{"entity": "publications", "timestamp": "2026-06-14T09:46:41.063Z", "year": "2011", "links": {"self": {"href": "https://publications.scilifelab.se/publications/2011.json"}, "display": {"href": "https://publications.scilifelab.se/publications/2011"}}, "publications_count": 163, "full": true, "publications": [{"entity": "publication", "iuid": "9ede859341ef44da83048f837f609d33", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ede859341ef44da83048f837f609d33.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ede859341ef44da83048f837f609d33"}}, "title": "A Complex Genomic Rearrangement Involving the Endothelin 3 Locus Causes Dermal Hyperpigmentation in the Chicken", "authors": [{"family": "Dorshorst", "given": "Ben", "initials": "B"}, {"family": "Molin", "given": "Anna Maja", "initials": "AM"}, {"family": "Rubin", "given": "Carl Johan", "initials": "CJ"}, {"family": "Johansson", "given": "Anna M", "initials": "AM"}, {"family": "Str\u00f6mstedt", "given": "Lina", "initials": "L"}, {"family": "Pham", "given": "Manh Hung", "initials": "MH"}, {"family": "Chen", "given": "Chih Feng", "initials": "CF"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F"}, {"family": "Ashwell", "given": "Chris", "initials": "C"}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal-article", "published": "2011-12-22", "journal": {"volume": "7", "issn": "1553-7404", "issue": "12", "pages": "e1002412", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Dermal hyperpigmentation or Fibromelanosis (FM) is one of the few examples of skin pigmentation phenotypes in the chicken, where most other pigmentation variants influence feather color and patterning. The Silkie chicken is the most widespread and well-studied breed displaying this phenotype. The presence of the dominant FM allele results in extensive pigmentation of the dermal layer of skin and the majority of internal connective tissue. Here we identify the causal mutation of FM as an inverted duplication and junction of two genomic regions separated by more than 400 kb in wild-type individuals. One of these duplicated regions contains endothelin 3 (EDN3), a gene with a known role in promoting melanoblast proliferation. We show that EDN3 expression is increased in the developing Silkie embryo during the time in which melanoblasts are migrating, and elevated levels of expression are maintained in the adult skin tissue. We have examined four different chicken breeds from both Asia and Europe displaying dermal hyperpigmentation and conclude that the same structural variant underlies this phenotype in all chicken breeds. This complex genomic rearrangement causing a specific monogenic trait in the chicken illustrates how novel mutations with major phenotypic effects have been reused during breed formation in domestic animals.", "doi": "10.1371/journal.pgen.1002412", "pmid": "22216010", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pmc", "key": "PMC3245302"}, {"db": "pii", "key": "PGENETICS-D-11-01394"}], "notes": [], "created": "2017-05-04T14:57:24.382Z", "modified": "2023-06-19T11:01:42.453Z"}, {"entity": "publication", "iuid": "fcddedebd2f947529567e84610e7b9bf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcddedebd2f947529567e84610e7b9bf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcddedebd2f947529567e84610e7b9bf"}}, "title": "Mechanisms underlying the sparing of masticatory versus limb muscle function in an experimental critical illness model.", "authors": [{"family": "Aare", "given": "Sudhakar", "initials": "S"}, {"family": "Ochala", "given": "Julien", "initials": "J"}, {"family": "Norman", "given": "Holly S", "initials": "HS"}, {"family": "Radell", "given": "Peter", "initials": "P"}, {"family": "Eriksson", "given": "Lars I", "initials": "LI"}, {"family": "G\u00f6ransson", "given": "Hanna", "initials": "H"}, {"family": "Chen", "given": "Yi-Wen", "initials": "YW"}, {"family": "Hoffman", "given": "Eric P", "initials": "EP"}, {"family": "Larsson", "given": "Lars", "initials": "L"}], "type": "comparative study", "published": "2011-12-16", "journal": {"volume": "43", "issn": "1531-2267", "issue": "24", "pages": "1334-1350", "title": "Physiol. Genomics", "issn-l": "1094-8341"}, "abstract": "Acute quadriplegic myopathy (AQM) is a common debilitating acquired disorder in critically ill intensive care unit (ICU) patients that is characterized by tetraplegia/generalized weakness of limb and trunk muscles. Masticatory muscles, on the other hand, are typically spared or less affected, yet the mechanisms underlying this striking muscle-specific difference remain unknown. This study aims to evaluate physiological parameters and the gene expression profiles of masticatory and limb muscles exposed to factors suggested to trigger AQM, such as mechanical ventilation, immobilization, neuromuscular blocking agents, corticosteroids (CS), and sepsis for 5 days by using a unique porcine model mimicking the ICU conditions. Single muscle fiber cross-sectional area and force-generating capacity, i.e., maximum force normalized to fiber cross-sectional area (specific force), revealed maintained masseter single muscle fiber cross-sectional area and specific-force after 5 days' exposure to all triggering factors. This is in sharp contrast to observations in limb and trunk muscles, showing a dramatic decline in specific force in response to 5 days' exposure to the triggering factors. Significant differences in gene expression were observed between craniofacial and limb muscles, indicating a highly complex and muscle-specific response involving transcription and growth factors, heat shock proteins, matrix metalloproteinase inhibitor, oxidative stress responsive elements, and sarcomeric proteins underlying the relative sparing of cranial vs. spinal nerve innervated muscles during exposure to the ICU intervention.", "doi": "10.1152/physiolgenomics.00116.2011", "pmid": "22010006", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "physiolgenomics.00116.2011"}], "notes": [], "created": "2017-05-04T15:02:53.851Z", "modified": "2017-05-30T12:36:12.391Z"}, {"entity": "publication", "iuid": "b83534b05e3b433d920a6dcd787ca276", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b83534b05e3b433d920a6dcd787ca276.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b83534b05e3b433d920a6dcd787ca276"}}, "title": "Polymorphisms in B3GAT1, SLC9A9 and MGAT5 are associated with variation within the human plasma N-glycome of 3533 European adults.", "authors": [{"family": "Huffman", "given": "Jennifer E", "initials": "JE"}, {"family": "Knezevic", "given": "Ana", "initials": "A"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Kattla", "given": "Jayesh", "initials": "J"}, {"family": "Adamczyk", "given": "Barbara", "initials": "B"}, {"family": "Novokmet", "given": "Mislav", "initials": "M"}, {"family": "Igl", "given": "Wilmar", "initials": "W"}, {"family": "Pucic", "given": "Maja", "initials": "M"}, {"family": "Zgaga", "given": "Lina", "initials": "L"}, {"family": "Johannson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Redzic", "given": "Irma", "initials": "I"}, {"family": "Gornik", "given": "Olga", "initials": "O"}, {"family": "Zemunik", "given": "Tatijana", "initials": "T"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Pehlic", "given": "Marina", "initials": "M"}, {"family": "Koeleman", "given": "Carolien A M", "initials": "CA"}, {"family": "Campbell", "given": "Susan", "initials": "S"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Hastie", "given": "Nicholas D", "initials": "ND"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Wuhrer", "given": "Manfred", "initials": "M"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Rudd", "given": "Pauline M", "initials": "PM"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Lauc", "given": "Gordan", "initials": "G"}], "type": "journal article", "published": "2011-12-15", "journal": {"volume": "20", "issn": "1460-2083", "issue": "24", "pages": "5000-5011", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "The majority of human proteins are post-translationally modified by covalent addition of one or more complex oligosaccharides (glycans). Alterations in glycosylation processing are associated with numerous diseases and glycans are attracting increasing attention both as disease biomarkers and as targets for novel therapeutic approaches. Using a recently developed high-throughput high-performance liquid chromatography (HPLC) analysis method, we have reported, in a pilot genome-wide association study of 13 glycan features in 2705 individuals from three European populations, that polymorphisms at three loci (FUT8, FUT6/FUT3 and HNF1A) affect plasma levels of N-glycans. Here, we extended the analysis to 33 directly measured and 13 derived glycosylation traits in 3533 individuals and identified three novel gene association (MGAT5, B3GAT1 and SLC9A9) as well as replicated the previous findings using an additional European cohort. MGAT5 (meta-analysis association P-value = 1.80 \u00d7 10(-10) for rs1257220) encodes a glycosyltransferase which is known to synthesize the associated glycans. In contrast, neither B3GAT1 (rs7928758, P = 1.66 \u00d7 10(-08)) nor SLC9A9 (rs4839604, P = 3.50 \u00d7 10(-13)) had previously been associated functionally with glycosylation of plasma proteins. Given the glucuronyl transferase activity of B3GAT1, we were able to show that glucuronic acid is present on antennae of plasma glycoproteins underlying the corresponding HPLC peak. SLC9A9 encodes a proton pump which affects pH in the endosomal compartment and it was recently reported that changes in Golgi pH can impair protein sialylation, giving a possible mechanism for the observed association.", "doi": "10.1093/hmg/ddr414", "pmid": "21908519", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "ddr414"}], "notes": [], "created": "2017-05-04T15:01:58.371Z", "modified": "2020-01-21T13:56:04.836Z"}, {"entity": "publication", "iuid": "63726d739c284fc0b2e763ada43dcfce", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63726d739c284fc0b2e763ada43dcfce.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63726d739c284fc0b2e763ada43dcfce"}}, "title": "Identification of immunogenic proteins in Treponema phagedenis-like strain V1 from digital dermatitis lesions by phage display.", "authors": [{"family": "Rosander", "given": "Anna", "initials": "A"}, {"family": "Guss", "given": "Bengt", "initials": "B"}, {"family": "Frykberg", "given": "Lars", "initials": "L"}, {"family": "Bj\u00f6rkman", "given": "Camilla", "initials": "C"}, {"family": "N\u00e4slund", "given": "Katarina", "initials": "K"}, {"family": "Pringle", "given": "M\u00e4rit", "initials": "M"}], "type": "journal article", "published": "2011-12-15", "journal": {"volume": "153", "issn": "1873-2542", "issue": "3-4", "pages": "315-322", "title": "Vet. Microbiol.", "issn-l": "0378-1135"}, "abstract": "Digital dermatitis (DD) is a contagious claw disease causing lameness in cattle, affecting both animal welfare and economics. In this study, shotgun phage display was used to identify immunogenic proteins in a strain (V1) of the Treponema phylotype closely related to Treponema phagedenis, indicated as a key agent in the pathogenesis of DD. A genomic phage library was constructed and selected against antibodies from a rabbit immunized with live strain V1 bacteria. A homolog to the immunogenic protein TmpA of Treponema pallidum subsp. pallidum was identified, as well as a putative phage tail tape measure protein (Ttm), and a putative proline-rich repeat lipoprotein (PrrA). The complete amino acid sequences of these proteins were predicted from a genomic sequence of strain V1 generated by 454 Sequencing\u2122. The presence of these genes in ten Treponema spp. field isolates was investigated by PCR. The tmpA and ttm genes were detected in all T. phagedenis-like isolates while prrA was detected in four out of seven. None of the genes were detected in the three Treponema pedis isolates investigated. Recombinant proteins were produced and used in indirect ELISAs. For all three proteins, a majority of serum samples from cattle with DD (n=8) showed higher optical density values than samples from cattle without DD (n=7).", "doi": "10.1016/j.vetmic.2011.06.005", "pmid": "21763087", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0378-1135(11)00333-6"}], "notes": [], "created": "2017-05-04T15:02:03.773Z", "modified": "2020-01-21T13:56:02.701Z"}, {"entity": "publication", "iuid": "1f50059e02074a5e873a48572d7e242e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f50059e02074a5e873a48572d7e242e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f50059e02074a5e873a48572d7e242e"}}, "title": "Association between body mass index and insulin receptor substrate-4 (IRS-4) gene polymorphisms in patients with schizophrenia.", "authors": [{"family": "Melkersson", "given": "Kristina", "initials": "K"}, {"family": "Persson", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2011-12-15", "journal": {"volume": "32", "issn": "0172-780X", "issue": "5", "pages": "634-640", "title": "Neuro Endocrinol. Lett.", "issn-l": null}, "abstract": "The insulin receptor substrate-4 (IRS-4) protein is highly expressed in the hypothalamus that plays a main role in the regulation of body weight. Therefore, as overweight and obesity are more frequent in patients with schizophrenia compared to the general population, this study was undertaken to investigate potential associations between body mass index (BMI) or height and polymorphisms in the IRS-4 gene in schizophrenia patients and healthy controls.\n\nThe IRS-4 gene of 93 patients and 59 controls was screened for DNA sequence variations, and then 10 detected single nucleotide polymorphisms (SNPs) were investigated in relation to BMI and height of patients and controls.\n\nMean BMI was higher in patients than in controls, whereas there was no difference regarding height. Significant associations were found between patients' BMI and genotypes of six SNPs (rs1801164, rs80131334, rs41307415, rs73253702, rs1801162, rs2073114) or a haplotype including these six SNPs. In contrast, no associations were found between BMI or height of controls, or height of patients, and the genotypes or haplotypes.\n\nThis study clearly demonstrates associations between BMI and IRS-4 variants in schizophrenia patients, but not in healthy controls, pointing to a possible involvement of IRS-4 in the control of body weight in schizophrenia.", "doi": null, "pmid": "22167131", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "NEL320511A07"}], "notes": [], "created": "2017-05-04T14:57:22.545Z", "modified": "2021-07-05T12:39:53.472Z"}, {"entity": "publication", "iuid": "6a9c4398ade546adae060121bcfffdbb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6a9c4398ade546adae060121bcfffdbb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6a9c4398ade546adae060121bcfffdbb"}}, "title": "The inner nuclear membrane proteins Man1 and Ima1 link to two different types of chromatin at the nuclear periphery in S. pombe.", "authors": [{"family": "Steglich", "given": "Babett", "initials": "B"}, {"family": "Filion", "given": "Guillaume J", "initials": "GJ"}, {"family": "van Steensel", "given": "Bas", "initials": "B"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2011-12-14", "journal": {"volume": "3", "issn": "1949-1042", "issue": "1", "pages": "77-87", "title": "Nucleus", "issn-l": null}, "abstract": "Metazoan chromatin at the nuclear periphery is generally characterized by lowly expressed genes and repressive chromatin marks and presents a sub-compartment with properties distinct from the nuclear interior. To test whether the S. pombe nuclear periphery behaves similarly, we used DNA adenine methyltransferase identification (DamID) to map the target loci of two inner nuclear membrane proteins, Ima1 and Man1. We found that peripheral chromatin shows low levels of RNA-Polymerase II and nucleosome occupancy, both characteristic of repressed chromatin regions. Consistently, lowly expressed genes preferentially associate with the periphery and highly expressed genes are depleted from it. When looking at peripheral intergenic regions (IGRs), we found that divergent IGRs are enriched compared with convergent IGRs, indicating that transcription preferentially points away from the periphery rather than toward it. Interestingly, we found that Ima1 and Man1 have common, but also separate target regions in the genome. Ima1-interacting loci were enriched for the RNAi components Dcr1 and Rdp1. This agrees with previous findings that Dcr1 is localized at the nuclear periphery. In contrast, Man1 target loci were bound by the heterochromatin protein Swi6, especially at subtelomeric regions. Subtelomeric chromatin was shown to form a unique chromatin type lacking both repressive and active chromatin features and containing low levels of the histone variant H2A.Z. Thus, we find that the fission yeast nuclear periphery shows similar properties to those of metazoan cells, despite the absence of a nuclear lamina. Our results point to a role of nuclear membrane proteins in organizing chromatin domains and loops.", "doi": "10.4161/nucl.18825", "pmid": "22156748", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "18825"}], "notes": [], "created": "2017-05-04T14:57:23.462Z", "modified": "2020-01-21T13:56:09.216Z"}, {"entity": "publication", "iuid": "4981f4e297634c109a11f7a33ef378df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4981f4e297634c109a11f7a33ef378df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4981f4e297634c109a11f7a33ef378df"}}, "title": "Muscle wasting and the temporal gene expression pattern in a novel rat intensive care unit model.", "authors": [{"family": "Llano-Diez", "given": "Monica", "initials": "M"}, {"family": "Gustafson", "given": "Ann-Marie", "initials": "AM"}, {"family": "Olsson", "given": "Carl", "initials": "C"}, {"family": "Goransson", "given": "Hanna", "initials": "H"}, {"family": "Larsson", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2011-12-13", "journal": {"volume": "12", "issn": "1471-2164", "issue": null, "pages": "602", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Acute quadriplegic myopathy (AQM) or critical illness myopathy (CIM) is frequently observed in intensive care unit (ICU) patients. To elucidate duration-dependent effects of the ICU intervention on molecular and functional networks that control the muscle wasting and weakness associated with AQM, a gene expression profile was analyzed at time points varying from 6 hours to 14 days in a unique experimental rat model mimicking ICU conditions, i.e., post-synaptically paralyzed, mechanically ventilated and extensively monitored animals.\n\nDuring the observation period, 1583 genes were significantly up- or down-regulated by factors of two or greater. A significant temporal gene expression pattern was constructed at short (6 h-4 days), intermediate (5-8 days) and long (9-14 days) durations. A striking early and maintained up-regulation (6 h-14d) of muscle atrogenes (muscle ring-finger 1/tripartite motif-containing 63 and F-box protein 32/atrogin-1) was observed, followed by an up-regulation of the proteolytic systems at intermediate and long durations (5-14d). Oxidative stress response genes and genes that take part in amino acid catabolism, cell cycle arrest, apoptosis, muscle development, and protein synthesis together with myogenic factors were significantly up-regulated from 5 to 14 days. At 9-14 d, genes involved in immune response and the caspase cascade were up-regulated. At 5-14d, genes related to contractile (myosin heavy chain and myosin binding protein C), regulatory (troponin, tropomyosin), developmental, caveolin-3, extracellular matrix, glycolysis/gluconeogenesis, cytoskeleton/sarcomere regulation and mitochondrial proteins were down-regulated. An activation of genes related to muscle growth and new muscle fiber formation (increase of myogenic factors and JunB and down-regulation of myostatin) and up-regulation of genes that code protein synthesis and translation factors were found from 5 to 14 days.\n\nNovel temporal patterns of gene expression have been uncovered, suggesting a unique, coordinated and highly complex mechanism underlying the muscle wasting associated with AQM in ICU patients and providing new target genes and avenues for intervention studies.", "doi": "10.1186/1471-2164-12-602", "pmid": "22165895", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "1471-2164-12-602"}, {"db": "pmc", "key": "PMC3266306"}], "notes": [], "created": "2017-05-04T15:02:51.187Z", "modified": "2017-05-30T14:49:24.252Z"}, {"entity": "publication", "iuid": "5aebe6334bed4654b7be912fbaa50694", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5aebe6334bed4654b7be912fbaa50694.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5aebe6334bed4654b7be912fbaa50694"}}, "title": "Blood pressure loci identified with a gene-centric array.", "authors": [{"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Gaunt", "given": "Tom R", "initials": "TR"}, {"family": "Newhouse", "given": "Stephen J", "initials": "SJ"}, {"family": "Padmanabhan", "given": "Sandosh", "initials": "S"}, {"family": "Tomaszewski", "given": "Maciej", "initials": "M"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Morris", "given": "Richard W", "initials": "RW"}, {"family": "Tzoulaki", "given": "Ioanna", "initials": "I"}, {"family": "O'Brien", "given": "Eoin T", "initials": "ET"}, {"family": "Poulter", "given": "Neil R", "initials": "NR"}, {"family": "Sever", "given": "Peter", "initials": "P"}, {"family": "Shields", "given": "Denis C", "initials": "DC"}, {"family": "Thom", "given": "Simon", "initials": "S"}, {"family": "Wannamethee", "given": "Sasiwarang G", "initials": "SG"}, {"family": "Whincup", "given": "Peter H", "initials": "PH"}, {"family": "Brown", "given": "Morris J", "initials": "MJ"}, {"family": "Connell", "given": "John M", "initials": "JM"}, {"family": "Dobson", "given": "Richard J", "initials": "RJ"}, {"family": "Howard", "given": "Philip J", "initials": "PJ"}, {"family": "Mein", "given": "Charles A", "initials": "CA"}, {"family": "Onipinla", "given": "Abiodun", "initials": "A"}, {"family": "Shaw-Hawkins", "given": "Sue", "initials": "S"}, {"family": "Zhang", "given": "Yun", "initials": "Y"}, {"family": "Davey Smith", "given": "George", "initials": "G"}, {"family": "Day", "given": "Ian N M", "initials": "IN"}, {"family": "Lawlor", "given": "Debbie A", "initials": "DA"}, {"family": "Goodall", "given": "Alison H", "initials": "AH"}, {"family": "Cardiogenics Consortium", "given": null, "initials": null}, {"family": "Fowkes", "given": "F Gerald", "initials": "FG"}, {"family": "Abecasis", "given": "Gon\u00e7alo R", "initials": "GR"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Gateva", "given": "Vesela", "initials": "V"}, {"family": "Global BPgen Consortium", "given": null, "initials": null}, {"family": "Braund", "given": "Peter S", "initials": "PS"}, {"family": "Burton", "given": "Paul R", "initials": "PR"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Tobin", "given": "Martin D", "initials": "MD"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Glorioso", "given": "Nicola", "initials": "N"}, {"family": "Neuvrith", "given": "Hani", "initials": "H"}, {"family": "Salvi", "given": "Erika", "initials": "E"}, {"family": "Staessen", "given": "Jan A", "initials": "JA"}, {"family": "Stucchi", "given": "Andrea", "initials": "A"}, {"family": "Devos", "given": "Nabila", "initials": "N"}, {"family": "Jeunemaitre", "given": "Xavier", "initials": "X"}, {"family": "Plouin", "given": "Pierre-Fran\u00e7ois", "initials": "PF"}, {"family": "Tichet", "given": "Jean", "initials": "J"}, {"family": "Juhanson", "given": "Peeter", "initials": "P"}, {"family": "Org", "given": "Elin", "initials": "E"}, {"family": "Putku", "given": "Margus", "initials": "M"}, {"family": "S\u00f5ber", "given": "Siim", "initials": "S"}, {"family": "Veldre", "given": "Gudrun", "initials": "G"}, {"family": "Viigimaa", "given": "Margus", "initials": "M"}, {"family": "Levinsson", "given": "Anna", "initials": "A"}, {"family": "Rosengren", "given": "Annika", "initials": "A"}, {"family": "Thelle", "given": "Dag S", "initials": "DS"}, {"family": "Hastie", "given": "Claire E", "initials": "CE"}, {"family": "Hedner", "given": "Thomas", "initials": "T"}, {"family": "Lee", "given": "Wai K", "initials": "WK"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Wahlstrand", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Hardy", "given": "Rebecca", "initials": "R"}, {"family": "Wong", "given": "Andrew", "initials": "A"}, {"family": "Cooper", "given": "Jackie A", "initials": "JA"}, {"family": "Palmen", "given": "Jutta", "initials": "J"}, {"family": "Chen", "given": "Li", "initials": "L"}, {"family": "Stewart", "given": "Alexandre F R", "initials": "AF"}, {"family": "Wells", "given": "George A", "initials": "GA"}, {"family": "Westra", "given": "Harm-Jan", "initials": "HJ"}, {"family": "Wolfs", "given": "Marcel G M", "initials": "MG"}, {"family": "Clarke", "given": "Robert", "initials": "R"}, {"family": "Franzosi", "given": "Maria Grazia", "initials": "MG"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Lathrop", "given": "Mark", "initials": "M"}, {"family": "Peden", "given": "John F", "initials": "JF"}, {"family": "Seedorf", "given": "Udo", "initials": "U"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Ouwehand", "given": "Willem H", "initials": "WH"}, {"family": "Sambrook", "given": "Jennifer", "initials": "J"}, {"family": "Stephens", "given": "Jonathan", "initials": "J"}, {"family": "Casas", "given": "Juan-Pablo", "initials": "JP"}, {"family": "Drenos", "given": "Fotios", "initials": "F"}, {"family": "Holmes", "given": "Michael V", "initials": "MV"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Shah", "given": "Sonia", "initials": "S"}, {"family": "Shah", "given": "Tina", "initials": "T"}, {"family": "Talmud", "given": "Philippa J", "initials": "PJ"}, {"family": "Whittaker", "given": "John", "initials": "J"}, {"family": "Wallace", "given": "Chris", "initials": "C"}, {"family": "Delles", "given": "Christian", "initials": "C"}, {"family": "Laan", "given": "Maris", "initials": "M"}, {"family": "Kuh", "given": "Diana", "initials": "D"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Nyberg", "given": "Fredrik", "initials": "F"}, {"family": "Cusi", "given": "Daniele", "initials": "D"}, {"family": "Roberts", "given": "Robert", "initials": "R"}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "Franke", "given": "Lude", "initials": "L"}, {"family": "Stanton", "given": "Alice V", "initials": "AV"}, {"family": "Dominiczak", "given": "Anna F", "initials": "AF"}, {"family": "Farrall", "given": "Martin", "initials": "M"}, {"family": "Hingorani", "given": "Aroon D", "initials": "AD"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}], "type": "journal article", "published": "2011-12-09", "journal": {"volume": "89", "issn": "1537-6605", "issue": "6", "pages": "688-700", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "Raised blood pressure (BP) is a major risk factor for cardiovascular disease. Previous studies have identified 47 distinct genetic variants robustly associated with BP, but collectively these explain only a few percent of the heritability for BP phenotypes. To find additional BP loci, we used a bespoke gene-centric array to genotype an independent discovery sample of 25,118 individuals that combined hypertensive case-control and general population samples. We followed up four SNPs associated with BP at our p < 8.56\u00a0\u00d7 10(-7) study-specific significance threshold and six suggestively associated SNPs in a further 59,349 individuals. We identified and replicated a SNP at LSP1/TNNT3, a SNP at MTHFR-NPPB independent (r(2) = 0.33) of previous reports, and replicated SNPs at AGT and ATP2B1 reported previously. An analysis of combined discovery and follow-up data identified SNPs significantly associated with BP at p < 8.56\u00a0\u00d7 10(-7) at four further loci (NPR3, HFE, NOS3, and SOX6). The high number of discoveries made with modest genotyping effort can be attributed to using a large-scale yet targeted genotyping array and to the development of a weighting scheme that maximized power when meta-analyzing results from samples ascertained with extreme phenotypes, in combination with results from nonascertained or population samples. Chromatin immunoprecipitation and transcript expression data highlight potential gene regulatory mechanisms at the MTHFR and NOS3 loci. These results provide candidates for further study to help dissect mechanisms affecting BP and highlight the utility of studying SNPs and samples that are independent of those studied previously even when the sample size is smaller than that in previous studies.", "doi": "10.1016/j.ajhg.2011.10.013", "pmid": "22100073", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0002-9297(11)00447-2"}, {"db": "pmc", "key": "PMC3234370"}], "notes": [], "created": "2017-05-04T15:00:39.882Z", "modified": "2020-01-21T13:56:02.489Z"}, {"entity": "publication", "iuid": "eeab66fda60e4471a39920006dc55659", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eeab66fda60e4471a39920006dc55659.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eeab66fda60e4471a39920006dc55659"}}, "title": "Common variants of the BRCA1 wild-type allele modify the risk of breast cancer in BRCA1 mutation carriers.", "authors": [{"family": "Cox", "given": "David G", "initials": "DG"}, {"family": "Simard", "given": "Jacques", "initials": "J"}, {"family": "Sinnett", "given": "Daniel", "initials": "D"}, {"family": "Hamdi", "given": "Yosr", "initials": "Y"}, {"family": "Soucy", "given": "Penny", "initials": "P"}, {"family": "Ouimet", "given": "Manon", "initials": "M"}, {"family": "Barjhoux", "given": "Laure", "initials": "L"}, {"family": "Verny-Pierre", "given": "Carole", "initials": "C"}, {"family": "McGuffog", "given": "Lesley", "initials": "L"}, {"family": "Healey", "given": "Sue", "initials": "S"}, {"family": "Szabo", "given": "Csilla", "initials": "C"}, {"family": "Greene", "given": "Mark H", "initials": "MH"}, {"family": "Mai", "given": "Phuong L", "initials": "PL"}, {"family": "Andrulis", "given": "Irene L", "initials": "IL"}, {"family": "Ontario Cancer Genetics Network", "given": null, "initials": null}, {"family": "Thomassen", "given": "Mads", "initials": "M"}, {"family": "Gerdes", "given": "Anne-Marie", "initials": "AM"}, {"family": "Caligo", "given": "Maria A", "initials": "MA"}, {"family": "Friedman", "given": "Eitan", "initials": "E"}, {"family": "Laitman", "given": "Yael", "initials": "Y"}, {"family": "Kaufman", "given": "Bella", "initials": "B"}, {"family": "Paluch", "given": "Shani S", "initials": "SS"}, {"family": "Borg", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Karlsson", "given": "Per", "initials": "P"}, {"family": "Askmalm", "given": "Marie Stenmark", "initials": "MS"}, {"family": "Bustinza", "given": "Gisela Barbany", "initials": "GB"}, {"family": "SWE-BRCA Collaborators", "given": null, "initials": null}, {"family": "Nathanson", "given": "Katherine L", "initials": "KL"}, {"family": "Domchek", "given": "Susan M", "initials": "SM"}, {"family": "Rebbeck", "given": "Timothy R", "initials": "TR"}, {"family": "Ben\u00edtez", "given": "Javier", "initials": "J"}, {"family": "Hamann", "given": "Ute", "initials": "U"}, {"family": "Rookus", "given": "Matti A", "initials": "MA"}, {"family": "van den Ouweland", "given": "Ans M W", "initials": "AM"}, {"family": "Ausems", "given": "Margreet G E M", "initials": "MG"}, {"family": "Aalfs", "given": "Cora M", "initials": "CM"}, {"family": "van Asperen", "given": "Christi J", "initials": "CJ"}, {"family": "Devilee", "given": "Peter", "initials": "P"}, {"family": "Gille", "given": "Hans J J P", "initials": "HJ"}, {"family": "HEBON", "given": null, "initials": null}, {"family": "EMBRACE", "given": null, "initials": null}, {"family": "Peock", "given": "Susan", "initials": "S"}, {"family": "Frost", "given": "Debra", "initials": "D"}, {"family": "Evans", "given": "D Gareth", "initials": "DG"}, {"family": "Eeles", "given": "Ros", "initials": "R"}, {"family": "Izatt", "given": "Louise", "initials": "L"}, {"family": "Adlard", "given": "Julian", "initials": "J"}, {"family": "Paterson", "given": "Joan", "initials": "J"}, {"family": "Eason", "given": "Jacqueline", "initials": "J"}, {"family": "Godwin", "given": "Andrew K", "initials": "AK"}, {"family": "Remon", "given": "Marie-Alice", "initials": "MA"}, {"family": "Moncoutier", "given": "Virginie", "initials": "V"}, {"family": "Gauthier-Villars", "given": "Marion", "initials": "M"}, {"family": "Lasset", "given": "Christine", "initials": "C"}, {"family": "Giraud", "given": "Sophie", "initials": "S"}, {"family": "Hardouin", "given": "Agn\u00e8s", "initials": "A"}, {"family": "Berthet", "given": "Pascaline", "initials": "P"}, {"family": "Sobol", "given": "Hagay", "initials": "H"}, {"family": "Eisinger", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Bressac de Paillerets", "given": "Brigitte", "initials": "B"}, {"family": "Caron", "given": "Olivier", "initials": "O"}, {"family": "Delnatte", "given": "Capucine", "initials": "C"}, {"family": "GEMO Study Collaborators", "given": null, "initials": null}, {"family": "Goldgar", "given": "David", "initials": "D"}, {"family": "Miron", "given": "Alex", "initials": "A"}, {"family": "Ozcelik", "given": "Hilmi", "initials": "H"}, {"family": "Buys", "given": "Saundra", "initials": "S"}, {"family": "Southey", "given": "Melissa C", "initials": "MC"}, {"family": "Terry", "given": "Mary Beth", "initials": "MB"}, {"family": "Breast Cancer Family Registry", "given": null, "initials": null}, {"family": "Singer", "given": "Christian F", "initials": "CF"}, {"family": "Dressler", "given": "Anne-Catharina", "initials": "AC"}, {"family": "Tea", "given": "Muy-Kheng", "initials": "MK"}, {"family": "Hansen", "given": "Thomas V O", "initials": "TV"}, {"family": "Johannsson", "given": "Oskar", "initials": "O"}, {"family": "Piedmonte", "given": "Marion", "initials": "M"}, {"family": "Rodriguez", "given": "Gustavo C", "initials": "GC"}, {"family": "Basil", "given": "Jack B", "initials": "JB"}, {"family": "Blank", "given": "Stephanie", "initials": "S"}, {"family": "Toland", "given": "Amanda E", "initials": "AE"}, {"family": "Montagna", "given": "Marco", "initials": "M"}, {"family": "Isaacs", "given": "Claudine", "initials": "C"}, {"family": "Blanco", "given": "Ignacio", "initials": "I"}, {"family": "Gayther", "given": "Simon A", "initials": "SA"}, {"family": "Moysich", "given": "Kirsten B", "initials": "KB"}, {"family": "Schmutzler", "given": "Rita K", "initials": "RK"}, {"family": "Wappenschmidt", "given": "Barbara", "initials": "B"}, {"family": "Engel", "given": "Christoph", "initials": "C"}, {"family": "Meindl", "given": "Alfons", "initials": "A"}, {"family": "Ditsch", "given": "Nina", "initials": "N"}, {"family": "Arnold", "given": "Norbert", "initials": "N"}, {"family": "Niederacher", "given": "Dieter", "initials": "D"}, {"family": "Sutter", "given": "Christian", "initials": "C"}, {"family": "Gadzicki", "given": "Dorothea", "initials": "D"}, {"family": "Fiebig", "given": "Britta", "initials": "B"}, {"family": "Caldes", "given": "Trinidad", "initials": "T"}, {"family": "Laframboise", "given": "Rachel", "initials": "R"}, {"family": "Nevanlinna", "given": "Heli", "initials": "H"}, {"family": "Chen", "given": "Xiaoqing", "initials": "X"}, {"family": "Beesley", "given": "Jonathan", "initials": "J"}, {"family": "Spurdle", "given": "Amanda B", "initials": "AB"}, {"family": "Neuhausen", "given": "Susan L", "initials": "SL"}, {"family": "Ding", "given": "Yuan C", "initials": "YC"}, {"family": "Couch", "given": "Fergus J", "initials": "FJ"}, {"family": "Wang", "given": "Xianshu", "initials": "X"}, {"family": "Peterlongo", "given": "Paolo", "initials": "P"}, {"family": "Manoukian", "given": "Siranoush", "initials": "S"}, {"family": "Bernard", "given": "Loris", "initials": "L"}, {"family": "Radice", "given": "Paolo", "initials": "P"}, {"family": "Easton", "given": "Douglas F", "initials": "DF"}, {"family": "Chenevix-Trench", "given": "Georgia", "initials": "G"}, {"family": "Antoniou", "given": "Antonis C", "initials": "AC"}, {"family": "Stoppa-Lyonnet", "given": "Dominique", "initials": "D"}, {"family": "Mazoyer", "given": "Sylvie", "initials": "S"}, {"family": "Sinilnikova", "given": "Olga M", "initials": "OM"}, {"family": "Consortium of Investigators of Modifiers of BRCA1/2", "given": null, "initials": null}], "type": "journal article", "published": "2011-12-01", "journal": {"volume": "20", "issn": "1460-2083", "issue": "23", "pages": "4732-4747", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "Mutations in the BRCA1 gene substantially increase a woman's lifetime risk of breast cancer. However, there is great variation in this increase in risk with several genetic and non-genetic modifiers identified. The BRCA1 protein plays a central role in DNA repair, a mechanism that is particularly instrumental in safeguarding cells against tumorigenesis. We hypothesized that polymorphisms that alter the expression and/or function of BRCA1 carried on the wild-type (non-mutated) copy of the BRCA1 gene would modify the risk of breast cancer in carriers of BRCA1 mutations. A total of 9874 BRCA1 mutation carriers were available in the Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA) for haplotype analyses of BRCA1. Women carrying the rare allele of single nucleotide polymorphism rs16942 on the wild-type copy of BRCA1 were at decreased risk of breast cancer (hazard ratio 0.86, 95% confidence interval 0.77-0.95, P = 0.003). Promoter in vitro assays of the major BRCA1 haplotypes showed that common polymorphisms in the regulatory region alter its activity and that this effect may be attributed to the differential binding affinity of nuclear proteins. In conclusion, variants on the wild-type copy of BRCA1 modify risk of breast cancer among carriers of BRCA1 mutations, possibly by altering the efficiency of BRCA1 transcription.", "doi": "10.1093/hmg/ddr388", "pmid": "21890493", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ddr388"}, {"db": "pmc", "key": "PMC3733139"}], "notes": [], "created": "2017-05-04T14:57:19.508Z", "modified": "2020-01-21T13:56:06.078Z"}, {"entity": "publication", "iuid": "4f7dadd5ad1e4faa87479d07cad1c76d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f7dadd5ad1e4faa87479d07cad1c76d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f7dadd5ad1e4faa87479d07cad1c76d"}}, "title": "Salt-inducible kinase 1 influences Na(+),K(+)-ATPase activity in vascular smooth muscle cells and associates with variations in blood pressure.", "authors": [{"family": "Popov", "given": "Sergej", "initials": "S"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "W\u00e5gs\u00e4ter", "given": "Dick", "initials": "D"}, {"family": "Takemori", "given": "Hiroshi", "initials": "H"}, {"family": "Oguro", "given": "Ryousuke", "initials": "R"}, {"family": "Matsumoto", "given": "Sachiko", "initials": "S"}, {"family": "Sugimoto", "given": "Ken", "initials": "K"}, {"family": "Kamide", "given": "Kei", "initials": "K"}, {"family": "Hirose", "given": "Takuo", "initials": "T"}, {"family": "Satoh", "given": "Michihiro", "initials": "M"}, {"family": "Metoki", "given": "Hirohito", "initials": "H"}, {"family": "Kikuya", "given": "Masahiro", "initials": "M"}, {"family": "Ohkubo", "given": "Takayoshi", "initials": "T"}, {"family": "Katsuya", "given": "Tomohiro", "initials": "T"}, {"family": "Rakugi", "given": "Hiromi", "initials": "H"}, {"family": "Imai", "given": "Yutaka", "initials": "Y"}, {"family": "Sanchez", "given": "Fabio", "initials": "F"}, {"family": "Leosdottir", "given": "Margret", "initials": "M"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Bertorello", "given": "Alejandro M", "initials": "AM"}], "type": "journal article", "published": "2011-12-00", "journal": {"volume": "29", "issn": "1473-5598", "issue": "12", "pages": "2395-2403", "title": "J. Hypertens.", "issn-l": "0263-6352"}, "abstract": "Essential hypertension is a complex condition whose cause involves the interaction of multiple genetic and environmental factors such as salt intake. Salt-inducible kinase 1 (SIK1) is a sucrose-nonfermenting-like kinase isoform that belongs to the AMPK (5' adenosine monophosphate-activated protein kinase) family. SIK1 activity is increased by high salt intake and plays an essential role in regulating the plasma membrane Na(+),K(+)-ATPase. The objective of this study was to examine whether SIK1 is present in vascular smooth muscle cells (VSMCs) and endothelial cells, whether it affects VSMC Na(+),K(+)-ATPase activity and whether human SIK1 (hSIK1) represents a potential candidate for blood pressure regulation.\n\nLocalization of SIK1 was performed using immunohistochemistry, mRNA and western blot. Functional assays (Na(+),K(+)-ATPase activity) were performed in VSMCs derived from rat aorta. Genotype-phenotype association studies were performed in three Swedish and one Japanese population-based cohorts.\n\nSIK1 was localized in human VSMCs and endothelial cells, as well as a cell line derived from rat aorta. A nonsynonymous single nucleotide polymorphism in the hSIK1 gene exon 3 (C\u2192T, rs3746951) results in the amino acid change (15)Gly\u2192Ser in the SIK1 protein. SIK1-(15)Ser was found to increase plasma membrane Na(+),K(+)-ATPase activity in cultured VSMC line from rat aorta. Genotype-phenotype association studies in three Swedish and one Japanese population-based cohorts suggested that T allele (coding for (15)Ser) was associated with lower blood pressure (P\u200a=\u200a0.005 for SBP and P\u200a=\u200a0.002 for DBP) and with a decrease in left ventricular mass (P\u200a=\u200a0.048).\n\nThe hSIK1 appears to be of potential relevance within VSMC function and blood pressure regulation.", "doi": "10.1097/HJH.0b013e32834d3d55", "pmid": "22045124", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:47.650Z", "modified": "2021-07-07T15:11:02.451Z"}, {"entity": "publication", "iuid": "01a2aabefb7442eab3fd126b52907d88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/01a2aabefb7442eab3fd126b52907d88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/01a2aabefb7442eab3fd126b52907d88"}}, "title": "Pathway-based analysis of genetic susceptibility to cervical cancer in situ: HLA-DPB1 affects risk in Swedish women.", "authors": [{"family": "Ivansson", "given": "E L", "initials": "EL"}, {"family": "Juko-Pecirep", "given": "I", "initials": "I"}, {"family": "Erlich", "given": "H A", "initials": "HA"}, {"family": "Gyllensten", "given": "U B", "initials": "UB"}], "type": "journal article", "published": "2011-12-00", "journal": {"volume": "12", "issn": "1476-5470", "issue": "8", "pages": "605-614", "title": "Genes Immun.", "issn-l": "1466-4879"}, "abstract": "We have conducted a pathway-based analysis of genome-wide single-nucleotide polymorphism (SNP) data in order to identify genetic susceptibility factors for cervical cancer in situ. Genotypes derived from Affymetrix 500k or 5.0 arrays for 1076 cases and 1426 controls were analyzed for association, and pathways with enriched signals were identified using the SNP ratio test. The most strongly associated KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were Asthma (empirical P=0.03), Folate biosynthesis (empirical P=0.04) and Graft-versus-host disease (empirical P=0.05). Among the 11 top-ranking pathways were 6 related to the immune response with the common denominator being genes in the major histocompatibility complex (MHC) region on chromosome 6. Further investigation of the MHC revealed a clear effect of HLA-DPB1 polymorphism on disease susceptibility. At a functional level, DPB1 alleles associated with risk and protection differ in key amino-acid residues affecting peptide-binding motifs in the extracellular domains. The results illustrate the value of pathway-based analysis to mine genome-wide data, and point to the importance of the MHC region and specifically the HLA-DPB1 locus for susceptibility to cervical cancer.", "doi": "10.1038/gene.2011.40", "pmid": "21716314", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "gene201140"}], "notes": [], "created": "2017-05-04T15:01:57.857Z", "modified": "2020-01-21T13:56:00.478Z"}, {"entity": "publication", "iuid": "51f66210bc9f4fdc8ad849038b7e87cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/51f66210bc9f4fdc8ad849038b7e87cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/51f66210bc9f4fdc8ad849038b7e87cc"}}, "title": "High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer.", "authors": [{"family": "Hjelm", "given": "Barbara", "initials": "B"}, {"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Zendehrokh", "given": "Nooreldin", "initials": "N"}, {"family": "Eberhard", "given": "Jakob", "initials": "J"}, {"family": "Nodin", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Gaber", "given": "Alexander", "initials": "A"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Smaragdi", "given": "Kristina", "initials": "K"}, {"family": "Frantz", "given": "Christian", "initials": "C"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Johnson", "given": "Louis B", "initials": "LB"}, {"family": "P\u00e5hlman", "given": "Sven", "initials": "S"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2011-12-00", "journal": {"volume": "5", "issn": "1862-8354", "issue": "11-12", "pages": "624-635", "title": "Proteomics Clin Appl", "issn-l": "1862-8346"}, "abstract": "In this study, we investigated the prognostic impact of human RBM3 expression in colorectal cancer using tissue microarray-based immunohistochemical analysis.\n\nOne polyclonal antibody and four monoclonal anti-RBM3 antibodies were generated and epitope mapped using two different methods. Bacterial display revealed five distinct epitopes for the polyclonal antibody, while the four mouse monoclonal antibodies were found to bind to three of the five epitopes. A peptide suspension bead array assay confirmed the five epitopes of the polyclonal antibody, while only one of the monoclonal antibodies could be mapped using this approach. Antibody specificity was confirmed by Western blotting and immunohistochemistry, including siRNA-mediated knock-down. Two of the antibodies (polyclonal and monoclonal) were subsequently used to analyze RBM3 expression in tumor samples from two independent colorectal cancer cohorts, one consecutive cohort (n=270) and one prospectively collected cohort of patients with cancer of the sigmoid colon (n=305). RBM3-expression was detected, with high correlation between both antibodies (R=0.81, p<0.001).\n\nIn both cohorts, tumors with high nuclear RBM3 staining had significantly prolonged the overall survival. This was also confirmed in multivariate analysis, adjusted for established prognostic factors.\n\nThese data demonstrate that high tumor-specific nuclear expression of RBM3 is an independent predictor of good prognosis in colorectal cancer.", "doi": "10.1002/prca.201100020", "pmid": "21956899", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:48.538Z", "modified": "2021-07-08T13:44:33.250Z"}, {"entity": "publication", "iuid": "b40b6662466c42fba773726d8fbdacee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b40b6662466c42fba773726d8fbdacee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b40b6662466c42fba773726d8fbdacee"}}, "title": "Targeting acetylcholinesterase: identification of chemical leads by high throughput screening, structure determination and molecular modeling.", "authors": [{"family": "Berg", "given": "Lotta", "initials": "L"}, {"family": "Andersson", "given": "C David", "initials": "CD"}, {"family": "Artursson", "given": "Elisabet", "initials": "E"}, {"family": "H\u00f6rnberg", "given": "Andreas", "initials": "A"}, {"family": "Tunemalm", "given": "Anna-Karin", "initials": "A"}, {"family": "Linusson", "given": "Anna", "initials": "A"}, {"family": "Ekstr\u00f6m", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2011-11-30", "journal": {"volume": "6", "issn": "1932-6203", "issue": "11", "pages": "e26039", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Acetylcholinesterase (AChE) is an essential enzyme that terminates cholinergic transmission by rapid hydrolysis of the neurotransmitter acetylcholine. Compounds inhibiting this enzyme can be used (inter alia) to treat cholinergic deficiencies (e.g. in Alzheimer's disease), but may also act as dangerous toxins (e.g. nerve agents such as sarin). Treatment of nerve agent poisoning involves use of antidotes, small molecules capable of reactivating AChE. We have screened a collection of organic molecules to assess their ability to inhibit the enzymatic activity of AChE, aiming to find lead compounds for further optimization leading to drugs with increased efficacy and/or decreased side effects. 124 inhibitors were discovered, with considerable chemical diversity regarding size, polarity, flexibility and charge distribution. An extensive structure determination campaign resulted in a set of crystal structures of protein-ligand complexes. Overall, the ligands have substantial interactions with the peripheral anionic site of AChE, and the majority form additional interactions with the catalytic site (CAS). Reproduction of the bioactive conformation of six of the ligands using molecular docking simulations required modification of the default parameter settings of the docking software. The results show that docking-assisted structure-based design of AChE inhibitors is challenging and requires crystallographic support to obtain reliable results, at least with currently available software. The complex formed between C5685 and Mus musculus AChE (C5685\u2022mAChE) is a representative structure for the general binding mode of the determined structures. The CAS binding part of C5685 could not be structurally determined due to a disordered electron density map and the developed docking protocol was used to predict the binding modes of this part of the molecule. We believe that chemical modifications of our discovered inhibitors, biochemical and biophysical characterization, crystallography and computational chemistry provide a route to novel AChE inhibitors and reactivators.", "doi": "10.1371/journal.pone.0026039", "pmid": "22140425", "labels": {"Chemical Biology Consortium Sweden": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-11-11581"}, {"db": "pmc", "key": "PMC3227566"}], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:37.320Z", "modified": "2025-10-17T13:04:30.728Z"}, {"entity": "publication", "iuid": "d11a70e0354c482ba76ccd807a782ea5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d11a70e0354c482ba76ccd807a782ea5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d11a70e0354c482ba76ccd807a782ea5"}}, "title": "Next-generation sequencing technologies and applications for human genetic history and forensics.", "authors": [{"family": "Berglund", "given": "Eva C", "initials": "EC"}, {"family": "Kiialainen", "given": "Anna", "initials": "A"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2011-11-24", "journal": {"volume": "2", "issn": "2041-2223", "issue": null, "pages": "23", "title": "Investig Genet", "issn-l": "2041-2223"}, "abstract": "Rapid advances in the development of sequencing technologies in recent years have enabled an increasing number of applications in biology and medicine. Here, we review key technical aspects of the preparation of DNA templates for sequencing, the biochemical reaction principles and assay formats underlying next-generation sequencing systems, methods for imaging and base calling, quality control, and bioinformatic approaches for sequence alignment, variant calling and assembly. We also discuss some of the most important advances that the new sequencing technologies have brought to the fields of human population genetics, human genetic history and forensic genetics.", "doi": "10.1186/2041-2223-2-23", "pmid": "22115430", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "2041-2223-2-23"}, {"db": "pmc", "key": "PMC3267688"}], "notes": [], "created": "2017-05-04T15:00:46.086Z", "modified": "2021-07-07T15:11:02.743Z"}, {"entity": "publication", "iuid": "0318de93d4474776aa4f1b4e4769dc0e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0318de93d4474776aa4f1b4e4769dc0e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0318de93d4474776aa4f1b4e4769dc0e"}}, "title": "Counting absolute numbers of molecules using unique molecular identifiers.", "authors": [{"family": "Kivioja", "given": "Teemu", "initials": "T"}, {"family": "V\u00e4h\u00e4rautio", "given": "Anna", "initials": "A"}, {"family": "Karlsson", "given": "Kasper", "initials": "K"}, {"family": "Bonke", "given": "Martin", "initials": "M"}, {"family": "Enge", "given": "Martin", "initials": "M"}, {"family": "Linnarsson", "given": "Sten", "initials": "S"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2011-11-20", "journal": {"volume": "9", "issn": "1548-7105", "issue": "1", "pages": "72-74", "title": "Nat. Methods", "issn-l": "1548-7091"}, "abstract": "Counting individual RNA or DNA molecules is difficult because they are hard to copy quantitatively for detection. To overcome this limitation, we applied unique molecular identifiers (UMIs), which make each molecule in a population distinct, to genome-scale human karyotyping and mRNA sequencing in Drosophila melanogaster. Use of this method can improve accuracy of almost any next-generation sequencing method, including chromatin immunoprecipitation-sequencing, genome assembly, diagnostics and manufacturing-process control and monitoring.", "doi": "10.1038/nmeth.1778", "pmid": "22101854", "labels": {"Karolinska High Throughput Center (KHTC)": null}, "xrefs": [{"db": "pii", "key": "nmeth.1778"}], "notes": [], "created": "2017-05-04T14:57:03.362Z", "modified": "2017-05-30T14:30:09.110Z"}, {"entity": "publication", "iuid": "c2e9c06ba1ef4c7882ff2869b01abad4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c2e9c06ba1ef4c7882ff2869b01abad4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c2e9c06ba1ef4c7882ff2869b01abad4"}}, "title": "Variance decomposition of protein profiles from antibody arrays using a longitudinal twin model.", "authors": [{"family": "Kato", "given": "Bernet S", "initials": "BS"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Rantalainen", "given": "Mattias", "initials": "M"}, {"family": "Holmes", "given": "Chris C", "initials": "CC"}, {"family": "Barrett", "given": "Amy", "initials": "A"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}], "type": "journal article", "published": "2011-11-17", "journal": {"volume": "9", "issn": "1477-5956", "issue": null, "pages": "73", "title": "Proteome Sci", "issn-l": "1477-5956"}, "abstract": "The advent of affinity-based proteomics technologies for global protein profiling provides the prospect of finding new molecular biomarkers for common, multifactorial disorders. The molecular phenotypes obtained from studies on such platforms are driven by multiple sources, including genetic, environmental, and experimental components. In characterizing the contribution of different sources of variation to the measured phenotypes, the aim is to facilitate the design and interpretation of future biomedical studies employing exploratory and multiplexed technologies. Thus, biometrical genetic modelling of twin or other family data can be used to decompose the variation underlying a phenotype into biological and experimental components.\n\nUsing antibody suspension bead arrays and antibodies from the Human Protein Atlas, we study unfractionated serum from a longitudinal study on 154 twins. In this study, we provide a detailed description of how the variation in a molecular phenotype in terms of protein profile can be decomposed into familial i.e. genetic and common environmental; individual environmental, short-term biological and experimental components. The results show that across 69 antibodies analyzed in the study, the median proportion of the total variation explained by familial sources is 12% (IQR 1-22%), and the median proportion of the total variation attributable to experimental sources is 63% (IQR 53-72%).\n\nThe variability analysis of antibody arrays highlights the importance to consider variability components and their relative contributions when designing and evaluating studies for biomarker discoveries with exploratory, high-throughput and multiplexed methods.", "doi": "10.1186/1477-5956-9-73", "pmid": "22093360", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [{"db": "pii", "key": "1477-5956-9-73"}, {"db": "pmc", "key": "PMC3247853"}], "notes": [], "created": "2017-10-30T10:37:06.896Z", "modified": "2021-07-08T13:44:33.591Z"}, {"entity": "publication", "iuid": "4209d57186b04e479f0e923cea37538c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4209d57186b04e479f0e923cea37538c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4209d57186b04e479f0e923cea37538c"}}, "title": "Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks.", "authors": [{"family": "Deneberg", "given": "Stefan", "initials": "S"}, {"family": "Guardiola", "given": "Philippe", "initials": "P"}, {"family": "Lennartsson", "given": "Andreas", "initials": "A"}, {"family": "Qu", "given": "Ying", "initials": "Y"}, {"family": "Gaidzik", "given": "Verena", "initials": "V"}, {"family": "Blanchet", "given": "Odile", "initials": "O"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Bengtz\u00e9n", "given": "Sofia", "initials": "S"}, {"family": "Nahi", "given": "Hareth", "initials": "H"}, {"family": "Uggla", "given": "Bertil", "initials": "B"}, {"family": "Tidefelt", "given": "Ulf", "initials": "U"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M"}, {"family": "Paul", "given": "Christer", "initials": "C"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "D\u00f6hner", "given": "Konstanze", "initials": "K"}, {"family": "Lehmann", "given": "S\u00f6ren", "initials": "S"}], "type": "journal article", "published": "2011-11-17", "journal": {"volume": "118", "issn": "1528-0020", "issue": "20", "pages": "5573-5582", "title": "Blood", "issn-l": "0006-4971"}, "abstract": "Cytogenetically normal acute myeloid leukemia (CN-AML) compose between 40% and 50% of all adult acute myeloid leukemia (AML) cases. In this clinically diverse group, molecular aberrations, such as FLT3-ITD, NPM1, and CEBPA mutations, recently have added to the prognostic accuracy. Aberrant DNA methylation is a hallmark of cancer, including AML. We investigated in total 118 CN-AML samples in a test and a validation cohort for genome-wide promoter DNA methylation with Illumina Methylation Bead arrays and compared them with normal myeloid precursors and global gene expression. IDH and NPM1 mutations were associated with different methylation patterns (P = .0004 and .04, respectively). Genome-wide methylation levels were elevated in IDH-mutated samples (P = .006). We observed a negative impact of DNA methylation on transcription. Genes targeted by Polycomb group (PcG) proteins and genes associated with bivalent histone marks in stem cells showed increased aberrant methylation in AML (P < .0001). Furthermore, high methylation levels of PcG target genes were independently associated with better progression-free survival (odds ratio = 0.47, P = .01) and overall survival (odds ratio = 0.36, P = .001). In summary, genome-wide methylation patterns show preferential methylation of PcG targets with prognostic impact in CN-AML.", "doi": "10.1182/blood-2011-01-332353", "pmid": "21960591", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "blood-2011-01-332353"}], "notes": [], "created": "2017-05-04T14:57:16.182Z", "modified": "2020-01-21T13:56:01.865Z"}, {"entity": "publication", "iuid": "b5f1106afe1545fd9cd8e46a5ea9932e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b5f1106afe1545fd9cd8e46a5ea9932e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b5f1106afe1545fd9cd8e46a5ea9932e"}}, "title": "Genome sequencing reveals a phage in Helicobacter pylori.", "authors": [{"family": "Lehours", "given": "Philippe", "initials": "P"}, {"family": "Vale", "given": "Filipa F", "initials": "FF"}, {"family": "Bjursell", "given": "Magnus K", "initials": "MK"}, {"family": "Melefors", "given": "Ojar", "initials": "O"}, {"family": "Advani", "given": "Reza", "initials": "R"}, {"family": "Glavas", "given": "Steve", "initials": "S"}, {"family": "Guegueniat", "given": "Julia", "initials": "J"}, {"family": "Gontier", "given": "Etienne", "initials": "E"}, {"family": "Lacomme", "given": "Sabrina", "initials": "S"}, {"family": "Alves Matos", "given": "Ant\u00f3nio", "initials": "A"}, {"family": "Menard", "given": "Armelle", "initials": "A"}, {"family": "M\u00e9graud", "given": "Francis", "initials": "F"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}], "type": "journal article", "published": "2011-11-15", "journal": {"volume": "2", "issn": "2150-7511", "issue": "6", "title": "MBio", "issn-l": null}, "abstract": "Helicobacter pylori chronically infects the gastric mucosa in more than half of the human population; in a subset of this population, its presence is associated with development of severe disease, such as gastric cancer. Genomic analysis of several strains has revealed an extensive H. pylori pan-genome, likely to grow as more genomes are sampled. Here we describe the draft genome sequence (63 contigs; 26\u00d7 mean coverage) of H. pylori strain B45, isolated from a patient with gastric mucosa-associated lymphoid tissue (MALT) lymphoma. The major finding was a 24.6-kb prophage integrated in the bacterial genome. The prophage shares most of its genes (22/27) with prophage region II of Helicobacter acinonychis strain Sheeba. After UV treatment of liquid cultures, circular DNA carrying the prophage integrase gene could be detected, and intracellular tailed phage-like particles were observed in H. pylori cells by transmission electron microscopy, indicating that phage production can be induced from the prophage. PCR amplification and sequencing of the integrase gene from 341 H. pylori strains from different geographic regions revealed a high prevalence of the prophage (21.4%). Phylogenetic reconstruction showed four distinct clusters in the integrase gene, three of which tended to be specific for geographic regions. Our study implies that phages may play important roles in the ecology and evolution of H. pylori.\n\nHelicobacter pylori chronically infects the gastric mucosa in more than half of the human population, and while most of the infected individuals do not develop disease, H. pylori infection doubles the risk of developing gastric cancer. An abundance and diversity of viruses (phages) infect microbial populations in most environments and are important mediators of microbial diversity. Our finding of a 24.6-kb prophage integrated inside an H. pylori genome and the observation of circular integrase gene-containing DNA and phage-like particles inside cells upon UV treatment demonstrate that we have discovered a viable H. pylori phage. The additional finding of integrase genes in a large proportion of screened isolates of diverse geographic origins indicates that the prevalence of prophages may have been underestimated in H. pylori. Since phages are important drivers of microbial evolution, the discovery should be important for understanding and predicting genetic diversity in H. pylori.", "doi": "10.1128/mBio.00239-11", "pmid": "22086490", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "mBio.00239-11"}, {"db": "pmc", "key": "PMC3221604"}, {"db": "GENBANK", "key": "AFAO01000001"}, {"db": "GENBANK", "key": "AFAO01000002"}, {"db": "GENBANK", "key": "AFAO01000003"}, {"db": "GENBANK", "key": "AFAO01000004"}, {"db": "GENBANK", "key": "AFAO01000005"}, {"db": "GENBANK", "key": "AFAO01000006"}, {"db": "GENBANK", "key": "AFAO01000007"}, {"db": "GENBANK", "key": "AFAO01000008"}, {"db": "GENBANK", "key": "AFAO01000009"}, {"db": "GENBANK", "key": "AFAO01000010"}, {"db": "GENBANK", "key": "AFAO01000011"}, {"db": "GENBANK", "key": "AFAO01000012"}, {"db": "GENBANK", "key": "AFAO01000013"}, {"db": "GENBANK", "key": "AFAO01000014"}, {"db": "GENBANK", "key": "AFAO01000015"}, {"db": "GENBANK", "key": "AFAO01000016"}, {"db": "GENBANK", "key": "AFAO01000017"}, {"db": "GENBANK", "key": "AFAO01000018"}, {"db": "GENBANK", "key": "AFAO01000019"}, {"db": "GENBANK", "key": "AFAO01000020"}, {"db": "GENBANK", "key": "AFAO01000021"}, {"db": "GENBANK", "key": "AFAO01000022"}, {"db": "GENBANK", "key": "AFAO01000023"}, {"db": "GENBANK", "key": "AFAO01000024"}, {"db": "GENBANK", "key": "AFAO01000025"}, {"db": "GENBANK", "key": "AFAO01000026"}, {"db": "GENBANK", "key": "AFAO01000027"}, {"db": "GENBANK", "key": "AFAO01000028"}, {"db": "GENBANK", "key": "AFAO01000029"}, {"db": "GENBANK", "key": "AFAO01000030"}, {"db": "GENBANK", "key": "AFAO01000031"}, {"db": "GENBANK", "key": "AFAO01000032"}, {"db": "GENBANK", "key": "AFAO01000033"}, {"db": "GENBANK", "key": "AFAO01000034"}, {"db": "GENBANK", "key": "AFAO01000035"}, {"db": "GENBANK", "key": "AFAO01000036"}, {"db": "GENBANK", "key": "AFAO01000037"}, {"db": "GENBANK", "key": "AFAO01000038"}, {"db": "GENBANK", "key": "AFAO01000039"}, {"db": "GENBANK", "key": "AFAO01000040"}, {"db": "GENBANK", "key": "AFAO01000041"}, {"db": "GENBANK", "key": "AFAO01000042"}, {"db": "GENBANK", "key": "AFAO01000043"}, {"db": "GENBANK", "key": "AFAO01000044"}, {"db": "GENBANK", "key": "AFAO01000045"}, {"db": "GENBANK", "key": "AFAO01000046"}, {"db": "GENBANK", "key": "AFAO01000047"}, {"db": "GENBANK", "key": "AFAO01000048"}, {"db": "GENBANK", "key": "AFAO01000049"}, {"db": "GENBANK", "key": "AFAO01000050"}, {"db": "GENBANK", "key": "AFAO01000051"}, {"db": "GENBANK", "key": "AFAO01000052"}, {"db": "GENBANK", "key": "AFAO01000053"}, {"db": "GENBANK", "key": "AFAO01000054"}, {"db": "GENBANK", "key": "AFAO01000055"}, {"db": "GENBANK", "key": "AFAO01000056"}, {"db": "GENBANK", "key": "AFAO01000057"}, {"db": "GENBANK", "key": "AFAO01000058"}, {"db": "GENBANK", "key": "AFAO01000059"}, {"db": "GENBANK", "key": "AFAO01000060"}, {"db": "GENBANK", "key": "AFAO01000061"}, {"db": "GENBANK", "key": "AFAO01000062"}, {"db": "GENBANK", "key": "AFAO01000063"}], "notes": [], "created": "2017-05-04T14:57:21.636Z", "modified": "2020-01-21T13:56:04.770Z"}, {"entity": "publication", "iuid": "a6b88208359d498db34ce8a14fa0d829", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a6b88208359d498db34ce8a14fa0d829.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a6b88208359d498db34ce8a14fa0d829"}}, "title": "Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1.", "authors": [{"family": "Bown", "given": "Matthew J", "initials": "MJ"}, {"family": "Jones", "given": "Gregory T", "initials": "GT"}, {"family": "Harrison", "given": "Seamus C", "initials": "SC"}, {"family": "Wright", "given": "Benjamin J", "initials": "BJ"}, {"family": "Bumpstead", "given": "Suzannah", "initials": "S"}, {"family": "Baas", "given": "Annette F", "initials": "AF"}, {"family": "Gretarsdottir", "given": "Solveig", "initials": "S"}, {"family": "Badger", "given": "Stephen A", "initials": "SA"}, {"family": "Bradley", "given": "Declan T", "initials": "DT"}, {"family": "Burnand", "given": "Kevin", "initials": "K"}, {"family": "Child", "given": "Anne H", "initials": "AH"}, {"family": "Clough", "given": "Rachel E", "initials": "RE"}, {"family": "Cockerill", "given": "Gillian", "initials": "G"}, {"family": "Hafez", "given": "Hany", "initials": "H"}, {"family": "Scott", "given": "D Julian A", "initials": "DJ"}, {"family": "Futers", "given": "Simon", "initials": "S"}, {"family": "Johnson", "given": "Anne", "initials": "A"}, {"family": "Sohrabi", "given": "Soroush", "initials": "S"}, {"family": "Smith", "given": "Alberto", "initials": "A"}, {"family": "Thompson", "given": "Matthew M", "initials": "MM"}, {"family": "van Bockxmeer", "given": "Frank M", "initials": "FM"}, {"family": "Waltham", "given": "Matthew", "initials": "M"}, {"family": "Matthiasson", "given": "Stefan E", "initials": "SE"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Blankensteijn", "given": "Jan D", "initials": "JD"}, {"family": "Teijink", "given": "Joep A W", "initials": "JA"}, {"family": "Wijmenga", "given": "Cisca", "initials": "C"}, {"family": "de Graaf", "given": "Jacqueline", "initials": "J"}, {"family": "Kiemeney", "given": "Lambertus A", "initials": "LA"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "McPherson", "given": "Ruth", "initials": "R"}, {"family": "CARDIoGRAM Consortium", "given": null, "initials": null}, {"family": "Global BPgen Consortium", "given": null, "initials": null}, {"family": "DIAGRAM Consortium", "given": null, "initials": null}, {"family": "VRCNZ Consortium", "given": null, "initials": null}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Palmen", "given": "Jutta", "initials": "J"}, {"family": "Smith", "given": "Andrew J", "initials": "AJ"}, {"family": "Sylvius", "given": "Nicolas", "initials": "N"}, {"family": "Wild", "given": "John B", "initials": "JB"}, {"family": "Refstrup", "given": "Mette", "initials": "M"}, {"family": "Edkins", "given": "Sarah", "initials": "S"}, {"family": "Gwilliam", "given": "Rhian", "initials": "R"}, {"family": "Hunt", "given": "Sarah E", "initials": "SE"}, {"family": "Potter", "given": "Simon", "initials": "S"}, {"family": "Lindholt", "given": "Jes S", "initials": "JS"}, {"family": "Frikke-Schmidt", "given": "Ruth", "initials": "R"}, {"family": "Tybj\u00e6rg-Hansen", "given": "Anne", "initials": "A"}, {"family": "Hughes", "given": "Anne E", "initials": "AE"}, {"family": "Golledge", "given": "Jonathan", "initials": "J"}, {"family": "Norman", "given": "Paul E", "initials": "PE"}, {"family": "van Rij", "given": "Andre", "initials": "A"}, {"family": "Powell", "given": "Janet T", "initials": "JT"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Thompson", "given": "John R", "initials": "JR"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Sayers", "given": "Robert D", "initials": "RD"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}], "type": "journal article", "published": "2011-11-11", "journal": {"volume": "89", "issn": "1537-6605", "issue": "5", "pages": "619-627", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "Abdominal aortic aneurysm (AAA) is a common cause of morbidity and mortality and has a significant heritability. We carried out a genome-wide association discovery study of 1866 patients with AAA and 5435 controls and replication of promising signals (lead SNP with a p value < 1\u00a0\u00d7 10(-5)) in 2871 additional cases and 32,687 controls and performed further follow-up in 1491 AAA and 11,060 controls. In the discovery study, nine loci demonstrated association with AAA (p < 1\u00a0\u00d7 10(-5)). In the replication sample, the lead SNP at one of these loci, rs1466535, located within intron 1 of low-density-lipoprotein receptor-related protein 1 (LRP1) demonstrated significant association (p = 0.0042). We confirmed the association of rs1466535 and AAA in our follow-up study (p = 0.035). In a combined analysis (6228 AAA and 49182 controls), rs1466535 had a consistent effect size and direction in all sample sets (combined p = 4.52\u00a0\u00d7 10(-10), odds ratio 1.15 [1.10-1.21]). No associations were seen for either rs1466535 or the 12q13.3 locus in independent association studies of coronary artery disease, blood pressure, diabetes, or hyperlipidaemia, suggesting that this locus is specific to AAA. Gene-expression studies demonstrated a trend toward increased LRP1 expression for the rs1466535 CC genotype in arterial tissues; there was a significant (p = 0.029) 1.19-fold (1.04-1.36) increase in LRP1 expression in CC homozygotes compared to TT homozygotes in aortic adventitia. Functional studies demonstrated that rs1466535 might alter a SREBP-1 binding site and influence enhancer activity at the locus. In conclusion, this study has identified a biologically plausible genetic variant associated specifically with AAA, and we suggest that this variant has a possible functional role in LRP1 expression.", "doi": "10.1016/j.ajhg.2011.10.002", "pmid": "22055160", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0002-9297(11)00436-8"}, {"db": "pmc", "key": "PMC3213391"}], "notes": [], "created": "2017-05-04T15:00:39.530Z", "modified": "2020-01-21T13:56:04.313Z"}, {"entity": "publication", "iuid": "bb6519b0dd8d478ebba28f1e622005ec", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb6519b0dd8d478ebba28f1e622005ec.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb6519b0dd8d478ebba28f1e622005ec"}}, "title": "Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.", "authors": [{"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Zaghlool", "given": "Ammar", "initials": "A"}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Wetterbom", "given": "Anna", "initials": "A"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2011-11-06", "journal": {"volume": "18", "issn": "1545-9985", "issue": "12", "pages": "1435-1440", "title": "Nat. Struct. Mol. Biol.", "issn-l": "1545-9985"}, "abstract": "Transcriptome sequencing allows for analysis of mature RNAs at base pair resolution. Here we show that RNA-seq can also be used for studying nascent RNAs undergoing transcription. We sequenced total RNA from human brain and liver and found a large fraction of reads (up to 40%) within introns. Intronic RNAs were abundant in brain tissue, particularly for genes involved in axonal growth and synaptic transmission. Moreover, we detected significant differences in intronic RNA levels between fetal and adult brains. We show that the pattern of intronic sequence read coverage is explained by nascent transcription in combination with co-transcriptional splicing. Further analysis of co-transcriptional splicing indicates a correlation between slowly removed introns and alternative splicing. Our data show that sequencing of total RNA provides unique insight into the transcriptional processes in the cell, with particular importance for normal brain development.", "doi": "10.1038/nsmb.2143", "pmid": "22056773", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "nsmb.2143"}], "notes": [], "created": "2017-05-04T14:57:22.242Z", "modified": "2021-07-08T12:52:24.403Z"}, {"entity": "publication", "iuid": "bb261b9837634c8da859d0e1b65915d9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb261b9837634c8da859d0e1b65915d9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb261b9837634c8da859d0e1b65915d9"}}, "title": "Inhibition of proteasome deubiquitinating activity as a new cancer therapy.", "authors": [{"family": "D'Arcy", "given": "P\u00e1draig", "initials": "P"}, {"family": "Brnjic", "given": "Slavica", "initials": "S"}, {"family": "Olofsson", "given": "Maria H\u00e4gg", "initials": "MH"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Lindsten", "given": "Kristina", "initials": "K"}, {"family": "De Cesare", "given": "Michelandrea", "initials": "M"}, {"family": "Perego", "given": "Paola", "initials": "P"}, {"family": "Sadeghi", "given": "Behnam", "initials": "B"}, {"family": "Hassan", "given": "Moustapha", "initials": "M"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Linder", "given": "Stig", "initials": "S"}], "type": "journal article", "published": "2011-11-06", "journal": {"volume": "17", "issn": "1546-170X", "issue": "12", "pages": "1636-1640", "title": "Nat. Med.", "issn-l": "1078-8956"}, "abstract": "Ubiquitin-tagged substrates are degraded by the 26S proteasome, which is a multisubunit complex comprising a proteolytic 20S core particle capped by 19S regulatory particles. The approval of bortezomib for the treatment of multiple myeloma validated the 20S core particle as an anticancer drug target. Here we describe the small molecule b-AP15 as a previously unidentified class of proteasome inhibitor that abrogates the deubiquitinating activity of the 19S regulatory particle. b-AP15 inhibited the activity of two 19S regulatory-particle-associated deubiquitinases, ubiquitin C-terminal hydrolase 5 (UCHL5) and ubiquitin-specific peptidase 14 (USP14), resulting in accumulation of polyubiquitin. b-AP15 induced tumor cell apoptosis that was insensitive to TP53 status and overexpression of the apoptosis inhibitor BCL2. We show that treatment with b-AP15 inhibited tumor progression in four different in vivo solid tumor models and inhibited organ infiltration in an acute myeloid leukemia model. Our results show that the deubiquitinating activity of the 19S regulatory particle is a new anticancer drug target.", "doi": "10.1038/nm.2536", "pmid": "22057347", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "nm.2536"}, {"db": "GEO", "key": "GSE24150"}], "notes": [], "created": "2017-05-04T15:02:53.335Z", "modified": "2017-05-30T14:49:33.477Z"}, {"entity": "publication", "iuid": "46874109988f4ab68218f77bac6175fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/46874109988f4ab68218f77bac6175fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/46874109988f4ab68218f77bac6175fb"}}, "title": "Plasma profiling reveals human fibulin-1 as candidate marker for renal impairment.", "authors": [{"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Hedberg", "given": "Jesper J", "initials": "JJ"}, {"family": "D\u00f6nnes", "given": "Pierre R", "initials": "PR"}, {"family": "Schuppe-Koistinen", "given": "Ina", "initials": "I"}, {"family": "Hanschke", "given": "Stephan", "initials": "S"}, {"family": "Schindler", "given": "Ralf", "initials": "R"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2011-11-04", "journal": {"volume": "10", "issn": "1535-3907", "issue": "11", "pages": "4925-4934", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "There is a need for reliable and sensitive biomarkers for renal impairments to detect early signs of kidney toxicity and to monitor progression of disease. Here, antibody suspension bead arrays were applied to profile plasma samples from patients with four types of kidney disorders: glomerulonephritis, diabetic nephropathy, obstructive uropathy, and analgesic abuse. In total, 200 clinical renal-associated cases and control plasma samples from different cohorts were profiled. Parallel plasma protein profiles were obtained using biotinylated and nonfractionated samples and a selected set of 94 proteins targeted by 129 antigen-purified polyclonal antibodies. Out of the analyzed target proteins, human fibulin-1 was detected at significantly higher levels in the glomerulonephritis patient group compared to the controls and with elevated levels in patient samples for all other renal disorders investigated. Two polyclonal antibodies and one monoclonal antibody directed toward separate, nonoverlapping epitopes showed the same trend in the discovery cohorts. A technical verification using Western blot analysis of selected patient plasma confirmed the trends toward higher abundance of the target protein in disease samples. Furthermore, a verification study was carried out in the context of glomerulonephritis using an independent case and control cohort, and this confirmed the results from the discovery cohort, suggesting that plasma levels of fibulin-1 could serve as a potential indicator to monitor kidney malfunction or kidney damage.", "doi": "10.1021/pr200286c", "pmid": "21888404", "labels": {"Affinity Proteomics Stockholm": "Collaborative"}, "xrefs": [], "notes": [], "created": "2017-10-30T10:36:18.646Z", "modified": "2021-07-08T13:44:33.201Z"}, {"entity": "publication", "iuid": "d7691a31556f4402bfbd57d406b08a8c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7691a31556f4402bfbd57d406b08a8c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7691a31556f4402bfbd57d406b08a8c"}}, "title": "SWI/SNF regulates the alternative processing of a specific subset of pre-mRNAs in Drosophila melanogaster.", "authors": [{"family": "Waldholm", "given": "Johan", "initials": "J"}, {"family": "Wang", "given": "Zhi", "initials": "Z"}, {"family": "Brodin", "given": "David", "initials": "D"}, {"family": "Tyagi", "given": "Anu", "initials": "A"}, {"family": "Yu", "given": "Simei", "initials": "S"}, {"family": "Theopold", "given": "Ulrich", "initials": "U"}, {"family": "Farrants", "given": "Ann Kristin \u00d6stlund", "initials": "AK"}, {"family": "Visa", "given": "Neus", "initials": "N"}], "type": "journal article", "published": "2011-11-02", "journal": {"volume": "12", "issn": "1471-2199", "issue": null, "pages": "46", "title": "BMC Mol. Biol.", "issn-l": "1471-2199"}, "abstract": "The SWI/SNF chromatin remodeling factors have the ability to remodel nucleosomes and play essential roles in key developmental processes. SWI/SNF complexes contain one subunit with ATPase activity, which in Drosophila melanogaster is called Brahma (Brm). The regulatory activities of SWI/SNF have been attributed to its influence on chromatin structure and transcription regulation, but recent observations have revealed that the levels of Brm affect the relative abundances of transcripts that are formed by alternative splicing and/or polyadenylation of the same pre-mRNA.\n\nWe have investigated whether the function of Brm in pre-mRNA processing in Drosophila melanogaster is mediated by Brm alone or by the SWI/SNF complex. We have analyzed the effects of depleting individual SWI/SNF subunits on pre-mRNA processing throughout the genome, and we have identified a subset of transcripts that are affected by depletion of the SWI/SNF core subunits Brm, Snr1 or Mor. The fact that depletion of different subunits targets a subset of common transcripts suggests that the SWI/SNF complex is responsible for the effects observed on pre-mRNA processing when knocking down Brm. We have also depleted Brm in larvae and we have shown that the levels of SWI/SNF affect the pre-mRNA processing outcome in vivo.\n\nWe have shown that SWI/SNF can modulate alternative pre-mRNA processing, not only in cultured cells but also in vivo. The effect is restricted to and specific for a subset of transcripts. Our results provide novel insights into the mechanisms by which SWI/SNF regulates transcript diversity and proteomic diversity in higher eukaryotes.", "doi": "10.1186/1471-2199-12-46", "pmid": "22047075", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "1471-2199-12-46"}, {"db": "pmc", "key": "PMC3221629"}], "notes": [], "created": "2017-05-04T15:03:09.546Z", "modified": "2017-05-30T14:50:43.929Z"}, {"entity": "publication", "iuid": "d9fa2ac7e63d4b53a6e2ab95554a276a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9fa2ac7e63d4b53a6e2ab95554a276a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9fa2ac7e63d4b53a6e2ab95554a276a"}}, "title": "Hypothalamic mitochondrial dysfunction associated with anorexia in the anx/anx mouse.", "authors": [{"family": "Lindfors", "given": "Charlotte", "initials": "C"}, {"family": "Nilsson", "given": "Ida A K", "initials": "IA"}, {"family": "Garcia-Roves", "given": "Pablo M", "initials": "PM"}, {"family": "Zuberi", "given": "Aamir R", "initials": "AR"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Donahue", "given": "Leah Rae", "initials": "LR"}, {"family": "Roopenian", "given": "Derry C", "initials": "DC"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Ekstr\u00f6m", "given": "Tomas J", "initials": "TJ"}, {"family": "Davisson", "given": "Muriel T", "initials": "MT"}, {"family": "H\u00f6kfelt", "given": "Tomas G M", "initials": "TG"}, {"family": "Schalling", "given": "Martin", "initials": "M"}, {"family": "Johansen", "given": "Jeanette E", "initials": "JE"}], "type": "journal article", "published": "2011-11-01", "journal": {"volume": "108", "issn": "1091-6490", "issue": "44", "pages": "18108-18113", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "The anorectic anx/anx mouse exhibits disturbed feeding behavior and aberrances, including neurodegeneration, in peptidergic neurons in the appetite regulating hypothalamic arcuate nucleus. Poor feeding in infants, as well as neurodegeneration, are common phenotypes in human disorders caused by dysfunction of the mitochondrial oxidative phosphorylation system (OXPHOS). We therefore hypothesized that the anorexia and degenerative phenotypes in the anx/anx mouse could be related to defects in the OXPHOS. In this study, we found reduced efficiency of hypothalamic OXPHOS complex I assembly and activity in the anx/anx mouse. We also recorded signs of increased oxidative stress in anx/anx hypothalamus, possibly as an effect of the decreased hypothalamic levels of fully assembled complex I, that were demonstrated by native Western blots. Furthermore, the Ndufaf1 gene, encoding a complex I assembly factor, was genetically mapped to the anx interval and found to be down-regulated in anx/anx mice. These results suggest that the anorexia and hypothalamic neurodegeneration of the anx/anx mouse are associated with dysfunction of mitochondrial complex I.", "doi": "10.1073/pnas.1114863108", "pmid": "22025706", "labels": {"Fluorescence Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1114863108"}, {"db": "pmc", "key": "PMC3207677"}], "notes": [], "created": "2017-05-04T14:55:18.035Z", "modified": "2021-07-08T13:44:33.684Z"}, {"entity": "publication", "iuid": "4ee3e6f46d4d45f2b05a33efaca4397e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4ee3e6f46d4d45f2b05a33efaca4397e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4ee3e6f46d4d45f2b05a33efaca4397e"}}, "title": "Abundant class of non-coding RNA regulates development in the social amoeba Dictyostelium discoideum.", "authors": [{"family": "Avesson", "given": "Lotta", "initials": "L"}, {"family": "Schumacher", "given": "Heiko T", "initials": "HT"}, {"family": "Fechter", "given": "Pierre", "initials": "P"}, {"family": "Romby", "given": "Pascale", "initials": "P"}, {"family": "Hellman", "given": "Ulf", "initials": "U"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2011-11-01", "journal": {"volume": "8", "issn": "1555-8584", "issue": "6", "pages": "1094-1104", "title": "RNA Biol", "issn-l": "1547-6286"}, "abstract": "Non-coding (nc)RNAs are important players in most biological processes. Although small RNAs such as microRNAs and small interfering RNAs have emerged as exceptionally important regulators of gene expression, great numbers of larger ncRNAs have also been identified. Many of these are abundant and differentially expressed but their functions have in most cases not been elucidated. The social amoeba Dictyostelium discoideum contain the ncRNAs commonly found in eukaryotes. In addition, we previously reported the identification of two novel classes of 42-65 nt long stem-loop forming RNAs, Class I and Class II RNAs, with unknown function. In this study we have further characterized these abundant ncRNAs, which are down regulated during development. We have confirmed expression of 29 Class I RNAs and experimentally verified the formation of the computationally predicted short conserved stem structure. Furthermore, we have for the first time created knockout strains for several small ncRNA genes in D. discoideum and found that deletion of one of the Class I RNAs, DdR-21, results in aberrant development. In addition we have shown that this Class I RNA forms a complex with one or several proteins but do not appear to be associated with ribosomes or polysomes. In a pull down assay, several proteins interacting with DdR-21 were identified, one of these has two RNA recognition motifs (RRMs). The purified RRM containing protein was demonstrated to bind directly and specifically to DdR-21.", "doi": "10.4161/rna.8.6.17214", "pmid": "21941123", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "17214"}], "notes": [], "created": "2017-05-04T14:57:27.385Z", "modified": "2020-01-21T13:56:10.288Z"}, {"entity": "publication", "iuid": "e85fbabce41642a5a4e00ff4b128069a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e85fbabce41642a5a4e00ff4b128069a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e85fbabce41642a5a4e00ff4b128069a"}}, "title": "Western blotting via proximity ligation for high performance protein analysis.", "authors": [{"family": "Liu", "given": "Yanling", "initials": "Y"}, {"family": "Gu", "given": "Jijuan", "initials": "J"}, {"family": "Hagner-McWhirter", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Sathiyanarayanan", "given": "Poojahrau", "initials": "P"}, {"family": "Gullberg", "given": "Mats", "initials": "M"}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O"}, {"family": "Johansson", "given": "Johan", "initials": "J"}, {"family": "Hammond", "given": "Maria", "initials": "M", "orcid": "0000-0002-8375-6676", "researcher": {"href": "https://publications.scilifelab.se/researcher/78703c93891e4827aabb35c2011be9f2.json"}}, {"family": "Ivansson", "given": "Daniel", "initials": "D"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "comparative study", "published": "2011-11-00", "journal": {"volume": "10", "issn": "1535-9484", "issue": "11", "pages": "O111.011031", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Western blotting is a powerful and widely used method, but limitations in detection sensitivity and specificity, and dependence upon high quality antibodies to detect targeted proteins, are hurdles to overcome. The in situ proximity ligation assay, based on dual antibody recognition and powerful localized signal amplification, offers increased detection sensitivity and specificity, along with an ability to identify complex targets such as phosphorylated or interacting proteins. Here we have applied the in situ proximity ligation assay mechanism in Western blotting. This combination allowed the use of isothermal rolling circle amplification of DNA molecules formed in target-specific ligation reaction, for 16-fold or greater increase in detection sensitivity. The increased specificity because of dual antibody recognition ensured highly selective assays, detecting the specific band when combinations of two cross-reactive antitubulin antibodies were used (i.e. both producing distinct nonspecific bands in traditional Western blotting). We also demonstrated detection of phosphorylated platelet-derived growth factor receptor \u03b2 by proximity ligation with one antibody directed against the receptor and another directed against the phosphorylated tyrosine residue. This avoided the need for stripping and re-probing the membrane or aligning two separate traditional blots. We demonstrate that the high-performance in situ proximity ligation-based Western blotting described herein is compatible with detection via enhanced chemiluminescence and fluorescence detection systems, and can thus be readily employed in any laboratory.", "doi": "10.1074/mcp.O111.011031", "pmid": "21813417", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "S1535-9476(20)30109-2"}, {"db": "pmc", "key": "PMC3226413"}], "notes": [], "created": "2017-05-04T14:55:21.367Z", "modified": "2023-04-14T13:56:31.236Z"}, {"entity": "publication", "iuid": "e07b816699de4cc785bc698cd13f8392", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e07b816699de4cc785bc698cd13f8392.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e07b816699de4cc785bc698cd13f8392"}}, "title": "The Human Protein Atlas as a proteomic resource for biomarker discovery.", "authors": [{"family": "Pont\u00e9n", "given": "F", "initials": "F"}, {"family": "Schwenk", "given": "J M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Asplund", "given": "A", "initials": "A"}, {"family": "Edqvist", "given": "P-H D", "initials": "PH"}], "type": "journal article", "published": "2011-11-00", "journal": {"volume": "270", "issn": "1365-2796", "issue": "5", "pages": "428-446", "title": "J. Intern. Med.", "issn-l": "0954-6820"}, "abstract": "The analysis of tissue-specific expression at both the gene and protein levels is vital for understanding human biology and disease. Antibody-based proteomics provides a strategy for the systematic generation of antibodies against all human proteins to combine with protein profiling in tissues and cells using tissue microarrays, immunohistochemistry and immunofluorescence. The Human Protein Atlas project was launched in 2003 with the aim of creating a map of protein expression patterns in normal cells, tissues and cancer. At present, 11,200 unique proteins corresponding to over 50% of all human protein-encoding genes have been analysed. All protein expression data, including underlying high-resolution images, are published on the free and publically available Human Protein Atlas portal (http://www.proteinatlas.org). This database provides an important source of information for numerous biomedical research projects, including biomarker discovery efforts. Moreover, the global analysis of how our genome is expressed at the protein level has provided basic knowledge on the ubiquitous expression of a large proportion of our proteins and revealed the paucity of cell- and tissue-type-specific proteins.", "doi": "10.1111/j.1365-2796.2011.02427.x", "pmid": "21752111", "labels": {"Tissue Profiling": null, "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:47.336Z", "modified": "2021-07-08T12:07:33.932Z"}, {"entity": "publication", "iuid": "0cd707a2aaa441a2a8b8d8ddcdec7fff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0cd707a2aaa441a2a8b8d8ddcdec7fff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0cd707a2aaa441a2a8b8d8ddcdec7fff"}}, "title": "Targeted enrichment of genomic DNA regions for next-generation sequencing.", "authors": [{"family": "Mertes", "given": "Florian", "initials": "F"}, {"family": "Elsharawy", "given": "Abdou", "initials": "A"}, {"family": "Sauer", "given": "Sascha", "initials": "S"}, {"family": "van Helvoort", "given": "Joop M L M", "initials": "JM"}, {"family": "van der Zaag", "given": "P J", "initials": "PJ"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}, {"family": "Lehrach", "given": "Hans", "initials": "H"}, {"family": "Brookes", "given": "Anthony J", "initials": "AJ"}], "type": "journal article", "published": "2011-11-00", "journal": {"volume": "10", "issn": "2041-2657", "issue": "6", "pages": "374-386", "title": "Brief Funct Genomics", "issn-l": "2041-2649"}, "abstract": "In this review, we discuss the latest targeted enrichment methods and aspects of their utilization along with second-generation sequencing for complex genome analysis. In doing so, we provide an overview of issues involved in detecting genetic variation, for which targeted enrichment has become a powerful tool. We explain how targeted enrichment for next-generation sequencing has made great progress in terms of methodology, ease of use and applicability, but emphasize the remaining challenges such as the lack of even coverage across targeted regions. Costs are also considered versus the alternative of whole-genome sequencing which is becoming ever more affordable. We conclude that targeted enrichment is likely to be the most economical option for many years to come in a range of settings.", "doi": "10.1093/bfgp/elr033", "pmid": "22121152", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "elr033"}, {"db": "pmc", "key": "PMC3245553"}], "notes": [], "created": "2017-05-04T14:57:17.678Z", "modified": "2021-07-07T13:54:46.041Z"}, {"entity": "publication", "iuid": "f1401f1407364e189b734a9b3e1582c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1401f1407364e189b734a9b3e1582c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1401f1407364e189b734a9b3e1582c0"}}, "title": "Generation of monospecific antibodies based on affinity capture of polyclonal antibodies.", "authors": [{"family": "Hjelm", "given": "Barbara", "initials": "B"}, {"family": "Forsstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Johannesson", "given": "Henrik", "initials": "H"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Sj\u00f6berg", "given": "Anna", "initials": "A"}, {"family": "Rockberg", "given": "Johan", "initials": "J"}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Johansson", "given": "Christine", "initials": "C"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2011-11-00", "journal": {"volume": "20", "issn": "1469-896X", "issue": "11", "pages": "1824-1835", "title": "Protein Sci.", "issn-l": "0961-8368"}, "abstract": "A method is described to generate and validate antibodies based on mapping the linear epitopes of a polyclonal antibody followed by sequential epitope-specific capture using synthetic peptides. Polyclonal antibodies directed towards four proteins RBM3, SATB2, ANLN, and CNDP1, potentially involved in human cancers, were selected and antibodies to several non-overlapping epitopes were generated and subsequently validated by Western blot, immunohistochemistry, and immunofluorescence. For all four proteins, a dramatic difference in functionality could be observed for these monospecific antibodies directed to the different epitopes. In each case, at least one antibody was obtained with full functionality across all applications, while other epitope-specific fractions showed no or little functionality. These results present a path forward to use the mapped binding sites of polyclonal antibodies to generate epitope-specific antibodies, providing an attractive approach for large-scale efforts to characterize the human proteome by antibodies.", "doi": "10.1002/pro.716", "pmid": "21898641", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Spatial Proteomics": null, "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC3267947"}], "notes": [], "created": "2017-05-04T14:55:09.271Z", "modified": "2021-07-08T13:44:33.721Z"}, {"entity": "publication", "iuid": "1e582e233a684cd7ac3a526fdb677dc9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1e582e233a684cd7ac3a526fdb677dc9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1e582e233a684cd7ac3a526fdb677dc9"}}, "title": "Gene copy number aberrations are associated with survival in histologic subgroups of non-small cell lung cancer.", "authors": [{"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Edlund", "given": "Karolina", "initials": "K"}, {"family": "Holmberg", "given": "Lars", "initials": "L"}, {"family": "Kultima", "given": "Hanna G\u00f6ransson", "initials": "HG"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Ekman", "given": "Simon", "initials": "S"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Scheibenflug", "given": "Lena", "initials": "L"}, {"family": "Lamberg", "given": "Kristina", "initials": "K"}, {"family": "Myrdal", "given": "Gunnar", "initials": "G"}, {"family": "Berglund", "given": "Anders", "initials": "A"}, {"family": "Andersson", "given": "Annsofie", "initials": "A"}, {"family": "Lambe", "given": "Mats", "initials": "M"}, {"family": "Nyberg", "given": "Fredrik", "initials": "F"}, {"family": "Thomas", "given": "Andrew", "initials": "A"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Botling", "given": "Johan", "initials": "J"}], "type": "comparative study", "published": "2011-11-00", "journal": {"volume": "6", "issn": "1556-1380", "issue": "11", "pages": "1833-1840", "title": "J Thorac Oncol", "issn-l": "1556-0864"}, "abstract": "Non-small cell lung cancer (NSCLC) is characterized by a multitude of genetic aberrations with unknown clinical impact. In this study, we aimed to identify gene copy number changes that correlate with clinical outcome in NSCLC. To maximize the chance to identify clinically relevant events, we applied a strategy involving two prognostically extreme patient groups.\n\nShort-term (<20 month; n = 53) and long-term survivors (>58 month; n = 47) were selected from a clinically well-characterized NSCLC patient cohort with available fresh frozen tumor specimens. The samples were analyzed using high-resolution single-nucleotide polymorphism array technology to assess gene copy number variations and array-based gene expression profiling. The molecular data were combined with information on clinical parameters.\n\nGenetic aberrations were strongly associated with tumor histology. In adenocarcinoma (n = 50), gene copy number gains on chromosome 8q21-q24.3 (177 genes) were more frequent in long-term than in short-term survivors. In squamous cell carcinoma (n = 28), gains on chromosome 14q23.1-24.3 (133 genes) were associated with shorter survival, whereas losses in a neighboring region, 14q31.1-32.33 (110 genes), correlated with favorable outcome. In accordance with copy number gains and losses, messenger RNA expression levels of corresponding genes were increased or decreased, respectively.\n\nComprehensive tumor profiling permits the integration of genomic, histologic, and clinical data. We identified gene copy number gains and losses, with corresponding changes in messenger RNA levels that were associated with prognosis in adenocarcinoma and squamous cell carcinoma of the lung.", "doi": "10.1097/JTO.0b013e3182295917", "pmid": "22011649", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "S1556-0864(15)32245-0"}], "notes": [], "created": "2017-05-04T15:02:52.434Z", "modified": "2017-05-30T12:35:49.266Z"}, {"entity": "publication", "iuid": "bb6fafd791694fa59add52f553a585f6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bb6fafd791694fa59add52f553a585f6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bb6fafd791694fa59add52f553a585f6"}}, "title": "Increasing the dynamic range of in situ PLA.", "authors": [{"family": "Clausson", "given": "Carl-Magnus", "initials": "C"}, {"family": "Allalou", "given": "Amin", "initials": "A"}, {"family": "Weibrecht", "given": "Irene", "initials": "I"}, {"family": "Mahmoudi", "given": "Salah", "initials": "S"}, {"family": "Farnebo", "given": "Marianne", "initials": "M"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "W\u00e4hlby", "given": "Carolina", "initials": "C", "orcid": "0000-0002-4139-7003", "researcher": {"href": "https://publications.scilifelab.se/researcher/c50194fbc8524d95b7152663ccf17f29.json"}}, {"family": "S\u00f6derberg", "given": "Ola", "initials": "O"}], "type": "letter", "published": "2011-10-28", "journal": {"volume": "8", "issn": "1548-7105", "issue": "11", "pages": "892-893", "title": "Nat. Methods", "issn-l": "1548-7091"}, "abstract": null, "doi": "10.1038/nmeth.1743", "pmid": "22036742", "labels": {"BioImage Informatics": "Collaborative", "PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Collaborative", "Bioinformatics (NBIS)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nmeth.1743"}], "notes": [], "created": "2017-05-04T14:55:21.665Z", "modified": "2023-04-14T13:56:31.396Z"}, {"entity": "publication", "iuid": "a8086f9ee6804106831134f4ea762e2d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8086f9ee6804106831134f4ea762e2d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8086f9ee6804106831134f4ea762e2d"}}, "title": "Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity.", "authors": [{"family": "Rasmussen", "given": "Markus", "initials": "M"}, {"family": "Sundstr\u00f6m", "given": "Magnus", "initials": "M"}, {"family": "G\u00f6ransson Kultima", "given": "Hanna", "initials": "H"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Micke", "given": "Patrick", "initials": "P"}, {"family": "Birgisson", "given": "Helgi", "initials": "H"}, {"family": "Glimelius", "given": "Bengt", "initials": "B"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2011-10-24", "journal": {"volume": "12", "issn": "1474-760X", "issue": "10", "pages": "R108", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "We describe a bioinformatic tool, Tumor Aberration Prediction Suite (TAPS), for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. It includes detailed visualization of genomic segment characteristics and iterative pattern recognition for copy number identification, and does not require patient-matched normal samples. TAPS can be used to identify chromosomal aberrations with high sensitivity even when the proportion of tumor cells is as low as 30%. Analysis of cancer samples indicates that TAPS is well suited to investigate samples with aneuploidy and tumor heterogeneity, which is commonly found in many types of solid tumors.", "doi": "10.1186/gb-2011-12-10-r108", "pmid": "22023820", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "gb-2011-12-10-r108"}, {"db": "pmc", "key": "PMC3333778"}], "notes": [], "created": "2017-05-04T15:02:51.918Z", "modified": "2017-05-30T14:49:28.836Z"}, {"entity": "publication", "iuid": "a8833ea487ae49f5b5ea4b85fde52c93", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8833ea487ae49f5b5ea4b85fde52c93.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8833ea487ae49f5b5ea4b85fde52c93"}}, "title": "Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.", "authors": [{"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Sehmi", "given": "Joban", "initials": "J"}, {"family": "Li", "given": "Xinzhong", "initials": "X"}, {"family": "Wass", "given": "Mark N", "initials": "MN"}, {"family": "Van der Harst", "given": "Pim", "initials": "P"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Kavousi", "given": "Maryam", "initials": "M"}, {"family": "Baumeister", "given": "Sebastian E", "initials": "SE"}, {"family": "Coin", "given": "Lachlan J", "initials": "LJ"}, {"family": "Deng", "given": "Guohong", "initials": "G"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Heard-Costa", "given": "Nancy L", "initials": "NL"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "K\u00fchnel", "given": "Brigitte", "initials": "B"}, {"family": "Kumar", "given": "Vinod", "initials": "V"}, {"family": "Lagou", "given": "Vasiliki", "initials": "V"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Vidal", "given": "Pedro Marques", "initials": "PM"}, {"family": "Mateo Leach", "given": "Irene", "initials": "I"}, {"family": "O'Reilly", "given": "Paul F", "initials": "PF"}, {"family": "Peden", "given": "John F", "initials": "JF"}, {"family": "Rahmioglu", "given": "Nilufer", "initials": "N"}, {"family": "Soininen", "given": "Pasi", "initials": "P"}, {"family": "Speliotes", "given": "Elizabeth K", "initials": "EK"}, {"family": "Yuan", "given": "Xin", "initials": "X"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Alizadeh", "given": "Behrooz Z", "initials": "BZ"}, {"family": "Atwood", "given": "Larry D", "initials": "LD"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Brown", "given": "Morris J", "initials": "MJ"}, {"family": "Charoen", "given": "Pimphen", "initials": "P"}, {"family": "Cucca", "given": "Francesco", "initials": "F"}, {"family": "Das", "given": "Debashish", "initials": "D"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJ"}, {"family": "Dixon", "given": "Anna L", "initials": "AL"}, {"family": "D\u00f6ring", "given": "Angela", "initials": "A"}, {"family": "Ehret", "given": "Georg", "initials": "G"}, {"family": "Eyjolfsson", "given": "Gudmundur I", "initials": "GI"}, {"family": "Farrall", "given": "Martin", "initials": "M"}, {"family": "Forouhi", "given": "Nita G", "initials": "NG"}, {"family": "Friedrich", "given": "Nele", "initials": "N"}, {"family": "Goessling", "given": "Wolfram", "initials": "W"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hartikainen", "given": "Anna-Liisa", "initials": "AL"}, {"family": "Heath", "given": "Simon", "initials": "S"}, {"family": "Hirschfield", "given": "Gideon M", "initials": "GM"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Hypp\u00f6nen", "given": "Elina", "initials": "E"}, {"family": "Janssen", "given": "Harry L A", "initials": "HL"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Kangas", "given": "Antti J", "initials": "AJ"}, {"family": "Kema", "given": "Ido P", "initials": "IP"}, {"family": "K\u00fchn", "given": "Jens P", "initials": "JP"}, {"family": "Lai", "given": "Sandra", "initials": "S"}, {"family": "Lathrop", "given": "Mark", "initials": "M"}, {"family": "Lerch", "given": "Markus M", "initials": "MM"}, {"family": "Li", "given": "Yun", "initials": "Y"}, {"family": "Liang", "given": "T Jake", "initials": "TJ"}, {"family": "Lin", "given": "Jing-Ping", "initials": "JP"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Moffatt", "given": "Miriam F", "initials": "MF"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Musunuru", "given": "Kiran", "initials": "K"}, {"family": "Nakamura", "given": "Yusuke", "initials": "Y"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Olafsson", "given": "Isleifur", "initials": "I"}, {"family": "Penninx", "given": "Brenda W", "initials": "BW"}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Prins", "given": "Bram P", "initials": "BP"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Puls", "given": "Ralf", "initials": "R"}, {"family": "Ruokonen", "given": "Aimo", "initials": "A"}, {"family": "Savolainen", "given": "Markku J", "initials": "MJ"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Schouten", "given": "Jeoffrey N L", "initials": "JN"}, {"family": "Seedorf", "given": "Udo", "initials": "U"}, {"family": "Sen-Chowdhry", "given": "Srijita", "initials": "S"}, {"family": "Siminovitch", "given": "Katherine A", "initials": "KA"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Tan", "given": "Wenting", "initials": "W"}, {"family": "Teslovich", "given": "Tanya M", "initials": "TM"}, {"family": "Tukiainen", "given": "Taru", "initials": "T"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Van der Klauw", "given": "Melanie M", "initials": "MM"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS"}, {"family": "Wallace", "given": "Chris", "initials": "C"}, {"family": "Wallaschofski", "given": "Henri", "initials": "H"}, {"family": "Wichmann", "given": "H-Erich", "initials": "HE"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "W\u00fcrtz", "given": "Peter", "initials": "P"}, {"family": "Xu", "given": "Chun", "initials": "C"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Alcohol Genome-wide Association (AlcGen) Consortium", "given": null, "initials": null}, {"family": "Diabetes Genetics Replication and Meta-analyses (DIAGRAM+) Study", "given": null, "initials": null}, {"family": "Genetic Investigation of Anthropometric Traits (GIANT) Consortium", "given": null, "initials": null}, {"family": "Global Lipids Genetics Consortium", "given": null, "initials": null}, {"family": "Genetics of Liver Disease (GOLD) Consortium", "given": null, "initials": null}, {"family": "International Consortium for Blood Pressure (ICBP-GWAS)", "given": null, "initials": null}, {"family": "Meta-analyses of Glucose and Insulin-Related Traits Consortium (MAGIC)", "given": null, "initials": null}, {"family": "Abecasis", "given": "Goncalo R", "initials": "GR"}, {"family": "Ahmadi", "given": "Kourosh R", "initials": "KR"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Caulfield", "given": "Mark", "initials": "M"}, {"family": "Cookson", "given": "William O", "initials": "WO"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Matsuda", "given": "Koichi", "initials": "K"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Meisinger", "given": "Christa", "initials": "C"}, {"family": "Mooser", "given": "Vincent", "initials": "V"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH"}, {"family": "Schumann", "given": "Gunter", "initials": "G"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Sternberg", "given": "Michael J E", "initials": "MJ"}, {"family": "Stolk", "given": "Ronald P", "initials": "RP"}, {"family": "Thomas", "given": "Howard C", "initials": "HC"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Uda", "given": "Manuela", "initials": "M"}, {"family": "Waeber", "given": "G\u00e9rard", "initials": "G"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "Wolffenbuttel", "given": "Bruce H R", "initials": "BH"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Ala-Korpela", "given": "Mika", "initials": "M"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Scott", "given": "James", "initials": "J"}, {"family": "J\u00e4rvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}], "type": "journal article", "published": "2011-10-16", "journal": {"volume": "43", "issn": "1546-1718", "issue": "11", "pages": "1131-1138", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Concentrations of liver enzymes in plasma are widely used as indicators of liver disease. We carried out a genome-wide association study in 61,089 individuals, identifying 42 loci associated with concentrations of liver enzymes in plasma, of which 32 are new associations (P = 10(-8) to P = 10(-190)). We used functional genomic approaches including metabonomic profiling and gene expression analyses to identify probable candidate genes at these regions. We identified 69 candidate genes, including genes involved in biliary transport (ATP8B1 and ABCB11), glucose, carbohydrate and lipid metabolism (FADS1, FADS2, GCKR, JMJD1C, HNF1A, MLXIPL, PNPLA3, PPP1R3B, SLC2A2 and TRIB1), glycoprotein biosynthesis and cell surface glycobiology (ABO, ASGR1, FUT2, GPLD1 and ST3GAL4), inflammation and immunity (CD276, CDH6, GCKR, HNF1A, HPR, ITGA1, RORA and STAT4) and glutathione metabolism (GSTT1, GSTT2 and GGT), as well as several genes of uncertain or unknown function (including ABHD12, EFHD1, EFNA1, EPHA2, MICAL3 and ZNF827). Our results provide new insight into genetic mechanisms and pathways influencing markers of liver function.", "doi": "10.1038/ng.970", "pmid": "22001757", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.970"}, {"db": "pmc", "key": "PMC3482372"}, {"db": "mid", "key": "NIHMS411128"}], "notes": [], "created": "2017-05-04T15:00:48.313Z", "modified": "2020-01-21T13:56:04.375Z"}, {"entity": "publication", "iuid": "6754e5e0fbbb4d85bc5707ec87f99a76", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6754e5e0fbbb4d85bc5707ec87f99a76.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6754e5e0fbbb4d85bc5707ec87f99a76"}}, "title": "MED12, the mediator complex subunit 12 gene, is mutated at high frequency in uterine leiomyomas.", "authors": [{"family": "M\u00e4kinen", "given": "Netta", "initials": "N"}, {"family": "Mehine", "given": "Miika", "initials": "M"}, {"family": "Tolvanen", "given": "Jaana", "initials": "J"}, {"family": "Kaasinen", "given": "Eevi", "initials": "E"}, {"family": "Li", "given": "Yilong", "initials": "Y"}, {"family": "Lehtonen", "given": "Heli J", "initials": "HJ"}, {"family": "Gentile", "given": "Massimiliano", "initials": "M"}, {"family": "Yan", "given": "Jian", "initials": "J"}, {"family": "Enge", "given": "Martin", "initials": "M"}, {"family": "Taipale", "given": "Minna", "initials": "M"}, {"family": "Aavikko", "given": "Mervi", "initials": "M"}, {"family": "Katainen", "given": "Riku", "initials": "R"}, {"family": "Virolainen", "given": "Elina", "initials": "E"}, {"family": "B\u00f6hling", "given": "Tom", "initials": "T"}, {"family": "Koski", "given": "Taru A", "initials": "TA"}, {"family": "Launonen", "given": "Virpi", "initials": "V"}, {"family": "Sj\u00f6berg", "given": "Jari", "initials": "J"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}, {"family": "Vahteristo", "given": "Pia", "initials": "P"}, {"family": "Aaltonen", "given": "Lauri A", "initials": "LA"}], "type": "journal article", "published": "2011-10-14", "journal": {"volume": "334", "issn": "1095-9203", "issue": "6053", "pages": "252-255", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Uterine leiomyomas, or fibroids, are benign tumors that affect millions of women worldwide and that can cause considerable morbidity. To study the genetic basis of this tumor type, we examined 18 uterine leiomyomas derived from 17 different patients by exome sequencing and identified tumor-specific mutations in the mediator complex subunit 12 (MED12) gene in 10. Through analysis of 207 additional tumors, we determined that MED12 is altered in 70% (159 of 225) of tumors from a total of 80 patients. The Mediator complex is a 26-subunit transcriptional regulator that bridges DNA regulatory sequences to the RNA polymerase II initiation complex. All mutations resided in exon 2, suggesting that aberrant function of this region of MED12 contributes to tumorigenesis.", "doi": "10.1126/science.1208930", "pmid": "21868628", "labels": {"Karolinska High Throughput Center (KHTC)": null}, "xrefs": [{"db": "pii", "key": "science.1208930"}, {"db": "GEO", "key": "GSE30673"}], "notes": [], "created": "2017-05-04T14:57:03.662Z", "modified": "2017-05-30T11:43:55.439Z"}, {"entity": "publication", "iuid": "ad9aced57e8c4591995ed1cdd8b2664d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ad9aced57e8c4591995ed1cdd8b2664d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ad9aced57e8c4591995ed1cdd8b2664d"}}, "title": "Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease.", "authors": [{"family": "Rivas", "given": "Manuel A", "initials": "MA"}, {"family": "Beaudoin", "given": "M\u00e9lissa", "initials": "M"}, {"family": "Gardet", "given": "Agnes", "initials": "A"}, {"family": "Stevens", "given": "Christine", "initials": "C"}, {"family": "Sharma", "given": "Yashoda", "initials": "Y"}, {"family": "Zhang", "given": "Clarence K", "initials": "CK"}, {"family": "Boucher", "given": "Gabrielle", "initials": "G"}, {"family": "Ripke", "given": "Stephan", "initials": "S"}, {"family": "Ellinghaus", "given": "David", "initials": "D"}, {"family": "Burtt", "given": "Noel", "initials": "N"}, {"family": "Fennell", "given": "Tim", "initials": "T"}, {"family": "Kirby", "given": "Andrew", "initials": "A"}, {"family": "Latiano", "given": "Anna", "initials": "A"}, {"family": "Goyette", "given": "Philippe", "initials": "P"}, {"family": "Green", "given": "Todd", "initials": "T"}, {"family": "Halfvarson", "given": "Jonas", "initials": "J"}, {"family": "Haritunians", "given": "Talin", "initials": "T"}, {"family": "Korn", "given": "Joshua M", "initials": "JM"}, {"family": "Kuruvilla", "given": "Finny", "initials": "F"}, {"family": "Lagac\u00e9", "given": "Caroline", "initials": "C"}, {"family": "Neale", "given": "Benjamin", "initials": "B"}, {"family": "Lo", "given": "Ken Sin", "initials": "KS"}, {"family": "Schumm", "given": "Phil", "initials": "P"}, {"family": "T\u00f6rkvist", "given": "Leif", "initials": "L"}, {"family": "National Institute of Diabetes and Digestive Kidney Diseases Inflammatory Bowel Disease Genetics Consortium (NIDDK IBDGC)", "given": null, "initials": null}, {"family": "United Kingdom Inflammatory Bowel Disease Genetics Consortium", "given": null, "initials": null}, {"family": "International Inflammatory Bowel Disease Genetics Consortium", "given": null, "initials": null}, {"family": "Dubinsky", "given": "Marla C", "initials": "MC"}, {"family": "Brant", "given": "Steven R", "initials": "SR"}, {"family": "Silverberg", "given": "Mark S", "initials": "MS"}, {"family": "Duerr", "given": "Richard H", "initials": "RH"}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "Gabriel", "given": "Stacey", "initials": "S"}, {"family": "Lettre", "given": "Guillaume", "initials": "G"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}, {"family": "McGovern", "given": "Dermot P B", "initials": "DP"}, {"family": "Cho", "given": "Judy H", "initials": "JH"}, {"family": "Rioux", "given": "John D", "initials": "JD"}, {"family": "Xavier", "given": "Ramnik J", "initials": "RJ"}, {"family": "Daly", "given": "Mark J", "initials": "MJ"}], "type": "journal article", "published": "2011-10-09", "journal": {"volume": "43", "issn": "1546-1718", "issue": "11", "pages": "1066-1073", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "More than 1,000 susceptibility loci have been identified through genome-wide association studies (GWAS) of common variants; however, the specific genes and full allelic spectrum of causal variants underlying these findings have not yet been defined. Here we used pooled next-generation sequencing to study 56 genes from regions associated with Crohn's disease in 350 cases and 350 controls. Through follow-up genotyping of 70 rare and low-frequency protein-altering variants in nine independent case-control series (16,054 Crohn's disease cases, 12,153 ulcerative colitis cases and 17,575 healthy controls), we identified four additional independent risk factors in NOD2, two additional protective variants in IL23R, a highly significant association with a protective splice variant in CARD9 (P < 1 \u00d7 10(-16), odds ratio \u2248 0.29) and additional associations with coding variants in IL18RAP, CUL2, C1orf106, PTPN22 and MUC19. We extend the results of successful GWAS by identifying new, rare and probably functional variants that could aid functional experiments and predictive models.", "doi": "10.1038/ng.952", "pmid": "21983784", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "ng.952"}, {"db": "pmc", "key": "PMC3378381"}, {"db": "mid", "key": "NIHMS335188"}], "notes": [], "created": "2017-05-04T15:03:31.881Z", "modified": "2017-05-30T14:52:07.911Z"}, {"entity": "publication", "iuid": "a370e55d30524cd8905f893b8dea60e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a370e55d30524cd8905f893b8dea60e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a370e55d30524cd8905f893b8dea60e9"}}, "title": "Pseudoceramines A-D, new antibacterial bromotyrosine alkaloids from the marine sponge Pseudoceratina sp.", "authors": [{"family": "Yin", "given": "Sheng", "initials": "S"}, {"family": "Davis", "given": "Rohan A", "initials": "RA"}, {"family": "Shelper", "given": "Todd", "initials": "T"}, {"family": "Sykes", "given": "Melissa L", "initials": "ML"}, {"family": "Avery", "given": "Vicky M", "initials": "VM"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}, {"family": "Sundin", "given": "Charlotta", "initials": "C"}, {"family": "Quinn", "given": "Ronald J", "initials": "RJ"}], "type": "journal article", "published": "2011-10-07", "journal": {"volume": "9", "issn": "1477-0539", "issue": "19", "pages": "6755-6760", "title": "Org. Biomol. Chem.", "issn-l": "1477-0520"}, "abstract": "Bioassay-guided fractionation of the CH(2)Cl(2)/MeOH extract of the Australian marine sponge Pseudoceratina sp. resulted in the purification of four new bromotyrosine alkaloids, pseudoceramines A-D (1-4), along with a known natural product, spermatinamine (5). The structures of 1-5 were determined by spectroscopic methods. Pseudoceramines A (1) and B (2) feature a rare bromotyrosyl-spermine-bromotyrosyl sequence, and pseudoceramine C (3) is the first example of bromotyrosine coupled with an N-methyl derivative of spermidine. Compounds 1-5 were screened for inhibition of toxin secretion by the type III secretion (T3S) pathway in Yersinia pseudotuberculosis. Compounds 2 and 5 inhibited secretion of the Yersinia outer protein YopE (IC(50) = 19 and 6 \u03bcM, respectively) and the enzyme activity of YopH (IC(50) = 33 and 6 \u03bcM, respectively).", "doi": "10.1039/c1ob05581j", "pmid": "21850326", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:37.017Z", "modified": "2025-10-17T13:04:30.741Z"}, {"entity": "publication", "iuid": "a59c07dadcad4fff829226e4e591f050", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a59c07dadcad4fff829226e4e591f050.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a59c07dadcad4fff829226e4e591f050"}}, "title": "Adenosine kinase deficiency disrupts the methionine cycle and causes hypermethioninemia, encephalopathy, and abnormal liver function.", "authors": [{"family": "Bjursell", "given": "Magnus K", "initials": "MK"}, {"family": "Blom", "given": "Henk J", "initials": "HJ", "orcid": "0000-0002-5584-9170", "researcher": {"href": "https://publications.scilifelab.se/researcher/3ce356a74dc84e0ea6af85397f11d869.json"}}, {"family": "Cayuela", "given": "Jordi Asin", "initials": "JA"}, {"family": "Engvall", "given": "Martin L", "initials": "ML"}, {"family": "Lesko", "given": "Nicole", "initials": "N"}, {"family": "Balasubramaniam", "given": "Shanti", "initials": "S"}, {"family": "Brandberg", "given": "G\u00f6ran", "initials": "G"}, {"family": "Halldin", "given": "Maria", "initials": "M"}, {"family": "Falkenberg", "given": "Maria", "initials": "M"}, {"family": "Jakobs", "given": "Cornelis", "initials": "C"}, {"family": "Smith", "given": "Desiree", "initials": "D"}, {"family": "Struys", "given": "Eduard", "initials": "E"}, {"family": "von D\u00f6beln", "given": "Ulrika", "initials": "U"}, {"family": "Gustafsson", "given": "Claes M", "initials": "CM"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Wedell", "given": "Anna", "initials": "A"}], "type": "case reports", "published": "2011-10-07", "journal": {"volume": "89", "issn": "1537-6605", "issue": "4", "pages": "507-515", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "Four inborn errors of metabolism (IEMs) are known to cause hypermethioninemia by directly interfering with the methionine cycle. Hypermethioninemia is occasionally discovered incidentally, but it is often disregarded as an unspecific finding, particularly if liver disease is involved. In many individuals the hypermethioninemia resolves without further deterioration, but it can also represent an early sign of a severe, progressive neurodevelopmental disorder. Further investigation of unclear hypermethioninemia is therefore important. We studied two siblings affected by severe developmental delay and liver dysfunction. Biochemical analysis revealed increased plasma levels of methionine, S-adenosylmethionine (AdoMet), and S-adenosylhomocysteine (AdoHcy) but normal or mildly elevated homocysteine (Hcy) levels, indicating a block in the methionine cycle. We excluded S-adenosylhomocysteine hydrolase (SAHH) deficiency, which causes a similar biochemical phenotype, by using genetic and biochemical techniques and hypothesized that there was a functional block in the SAHH enzyme as a result of a recessive mutation in a different gene. Using exome sequencing, we identified a homozygous c.902C>A (p.Ala301Glu) missense mutation in the adenosine kinase gene (ADK), the function of which fits perfectly with this hypothesis. Increased urinary adenosine excretion confirmed ADK deficiency in the siblings. Four additional individuals from two unrelated families with a similar presentation were identified and shown to have a homozygous c.653A>C (p.Asp218Ala) and c.38G>A (p.Gly13Glu) mutation, respectively, in the same gene. All three missense mutations were deleterious, as shown by activity measurements on recombinant enzymes. ADK deficiency is a previously undescribed, severe IEM shedding light on a functional link between the methionine cycle and adenosine metabolism.", "doi": "10.1016/j.ajhg.2011.09.004", "pmid": "21963049", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0002-9297(11)00394-6"}, {"db": "pmc", "key": "PMC3188832"}], "notes": [], "created": "2017-05-04T14:57:15.579Z", "modified": "2021-07-08T13:26:08.274Z"}, {"entity": "publication", "iuid": "7dabadd6e20b4d3fbee23713a92308c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7dabadd6e20b4d3fbee23713a92308c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7dabadd6e20b4d3fbee23713a92308c6"}}, "title": "Tracking Phytophthora infestans with SSR markers within and between seasons - a field study in Sweden", "authors": [{"family": "Widmark", "given": "A K", "initials": "AK"}, {"family": "Andersson", "given": "B", "initials": "B"}, {"family": "Sandstr\u00f6m", "given": "M", "initials": "M"}, {"family": "Yuen", "given": "J E", "initials": "JE"}], "type": "journal-article", "published": "2011-10-00", "journal": {"volume": "60", "issn": "0032-0862", "issue": "5", "pages": "938-945", "title": "Plant Pathol", "issn-l": null}, "abstract": null, "doi": "10.1111/j.1365-3059.2011.02446.x", "pmid": null, "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:01.535Z", "modified": "2021-06-22T12:07:36.898Z"}, {"entity": "publication", "iuid": "7f12eda95a1d4529a826f3741d211f89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f12eda95a1d4529a826f3741d211f89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f12eda95a1d4529a826f3741d211f89"}}, "title": "No evidence for an association between genetic variation at the SERPINI1 locus and ischemic stroke.", "authors": [{"family": "Tj\u00e4rnlund-Wolf", "given": "A", "initials": "A"}, {"family": "Olsson", "given": "S", "initials": "S"}, {"family": "Jood", "given": "K", "initials": "K"}, {"family": "Blomstrand", "given": "C", "initials": "C"}, {"family": "Jern", "given": "C", "initials": "C"}], "type": "letter", "published": "2011-10-00", "journal": {"volume": "258", "issn": "1432-1459", "issue": "10", "pages": "1885-1887", "title": "J. Neurol.", "issn-l": "0340-5354"}, "abstract": null, "doi": "10.1007/s00415-011-6022-0", "pmid": "21487809", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:47.953Z", "modified": "2020-01-21T13:56:03.301Z"}, {"entity": "publication", "iuid": "eb5b9988743c4ed5b258d118de89957a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb5b9988743c4ed5b258d118de89957a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb5b9988743c4ed5b258d118de89957a"}}, "title": "Histone modifications influence mediator interactions with chromatin.", "authors": [{"family": "Zhu", "given": "Xuefeng", "initials": "X"}, {"family": "Zhang", "given": "Yongqiang", "initials": "Y"}, {"family": "Bjornsdottir", "given": "Gudrun", "initials": "G"}, {"family": "Liu", "given": "Zhongle", "initials": "Z"}, {"family": "Quan", "given": "Amy", "initials": "A"}, {"family": "Costanzo", "given": "Michael", "initials": "M"}, {"family": "D\u00e1vila L\u00f3pez", "given": "Marcela", "initials": "M"}, {"family": "Westholm", "given": "Jakub Orzechowski", "initials": "JO"}, {"family": "Ronne", "given": "Hans", "initials": "H"}, {"family": "Boone", "given": "Charles", "initials": "C"}, {"family": "Gustafsson", "given": "Claes M", "initials": "CM"}, {"family": "Myers", "given": "Lawrence C", "initials": "LC"}], "type": "journal article", "published": "2011-10-00", "journal": {"volume": "39", "issn": "1362-4962", "issue": "19", "pages": "8342-8354", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild-type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator-histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization.", "doi": "10.1093/nar/gkr551", "pmid": "21742760", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "gkr551"}, {"db": "pmc", "key": "PMC3201872"}], "notes": [], "created": "2017-05-04T15:03:10.986Z", "modified": "2017-05-30T12:40:21.217Z"}, {"entity": "publication", "iuid": "e30557a2e2d34a3b9fb377220a25ec13", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e30557a2e2d34a3b9fb377220a25ec13.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e30557a2e2d34a3b9fb377220a25ec13"}}, "title": "High-risk HPV infection and CIN grade correlates to the expression of c-myc, CD4+, FHIT, E-cadherin, Ki-67, and p16INK4a.", "authors": [{"family": "Samir", "given": "Raghad", "initials": "R"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Tot", "given": "Tibor", "initials": "T"}, {"family": "Pekar", "given": "Gyula", "initials": "G"}, {"family": "Hellberg", "given": "Dan", "initials": "D"}], "type": "journal article", "published": "2011-10-00", "journal": {"volume": "15", "issn": "1526-0976", "issue": "4", "pages": "280-286", "title": "J Low Genit Tract Dis", "issn-l": "1089-2591"}, "abstract": ": This study aimed to investigate correlations between a panel of biomarkers/tumor markers and high-risk (HR) human papillomavirus (HPV)-positive versus HR-HPV-negative cervical lesions.\n\n: The study included 188 women who consecutively attended a colposcopy clinic because of PAP smears suggesting cervical intraepithelial neoplasia (CIN), and 40 women with normal vaginal cytology. Tissue microarray blocks were prepared from representative cervical cone or punch biopsies. Sections were stained for 12 biological markers, previously shown to be relevant in cervical neoplasms, and expression was correlated to the presence or absence of HR-HPV in cervical lesions.\n\n: No correlations between expression of biomarkers and HPV status were found in normal epithelium. Expression of c-myc, CD4, Ki-67, and p16 correlated significantly to HR-HPV-infected epithelium compared with HR-HPV-negative epithelium. When adjustment was made for CIN grade, only the expression of Ki-67 correlated significantly with HPV status and CIN grade. Human papillomavirus status was stratified to normal epithelium, low-grade CIN, and high-grade CIN. Fragile histidine triad (FHIT), E-cadherin, Rb, Ki-67, and p16 expression was significantly increased in HPV-positive tissue by increasing CIN grade. No correlation to tumor marker expression was observed in the HPV-negative tissue.\n\n: This study described correlations, previously not investigated, between HPV status and tumor marker expression, that is, E-cadherin, Rb, and fragile histidine triad. Surprisingly, p16 was not, although Ki-67 expression was, independently correlated to HPV positivity. The results of this study suggest that p16 instead correlates independently with increasing CIN grade.", "doi": "10.1097/LGT.0b013e318215170c", "pmid": "21558960", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:47.638Z", "modified": "2017-05-30T12:57:44.937Z"}, {"entity": "publication", "iuid": "d50c494f0bb9439bbaf8cbc5379effbe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d50c494f0bb9439bbaf8cbc5379effbe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d50c494f0bb9439bbaf8cbc5379effbe"}}, "title": "Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.", "authors": [{"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Barker", "given": "Adam", "initials": "A"}, {"family": "Ahlqvist", "given": "Emma", "initials": "E"}, {"family": "Rybin", "given": "Denis", "initials": "D"}, {"family": "Petrie", "given": "John R", "initials": "JR"}, {"family": "Travers", "given": "Mary E", "initials": "ME"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N"}, {"family": "Dimas", "given": "Antigone S", "initials": "AS"}, {"family": "Nica", "given": "Alexandra", "initials": "A"}, {"family": "Wheeler", "given": "Eleanor", "initials": "E"}, {"family": "Chen", "given": "Han", "initials": "H"}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Taneera", "given": "Jalal", "initials": "J"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Peden", "given": "John F", "initials": "JF"}, {"family": "Turrini", "given": "Fabiola", "initials": "F"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Zabena", "given": "Carina", "initials": "C"}, {"family": "Almgren", "given": "Peter", "initials": "P"}, {"family": "Barker", "given": "David J P", "initials": "DJ"}, {"family": "Barnes", "given": "Daniel", "initials": "D"}, {"family": "Dennison", "given": "Elaine M", "initials": "EM"}, {"family": "Eriksson", "given": "Johan G", "initials": "JG"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Eury", "given": "Elodie", "initials": "E"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Gu", "given": "Harvest F", "initials": "HF"}, {"family": "Horikoshi", "given": "Momoko", "initials": "M"}, {"family": "Isomaa", "given": "Bo", "initials": "B"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Jameson", "given": "Karen A", "initials": "KA"}, {"family": "Kajantie", "given": "Eero", "initials": "E"}, {"family": "Kerr-Conte", "given": "Julie", "initials": "J"}, {"family": "Kuulasmaa", "given": "Teemu", "initials": "T"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Makrilakis", "given": "Konstantinos", "initials": "K"}, {"family": "Manning", "given": "Alisa K", "initials": "AK"}, {"family": "Mart\u00ednez-Larrad", "given": "Mar\u00eda Teresa", "initials": "MT"}, {"family": "Narisu", "given": "Narisu", "initials": "N"}, {"family": "Nastase Mannila", "given": "Maria", "initials": "M"}, {"family": "Ohrvik", "given": "John", "initials": "J"}, {"family": "Osmond", "given": "Clive", "initials": "C"}, {"family": "Pascoe", "given": "Laura", "initials": "L"}, {"family": "Payne", "given": "Felicity", "initials": "F"}, {"family": "Sayer", "given": "Avan A", "initials": "AA"}, {"family": "Sennblad", "given": "Bengt", "initials": "B"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Stanc\u00e1kov\u00e1", "given": "Alena", "initials": "A"}, {"family": "Stirrups", "given": "Kathy", "initials": "K"}, {"family": "Swift", "given": "Amy J", "initials": "AJ"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T"}, {"family": "van 't Hooft", "given": "Ferdinand M", "initials": "FM"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Weedon", "given": "Michael N", "initials": "MN"}, {"family": "Xie", "given": "Weijia", "initials": "W"}, {"family": "Zethelius", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "DIAGRAM Consortium", "given": null, "initials": null}, {"family": "GIANT Consortium", "given": null, "initials": null}, {"family": "MuTHER Consortium", "given": null, "initials": null}, {"family": "CARDIoGRAM Consortium", "given": null, "initials": null}, {"family": "C4D Consortium", "given": null, "initials": null}, {"family": "Ongen", "given": "Halit", "initials": "H"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A"}, {"family": "Hopewell", "given": "Jemma C", "initials": "JC"}, {"family": "Saleheen", "given": "Danish", "initials": "D"}, {"family": "Chambers", "given": "John", "initials": "J"}, {"family": "Parish", "given": "Sarah", "initials": "S"}, {"family": "Danesh", "given": "John", "initials": "J"}, {"family": "Kooner", "given": "Jaspal", "initials": "J"}, {"family": "Ostenson", "given": "Claes-G\u00f6ran", "initials": "CG"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Cooper", "given": "Cyrus C", "initials": "CC"}, {"family": "Serrano-R\u00edos", "given": "Manuel", "initials": "M"}, {"family": "Ferrannini", "given": "Ele", "initials": "E"}, {"family": "Forsen", "given": "Tom J", "initials": "TJ"}, {"family": "Clarke", "given": "Robert", "initials": "R"}, {"family": "Franzosi", "given": "Maria Grazia", "initials": "MG"}, {"family": "Seedorf", "given": "Udo", "initials": "U"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Johnson", "given": "Paul", "initials": "P"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Dermitzakis", "given": "Emmanouil T", "initials": "ET"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Pattou", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Gloyn", "given": "Anna L", "initials": "AL"}, {"family": "Dedoussis", "given": "George V", "initials": "GV"}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Watanabe", "given": "Richard M", "initials": "RM"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}], "type": "journal article", "published": "2011-10-00", "journal": {"volume": "60", "issn": "1939-327X", "issue": "10", "pages": "2624-2634", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": "Proinsulin is a precursor of mature insulin and C-peptide. Higher circulating proinsulin levels are associated with impaired \u03b2-cell function, raised glucose levels, insulin resistance, and type 2 diabetes (T2D). Studies of the insulin processing pathway could provide new insights about T2D pathophysiology.\n\nWe have conducted a meta-analysis of genome-wide association tests of \u223c2.5 million genotyped or imputed single nucleotide polymorphisms (SNPs) and fasting proinsulin levels in 10,701 nondiabetic adults of European ancestry, with follow-up of 23 loci in up to 16,378 individuals, using additive genetic models adjusted for age, sex, fasting insulin, and study-specific covariates.\n\nNine SNPs at eight loci were associated with proinsulin levels (P < 5 \u00d7 10(-8)). Two loci (LARP6 and SGSM2) have not been previously related to metabolic traits, one (MADD) has been associated with fasting glucose, one (PCSK1) has been implicated in obesity, and four (TCF7L2, SLC30A8, VPS13C/C2CD4A/B, and ARAP1, formerly CENTD2) increase T2D risk. The proinsulin-raising allele of ARAP1 was associated with a lower fasting glucose (P = 1.7 \u00d7 10(-4)), improved \u03b2-cell function (P = 1.1 \u00d7 10(-5)), and lower risk of T2D (odds ratio 0.88; P = 7.8 \u00d7 10(-6)). Notably, PCSK1 encodes the protein prohormone convertase 1/3, the first enzyme in the insulin processing pathway. A genotype score composed of the nine proinsulin-raising alleles was not associated with coronary disease in two large case-control datasets.\n\nWe have identified nine genetic variants associated with fasting proinsulin. Our findings illuminate the biology underlying glucose homeostasis and T2D development in humans and argue against a direct role of proinsulin in coronary artery disease pathogenesis.", "doi": "10.2337/db11-0415", "pmid": "21873549", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "db11-0415"}, {"db": "pmc", "key": "PMC3178302"}], "notes": [], "created": "2017-05-04T15:00:42.696Z", "modified": "2021-07-07T15:11:02.753Z"}, {"entity": "publication", "iuid": "3e31cf6c2c144c12ae03f5f06cc3c661", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3e31cf6c2c144c12ae03f5f06cc3c661.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3e31cf6c2c144c12ae03f5f06cc3c661"}}, "title": "Genetic variation in complement component C3 shows association with ischaemic stroke.", "authors": [{"family": "Olsson", "given": "S", "initials": "S"}, {"family": "Stokowska", "given": "A", "initials": "A"}, {"family": "Holmegaard", "given": "L", "initials": "L"}, {"family": "Jood", "given": "K", "initials": "K"}, {"family": "Blomstrand", "given": "C", "initials": "C"}, {"family": "Pekna", "given": "M", "initials": "M"}, {"family": "Jern", "given": "C", "initials": "C"}], "type": "journal article", "published": "2011-10-00", "journal": {"volume": "18", "issn": "1468-1331", "issue": "10", "pages": "1272-1274", "title": "Eur. J. Neurol.", "issn-l": "1351-5101"}, "abstract": "The aim of this study was to investigate whether genetic variation at the third complement component (C3) locus is associated with ischaemic stroke (IS).\n\nThe Sahlgrenska Academy Study on Ischaemic Stroke comprises 844 patients with IS, and 668 healthy controls. Sixteen SNPs were analyzed.\n\nTwo SNPs, rs2277984 and rs3745565, showed a significant association with overall IS. The SNP rs2277984 also showed association with the IS subtype cryptogenic stroke. These associations were independent of hypertension, diabetes, and smoking. The independent association between rs3745565 and overall IS withstands correction for multiple testing.\n\nIn this sample of patients with IS, genetic variation in C3 is associated with IS.", "doi": "10.1111/j.1468-1331.2011.03377.x", "pmid": "21414106", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:43.673Z", "modified": "2020-01-21T13:56:01.776Z"}, {"entity": "publication", "iuid": "503caecdb0514b91afe0340f76837aad", "links": {"self": {"href": "https://publications.scilifelab.se/publication/503caecdb0514b91afe0340f76837aad.json"}, "display": {"href": "https://publications.scilifelab.se/publication/503caecdb0514b91afe0340f76837aad"}}, "title": "Evidence for involvement of Dicer-like, Argonaute and histone deacetylase proteins in gene silencing in Phytophthora infestans.", "authors": [{"family": "Vetukuri", "given": "Ramesh R", "initials": "RR"}, {"family": "Avrova", "given": "Anna O", "initials": "AO"}, {"family": "Grenville-Briggs", "given": "Laura J", "initials": "LJ"}, {"family": "Van West", "given": "Pieter", "initials": "P"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F"}, {"family": "Savenkov", "given": "Eugene I", "initials": "EI"}, {"family": "Whisson", "given": "Stephen C", "initials": "SC"}, {"family": "Dixelius", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2011-10-00", "journal": {"volume": "12", "issn": "1364-3703", "issue": "8", "pages": "772-785", "title": "Mol. Plant Pathol.", "issn-l": null}, "abstract": "Gene silencing may have a direct or indirect impact on many biological processes in eukaryotic cells, and is a useful tool for the determination of the roles of specific genes. In this article, we report silencing in Phytophthora infestans, an oomycete pathogen of potato and tomato. Gene silencing is known to occur in P. infestans, but its genetic basis has yet to be determined. Genes encoding the major components of the RNA interference (RNAi) pathway, Dicer-like (Pidcl1), Argonaute (Piago1-5) and RNA-directed RNA polymerase (Pirdr1), were identified in the P. infestans genome by comparative genomics, together with families of other genes potentially involved in gene silencing, such as histone deacetylases, histone methyltransferases, DEAD helicases, chromodomain proteins and a class 1 RNaseIII. Real-time reverse transcription-polymerase chain reaction demonstrated transcript accumulation for all candidate genes throughout the asexual lifecycle and plant infection, but at different levels of mRNA abundance. A functional assay was developed in which silencing of the sporulation-associated Picdc14 gene was released by the treatment of protoplasts with in vitro-synthesized double-stranded RNAs homologous to Pidcl1, Piago1/2 and histone deacetylase Pihda1. These results suggest that the components of gene silencing, namely Dicer-like, Argonaute and histone deacetylase, are functional in P. infestans. Our data demonstrate that this oomycete possesses canonical gene silencing pathways similar to those of other eukaryotes.", "doi": "10.1111/j.1364-3703.2011.00710.x", "pmid": "21726377", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:21.937Z", "modified": "2020-01-21T13:56:02.266Z"}, {"entity": "publication", "iuid": "a6893171608b4336ab4fdda687c6e575", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a6893171608b4336ab4fdda687c6e575.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a6893171608b4336ab4fdda687c6e575"}}, "title": "Early transcriptional regulation by C-peptide in freshly isolated rat proximal tubular cells.", "authors": [{"family": "Lindahl", "given": "Emma", "initials": "E"}, {"family": "Nordquist", "given": "Lina", "initials": "L"}, {"family": "M\u00fcller", "given": "Patrick", "initials": "P"}, {"family": "El Agha", "given": "Eli", "initials": "E"}, {"family": "Friederich", "given": "Malou", "initials": "M"}, {"family": "Dahlman-Wright", "given": "Karin", "initials": "K"}, {"family": "Palm", "given": "Fredrik", "initials": "F"}, {"family": "J\u00f6rnvall", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2011-10-00", "journal": {"volume": "27", "issn": "1520-7560", "issue": "7", "pages": "697-704", "title": "Diabetes Metab. Res. Rev.", "issn-l": "1520-7552"}, "abstract": "Clinical studies have shown that proinsulin C-peptide exerts renoprotective effects in type 1 diabetes, although the underlying mechanisms are poorly understood. As C-peptide has been shown to induce several intracellular events and to localize to nuclei, we aimed to determine whether gene transcription is affected in proximal tubular kidney cells, and if so, whether the genes with altered transcription include those related to protective mechanisms.\n\nThe effect of C-peptide incubation (2 h) on gene expression was investigated in freshly isolated proximal tubular cells from streptozotocin-diabetic Sprague-Dawley rats using global gene expression profiling and real-time quantitative polymerase chain reaction. Protein expression was assayed using western blotting. Different bioinformatic strategies were employed.\n\nGene transcription profiling demonstrated differential transcription of 492 genes (p < 0.01) after 2 h of C-peptide exposure, with the majority of these genes repressed (83%). Real-time quantitative polymerase chain reaction validation supported a trend of several G protein-coupled receptors being activated, and certain transcription factors being repressed. Also, C-peptide repressed the transcription of genes associated with the pathways of circulatory and inflammatory diseases.\n\nThis study shows that C-peptide exerts early effects on gene transcription in proximal tubular cells. The findings also bring further knowledge to the renoprotective mechanisms of C-peptide in type 1 diabetes, and support a transcriptional activity for C-peptide. It is suggested that C-peptide may play a regulatory role in the gene expression of proximal tubular cells.", "doi": "10.1002/dmrr.1220", "pmid": "21618400", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:10.149Z", "modified": "2017-05-30T12:40:11.802Z"}, {"entity": "publication", "iuid": "26465db735494c02b2ad1f38180a9d7d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/26465db735494c02b2ad1f38180a9d7d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/26465db735494c02b2ad1f38180a9d7d"}}, "title": "The Lin28/let-7 axis regulates glucose metabolism.", "authors": [{"family": "Zhu", "given": "Hao", "initials": "H"}, {"family": "Shyh-Chang", "given": "Ng", "initials": "N"}, {"family": "Segr\u00e8", "given": "Ayellet V", "initials": "AV"}, {"family": "Shinoda", "given": "Gen", "initials": "G"}, {"family": "Shah", "given": "Samar P", "initials": "SP"}, {"family": "Einhorn", "given": "William S", "initials": "WS"}, {"family": "Takeuchi", "given": "Ayumu", "initials": "A"}, {"family": "Engreitz", "given": "Jesse M", "initials": "JM"}, {"family": "Hagan", "given": "John P", "initials": "JP"}, {"family": "Kharas", "given": "Michael G", "initials": "MG"}, {"family": "Urbach", "given": "Achia", "initials": "A"}, {"family": "Thornton", "given": "James E", "initials": "JE"}, {"family": "Triboulet", "given": "Robinson", "initials": "R"}, {"family": "Gregory", "given": "Richard I", "initials": "RI"}, {"family": "DIAGRAM Consortium", "given": null, "initials": null}, {"family": "MAGIC Investigators", "given": null, "initials": null}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "Daley", "given": "George Q", "initials": "GQ"}], "type": "journal article", "published": "2011-09-30", "journal": {"volume": "147", "issn": "1097-4172", "issue": "1", "pages": "81-94", "title": "Cell", "issn-l": "0092-8674"}, "abstract": "The let-7 tumor suppressor microRNAs are known for their regulation of oncogenes, while the RNA-binding proteins Lin28a/b promote malignancy by inhibiting let-7 biogenesis. We have uncovered unexpected roles for the Lin28/let-7 pathway in regulating metabolism. When overexpressed in mice, both Lin28a and LIN28B promote an insulin-sensitized state that resists high-fat-diet induced diabetes. Conversely, muscle-specific loss of Lin28a or overexpression of let-7 results in insulin resistance and impaired glucose tolerance. These phenomena occur, in part, through the let-7-mediated repression of multiple components of the insulin-PI3K-mTOR pathway, including IGF1R, INSR, and IRS2. In addition, the mTOR inhibitor, rapamycin, abrogates Lin28a-mediated insulin sensitivity and enhanced glucose uptake. Moreover, let-7 targets are enriched for genes containing SNPs associated with type 2 diabetes and control of fasting glucose in human genome-wide association studies. These data establish the Lin28/let-7 pathway as a central regulator of mammalian glucose metabolism.", "doi": "10.1016/j.cell.2011.08.033", "pmid": "21962509", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0092-8674(11)01003-8"}, {"db": "pmc", "key": "PMC3353524"}, {"db": "mid", "key": "NIHMS322292"}], "notes": [], "created": "2017-05-04T15:00:41.409Z", "modified": "2020-01-21T13:56:01.145Z"}, {"entity": "publication", "iuid": "f31c7353d64b4670a6aeec535daabd05", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f31c7353d64b4670a6aeec535daabd05.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f31c7353d64b4670a6aeec535daabd05"}}, "title": "ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing.", "authors": [{"family": "Darmanis", "given": "Spyros", "initials": "S"}, {"family": "Nong", "given": "Rachel Yuan", "initials": "RY"}, {"family": "V\u00e4nelid", "given": "Johan", "initials": "J"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Ericsson", "given": "Olle", "initials": "O"}, {"family": "Fredriksson", "given": "Simon", "initials": "S"}, {"family": "B\u00e4cklin", "given": "Christofer", "initials": "C"}, {"family": "Gut", "given": "Marta", "initials": "M"}, {"family": "Heath", "given": "Simon", "initials": "S"}, {"family": "Gut", "given": "Ivo Glynne", "initials": "IG"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Gustafsson", "given": "Mats G", "initials": "MG"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2011-09-29", "journal": {"volume": "6", "issn": "1932-6203", "issue": "9", "pages": "e25583", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Despite intense interest, methods that provide enhanced sensitivity and specificity in parallel measurements of candidate protein biomarkers in numerous samples have been lacking. We present herein a multiplex proximity ligation assay with readout via realtime PCR or DNA sequencing (ProteinSeq). We demonstrate improved sensitivity over conventional sandwich assays for simultaneous analysis of sets of 35 proteins in 5 \u00b5l of blood plasma. Importantly, we observe a minimal tendency to increased background with multiplexing, compared to a sandwich assay, suggesting that higher levels of multiplexing are possible. We used ProteinSeq to analyze proteins in plasma samples from cardiovascular disease (CVD) patient cohorts and matched controls. Three proteins, namely P-selectin, Cystatin-B and Kallikrein-6, were identified as putative diagnostic biomarkers for CVD. The latter two have not been previously reported in the literature and their potential roles must be validated in larger patient cohorts. We conclude that ProteinSeq is promising for screening large numbers of proteins and samples while the technology can provide a much-needed platform for validation of diagnostic markers in biobank samples and in clinical use.", "doi": "10.1371/journal.pone.0025583", "pmid": "21980495", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "PONE-D-11-10457"}, {"db": "pmc", "key": "PMC3183061"}], "notes": [], "created": "2017-05-04T14:55:22.262Z", "modified": "2023-04-14T13:56:31.562Z"}, {"entity": "publication", "iuid": "bd893df429b04bdaa7b14f91038c1707", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd893df429b04bdaa7b14f91038c1707.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd893df429b04bdaa7b14f91038c1707"}}, "title": "High RBM3 expression in prostate cancer independently predicts a reduced risk of biochemical recurrence and disease progression.", "authors": [{"family": "Jonsson", "given": "Liv", "initials": "L"}, {"family": "Gaber", "given": "Alexander", "initials": "A"}, {"family": "Ulmert", "given": "David", "initials": "D"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2011-09-28", "journal": {"volume": "6", "issn": "1746-1596", "issue": null, "pages": "91", "title": "Diagn Pathol", "issn-l": "1746-1596"}, "abstract": "High expression of the RNA-binding protein RBM3 has previously been found to be associated with good prognosis in breast cancer, ovarian cancer, malignant melanoma and colorectal cancer. The aim of this study was to examine the prognostic impact of immunohistochemical RBM3 expression in prostate cancer.\n\nImmunohistochemical RBM3 expression was examined in a tissue microarray with malignant and benign prostatic specimens from 88 patients treated with radical prostatectomy for localized disease. While rarely expressed in benign prostate gland epithelium, RBM3 was found to be up-regulated in prostate intraepithelial neoplasia and present in various fractions and intensities in invasive prostate cancer. High nuclear RBM3 expression was significantly associated with a prolonged time to biochemical recurrence (BCR) (HR 0.56, 95% CI: 0.34-0.93, p = 0.024) and clinical progression (HR 0.09, 95% CI: 0.01-0.71, p = 0.021). These associations remained significant in multivariate analysis, adjusted for preoperative PSA level in blood, pathological Gleason score and presence or absence of extracapsular extension, seminal vesicle invasion and positive surgical margin (HR 0.41, 95% CI: 0.19-0.89, p = 0.024 for BCR and HR 0.06, 95% CI: 0.01-0.50, p = 0.009 for clinical progression).\n\nOur results demonstrate that high nuclear expression of RBM3 in prostate cancer is associated with a prolonged time to disease progression and, thus, a potential biomarker of favourable prognosis. The value of RBM3 for prognostication, treatment stratification and follow-up of prostate cancer patients should be further validated in larger studies.", "doi": "10.1186/1746-1596-6-91", "pmid": "21955582", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1746-1596-6-91"}, {"db": "pmc", "key": "PMC3195697"}], "notes": [], "created": "2017-05-04T14:55:46.742Z", "modified": "2021-07-08T13:44:33.574Z"}, {"entity": "publication", "iuid": "5d41d0cc474541e9afaa45f363ded507", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d41d0cc474541e9afaa45f363ded507.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d41d0cc474541e9afaa45f363ded507"}}, "title": "Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.", "authors": [{"family": "Wain", "given": "Louise V", "initials": "LV"}, {"family": "Verwoert", "given": "Germaine C", "initials": "GC"}, {"family": "O'Reilly", "given": "Paul F", "initials": "PF"}, {"family": "Shi", "given": "Gang", "initials": "G"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Rice", "given": "Kenneth M", "initials": "KM"}, {"family": "Henneman", "given": "Peter", "initials": "P"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Ehret", "given": "Georg B", "initials": "GB"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Larson", "given": "Martin G", "initials": "MG"}, {"family": "Mooser", "given": "Vincent", "initials": "V"}, {"family": "Hadley", "given": "David", "initials": "D"}, {"family": "D\u00f6rr", "given": "Marcus", "initials": "M"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Aspelund", "given": "Thor", "initials": "T"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Janssens", "given": "A Cecile J W", "initials": "AC"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Heath", "given": "Simon", "initials": "S"}, {"family": "Laan", "given": "Maris", "initials": "M"}, {"family": "Fu", "given": "Jingyuan", "initials": "J"}, {"family": "Pistis", "given": "Giorgio", "initials": "G"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Arora", "given": "Pankaj", "initials": "P"}, {"family": "Lucas", "given": "Gavin", "initials": "G"}, {"family": "Pirastu", "given": "Nicola", "initials": "N"}, {"family": "Pichler", "given": "Irene", "initials": "I"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Webster", "given": "Rebecca J", "initials": "RJ"}, {"family": "Zhang", "given": "Feng", "initials": "F"}, {"family": "Peden", "given": "John F", "initials": "JF"}, {"family": "Schmidt", "given": "Helena", "initials": "H"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Igl", "given": "Wilmar", "initials": "W"}, {"family": "Milaneschi", "given": "Yuri", "initials": "Y"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Trompet", "given": "Stella", "initials": "S"}, {"family": "Bragg-Gresham", "given": "Jennifer L", "initials": "JL"}, {"family": "Alizadeh", "given": "Behrooz Z", "initials": "BZ"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Lehtim\u00e4ki", "given": "Terho", "initials": "T"}, {"family": "K\u00fchnel", "given": "Brigitte", "initials": "B"}, {"family": "Lopez", "given": "Lorna M", "initials": "LM"}, {"family": "Pola\u0161ek", "given": "Ozren", "initials": "O"}, {"family": "Boban", "given": "Mladen", "initials": "M"}, {"family": "Nelson", "given": "Christopher P", "initials": "CP"}, {"family": "Morrison", "given": "Alanna C", "initials": "AC"}, {"family": "Pihur", "given": "Vasyl", "initials": "V"}, {"family": "Ganesh", "given": "Santhi K", "initials": "SK"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Kundu", "given": "Suman", "initials": "S"}, {"family": "Mattace-Raso", "given": "Francesco U S", "initials": "FU"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Sijbrands", "given": "Eric J G", "initials": "EJ"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS"}, {"family": "Wang", "given": "Thomas J", "initials": "TJ"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Waeber", "given": "G\u00e9rard", "initials": "G"}, {"family": "Laitinen", "given": "Jaana", "initials": "J"}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Zitting", "given": "Paavo", "initials": "P"}, {"family": "McArdle", "given": "Wendy L", "initials": "WL"}, {"family": "Kroemer", "given": "Heyo K", "initials": "HK"}, {"family": "V\u00f6lker", "given": "Uwe", "initials": "U"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Glazer", "given": "Nicole L", "initials": "NL"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Alavere", "given": "Helene", "initials": "H"}, {"family": "Haller", "given": "Toomas", "initials": "T"}, {"family": "Keis", "given": "Aime", "initials": "A"}, {"family": "Tammesoo", "given": "Mari-Liis", "initials": "ML"}, {"family": "Aulchenko", "given": "Yurii", "initials": "Y"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "KT"}, {"family": "Galan", "given": "Pilar", "initials": "P"}, {"family": "Hercberg", "given": "Serge", "initials": "S"}, {"family": "Lathrop", "given": "Mark", "initials": "M"}, {"family": "Eyheramendy", "given": "Susana", "initials": "S"}, {"family": "Org", "given": "Elin", "initials": "E"}, {"family": "S\u00f5ber", "given": "Siim", "initials": "S"}, {"family": "Lu", "given": "Xiaowen", "initials": "X"}, {"family": "Nolte", "given": "Ilja M", "initials": "IM"}, {"family": "Penninx", "given": "Brenda W", "initials": "BW"}, {"family": "Corre", "given": "Tanguy", "initials": "T"}, {"family": "Masciullo", "given": "Corrado", "initials": "C"}, {"family": "Sala", "given": "Cinzia", "initials": "C"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "d'Adamo", "given": "Adamo Pio", "initials": "AP"}, {"family": "Fabretto", "given": "Antonella", "initials": "A"}, {"family": "Faletra", "given": "Flavio", "initials": "F"}, {"family": "Ulivi", "given": "Sheila", "initials": "S"}, {"family": "Del Greco", "given": "Fabiola M", "initials": "F"}, {"family": "Facheris", "given": "Maurizio", "initials": "M"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Bergman", "given": "Richard N", "initials": "RN"}, {"family": "Beilby", "given": "John P", "initials": "JP"}, {"family": "Hung", "given": "Joseph", "initials": "J"}, {"family": "Musk", "given": "A William", "initials": "AW"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Shin", "given": "So-Youn", "initials": "SY"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Gider", "given": "Pierre", "initials": "P"}, {"family": "Loitfelder", "given": "Marisa", "initials": "M"}, {"family": "Zeginigg", "given": "Marion", "initials": "M"}, {"family": "Hernandez", "given": "Dena", "initials": "D"}, {"family": "Najjar", "given": "Samer S", "initials": "SS"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Corsi", "given": "Anna Maria", "initials": "AM"}, {"family": "Singleton", "given": "Andrew", "initials": "A"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJ"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Parker", "given": "Alex N", "initials": "AN"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Buckley", "given": "Brendan", "initials": "B"}, {"family": "Stott", "given": "David", "initials": "D"}, {"family": "Orru", "given": "Marco", "initials": "M"}, {"family": "Uda", "given": "Manuela", "initials": "M"}, {"family": "LifeLines Cohort Study", "given": "", "initials": ""}, {"family": "van der Klauw", "given": "Melanie M", "initials": "MM"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Li", "given": "Xinzhong", "initials": "X"}, {"family": "Scott", "given": "James", "initials": "J"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YD"}, {"family": "Burke", "given": "Gregory L", "initials": "GL"}, {"family": "K\u00e4h\u00f6nen", "given": "Mika", "initials": "M"}, {"family": "Viikari", "given": "Jorma", "initials": "J"}, {"family": "D\u00f6ring", "given": "Angela", "initials": "A"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Davies", "given": "Gail", "initials": "G"}, {"family": "Starr", "given": "John M", "initials": "JM"}, {"family": "Emilsson", "given": "Valur", "initials": "V"}, {"family": "Plump", "given": "Andrew", "initials": "A"}, {"family": "Lindeman", "given": "Jan H", "initials": "JH"}, {"family": "Hoen", "given": "Peter A C 't", "initials": "PA"}, {"family": "K\u00f6nig", "given": "Inke R", "initials": "IR"}, {"family": "EchoGen consortium", "given": "", "initials": ""}, {"family": "Felix", "given": "Janine F", "initials": "JF"}, {"family": "Clarke", "given": "Robert", "initials": "R"}, {"family": "Hopewell", "given": "Jemma C", "initials": "JC"}, {"family": "Ongen", "given": "Halit", "initials": "H"}, {"family": "Breteler", "given": "Monique", "initials": "M"}, {"family": "Debette", "given": "St\u00e9phanie", "initials": "S"}, {"family": "Destefano", "given": "Anita L", "initials": "AL"}, {"family": "Fornage", "given": "Myriam", "initials": "M"}, {"family": "AortaGen Consortium", "given": "", "initials": ""}, {"family": "Mitchell", "given": "Gary F", "initials": "GF"}, {"family": "CHARGE Consortium Heart Failure Working Group", "given": "", "initials": ""}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "KidneyGen consortium", "given": "", "initials": ""}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "CKDGen consortium", "given": "", "initials": ""}, {"family": "Cardiogenics consortium", "given": "", "initials": ""}, {"family": "CardioGram", "given": "", "initials": ""}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Preuss", "given": "Michael", "initials": "M"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Deary", "given": "Ian J", "initials": "IJ"}, {"family": "Wichmann", "given": "H-Erich", "initials": "HE"}, {"family": "Raitakari", "given": "Olli T", "initials": "OT"}, {"family": "Palmas", "given": "Walter", "initials": "W"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Stolk", "given": "Ronald P", "initials": "RP"}, {"family": "Jukema", "given": "J Wouter", "initials": "JW"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Gyllensten", "given": "Ulf B", "initials": "UB"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Schmidt", "given": "Reinhold", "initials": "R"}, {"family": "Farrall", "given": "Martin", "initials": "M"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Palmer", "given": "Lyle J", "initials": "LJ"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Pfeufer", "given": "Arne", "initials": "A"}, {"family": "Gasparini", "given": "Paolo", "initials": "P"}, {"family": "Siscovick", "given": "David", "initials": "D"}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Toniolo", "given": "Daniela", "initials": "D"}, {"family": "Snieder", "given": "Harold", "initials": "H"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Meneton", "given": "Pierre", "initials": "P"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Launer", "given": "Lenore", "initials": "L"}, {"family": "Rettig", "given": "Rainer", "initials": "R"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Beckmann", "given": "Jacques S", "initials": "JS"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "van Dijk", "given": "Ko Willems", "initials": "KW"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Chakravarti", "given": "Aravinda", "initials": "A"}, {"family": "Abecasis", "given": "Goncalo R", "initials": "GR"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Newton-Cheh", "given": "Christopher", "initials": "C"}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Rao", "given": "Dabeeru C", "initials": "DC"}, {"family": "Tobin", "given": "Martin D", "initials": "MD"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}], "type": "journal article", "published": "2011-09-11", "journal": {"volume": "43", "issn": "1546-1718", "issue": "10", "pages": "1005-1011", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Numerous genetic loci have been associated with systolic blood pressure (SBP) and diastolic blood pressure (DBP) in Europeans. We now report genome-wide association studies of pulse pressure (PP) and mean arterial pressure (MAP). In discovery (N = 74,064) and follow-up studies (N = 48,607), we identified at genome-wide significance (P = 2.7 \u00d7 10(-8) to P = 2.3 \u00d7 10(-13)) four new PP loci (at 4q12 near CHIC2, 7q22.3 near PIK3CG, 8q24.12 in NOV and 11q24.3 near ADAMTS8), two new MAP loci (3p21.31 in MAP4 and 10q25.3 near ADRB1) and one locus associated with both of these traits (2q24.3 near FIGN) that has also recently been associated with SBP in east Asians. For three of the new PP loci, the estimated effect for SBP was opposite of that for DBP, in contrast to the majority of common SBP- and DBP-associated variants, which show concordant effects on both traits. These findings suggest new genetic pathways underlying blood pressure variation, some of which may differentially influence SBP and DBP.", "doi": "10.1038/ng.922", "pmid": "21909110", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ng.922"}, {"db": "pmc", "key": "PMC3445021"}, {"db": "mid", "key": "NIHMS316759"}], "notes": [], "created": "2017-10-30T13:49:09.433Z", "modified": "2020-01-21T13:56:08.436Z"}, {"entity": "publication", "iuid": "8e439b7d2309467a875a218e7ba3b1fe", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8e439b7d2309467a875a218e7ba3b1fe.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8e439b7d2309467a875a218e7ba3b1fe"}}, "title": "Engineering GST M2-2 for high activity with indene 1,2-oxide and indication of an H-site residue sustaining catalytic promiscuity.", "authors": [{"family": "Norrg\u00e5rd", "given": "Malena A", "initials": "MA"}, {"family": "Mannervik", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2011-09-09", "journal": {"volume": "412", "issn": "1089-8638", "issue": "1", "pages": "111-120", "title": "J. Mol. Biol.", "issn-l": "0022-2836"}, "abstract": "The substrate-binding H-site of human glutathione transferase (GST) M2-2 was subjected to iterative saturation mutagenesis in order to obtain an efficient enzyme with the novel epoxide substrate indene 1,2-oxide. Residues 10, 116, and 210 were targeted, and the activities with the alternative substrates, benzyl isothiocyanate and the prodrug azathioprine, undergoing divergent chemical reactions were monitored for comparison. In general, increased activities were found when the smaller residues Gly, Ser, and Ala replaced the original Thr210. The most active mutant T210G was further mutated at position 116, but no mutant showed enhanced catalytic activity. However, saturation mutagenesis of position 10 identified one double mutant T210G/I10C with 100-fold higher specific activity with indene 1,2-oxide than wild-type GST M2-2. This enhanced epoxide activity of 50 \u03bcmol min(-1) mg(-1) resulted primarily from an increased k(cat) value (70 s(-1)). The specific activity is 24-fold higher than that of wild-type GST M1-1, which is otherwise the most proficient GST enzyme with epoxide substrates. A second double mutant T210G/I10W displayed 30-fold increased activity with azathioprine, 0.56 \u03bcmol min(-1) mg(-1). In both double mutants, the replacement of Ile10 led to narrowed acceptance of alternative substrates. Ile10 is evolutionarily conserved in related class Mu GSTs. Conservation usually indicates preservation of a particular function, and in the Mu class, it would appear that the conserved Ile10 is not necessary to maintain catalytic functions but to prevent loss of broad substrate acceptance. In summary, our data underscore the facile transition between alternative substrate selectivity profiles in GSTs by a few mutations.", "doi": "10.1016/j.jmb.2011.07.039", "pmid": "21821040", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0022-2836(11)00804-7"}], "notes": [], "created": "2017-05-04T15:01:59.713Z", "modified": "2020-01-21T13:56:03.664Z"}, {"entity": "publication", "iuid": "cbad22e00c3f4d66847be8d00ab25dc7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cbad22e00c3f4d66847be8d00ab25dc7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cbad22e00c3f4d66847be8d00ab25dc7"}}, "title": "Large-scale protein profiling in human cell lines using antibody-based proteomics.", "authors": [{"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Str\u00f6mberg", "given": "Sara", "initials": "S"}, {"family": "El-Obeid", "given": "Adila", "initials": "A"}, {"family": "Gry", "given": "Marcus", "initials": "M"}, {"family": "Nilsson", "given": "Kenneth", "initials": "K"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Asplund", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2011-09-02", "journal": {"volume": "10", "issn": "1535-3907", "issue": "9", "pages": "4066-4075", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "Human cancer cell lines grown in vitro are frequently used to decipher basic cell biological phenomena and to also specifically study different forms of cancer. Here we present the first large-scale study of protein expression patterns in cell lines using an antibody-based proteomics approach. We analyzed the expression pattern of 5436 proteins in 45 different cell lines using hierarchical clustering, principal component analysis, and two-group comparisons for the identification of differentially expressed proteins. Our results show that immunohistochemically determined protein profiles can categorize cell lines into groups that overall reflect the tumor tissue of origin and that hematological cell lines appear to retain their protein profiles to a higher degree than cell lines established from solid tumors. The two-group comparisons reveal well-characterized proteins as well as previously unstudied proteins that could be of potential interest for further investigations. Moreover, multiple myeloma cells and cells of myeloid origin were found to share a protein profile, relative to the protein profile of lymphoid leukemia and lymphoma cells, possibly reflecting their common dependency of bone marrow microenvironment. This work also provides an extensive list of antibodies, for which high-resolution images as well as validation data are available on the Human Protein Atlas ( www.proteinatlas.org ), that are of potential use in cell line studies.", "doi": "10.1021/pr200259v", "pmid": "21726073", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:47.937Z", "modified": "2021-07-08T13:44:33.629Z"}, {"entity": "publication", "iuid": "457a79d276644f8385739cf57840531b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/457a79d276644f8385739cf57840531b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/457a79d276644f8385739cf57840531b"}}, "title": "Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport.", "authors": [{"family": "Phirke", "given": "Prasad", "initials": "P"}, {"family": "Efimenko", "given": "Evgeni", "initials": "E"}, {"family": "Mohan", "given": "Swetha", "initials": "S"}, {"family": "Burghoorn", "given": "Jan", "initials": "J"}, {"family": "Crona", "given": "Filip", "initials": "F"}, {"family": "Bakhoum", "given": "Mathieu W", "initials": "MW"}, {"family": "Trieb", "given": "Maria", "initials": "M"}, {"family": "Schuske", "given": "Kim", "initials": "K"}, {"family": "Jorgensen", "given": "Erik M", "initials": "EM"}, {"family": "Piasecki", "given": "Brian P", "initials": "BP"}, {"family": "Leroux", "given": "Michel R", "initials": "MR"}, {"family": "Swoboda", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2011-09-01", "journal": {"volume": "357", "issn": "1095-564X", "issue": "1", "pages": "235-247", "title": "Dev. Biol.", "issn-l": "0012-1606"}, "abstract": "Cilia are ubiquitous cell surface projections that mediate various sensory- and motility-based processes and are implicated in a growing number of multi-organ genetic disorders termed ciliopathies. To identify new components required for cilium biogenesis and function, we sought to further define and validate the transcriptional targets of DAF-19, the ciliogenic C. elegans RFX transcription factor. Transcriptional profiling of daf-19 mutants (which do not form cilia) and wild-type animals was performed using embryos staged to when the cell types developing cilia in the worm, the ciliated sensory neurons (CSNs), still differentiate. Comparisons between the two populations revealed 881 differentially regulated genes with greater than a 1.5-fold increase or decrease in expression. A subset of these was confirmed by quantitative RT-PCR. Transgenic worms expressing transcriptional GFP fusions revealed CSN-specific expression patterns for 11 of 14 candidate genes. We show that two uncharacterized candidate genes, termed dyf-17 and dyf-18 because their corresponding mutants display dye-filling (Dyf) defects, are important for ciliogenesis. DYF-17 localizes at the base of cilia and is specifically required for building the distal segment of sensory cilia. DYF-18 is an evolutionarily conserved CDK7/CCRK/LF2p-related serine/threonine kinase that is necessary for the proper function of intraflagellar transport, a process critical for cilium biogenesis. Together, our microarray study identifies targets of the evolutionarily conserved RFX transcription factor, DAF-19, providing a rich dataset from which to uncover-in addition to DYF-17 and DYF-18-cellular components important for cilium formation and function.", "doi": "10.1016/j.ydbio.2011.06.028", "pmid": "21740898", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "S0012-1606(11)01088-8"}, {"db": "pmc", "key": "PMC3888451"}, {"db": "mid", "key": "NIHMS540805"}], "notes": [], "created": "2017-05-04T15:03:09.848Z", "modified": "2017-05-30T12:40:07.051Z"}, {"entity": "publication", "iuid": "aefd890bfba14f1c884cfa73bfe11a17", "links": {"self": {"href": "https://publications.scilifelab.se/publication/aefd890bfba14f1c884cfa73bfe11a17.json"}, "display": {"href": "https://publications.scilifelab.se/publication/aefd890bfba14f1c884cfa73bfe11a17"}}, "title": "Variants in STAT5B associate with serum TC and LDL-C levels.", "authors": [{"family": "Kornfeld", "given": "Jan-Wilhelm", "initials": "JW"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Pospisilik", "given": "J Andrew", "initials": "JA"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Penninger", "given": "Josef M", "initials": "JM"}, {"family": "Sexl", "given": "Veronika", "initials": "V"}, {"family": "Moriggl", "given": "Richard", "initials": "R"}, {"family": "van Duijn", "given": "Cornelia", "initials": "C"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}], "type": "journal article", "published": "2011-09-00", "journal": {"volume": "96", "issn": "1945-7197", "issue": "9", "pages": "E1496-E1501", "title": "J. Clin. Endocrinol. Metab.", "issn-l": "0021-972X"}, "abstract": "Known genetic variants influencing serum lipid levels do not adequately account for the observed population variability of these phenotypes. The GH/signal transducers and activators of transcription (STAT) signaling pathway is an evolutionary conserved system that exerts strong effects on metabolism, including that of lipids.\n\nWe analyzed the association of 11 single-nucleotide polymorphisms (SNP) spanning the STAT5B/STAT5A/STAT3 locus with serum lipid levels in six European populations (n = 5162 nondiabetic individuals).\n\nAfter adjustment for age, sex, alcohol use, smoking, and body mass index, we identified STAT5B variants (rs8082391 and rs8064638) in novel association with total cholesterol (TC; P = 0.001 and P = 0.002) and low-density lipoprotein cholesterol (P = 0.002 and P = 0.004) levels. The minor alleles of these single-nucleotide polymorphisms were significantly enriched in hyperlipidemic individuals across the six discovery populations (P = 0.004 and P = 0.006). In transgenic mice deficient for hepatic STAT5A and STAT5B, reduced serum TC levels coincided with reduced hepatic cholesterol biosynthesis as demonstrated using gene expression profiling and pathway enrichment analysis.\n\nGenetic variants in STAT5B are associated with TC and low-density lipoprotein cholesterol levels among six populations. Mechanistically, STAT5B transcriptionally regulates hepatic cholesterol homeostasis.", "doi": "10.1210/jc.2011-0322", "pmid": "21752895", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "jc.2011-0322"}], "notes": [], "created": "2017-05-04T15:01:59.199Z", "modified": "2020-01-21T13:56:04.609Z"}, {"entity": "publication", "iuid": "f37b1c10ed744c518eed964c839c42c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f37b1c10ed744c518eed964c839c42c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f37b1c10ed744c518eed964c839c42c7"}}, "title": "Total zinc intake may modify the glucose-raising effect of a zinc transporter (SLC30A8) variant: a 14-cohort meta-analysis.", "authors": [{"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Nettleton", "given": "Jennifer A", "initials": "JA"}, {"family": "Hivert", "given": "Marie-France", "initials": "MF"}, {"family": "Ye", "given": "Zheng", "initials": "Z"}, {"family": "van Rooij", "given": "Frank J A", "initials": "FJ"}, {"family": "Shungin", "given": "Dmitry", "initials": "D"}, {"family": "Sonestedt", "given": "Emily", "initials": "E"}, {"family": "Ngwa", "given": "Julius S", "initials": "JS"}, {"family": "Wojczynski", "given": "Mary K", "initials": "MK"}, {"family": "Lemaitre", "given": "Rozenn N", "initials": "RN"}, {"family": "Gustafsson", "given": "Stefan", "initials": "S"}, {"family": "Anderson", "given": "Jennifer S", "initials": "JS"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Hindy", "given": "George", "initials": "G"}, {"family": "Saylor", "given": "Georgia", "initials": "G"}, {"family": "Renstrom", "given": "Frida", "initials": "F"}, {"family": "Bennett", "given": "Amanda J", "initials": "AJ"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Hoogeveen", "given": "Ron C", "initials": "RC"}, {"family": "Houston", "given": "Denise K", "initials": "DK"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Jacques", "given": "Paul F", "initials": "PF"}, {"family": "Johansson", "given": "Ingegerd", "initials": "I"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "McKeown", "given": "Nicola", "initials": "N"}, {"family": "Ordovas", "given": "Jose", "initials": "J"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Sijbrands", "given": "Eric J G", "initials": "EJ"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Yannakoulia", "given": "Mary", "initials": "M"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "MAGIC Investigators", "given": null, "initials": null}, {"family": "Wareham", "given": "Nick J", "initials": "NJ"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Forouhi", "given": "Nita G", "initials": "NG"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Loos", "given": "Ruth J", "initials": "RJ"}, {"family": "Hallmans", "given": "Goran", "initials": "G"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Dedoussis", "given": "George V", "initials": "GV"}], "type": "journal article", "published": "2011-09-00", "journal": {"volume": "60", "issn": "1939-327X", "issue": "9", "pages": "2407-2416", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": "Many genetic variants have been associated with glucose homeostasis and type 2 diabetes in genome-wide association studies. Zinc is an essential micronutrient that is important for \u03b2-cell function and glucose homeostasis. We tested the hypothesis that zinc intake could influence the glucose-raising effect of specific variants.\n\nWe conducted a 14-cohort meta-analysis to assess the interaction of 20 genetic variants known to be related to glycemic traits and zinc metabolism with dietary zinc intake (food sources) and a 5-cohort meta-analysis to assess the interaction with total zinc intake (food sources and supplements) on fasting glucose levels among individuals of European ancestry without diabetes.\n\nWe observed a significant association of total zinc intake with lower fasting glucose levels (\u03b2-coefficient \u00b1 SE per 1 mg/day of zinc intake: -0.0012 \u00b1 0.0003 mmol/L, summary P value = 0.0003), while the association of dietary zinc intake was not significant. We identified a nominally significant interaction between total zinc intake and the SLC30A8 rs11558471 variant on fasting glucose levels (\u03b2-coefficient \u00b1 SE per A allele for 1 mg/day of greater total zinc intake: -0.0017 \u00b1 0.0006 mmol/L, summary interaction P value = 0.005); this result suggests a stronger inverse association between total zinc intake and fasting glucose in individuals carrying the glucose-raising A allele compared with individuals who do not carry it. None of the other interaction tests were statistically significant.\n\nOur results suggest that higher total zinc intake may attenuate the glucose-raising effect of the rs11558471 SLC30A8 (zinc transporter) variant. Our findings also support evidence for the association of higher total zinc intake with lower fasting glucose levels.", "doi": "10.2337/db11-0176", "pmid": "21810599", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "db11-0176"}, {"db": "pmc", "key": "PMC3161318"}], "notes": [], "created": "2017-05-04T15:00:42.342Z", "modified": "2021-07-07T15:11:02.792Z"}, {"entity": "publication", "iuid": "bd08d776fa434ae89b3d06f940278595", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd08d776fa434ae89b3d06f940278595.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd08d776fa434ae89b3d06f940278595"}}, "title": "Structural features determining the intestinal epithelial permeability and efflux of novel HIV-1 protease inhibitors.", "authors": [{"family": "Lazorova", "given": "Lucia", "initials": "L"}, {"family": "Hubatsch", "given": "Ina", "initials": "I"}, {"family": "Ekegren", "given": "Jenny K", "initials": "JK"}, {"family": "Gising", "given": "Johan", "initials": "J"}, {"family": "Nakai", "given": "Daisuke", "initials": "D"}, {"family": "Zaki", "given": "Noha M", "initials": "NM"}, {"family": "Bergstr\u00f6m", "given": "Christel A S", "initials": "CAS"}, {"family": "Norinder", "given": "Ulf", "initials": "U"}, {"family": "Larhed", "given": "Mats", "initials": "M"}, {"family": "Artursson", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2011-09-00", "journal": {"volume": "100", "issn": "1520-6017", "issue": "9", "pages": "3763-3772", "title": "J Pharm Sci", "issn-l": "0022-3549"}, "abstract": "The primary aim of this study was to identify structural features that alter the intestinal epithelial permeability and efflux in a series of novel HIV-1 protease inhibitors (PIs). Eleven PIs were selected containing a tertiary alcohol in a transition-state mimicking scaffold, in which two substituents (R(1) and R(2) ) were varied systematically. Indinavir was selected as a reference compound. The apical-to-basolateral permeability was investigated in 2/4/A1 and Caco-2 monolayers. In addition, the basolateral-to-apical permeability was investigated in the Caco-2 monolayers and the efflux ratios were calculated. The absence of active drug transport processes in 2/4/A1 cells allowed identification and modeling of structural elements affecting the passive permeability. For instance, small aromatic R(1) substituents and a small (bromo-) R(2) substituent were associated with a high passive permeability. Efflux studies in Caco-2 cells indicated that amide-substituted neutral hydrophobic amino acids, such as valine and leucine, in the R(1) position, reduced the apical-to-basolateral transport and enhanced the efflux. We conclude that our investigation revealed structural features that alter the intestinal epithelial permeability and efflux in the series of PIs and hope that these results can contribute to the synthesis of PIs with improved permeability and limited efflux properties.", "doi": "10.1002/jps.22570", "pmid": "21491458", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pmc", "key": "PMC3210832"}, {"db": "pii", "key": "S0022-3549(15)31944-4"}], "notes": "Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)\r\nADME of Therapeutics (UDOPP)", "created": "2017-05-04T14:56:44.698Z", "modified": "2025-10-17T13:04:30.753Z"}, {"entity": "publication", "iuid": "e9129eb207414720af691c5ae6d3c0c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e9129eb207414720af691c5ae6d3c0c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e9129eb207414720af691c5ae6d3c0c1"}}, "title": "Large-scale gene-centric analysis identifies novel variants for coronary artery disease.", "authors": [{"family": "IBC 50K CAD Consortium", "given": "None", "initials": "N"}], "type": "journal article", "published": "2011-09-00", "journal": {"volume": "7", "issn": "1553-7404", "issue": "9", "pages": "e1002260", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Coronary artery disease (CAD) has a significant genetic contribution that is incompletely characterized. To complement genome-wide association (GWA) studies, we conducted a large and systematic candidate gene study of CAD susceptibility, including analysis of many uncommon and functional variants. We examined 49,094 genetic variants in \u223c2,100 genes of cardiovascular relevance, using a customised gene array in 15,596 CAD cases and 34,992 controls (11,202 cases and 30,733 controls of European descent; 4,394 cases and 4,259 controls of South Asian origin). We attempted to replicate putative novel associations in an additional 17,121 CAD cases and 40,473 controls. Potential mechanisms through which the novel variants could affect CAD risk were explored through association tests with vascular risk factors and gene expression. We confirmed associations of several previously known CAD susceptibility loci (eg, 9p21.3:p<10(-33); LPA:p<10(-19); 1p13.3:p<10(-17)) as well as three recently discovered loci (COL4A1/COL4A2, ZC3HC1, CYP17A1:p<5\u00d710(-7)). However, we found essentially null results for most previously suggested CAD candidate genes. In our replication study of 24 promising common variants, we identified novel associations of variants in or near LIPA, IL5, TRIB1, and ABCG5/ABCG8, with per-allele odds ratios for CAD risk with each of the novel variants ranging from 1.06-1.09. Associations with variants at LIPA, TRIB1, and ABCG5/ABCG8 were supported by gene expression data or effects on lipid levels. Apart from the previously reported variants in LPA, none of the other \u223c4,500 low frequency and functional variants showed a strong effect. Associations in South Asians did not differ appreciably from those in Europeans, except for 9p21.3 (per-allele odds ratio: 1.14 versus 1.27 respectively; P for heterogeneity\u200a=\u200a0.003). This large-scale gene-centric analysis has identified several novel genes for CAD that relate to diverse biochemical and cellular functions and clarified the literature with regard to many previously suggested genes.", "doi": "10.1371/journal.pgen.1002260", "pmid": "21966275", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pmc", "key": "PMC3178591"}], "notes": [], "created": "2017-05-04T15:00:50.521Z", "modified": "2020-01-21T13:56:09.208Z"}, {"entity": "publication", "iuid": "28081e743c0d419d98e741189dd798b0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/28081e743c0d419d98e741189dd798b0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/28081e743c0d419d98e741189dd798b0"}}, "title": "Genomic and clinical characteristics of six patients with partially overlapping interstitial deletions at 10p12p11.", "authors": [{"family": "Wentzel", "given": "Christian", "initials": "C"}, {"family": "Rajcan-Separovic", "given": "Evica", "initials": "E"}, {"family": "Ruivenkamp", "given": "Claudia A L", "initials": "CA"}, {"family": "Chantot-Bastaraud", "given": "Sandra", "initials": "S"}, {"family": "Metay", "given": "Corinne", "initials": "C"}, {"family": "Andrieux", "given": "Joris", "initials": "J"}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Gijsbers", "given": "Antoinet C J", "initials": "AC"}, {"family": "Druart", "given": "Luc", "initials": "L"}, {"family": "Hyon", "given": "Capucine", "initials": "C"}, {"family": "Portnoi", "given": "Marie-France", "initials": "MF"}, {"family": "Stattin", "given": "Eva-Lena", "initials": "EL"}, {"family": "Vincent-Delorme", "given": "Catherine", "initials": "C"}, {"family": "Kant", "given": "Sarina G", "initials": "SG"}, {"family": "Steinraths", "given": "Michelle", "initials": "M"}, {"family": "Marlin", "given": "Sandrine", "initials": "S"}, {"family": "Giurgea", "given": "Irina", "initials": "I"}, {"family": "Thuresson", "given": "Ann-Charlotte", "initials": "AC"}], "type": "case reports", "published": "2011-09-00", "journal": {"volume": "19", "issn": "1476-5438", "issue": "9", "pages": "959-964", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "With the clinical implementation of genomic microarrays, the detection of cryptic unbalanced rearrangements in patients with syndromic developmental delay has improved considerably. Here we report the molecular karyotyping and phenotypic description of six new unrelated patients with partially overlapping microdeletions at 10p12.31p11.21 ranging from 1.0 to 10.6\u2009Mb. The smallest region of overlap is 306\u2009kb, which includes WAC gene, known to be associated with microtubule function and to have a role in cell division. Another patient has previously been described with a 10\u2009Mb deletion, partially overlapping with our six patients. All seven patients have developmental delay and a majority of the patients have abnormal behaviour and dysmorphic features, including bulbous nasal tip, deep set eyes, synophrys/thick eyebrows and full cheeks, whereas other features varied. All patients also displayed various visual impairments and six out of seven patients had cardiac malformations. Taken together with the previously reported patient, our study suggests that the detected deletions may represent a new contiguous gene syndrome caused by dosage-sensitive genes that predispose to developmental delay.", "doi": "10.1038/ejhg.2011.71", "pmid": "21522184", "labels": {"National Genomics Infrastructure": null, "Array and Analysis Facility": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "ejhg201171"}, {"db": "pmc", "key": "PMC3179368"}], "notes": [], "created": "2017-05-04T15:01:57.258Z", "modified": "2020-01-21T13:56:01.163Z"}, {"entity": "publication", "iuid": "8ea9018926f340969057657f66916509", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ea9018926f340969057657f66916509.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ea9018926f340969057657f66916509"}}, "title": "Dystrobrevin-binding protein 1 gene (DTNBP1) variants associated with cerebrospinal fluid homovanillic acid and 5-hydroxyindoleacetic acid concentrations in healthy volunteers.", "authors": [{"family": "Andreou", "given": "Dimitrios", "initials": "D"}, {"family": "Saetre", "given": "Peter", "initials": "P"}, {"family": "K\u00e4hler", "given": "Anna K", "initials": "AK"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Sedvall", "given": "G\u00f6ran C", "initials": "GC"}, {"family": "Hall", "given": "H\u00e5kan", "initials": "H"}, {"family": "Terenius", "given": "Lars", "initials": "L"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}], "type": "journal article", "published": "2011-09-00", "journal": {"volume": "21", "issn": "1873-7862", "issue": "9", "pages": "700-704", "title": "Eur Neuropsychopharmacol", "issn-l": "0924-977X"}, "abstract": "The dystrobrevin binding protein-1 (DTNBP1) gene encodes dysbindin-1, a protein involved in neurodevelopmental and neurochemical processes related mainly to the monoamine dopamine. We investigated possible associations between eleven DTNBP1 polymorphisms and cerebrospinal fluid (CSF) concentrations of the major dopamine metabolite homovanillic acid (HVA), the major serotonin metabolite 5-hydroxyindoleacetic acid (5-HIAA), and the major noradrenaline metabolite 3-methoxy-4-hydroxyphenylglycol (MHPG) in healthy human subjects (n=132). Two polymorphisms, rs2619538 and rs760666, were nominally associated with CSF HVA and 5-HIAA concentrations, whereas a third polymorphism, rs909706, showed association only with HVA. After correction for multiple testing only the associations between rs2619538 and HVA and 5-HIAA concentrations remained significant. No significant association was found between any of the investigated DTNBP1 polymorphisms and CSF MHPG concentrations. The results suggest that genetic variation in DTNBP1 gene affects the regulation of dopamine and serotonin turnover in the central nervous system of healthy volunteers.", "doi": "10.1016/j.euroneuro.2010.12.008", "pmid": "21295953", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0924-977X(11)00004-6"}], "notes": [], "created": "2017-05-04T15:00:43.974Z", "modified": "2020-01-21T13:56:03.671Z"}, {"entity": "publication", "iuid": "70ec8d14993e49d2aa57009ad74f8c99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/70ec8d14993e49d2aa57009ad74f8c99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/70ec8d14993e49d2aa57009ad74f8c99"}}, "title": "Combinations of SNPs related to signal transduction in bipolar disorder.", "authors": [{"family": "Koefoed", "given": "Pernille", "initials": "P"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Bennike", "given": "Bente", "initials": "B"}, {"family": "Dam", "given": "Henrik", "initials": "H"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Hansen", "given": "Thomas", "initials": "T"}, {"family": "Jorgensen", "given": "Martin Balslev", "initials": "MB"}, {"family": "Kessing", "given": "Lars Vedel", "initials": "LV"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "M\u00f8ller", "given": "Gert Lykke", "initials": "GL"}, {"family": "Mors", "given": "Ole", "initials": "O"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Mellerup", "given": "Erling", "initials": "E"}], "type": "journal article", "published": "2011-08-29", "journal": {"volume": "6", "issn": "1932-6203", "issue": "8", "pages": "e23812", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Any given single nucleotide polymorphism (SNP) in a genome may have little or no functional impact. A biologically significant effect may possibly emerge only when a number of key SNP-related genotypes occur together in a single organism. Thus, in analysis of many SNPs in association studies of complex diseases, it may be useful to look at combinations of genotypes. Genes related to signal transmission, e.g., ion channel genes, may be of interest in this respect in the context of bipolar disorder. In the present study, we analysed 803 SNPs in 55 genes related to aspects of signal transmission and calculated all combinations of three genotypes from the 3\u00d7803 SNP genotypes for 1355 controls and 607 patients with bipolar disorder. Four clusters of patient-specific combinations were identified. Permutation tests indicated that some of these combinations might be related to bipolar disorder. The WTCCC bipolar dataset were use for replication, 469 of the 803 SNP were present in the WTCCC dataset either directly (n\u200a=\u200a132) or by imputation (n\u200a=\u200a337) covering 51 of our selected genes. We found three clusters of patient-specific 3\u00d7SNP combinations in the WTCCC dataset. Different SNPs were involved in the clusters in the two datasets. The present analyses of the combinations of SNP genotypes support a role for both genetic heterogeneity and interactions in the genetic architecture of bipolar disorder.", "doi": "10.1371/journal.pone.0023812", "pmid": "21897858", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10-PONE-RA-20023"}, {"db": "pmc", "key": "PMC3163586"}], "notes": [], "created": "2017-10-30T13:48:15.554Z", "modified": "2020-01-21T13:56:08.426Z"}, {"entity": "publication", "iuid": "d7bd1c5050d3453eb235b0dd54f012bc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d7bd1c5050d3453eb235b0dd54f012bc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d7bd1c5050d3453eb235b0dd54f012bc"}}, "title": "Identification of Bacterial Target Proteins for the Salicylidene Acylhydrazide Class of Virulence-blocking Compounds", "authors": [{"family": "Wang", "given": "Dai", "initials": "D"}, {"family": "Zetterstr\u00f6m", "given": "Caroline E", "initials": "CE"}, {"family": "Gabrielsen", "given": "Mads", "initials": "M"}, {"family": "Beckham", "given": "Katherine S H", "initials": "KSH"}, {"family": "Tree", "given": "Jai J", "initials": "JJ"}, {"family": "Macdonald", "given": "Sarah E", "initials": "SE"}, {"family": "Byron", "given": "Olwyn", "initials": "O"}, {"family": "Mitchell", "given": "Tim J", "initials": "TJ"}, {"family": "Gally", "given": "David L", "initials": "DL"}, {"family": "Herzyk", "given": "Pawel", "initials": "P"}, {"family": "Mahajan", "given": "Arvind", "initials": "A"}, {"family": "Uvell", "given": "Hanna", "initials": "H"}, {"family": "Burchmore", "given": "Richard", "initials": "R"}, {"family": "Smith", "given": "Brian O", "initials": "BO"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}, {"family": "Roe", "given": "Andrew J", "initials": "AJ"}], "type": "journal-article", "published": "2011-08-26", "journal": {"volume": "286", "issn": "1083-351X", "issue": "34", "pages": "29922-29931", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": null, "doi": "10.1074/jbc.m111.233858", "pmid": "21724850", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:36.719Z", "modified": "2025-10-17T13:04:30.765Z"}, {"entity": "publication", "iuid": "3aff75dc3c16442eb233d9aad15df027", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3aff75dc3c16442eb233d9aad15df027.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3aff75dc3c16442eb233d9aad15df027"}}, "title": "Changes in the acetogenic population in a mesophilic anaerobic digester in response to increasing ammonia concentration.", "authors": [{"family": "Westerholm", "given": "Maria", "initials": "M"}, {"family": "M\u00fcller", "given": "Bettina", "initials": "B"}, {"family": "Arthurson", "given": "Veronica", "initials": "V"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2011-08-24", "journal": {"volume": "26", "issn": "1347-4405", "issue": "4", "pages": "347-353", "title": "Microbes Environ.", "issn-l": "1342-6311"}, "abstract": "Changes in the acetogenic population were investigated in an experimental laboratory-scale biogas reactor (37\u00b0C) subjected to gradually elevated ammonia levels (0.8 to 6.9 g NH(4)(+)-N L(-1)). A shift from aceticlastic acetate degradation to syntrophic acetate oxidation had previously been confirmed in this reactor. In a parallel control reactor, operating at constant ammonia levels (0.65-0.90 g NH(4)(+)-N L(-1)), acetate degradation proceeded via the aceticlastic pathway throughout the operating period (660 d). The acetogenic populations in the reactors were analysed using degenerated primers designed to target the functional gene encoding a key enzyme of the acetyl-CoA pathway, 10-formyltetrahydrofolate synthetase (FTHFS). The analysis consisted of terminal restriction fragment length polymorphism (T-RFLP) analysis coupled with the construction of clone libraries, and quantitative PCR (qPCR) analysis. The T-RFLP data obtained were statistically analysed by non-metric multidimensional scaling. The most abundant FTHFS genes recovered in the clone libraries were assigned to terminal restriction fragments of the T-RFLP profile. The results of the investigation clearly indicated that increased ammonia concentration substantially influenced the putative acetogenic population structure and caused two distinct shifts of the most abundant members; however, the identity of the dominating species remains unknown, as none of the genes had been identified previously. Despite the shifts in the population, the qPCR analysis revealed a relatively stable abundance of the acetogenic population throughout the operation.", "doi": "10.1264/jsme2.ME11123", "pmid": "21869569", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "JST.JSTAGE/jsme2/ME11123"}, {"db": "GENBANK", "key": "HM365334"}, {"db": "GENBANK", "key": "HM365335"}, {"db": "GENBANK", "key": "HM365336"}, {"db": "GENBANK", "key": "HM365337"}, {"db": "GENBANK", "key": "HM365339"}, {"db": "GENBANK", "key": "HM365340"}, {"db": "GENBANK", "key": "HQ156223"}], "notes": [], "created": "2017-05-04T15:02:00.321Z", "modified": "2020-01-21T13:56:09.200Z"}, {"entity": "publication", "iuid": "a19b8f04ff8a4fa8902afc4c54a0627f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a19b8f04ff8a4fa8902afc4c54a0627f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a19b8f04ff8a4fa8902afc4c54a0627f"}}, "title": "Identification of cis- and trans-acting genetic variants explaining up to half the variation in circulating vascular endothelial growth factor levels.", "authors": [{"family": "Debette", "given": "Stephanie", "initials": "S"}, {"family": "Visvikis-Siest", "given": "Sophie", "initials": "S"}, {"family": "Chen", "given": "Ming-Huen", "initials": "MH"}, {"family": "Ndiaye", "given": "Ndeye-Coumba", "initials": "NC"}, {"family": "Song", "given": "Ci", "initials": "C"}, {"family": "Destefano", "given": "Anita", "initials": "A"}, {"family": "Safa", "given": "Radwan", "initials": "R"}, {"family": "Azimi Nezhad", "given": "Mohsen", "initials": "M"}, {"family": "Sawyer", "given": "Douglas", "initials": "D"}, {"family": "Marteau", "given": "Jean-Brice", "initials": "JB"}, {"family": "Xanthakis", "given": "Vanessa", "initials": "V"}, {"family": "Siest", "given": "Gerard", "initials": "G"}, {"family": "Sullivan", "given": "Lisa", "initials": "L"}, {"family": "Pfister", "given": "Michele", "initials": "M"}, {"family": "Smith", "given": "Holly", "initials": "H"}, {"family": "Choi", "given": "Seung-Hoan", "initials": "SH"}, {"family": "Lamont", "given": "John", "initials": "J"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Fitzgerald", "given": "Peter", "initials": "P"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Vasan", "given": "Ramachandran S", "initials": "RS"}, {"family": "Seshadri", "given": "Sudha", "initials": "S"}], "type": "comparative study", "published": "2011-08-19", "journal": {"volume": "109", "issn": "1524-4571", "issue": "5", "pages": "554-563", "title": "Circ. Res.", "issn-l": "0009-7330"}, "abstract": "Vascular endothelial growth factor (VEGF) affects angiogenesis, atherosclerosis, and cancer. Although the heritability of circulating VEGF levels is high, little is known about its genetic underpinnings.\n\nOur aim was to identify genetic variants associated with circulating VEGF levels, using an unbiased genome-wide approach, and to explore their functional significance with gene expression and pathway analysis.\n\nWe undertook a genome-wide association study of serum VEGF levels in 3527 participants of the Framingham Heart Study, with preplanned replication in 1727 participants from 2 independent samples, the STANISLAS Family Study and the Prospective Investigation of the Vasculature in Uppsala Seniors study. One hundred forty single nucleotide polymorphism (SNPs) reached genome-wide significance (P<5\u00d710(-8)). We found evidence of replication for the most significant associations in both replication datasets. In a conditional genome-wide association study, 4 SNPs mapping to 3 chromosomal regions were independently associated with circulating VEGF levels: rs6921438 and rs4416670 (6p21.1, P=6.11\u00d710(-506) and P=1.47\u00d710(-12)), rs6993770 (8q23.1, P=2.50\u00d710(-16)), and rs10738760 (9p24.2, P=1.96\u00d710(-34)). A genetic score including these 4 SNPs explained 48% of the heritability of serum VEGF levels. Six of the SNPs that reached genome-wide significance in the genome-wide association study were significantly associated with VEGF messenger RNA levels in peripheral blood mononuclear cells. Ingenuity pathway analyses showed found plausible biological links between VEGF and 2 novel genes in these loci (ZFPM2 and VLDLR).\n\nGenetic variants explaining up to half the heritability of serum VEGF levels were identified. These new insights provide important clues to the pathways regulating circulating VEGF levels.", "doi": "10.1161/CIRCRESAHA.111.243790", "pmid": "21757650", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "CIRCRESAHA.111.243790"}, {"db": "pmc", "key": "PMC3193930"}, {"db": "mid", "key": "NIHMS315529"}], "notes": [], "created": "2017-05-04T15:00:41.730Z", "modified": "2020-01-21T13:56:04.152Z"}, {"entity": "publication", "iuid": "e5d5b927ec6340288650334b6f1e3e0a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e5d5b927ec6340288650334b6f1e3e0a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e5d5b927ec6340288650334b6f1e3e0a"}}, "title": "Characterization of a 8q21.11 microdeletion syndrome associated with intellectual disability and a recognizable phenotype.", "authors": [{"family": "Palomares", "given": "Mar\u00eda", "initials": "M"}, {"family": "Delicado", "given": "Alicia", "initials": "A"}, {"family": "Mansilla", "given": "Elena", "initials": "E"}, {"family": "de Torres", "given": "Mar\u00eda Luisa", "initials": "ML"}, {"family": "Vallesp\u00edn", "given": "Elena", "initials": "E"}, {"family": "Fernandez", "given": "Luis", "initials": "L"}, {"family": "Martinez-Glez", "given": "Victor", "initials": "V"}, {"family": "Garc\u00eda-Mi\u00f1aur", "given": "Sixto", "initials": "S"}, {"family": "Nevado", "given": "Juli\u00e1n", "initials": "J"}, {"family": "Simarro", "given": "Fernando Santos", "initials": "FS"}, {"family": "Ruiz-Perez", "given": "Victor L", "initials": "VL"}, {"family": "Lynch", "given": "Sally Ann", "initials": "SA"}, {"family": "Sharkey", "given": "Freddie H", "initials": "FH"}, {"family": "Thuresson", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Belligni", "given": "Elga F", "initials": "EF"}, {"family": "Mart\u00ednez-Fern\u00e1ndez", "given": "Mar\u00eda Luisa", "initials": "ML"}, {"family": "Bermejo", "given": "Eva", "initials": "E"}, {"family": "Nowakowska", "given": "Beata", "initials": "B"}, {"family": "Kutkowska-Kazmierczak", "given": "Anna", "initials": "A"}, {"family": "Bocian", "given": "Ewa", "initials": "E"}, {"family": "Obersztyn", "given": "Ewa", "initials": "E"}, {"family": "Mart\u00ednez-Fr\u00edas", "given": "Mar\u00eda Luisa", "initials": "ML"}, {"family": "Hennekam", "given": "Raoul C M", "initials": "RC"}, {"family": "Lapunzina", "given": "Pablo", "initials": "P"}], "type": "journal article", "published": "2011-08-12", "journal": {"volume": "89", "issn": "1537-6605", "issue": "2", "pages": "295-301", "title": "Am. J. Hum. Genet.", "issn-l": "0002-9297"}, "abstract": "We report eight unrelated individuals with intellectual disability and overlapping submicroscopic deletions of 8q21.11 (0.66-13.55 Mb in size). The deletion was familial in one and simplex in seven individuals. The phenotype was remarkably similar and consisted of a round face with full cheeks, a high forehead, ptosis, cornea opacities, an underdeveloped alae, a short philtrum, a cupid's bow of the upper lip, down-turned corners of the mouth, micrognathia, low-set and prominent ears, and mild finger and toe anomalies (camptodactyly, syndactyly, and broadening of the first rays). Intellectual disability, hypotonia, decreased balance, sensorineural hearing loss, and unusual behavior were frequently observed. A high-resolution oligonucleotide array showed different proximal and distal breakpoints in all of the individuals. Sequencing studies in three of the individuals revealed that proximal and distal breakpoints were located in unique sequences with no apparent homology. The smallest region of overlap was a 539.7 kb interval encompassing three genes: a Zinc Finger Homeobox 4 (ZFHX4), one microRNA of unknown function, and one nonfunctional pseudogen. ZFHX4 encodes a transcription factor expressed in the adult human brain, skeletal muscle, and liver. It has been suggested as a candidate gene for congenital bilateral isolated ptosis. Our results suggest that the 8q21.11 submicroscopic deletion represents a clinically recognizable entity and that a haploinsufficient gene or genes within the minimal deletion region could underlie this syndrome.", "doi": "10.1016/j.ajhg.2011.06.012", "pmid": "21802062", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0002-9297(11)00266-7"}, {"db": "pmc", "key": "PMC3155189"}], "notes": [], "created": "2017-05-04T15:01:53.531Z", "modified": "2020-01-21T13:56:05.887Z"}, {"entity": "publication", "iuid": "63510104f3784bf9b3a3a73f29b7ae65", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63510104f3784bf9b3a3a73f29b7ae65.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63510104f3784bf9b3a3a73f29b7ae65"}}, "title": "Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.", "authors": [{"family": "International Multiple Sclerosis Genetics Consortium", "given": "None", "initials": "N"}, {"family": "Wellcome Trust Case Control Consortium 2", "given": "None", "initials": "N"}, {"family": "Sawcer", "given": "Stephen", "initials": "S"}, {"family": "Hellenthal", "given": "Garrett", "initials": "G"}, {"family": "Pirinen", "given": "Matti", "initials": "M"}, {"family": "Spencer", "given": "Chris C A", "initials": "CCA"}, {"family": "Patsopoulos", "given": "Nikolaos A", "initials": "NA"}, {"family": "Moutsianas", "given": "Loukas", "initials": "L"}, {"family": "Dilthey", "given": "Alexander", "initials": "A"}, {"family": "Su", "given": "Zhan", "initials": "Z"}, {"family": "Freeman", "given": "Colin", "initials": "C"}, {"family": "Hunt", "given": "Sarah E", "initials": "SE"}, {"family": "Edkins", "given": "Sarah", "initials": "S"}, {"family": "Gray", "given": "Emma", "initials": "E"}, {"family": "Booth", "given": "David R", "initials": "DR"}, {"family": "Potter", "given": "Simon C", "initials": "SC"}, {"family": "Goris", "given": "An", "initials": "A"}, {"family": "Band", "given": "Gavin", "initials": "G"}, {"family": "Oturai", "given": "Annette Bang", "initials": "AB"}, {"family": "Strange", "given": "Amy", "initials": "A"}, {"family": "Saarela", "given": "Janna", "initials": "J"}, {"family": "Bellenguez", "given": "C\u00e9line", "initials": "C"}, {"family": "Fontaine", "given": "Bertrand", "initials": "B"}, {"family": "Gillman", "given": "Matthew", "initials": "M"}, {"family": "Hemmer", "given": "Bernhard", "initials": "B"}, {"family": "Gwilliam", "given": "Rhian", "initials": "R"}, {"family": "Zipp", "given": "Frauke", "initials": "F"}, {"family": "Jayakumar", "given": "Alagurevathi", "initials": "A"}, {"family": "Martin", "given": "Roland", "initials": "R"}, {"family": "Leslie", "given": "Stephen", "initials": "S"}, {"family": "Hawkins", "given": "Stanley", "initials": "S"}, {"family": "Giannoulatou", "given": "Eleni", "initials": "E"}, {"family": "D'alfonso", "given": "Sandra", "initials": "S"}, {"family": "Blackburn", "given": "Hannah", "initials": "H"}, {"family": "Martinelli Boneschi", "given": "Filippo", "initials": "F"}, {"family": "Liddle", "given": "Jennifer", "initials": "J"}, {"family": "Harbo", "given": "Hanne F", "initials": "HF"}, {"family": "Perez", "given": "Marc L", "initials": "ML"}, {"family": "Spurkland", "given": "Anne", "initials": "A"}, {"family": "Waller", "given": "Matthew J", "initials": "MJ"}, {"family": "Mycko", "given": "Marcin P", "initials": "MP"}, {"family": "Ricketts", "given": "Michelle", "initials": "M"}, {"family": "Comabella", "given": "Manuel", "initials": "M"}, {"family": "Hammond", "given": "Naomi", "initials": "N"}, {"family": "Kockum", "given": "Ingrid", "initials": "I"}, {"family": "McCann", "given": "Owen T", "initials": "OT"}, {"family": "Ban", "given": "Maria", "initials": "M"}, {"family": "Whittaker", "given": "Pamela", "initials": "P"}, {"family": "Kemppinen", "given": "Anu", "initials": "A"}, {"family": "Weston", "given": "Paul", "initials": "P"}, {"family": "Hawkins", "given": "Clive", "initials": "C"}, {"family": "Widaa", "given": "Sara", "initials": "S"}, {"family": "Zajicek", "given": "John", "initials": "J"}, {"family": "Dronov", "given": "Serge", "initials": "S"}, {"family": "Robertson", "given": "Neil", "initials": "N"}, {"family": "Bumpstead", "given": "Suzannah J", "initials": "SJ"}, {"family": "Barcellos", "given": "Lisa F", "initials": "LF"}, {"family": "Ravindrarajah", "given": "Rathi", "initials": "R"}, {"family": "Abraham", "given": "Roby", "initials": "R"}, {"family": "Alfredsson", "given": "Lars", "initials": "L"}, {"family": "Ardlie", "given": "Kristin", "initials": "K"}, {"family": "Aubin", "given": "Cristin", "initials": "C"}, {"family": "Baker", "given": "Amie", "initials": "A"}, {"family": "Baker", "given": "Katharine", "initials": "K"}, {"family": "Baranzini", "given": "Sergio E", "initials": "SE"}, {"family": "Bergamaschi", "given": "Laura", "initials": "L"}, {"family": "Bergamaschi", "given": "Roberto", "initials": "R"}, {"family": "Bernstein", "given": "Allan", "initials": "A"}, {"family": "Berthele", "given": "Achim", "initials": "A"}, {"family": "Boggild", "given": "Mike", "initials": "M"}, {"family": "Bradfield", "given": "Jonathan P", "initials": "JP"}, {"family": "Brassat", "given": "David", "initials": "D"}, {"family": "Broadley", "given": "Simon A", "initials": "SA"}, {"family": "Buck", "given": "Dorothea", "initials": "D"}, {"family": "Butzkueven", "given": "Helmut", "initials": "H"}, {"family": "Capra", "given": "Ruggero", "initials": "R"}, {"family": "Carroll", "given": "William M", "initials": "WM"}, {"family": "Cavalla", "given": "Paola", "initials": "P"}, {"family": "Celius", "given": "Elisabeth G", "initials": "EG"}, {"family": "Cepok", "given": "Sabine", "initials": "S"}, {"family": "Chiavacci", "given": "Rosetta", "initials": "R"}, {"family": "Clerget-Darpoux", "given": "Fran\u00e7oise", "initials": "F"}, {"family": "Clysters", "given": "Katleen", "initials": "K"}, {"family": "Comi", "given": "Giancarlo", "initials": "G"}, {"family": "Cossburn", "given": "Mark", "initials": "M"}, {"family": "Cournu-Rebeix", "given": "Isabelle", "initials": "I"}, {"family": "Cox", "given": "Mathew B", "initials": "MB"}, {"family": "Cozen", "given": "Wendy", "initials": "W"}, {"family": "Cree", "given": "Bruce A C", "initials": "BAC"}, {"family": "Cross", "given": "Anne H", "initials": "AH"}, {"family": "Cusi", "given": "Daniele", "initials": "D"}, {"family": "Daly", "given": "Mark J", "initials": "MJ"}, {"family": "Davis", "given": "Emma", "initials": "E"}, {"family": "de Bakker", "given": "Paul I W", "initials": "PIW"}, {"family": "Debouverie", "given": "Marc", "initials": "M"}, {"family": "D'hooghe", "given": "Marie Beatrice", "initials": "MB"}, {"family": "Dixon", "given": "Katherine", "initials": "K"}, {"family": "Dobosi", "given": "Rita", "initials": "R"}, {"family": "Dubois", "given": "B\u00e9n\u00e9dicte", "initials": "B"}, {"family": "Ellinghaus", "given": "David", "initials": "D"}, {"family": "Elovaara", "given": "Irina", "initials": "I"}, {"family": "Esposito", "given": "Federica", "initials": "F"}, {"family": "Fontenille", "given": "Claire", "initials": "C"}, {"family": "Foote", "given": "Simon", "initials": "S"}, {"family": "Franke", "given": "Andre", "initials": "A"}, {"family": "Galimberti", "given": "Daniela", "initials": "D"}, {"family": "Ghezzi", "given": "Angelo", "initials": "A"}, {"family": "Glessner", "given": "Joseph", "initials": "J"}, {"family": "Gomez", "given": "Refujia", "initials": "R"}, {"family": "Gout", "given": "Olivier", "initials": "O"}, {"family": "Graham", "given": "Colin", "initials": "C"}, {"family": "Grant", "given": "Struan F A", "initials": "SFA"}, {"family": "Guerini", "given": "Franca Rosa", "initials": "FR"}, {"family": "Hakonarson", "given": "Hakon", "initials": "H"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Hartung", "given": "Hans-Peter", "initials": "H"}, {"family": "Heard", "given": "Rob N", "initials": "RN"}, {"family": "Heath", "given": "Simon", "initials": "S"}, {"family": "Hobart", "given": "Jeremy", "initials": "J"}, {"family": "Hoshi", "given": "Muna", "initials": "M"}, {"family": "Infante-Duarte", "given": "Carmen", "initials": "C"}, {"family": "Ingram", "given": "Gillian", "initials": "G"}, {"family": "Ingram", "given": "Wendy", "initials": "W"}, {"family": "Islam", "given": "Talat", "initials": "T"}, {"family": "Jagodic", "given": "Maja", "initials": "M"}, {"family": "Kabesch", "given": "Michael", "initials": "M"}, {"family": "Kermode", "given": "Allan G", "initials": "AG"}, {"family": "Kilpatrick", "given": "Trevor J", "initials": "TJ"}, {"family": "Kim", "given": "Cecilia", "initials": "C"}, {"family": "Klopp", "given": "Norman", "initials": "N"}, {"family": "Koivisto", "given": "Keijo", "initials": "K"}, {"family": "Larsson", "given": "Malin", "initials": "M"}, {"family": "Lathrop", "given": "Mark", "initials": "M"}, {"family": "Lechner-Scott", "given": "Jeannette S", "initials": "JS"}, {"family": "Leone", "given": "Maurizio A", "initials": "MA"}, {"family": "Lepp\u00e4", "given": "Virpi", "initials": "V"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-1250-392X", "researcher": {"href": "https://publications.scilifelab.se/researcher/241618974ae142b38e5fe84236819f2b.json"}}, {"family": "Bomfim", "given": "Izaura Lima", "initials": "IL"}, {"family": "Lincoln", "given": "Robin R", "initials": "RR"}, {"family": "Link", "given": "Jenny", "initials": "J"}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "Lorentzen", "given": "Aslaug R", "initials": "AR"}, {"family": "Lupoli", "given": "Sara", "initials": "S"}, {"family": "Macciardi", "given": "Fabio", "initials": "F"}, {"family": "Mack", "given": "Thomas", "initials": "T"}, {"family": "Marriott", "given": "Mark", "initials": "M"}, {"family": "Martinelli", "given": "Vittorio", "initials": "V"}, {"family": "Mason", "given": "Deborah", "initials": "D"}, {"family": "McCauley", "given": "Jacob L", "initials": "JL"}, {"family": "Mentch", "given": "Frank", "initials": "F"}, {"family": "Mero", "given": "Inger-Lise", "initials": "I"}, {"family": "Mihalova", "given": "Tania", "initials": "T"}, {"family": "Montalban", "given": "Xavier", "initials": "X"}, {"family": "Mottershead", "given": "John", "initials": "J"}, {"family": "Myhr", "given": "Kjell-Morten", "initials": "K"}, {"family": "Naldi", "given": "Paola", "initials": "P"}, {"family": "Ollier", "given": "William", "initials": "W"}, {"family": "Page", "given": "Alison", "initials": "A"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Pelletier", "given": "Jean", "initials": "J"}, {"family": "Piccio", "given": "Laura", "initials": "L"}, {"family": "Pickersgill", "given": "Trevor", "initials": "T"}, {"family": "Piehl", "given": "Fredrik", "initials": "F"}, {"family": "Pobywajlo", "given": "Susan", "initials": "S"}, {"family": "Quach", "given": "Hong L", "initials": "HL"}, {"family": "Ramsay", "given": "Patricia P", "initials": "PP"}, {"family": "Reunanen", "given": "Mauri", "initials": "M"}, {"family": "Reynolds", "given": "Richard", "initials": "R"}, {"family": "Rioux", "given": "John D", "initials": "JD"}, {"family": "Rodegher", "given": "Mariaemma", "initials": "M"}, {"family": "Roesner", "given": "Sabine", "initials": "S"}, {"family": "Rubio", "given": "Justin P", "initials": "JP"}, {"family": "R\u00fcckert", "given": "Ina-Maria", "initials": "I"}, {"family": "Salvetti", "given": "Marco", "initials": "M"}, {"family": "Salvi", "given": "Erika", "initials": "E"}, {"family": "Santaniello", "given": "Adam", "initials": "A"}, {"family": "Schaefer", "given": "Catherine A", "initials": "CA"}, {"family": "Schreiber", "given": "Stefan", "initials": "S"}, {"family": "Schulze", "given": "Christian", "initials": "C"}, {"family": "Scott", "given": "Rodney J", "initials": "RJ"}, {"family": "Sellebjerg", "given": "Finn", "initials": "F"}, {"family": "Selmaj", "given": "Krzysztof W", "initials": "KW"}, {"family": "Sexton", "given": "David", "initials": "D"}, {"family": "Shen", "given": "Ling", "initials": "L"}, {"family": "Simms-Acuna", "given": "Brigid", "initials": "B"}, {"family": "Skidmore", "given": "Sheila", "initials": "S"}, {"family": "Sleiman", "given": "Patrick M A", "initials": "PMA"}, {"family": "Smestad", "given": "Cathrine", "initials": "C"}, {"family": "S\u00f8rensen", "given": "Per Soelberg", "initials": "PS"}, {"family": "S\u00f8ndergaard", "given": "Helle Bach", "initials": "HB"}, {"family": "Stankovich", "given": "Jim", "initials": "J"}, {"family": "Strange", "given": "Richard C", "initials": "RC"}, {"family": "Sulonen", "given": "Anna-Maija", "initials": "A"}, {"family": "Sundqvist", "given": "Emilie", "initials": "E"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "A"}, {"family": "Taddeo", "given": "Francesca", "initials": "F"}, {"family": "Taylor", "given": "Bruce", "initials": "B"}, {"family": "Blackwell", "given": "Jenefer M", "initials": "JM"}, {"family": "Tienari", "given": "Pentti", "initials": "P"}, {"family": "Bramon", "given": "Elvira", "initials": "E"}, {"family": "Tourbah", "given": "Ayman", "initials": "A"}, {"family": "Brown", "given": "Matthew A", "initials": "MA"}, {"family": "Tronczynska", "given": "Ewa", "initials": "E"}, {"family": "Casas", "given": "Juan P", "initials": "JP"}, {"family": "Tubridy", "given": "Niall", "initials": "N"}, {"family": "Corvin", "given": "Aiden", "initials": "A"}, {"family": "Vickery", "given": "Jane", "initials": "J"}, {"family": "Jankowski", "given": "Janusz", "initials": "J"}, {"family": "Villoslada", "given": "Pablo", "initials": "P"}, {"family": "Markus", "given": "Hugh S", "initials": "HS"}, {"family": "Wang", "given": "Kai", "initials": "K"}, {"family": "Mathew", "given": "Christopher G", "initials": "CG"}, {"family": "Wason", "given": "James", "initials": "J"}, {"family": "Palmer", "given": "Colin N A", "initials": "CNA"}, {"family": "Wichmann", "given": "H-Erich", "initials": "H"}, {"family": "Plomin", "given": "Robert", "initials": "R"}, {"family": "Willoughby", "given": "Ernest", "initials": "E"}, {"family": "Rautanen", "given": "Anna", "initials": "A"}, {"family": "Winkelmann", "given": "Juliane", "initials": "J"}, {"family": "Wittig", "given": "Michael", "initials": "M"}, {"family": "Trembath", "given": "Richard C", "initials": "RC"}, {"family": "Yaouanq", "given": "Jacqueline", "initials": "J"}, {"family": "Viswanathan", "given": "Ananth C", "initials": "AC"}, {"family": "Zhang", "given": "Haitao", "initials": "H"}, {"family": "Wood", "given": "Nicholas W", "initials": "NW"}, {"family": "Zuvich", "given": "Rebecca", "initials": "R"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Langford", "given": "Cordelia", "initials": "C"}, {"family": "Duncanson", "given": "Audrey", "initials": "A"}, {"family": "Oksenberg", "given": "Jorge R", "initials": "JR"}, {"family": "Pericak-Vance", "given": "Margaret A", "initials": "MA"}, {"family": "Haines", "given": "Jonathan L", "initials": "JL"}, {"family": "Olsson", "given": "Tomas", "initials": "T"}, {"family": "Hillert", "given": "Jan", "initials": "J"}, {"family": "Ivinson", "given": "Adrian J", "initials": "AJ"}, {"family": "De Jager", "given": "Philip L", "initials": "PL"}, {"family": "Peltonen", "given": "Leena", "initials": "L"}, {"family": "Stewart", "given": "Graeme J", "initials": "GJ"}, {"family": "Hafler", "given": "David A", "initials": "DA"}, {"family": "Hauser", "given": "Stephen L", "initials": "SL"}, {"family": "McVean", "given": "Gil", "initials": "G"}, {"family": "Donnelly", "given": "Peter", "initials": "P"}, {"family": "Compston", "given": "Alastair", "initials": "A"}], "type": "journal article", "published": "2011-08-10", "journal": {"title": "Nature", "issn": "1476-4687", "issn-l": "0028-0836", "volume": "476", "issue": "7359", "pages": "214-219"}, "abstract": "Multiple sclerosis is a common disease of the central nervous system in which the interplay between inflammatory and neurodegenerative processes typically results in intermittent neurological disturbance followed by progressive accumulation of disability. Epidemiological studies have shown that genetic factors are primarily responsible for the substantially increased frequency of the disease seen in the relatives of affected individuals, and systematic attempts to identify linkage in multiplex families have confirmed that variation within the major histocompatibility complex (MHC) exerts the greatest individual effect on risk. Modestly powered genome-wide association studies (GWAS) have enabled more than 20 additional risk loci to be identified and have shown that multiple variants exerting modest individual effects have a key role in disease susceptibility. Most of the genetic architecture underlying susceptibility to the disease remains to be defined and is anticipated to require the analysis of sample sizes that are beyond the numbers currently available to individual research groups. In a collaborative GWAS involving 9,772 cases of European descent collected by 23 research groups working in 15 different countries, we have replicated almost all of the previously suggested associations and identified at least a further 29 novel susceptibility loci. Within the MHC we have refined the identity of the HLA-DRB1 risk alleles and confirmed that variation in the HLA-A gene underlies the independent protective effect attributable to the class I region. Immunologically relevant genes are significantly overrepresented among those mapping close to the identified loci and particularly implicate T-helper-cell differentiation in the pathogenesis of multiple sclerosis.", "doi": "10.1038/nature10251", "pmid": "21833088", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "nature10251"}, {"db": "pmc", "key": "PMC3182531"}, {"db": "mid", "key": "UKMS36028"}], "notes": [], "created": "2017-05-04T15:00:49.499Z", "modified": "2022-03-31T15:22:21.771Z"}, {"entity": "publication", "iuid": "952052b847a94bd796d1d8a6943902b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/952052b847a94bd796d1d8a6943902b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/952052b847a94bd796d1d8a6943902b9"}}, "title": "Functional and prognostic relevance of the homeobox protein MSX2 in malignant melanoma.", "authors": [{"family": "Gremel", "given": "G", "initials": "G"}, {"family": "Ryan", "given": "D", "initials": "D"}, {"family": "Rafferty", "given": "M", "initials": "M"}, {"family": "Lanigan", "given": "F", "initials": "F"}, {"family": "Hegarty", "given": "S", "initials": "S"}, {"family": "Lavelle", "given": "M", "initials": "M"}, {"family": "Murphy", "given": "I", "initials": "I"}, {"family": "Unwin", "given": "L", "initials": "L"}, {"family": "Joyce", "given": "C", "initials": "C"}, {"family": "Faller", "given": "W", "initials": "W"}, {"family": "McDermott", "given": "E W", "initials": "EW"}, {"family": "Sheahan", "given": "K", "initials": "K"}, {"family": "Ponten", "given": "F", "initials": "F"}, {"family": "Gallagher", "given": "W M", "initials": "WM"}], "type": "journal article", "published": "2011-08-09", "journal": {"volume": "105", "issn": "1532-1827", "issue": "4", "pages": "565-574", "title": "Br. J. Cancer", "issn-l": "0007-0920"}, "abstract": "The homeobox containing transcription factor MSX2 is a key regulator of embryonic development and has been implicated to have a role in breast and pancreatic cancer.\n\nUsing a selection of two- and three-dimensional in vitro assays and tissue microarrays (TMAs), the clinical and functional relevance of MSX2 in malignant melanoma was explored. A doxycyline-inducible over-expression system was applied to study the relevance of MSX2 in vitro. For TMA construction, tumour material from 218 melanoma patients was used.\n\nEctopic expression of MSX2 resulted in the induction of apoptosis and reduced the invasive capacity of melanoma cells in three-dimensional culture. MSX2 over-expression was shown to affect several signalling pathways associated with cell invasion and survival. Downregulation of N-Cadherin, induction of p21 and inhibition of both BCL2 and Survivin were observed. Cytoplasmic MSX2 expression was found to correlate significantly with increased recurrence-free survival (P=0.008). Nuclear expression of MSX2 did not result in significant survival correlations, suggesting that the beneficial effect of MSX2 may be independent of its DNA binding activity.\n\nMSX2 may be an important regulator of melanoma cell invasion and survival. Cytoplasmic expression of the protein was identified as biomarker for good prognosis in malignant melanoma patients.", "doi": "10.1038/bjc.2011.249", "pmid": "21730974", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "bjc2011249"}, {"db": "pmc", "key": "PMC3170959"}], "notes": [], "created": "2017-05-04T14:55:46.127Z", "modified": "2017-05-30T12:55:34.493Z"}, {"entity": "publication", "iuid": "24d391bebc0340e9b9fb89683845c7d2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24d391bebc0340e9b9fb89683845c7d2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24d391bebc0340e9b9fb89683845c7d2"}}, "title": "Mapping the subcellular protein distribution in three human cell lines.", "authors": [{"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Stadler", "given": "Charlotte", "initials": "C", "orcid": "0000-0002-6781-1938", "researcher": {"href": "https://publications.scilifelab.se/researcher/2db3b27c7d7143cbacc8c1dd8ac90a31.json"}}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Hjelmare", "given": "Martin", "initials": "M"}, {"family": "Jonasson", "given": "Kalle", "initials": "K"}, {"family": "Wiking", "given": "Mikaela", "initials": "M"}, {"family": "Abergh", "given": "Annica", "initials": "A"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}], "type": "journal article", "published": "2011-08-05", "journal": {"volume": "10", "issn": "1535-3907", "issue": "8", "pages": "3766-3777", "title": "J. Proteome Res.", "issn-l": "1535-3893"}, "abstract": "The subcellular locations of proteins are closely related to their function and constitute an essential aspect for understanding the complex machinery of living cells. A systematic effort has been initiated to map the protein distribution in three functionally different cell lines with the aim to provide a subcellular localization index for at least one representative protein from all human protein-encoding genes. Here, we present the results of more than 3500 proteins mapped to 16 subcellular compartments. The results indicate a ubiquitous protein expression with a majority of the proteins found in all three cell lines and a large portion localized to two or more compartments. The inter-relationships between the subcellular compartments are visualized in a protein-compartment network based on all detected proteins. Hierarchical clustering was performed to determine how closely related the organelles are in terms of protein constituents and compare the proteins detected in each cell type. Our results show distinct organelle proteomes, well conserved across the cell types, and demonstrate that biochemically similar organelles are grouped together.", "doi": "10.1021/pr200379a", "pmid": "21675716", "labels": {"Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:08.969Z", "modified": "2021-07-08T13:44:33.089Z"}, {"entity": "publication", "iuid": "efde3eebca04451982a1cd12962eea84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/efde3eebca04451982a1cd12962eea84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/efde3eebca04451982a1cd12962eea84"}}, "title": "The genetic structure of the Swedish population.", "authors": [{"family": "Humphreys", "given": "Keith", "initials": "K"}, {"family": "Grankvist", "given": "Alexander", "initials": "A"}, {"family": "Leu", "given": "Monica", "initials": "M"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Rehnstr\u00f6m", "given": "Karola", "initials": "K"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Ding", "given": "Bo", "initials": "B"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Xu", "given": "Jianfeng", "initials": "J"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}, {"family": "Mattingsdal", "given": "Morten", "initials": "M"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "O'Dushlaine", "given": "Colm", "initials": "C"}, {"family": "Purcell", "given": "Shaun M", "initials": "SM"}, {"family": "Sklar", "given": "Pamela", "initials": "P"}, {"family": "Sullivan", "given": "Patrick F", "initials": "PF"}, {"family": "Hultman", "given": "Christina M", "initials": "CM"}, {"family": "Palmgren", "given": "Juni", "initials": "J"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}], "type": "journal article", "published": "2011-08-04", "journal": {"volume": "6", "issn": "1932-6203", "issue": "8", "pages": "e22547", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Patterns of genetic diversity have previously been shown to mirror geography on a global scale and within continents and individual countries. Using genome-wide SNP data on 5174 Swedes with extensive geographical coverage, we analyzed the genetic structure of the Swedish population. We observed strong differences between the far northern counties and the remaining counties. The population of Dalarna county, in north middle Sweden, which borders southern Norway, also appears to differ markedly from other counties, possibly due to this county having more individuals with remote Finnish or Norwegian ancestry than other counties. An analysis of genetic differentiation (based on pairwise F(st)) indicated that the population of Sweden's southernmost counties are genetically closer to the HapMap CEU samples of Northern European ancestry than to the populations of Sweden's northernmost counties. In a comparison of extended homozygous segments, we detected a clear divide between southern and northern Sweden with small differences between the southern counties and considerably more segments in northern Sweden. Both the increased degree of homozygosity in the north and the large genetic differences between the south and the north may have arisen due to a small population in the north and the vast geographical distances between towns and villages in the north, in contrast to the more densely settled southern parts of Sweden. Our findings have implications for future genome-wide association studies (GWAS) with respect to the matching of cases and controls and the need for within-county matching. We have shown that genetic differences within a single country may be substantial, even when viewed on a European scale. Thus, population stratification needs to be accounted for, even within a country like Sweden, which is often perceived to be relatively homogenous and a favourable resource for genetic mapping, otherwise inferences based on genetic data may lead to false conclusions.", "doi": "10.1371/journal.pone.0022547", "pmid": "21829632", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "PONE-D-11-01309"}, {"db": "pmc", "key": "PMC3150368"}], "notes": [], "created": "2017-10-30T13:50:22.133Z", "modified": "2020-01-21T13:56:08.449Z"}, {"entity": "publication", "iuid": "d80b83743fac433cbc81d4d3f3724da1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d80b83743fac433cbc81d4d3f3724da1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d80b83743fac433cbc81d4d3f3724da1"}}, "title": "Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer.", "authors": [{"family": "H\u00e5fstr\u00f6m", "given": "Therese", "initials": "T"}, {"family": "Jansson", "given": "D\u00e9sir\u00e9e S", "initials": "DS"}, {"family": "Segerman", "given": "Bo", "initials": "B"}], "type": "journal article", "published": "2011-08-04", "journal": {"volume": "12", "issn": "1471-2164", "issue": null, "pages": "395", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Brachyspira spp. colonize the intestines of some mammalian and avian species and show different degrees of enteropathogenicity. Brachyspira intermedia can cause production losses in chickens and strain PWS/AT now becomes the fourth genome to be completed in the genus Brachyspira.\n\n15 classes of unique and shared genes were analyzed in B. intermedia, B. murdochii, B. hyodysenteriae and B. pilosicoli. The largest number of unique genes was found in B. intermedia and B. murdochii. This indicates the presence of larger pan-genomes. In general, hypothetical protein annotations are overrepresented among the unique genes. A 3.2 kb plasmid was found in B. intermedia strain PWS/AT. The plasmid was also present in the B. murdochii strain but not in nine other Brachyspira isolates. Within the Brachyspira genomes, genes had been translocated and also frequently switched between leading and lagging strands, a process that can be followed by different AT-skews in the third positions of synonymous codons. We also found evidence that bacteriophages were being remodeled and genes incorporated into them.\n\nThe accessory gene pool shapes species-specific traits. It is also influenced by reductive genome evolution and horizontal gene transfer. Gene-transfer events can cross both species and genus boundaries and bacteriophages appear to play an important role in this process. A mechanism for horizontal gene transfer appears to be gene translocations leading to remodeling of bacteriophages in combination with broad tropism.", "doi": "10.1186/1471-2164-12-395", "pmid": "21816042", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-12-395"}, {"db": "pmc", "key": "PMC3163572"}], "notes": [], "created": "2017-05-04T14:57:16.486Z", "modified": "2020-01-21T13:56:05.540Z"}, {"entity": "publication", "iuid": "54847b9b8a9d4f5e95bfd6ea007f45fb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/54847b9b8a9d4f5e95bfd6ea007f45fb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/54847b9b8a9d4f5e95bfd6ea007f45fb"}}, "title": "Influence of the COMT genotype on working memory and brain activity changes during development.", "authors": [{"family": "Dumontheil", "given": "Iroise", "initials": "I"}, {"family": "Roggeman", "given": "Chantal", "initials": "C"}, {"family": "Ziermans", "given": "Tim", "initials": "T"}, {"family": "Peyrard-Janvid", "given": "Myriam", "initials": "M"}, {"family": "Matsson", "given": "Hans", "initials": "H"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Klingberg", "given": "Torkel", "initials": "T"}], "type": "journal article", "published": "2011-08-01", "journal": {"volume": "70", "issn": "1873-2402", "issue": "3", "pages": "222-229", "title": "Biol. Psychiatry", "issn-l": "0006-3223"}, "abstract": "The Valine158Methionine (Val158Met) polymorphism of the COMT gene leads to lower enzymatic activity and higher dopamine availability in Met carriers. The Met allele is associated with better performance and reduced prefrontal cortex activation during working memory (WM) tasks in adults. Dopaminergic system changes during adolescence may lead to a reduction of basal dopamine levels, potentially affecting Met allele benefits during development.\n\nWe investigated the association of COMT genotype with behavioral (n = 322) and magnetic resonance imaging data (n = 81-84) collected during performance of a visuospatial WM task and potential changes in these effects during development (reflected in age \u00d7 genotype interactions). Data were collected from a cross-sectional and longitudinal typically developing sample of 6- to 20-year-olds.\n\nVisuospatial WM capacity exhibited an age \u00d7 genotype interaction, with a benefit of the Met allele emerging after 10 years of age. There was a parallel age \u00d7 genotype interaction on WM-related activation in the right inferior frontal gyrus and intraparietal sulcus (IPS), with increases in activation with age in the Val/Val group only. Main effects of COMT genotype were also observed in the IPS, with greater gray matter volumes bilaterally and greater right IPS activation in the Val/Val group compared with the Met carriers.\n\nThese results suggest that COMT genotype effects on WM brain activity and behavior are not static during development. The full developmental picture should be considered when trying to understand the impact of genetic polymorphisms on the mature cognition of healthy adult or psychiatric populations.", "doi": "10.1016/j.biopsych.2011.02.027", "pmid": "21514925", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "S0006-3223(11)00202-2"}], "notes": [], "created": "2017-05-04T15:03:29.544Z", "modified": "2017-05-30T12:44:05.009Z"}, {"entity": "publication", "iuid": "74a2c5d345704611b48c394e247dc4d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/74a2c5d345704611b48c394e247dc4d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/74a2c5d345704611b48c394e247dc4d7"}}, "title": "The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi.", "authors": [{"family": "Franz\u00e9n", "given": "Oscar", "initials": "O"}, {"family": "Arner", "given": "Erik", "initials": "E"}, {"family": "Ferella", "given": "Marcela", "initials": "M"}, {"family": "Nilsson", "given": "Daniel", "initials": "D"}, {"family": "Respuela", "given": "Patricia", "initials": "P"}, {"family": "Carninci", "given": "Piero", "initials": "P"}, {"family": "Hayashizaki", "given": "Yoshihide", "initials": "Y"}, {"family": "Aslund", "given": "Lena", "initials": "L"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Daub", "given": "Carsten O", "initials": "CO"}], "type": "journal article", "published": "2011-08-00", "journal": {"volume": "5", "issn": "1935-2735", "issue": "8", "pages": "e1283", "title": "PLoS Negl Trop Dis", "issn-l": "1935-2727"}, "abstract": "The pathway for RNA interference is widespread in metazoans and participates in numerous cellular tasks, from gene silencing to chromatin remodeling and protection against retrotransposition. The unicellular eukaryote Trypanosoma cruzi is missing the canonical RNAi pathway and is unable to induce RNAi-related processes. To further understand alternative RNA pathways operating in this organism, we have performed deep sequencing and genome-wide analyses of a size-fractioned cDNA library (16-61 nt) from the epimastigote life stage. Deep sequencing generated 582,243 short sequences of which 91% could be aligned with the genome sequence. About 95-98% of the aligned data (depending on the haplotype) corresponded to small RNAs derived from tRNAs, rRNAs, snRNAs and snoRNAs. The largest class consisted of tRNA-derived small RNAs which primarily originated from the 3' end of tRNAs, followed by small RNAs derived from rRNA. The remaining sequences revealed the presence of 92 novel transcribed loci, of which 79 did not show homology to known RNA classes.", "doi": "10.1371/journal.pntd.0001283", "pmid": "21912713", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PNTD-D-11-00417"}, {"db": "pmc", "key": "PMC3166047"}], "notes": [], "created": "2017-05-04T14:57:24.991Z", "modified": "2020-01-21T13:56:03.019Z"}, {"entity": "publication", "iuid": "f52e06e45f5441fd85c12a288c5606c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f52e06e45f5441fd85c12a288c5606c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f52e06e45f5441fd85c12a288c5606c4"}}, "title": "RBM3-regulated genes promote DNA integrity and affect clinical outcome in epithelial ovarian cancer.", "authors": [{"family": "Ehl\u00e9n", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Nodin", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Br\u00e4ndstedt", "given": "Jenny", "initials": "J"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Alvarado-Kristensson", "given": "Maria", "initials": "M", "orcid": "0000-0003-0598-7986", "researcher": {"href": "https://publications.scilifelab.se/researcher/70ee81797eff452fa037821f293d8673.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2011-08-00", "journal": {"volume": "4", "issn": "1936-5233", "issue": "4", "pages": "212-221", "title": "Transl Oncol", "issn-l": null}, "abstract": "The RNA-binding motif protein 3 (RBM3) was initially discovered as a putative cancer biomarker based on its differential expression in various cancer forms in the Human Protein Atlas (HPA). We previously reported an association between high expression of RBM3 and prolonged survival in breast and epithelial ovarian cancer (EOC). Because the function of RBM3 has not been fully elucidated, the aim of this study was to use gene set enrichment analysis to identify the underlying biologic processes associated with RBM3 expression in a previously analyzed EOC cohort (cohort 1, n = 267). This revealed an association between RBM3 expression and several cellular processes involved in the maintenance of DNA integrity. RBM3-regulated genes were subsequently screened in the HPA to select for putative prognostic markers, and candidate proteins were analyzed in the ovarian cancer cell line A2780, whereby an up-regulation of Chk1, Chk2, and MCM3 was demonstrated in siRBM3-treated cells compared to controls. The prognostic value of these markers was assessed at the messenger RNA level in cohort 1 and the protein level in an independent EOC cohort (cohort 2, n = 154). High expression levels of Chk1, Chk2, and MCM3 were associated with a significantly shorter survival in both cohorts, and phosphorylated Chk2 was an adverse prognostic marker in cohort 2. These results uncover a putative role for RBM3 in DNA damage response, which might, in part, explain its cisplatin-sensitizing properties and good prognostic value in EOC. Furthermore, it is demonstrated that Chk1, Chk2, and MCM3 are poor prognostic markers in EOC.", "doi": "10.1593/tlo.11106", "pmid": "21804916", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pmc", "key": "PMC3140008"}], "notes": [], "created": "2017-05-04T14:55:49.446Z", "modified": "2021-06-22T12:17:19.596Z"}, {"entity": "publication", "iuid": "34c5fbe40d8c4a67994933bef70f3526", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34c5fbe40d8c4a67994933bef70f3526.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34c5fbe40d8c4a67994933bef70f3526"}}, "title": "Lack of association between two dopamine D2 receptor gene polymorphisms and schizophrenia.", "authors": [{"family": "Caprini", "given": "Sara", "initials": "S"}, {"family": "Saetre", "given": "Peter", "initials": "P"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Skj\u00f8dt", "given": "Celina", "initials": "C"}, {"family": "Duong", "given": "Linh", "initials": "L"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Hall", "given": "Hakan", "initials": "H"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Terenius", "given": "Lars", "initials": "L"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}], "type": "letter", "published": "2011-08-00", "journal": {"volume": "21", "issn": "1473-5873", "issue": "4", "pages": "214-215", "title": "Psychiatr. Genet.", "issn-l": "0955-8829"}, "abstract": null, "doi": "10.1097/YPG.0b013e328341e020", "pmid": "21712758", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "00041444-201108000-00008"}], "notes": [], "created": "2017-05-04T15:00:51.649Z", "modified": "2020-01-21T13:56:01.519Z"}, {"entity": "publication", "iuid": "d8c3d87f73874cce97d189292f4e7bb8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d8c3d87f73874cce97d189292f4e7bb8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d8c3d87f73874cce97d189292f4e7bb8"}}, "title": "Lack of association between genetic variations in the KALRN region and ischemic stroke.", "authors": [{"family": "Olsson", "given": "Sandra", "initials": "S"}, {"family": "Jood", "given": "Katarina", "initials": "K"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Sj\u00f6gren", "given": "Marketa", "initials": "M"}, {"family": "Norrving", "given": "Bo", "initials": "B"}, {"family": "Nilsson", "given": "Michael", "initials": "M"}, {"family": "Lindgren", "given": "Arne", "initials": "A"}, {"family": "Jern", "given": "Christina", "initials": "C"}], "type": "journal article", "published": "2011-08-00", "journal": {"volume": "44", "issn": "1873-2933", "issue": "12", "pages": "1018-1020", "title": "Clin. Biochem.", "issn-l": "0009-9120"}, "abstract": "To investigate whether KALRN gene variation is associated with ischemic stroke (IS).\n\nAssociations to overall IS and IS subtypes were investigated in SAHLSIS, which comprises 844 patients with IS and 668 controls.\n\nAssociations between KALRN SNPs and overall IS and cardioembolic stroke were detected. Associations for overall IS were investigated in two additional Swedish samples, but could not be replicated.\n\nKALRN gene variation is not associated with overall IS.", "doi": "10.1016/j.clinbiochem.2011.05.025", "pmid": "21664346", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0009-9120(11)00376-6"}], "notes": [], "created": "2017-05-04T15:00:42.033Z", "modified": "2021-07-07T13:54:18.974Z"}, {"entity": "publication", "iuid": "6f6bece2b52d42f6b7cb4126f462b00e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f6bece2b52d42f6b7cb4126f462b00e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f6bece2b52d42f6b7cb4126f462b00e"}}, "title": "Hyphae-colonizing Burkholderia sp.--a new source of biological control agents against sheath blight disease (Rhizoctonia solani AG1-IA) in rice.", "authors": [{"family": "Cuong", "given": "Nguyen Duc", "initials": "ND"}, {"family": "Nicolaisen", "given": "Mette Haubjerg", "initials": "MH"}, {"family": "S\u00f8rensen", "given": "Jan", "initials": "J"}, {"family": "Olsson", "given": "Stefan", "initials": "S"}], "type": "comparative study", "published": "2011-08-00", "journal": {"volume": "62", "issn": "1432-184X", "issue": "2", "pages": "425-434", "title": "Microb. Ecol.", "issn-l": "0095-3628"}, "abstract": "Sheath blight infection of rice by Rhizoctonia solani K\u00fchn AG1-IA often results in serious yield losses in intensive rice cultivation. Biological control agents (BCAs) have previously been isolated but poor efficiency is often observed when applied under field conditions. This study compares a traditional dual-culture plate assay and a new water-surface microcosm assay for isolation of antagonistic soil bacteria. In the water-surface microcosm assay, floating pathogen mycelium is used as a source for isolation of hyphae-colonizing soil bacteria (HCSB), which are subsequently screened for antagonism. Ten antagonistic soil bacteria (ASB) isolated from a variety of Vietnamese rice soils using dual-culture plates were found to be affiliated with Bacillus based on 16S rRNA gene sequencing. However, all the ASB isolates grew poorly and showed no antagonism in the water-surface microcosm assay. In contrast, 11 (out of 13) HCSB isolates affiliated with Burkholderia sp. all grew well by colonizing the hyphae in the microcosms. Two of the Burkholderia sp. isolates, assigned to B. vietnamiensis based on recA gene sequencing, strongly inhibited fungal growth in both the dual-culture and water-surface microcosm assays; HCSB isolates affiliated to other species or species groups showed limited or no inhibition of R. solani in the microcosms. Our results suggest that HCSB obtained from floating pathogen hyphae can be a new source for isolation of efficient BCAs against R. solani, as the isolation assay mimics the natural habitat for fungal-bacterial interaction in the fields.", "doi": "10.1007/s00248-011-9823-x", "pmid": "21365233", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:00.013Z", "modified": "2020-01-21T13:56:02.912Z"}, {"entity": "publication", "iuid": "488c351a1c714b168070854f0ee5956a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/488c351a1c714b168070854f0ee5956a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/488c351a1c714b168070854f0ee5956a"}}, "title": "Gene-environment interactions between CRHR1 variants and physical assault in suicide attempts.", "authors": [{"family": "Ben-Efraim", "given": "Y J", "initials": "YJ"}, {"family": "Wasserman", "given": "D", "initials": "D"}, {"family": "Wasserman", "given": "J", "initials": "J"}, {"family": "Sokolowski", "given": "M", "initials": "M"}], "type": "journal article", "published": "2011-08-00", "journal": {"volume": "10", "issn": "1601-183X", "issue": "6", "pages": "663-672", "title": "Genes Brain Behav.", "issn-l": null}, "abstract": "Risk factors for suicidal behaviors are partly heritable, including genetic variants that drive diathesis-stress in addition to, or by interaction with, exposure to certain stressful life events (SLEs). Hypothalamic-pituitary-adrenal (HPA) axis regulatory genes are candidates for association with suicide as well as its endophenotypes. Using a family-based design of offspring who attempted suicide (SA) and both parents, we investigated gene-environment interactions (G\u00d7Es) of SLE exposures with single nucleotide polymorphisms (SNPs) in corticotropin-releasing hormone receptor-1 (CRHR1), a major HPA axis regulatory gene. We observed a novel G\u00d7E among predominantly female SA between 5'-SNP rs7209436 and childhood/adolescence physical assault or attack (PA), as well as a second novel and male-specific G\u00d7E between 3'-SNP rs16940665 and adulthood PA exposure. A third male-specific G\u00d7E previously reported by us among depressed SA, between SNP rs4792887 and cumulative SLEs, was also further confirmed. The two novel G\u00d7Es presented here shared the SA characteristic of aggression, while showing differences on other aspects of SA heterogeneity. We conclude that different SA subjects were observed to differentially associate with two novel G\u00d7Es involving exposures to PA with different life timing and SNPs located in opposite ends of CRHR1. Concerning sex differences, we observed three subsets of distinct male SA that associated with each of the three observed G\u00d7Es, whereas female SAs were affected by only one of the G\u00d7Es. These results are consistent with a diathesis-stress model of suicidal behavior and may help to explain SA heterogeneity.", "doi": "10.1111/j.1601-183X.2011.00703.x", "pmid": "21605337", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:44.577Z", "modified": "2020-01-21T13:56:02.093Z"}, {"entity": "publication", "iuid": "24df8269ff104672b5f3ba0f7b3aeef6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24df8269ff104672b5f3ba0f7b3aeef6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24df8269ff104672b5f3ba0f7b3aeef6"}}, "title": "Evaluation of Fanconi anaemia genes FANCA, FANCC and FANCL in cervical cancer susceptibility.", "authors": [{"family": "Juko-Pecirep", "given": "Ivana", "initials": "I"}, {"family": "Ivansson", "given": "Emma L", "initials": "EL"}, {"family": "Gyllensten", "given": "Ulf B", "initials": "UB"}], "type": "journal article", "published": "2011-08-00", "journal": {"volume": "122", "issn": "1095-6859", "issue": "2", "pages": "377-381", "title": "Gynecol. Oncol.", "issn-l": "0090-8258"}, "abstract": "Disrupting the function of any of the 13 Fanconi anaemia (FA) genes causes a DNA repair deficiency disorder, with patients being susceptible to a number of cancer types. Variation in the family of FA genes has been suggested to affect risk of cervical cancer. The current study evaluates the influence of three genes in the FA pathway on cervical cancer risk in Swedish women.\r\n\r\nTagSNPs in FANCA, FANCC and FANCL were selected using the Tagger algorithm in Haploview. A total of 81 tagSNPs were genotyped in 782 cases (CIN3 or ICC) and 775 controls using the Illumina GoldenGate Assay and statistically analyzed for association with cervical cancer.\r\n\r\n72 SNPs were successfully genotyped in >98% of the samples. Nominal associations were detected for FANCA rs11649196 (p=0.05) and rs4128763 in FANCC (p=0.02). The associations did not withstand correction for multiple testing.\r\n\r\nThe current study does not support that genetic variation in FANCA, FANCC or FANCL genes affects susceptibility to cervical cancer in the Swedish population.", "doi": "10.1016/j.ygyno.2011.04.014", "pmid": "21543111", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0090-8258(11)00276-9"}], "notes": [], "created": "2017-05-04T15:00:45.482Z", "modified": "2020-01-21T13:56:09.048Z"}, {"entity": "publication", "iuid": "899359c579ff4acd9c8aa1d39b9d6060", "links": {"self": {"href": "https://publications.scilifelab.se/publication/899359c579ff4acd9c8aa1d39b9d6060.json"}, "display": {"href": "https://publications.scilifelab.se/publication/899359c579ff4acd9c8aa1d39b9d6060"}}, "title": "Correlation between LRIG1 and LRIG2 expressions and expression of 11 tumor markers, with special reference to tumor suppressors, in CIN and normal cervical epithelium.", "authors": [{"family": "Lindstr\u00f6m", "given": "A K", "initials": "AK"}, {"family": "Asplund", "given": "A", "initials": "A"}, {"family": "Hellberg", "given": "D", "initials": "D"}], "type": "journal article", "published": "2011-08-00", "journal": {"volume": "122", "issn": "1095-6859", "issue": "2", "pages": "372-376", "title": "Gynecol. Oncol.", "issn-l": "0090-8258"}, "abstract": "Novel biological markers LRIG1 and LRIG2 have been associated with favorable as well as poor prognosis, respectively, in different cancer types, including cervical cancer. The aim of this study was to investigate possible interactions between these proteins and other tumor markers, and as diagnostic adjuncts in CIN.\n\nCervical biopsies from 171 women, with normal epithelium, and low-grade and high-grade CIN were stained for LRIG1 and LRIG2, and 11 additional tumor markers. The tumor markers were chosen to be relevant in cervical neoplasms. Staining was evaluated semiquantitatively.\n\nExpression of LRIG1 and LRIG2 was found to correlate with increasing CIN grade, as well as with expression of tumor suppressor FHIT, independent of histological grade. In addition, tumor promoter LRIG2 expression correlated negatively with expression of tumor suppressor retinoblastoma protein and positively with IL-10. The latter correlation did not however remain after adjustment for CIN grade. p53 and p16 expressions correlated positively with LRIG1 expression in univariate analyses, but significance did not hold after adjustment for CIN grade.\n\nLRIG1 and LRIG2 expressions were seen in precancerous cervical epithelium and found to increase with increasing grade. There was an association between expression of these glycoproteins and FHIT tumor suppressor protein, independently of histological grade.", "doi": "10.1016/j.ygyno.2011.04.049", "pmid": "21632100", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "S0090-8258(11)00350-7"}], "notes": [], "created": "2017-05-04T14:55:47.041Z", "modified": "2017-05-30T12:55:25.269Z"}, {"entity": "publication", "iuid": "29c2577bd03d479a8b23a8a06f02054a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/29c2577bd03d479a8b23a8a06f02054a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/29c2577bd03d479a8b23a8a06f02054a"}}, "title": "Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia.", "authors": [{"family": "Gunnarsson", "given": "Rebeqa", "initials": "R"}, {"family": "Mansouri", "given": "Larry", "initials": "L"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "G\u00f6ransson", "given": "Hanna", "initials": "H"}, {"family": "Cahill", "given": "Nicola", "initials": "N"}, {"family": "Jansson", "given": "Mattias", "initials": "M"}, {"family": "Rasmussen", "given": "Markus", "initials": "M"}, {"family": "Lundin", "given": "Jeanette", "initials": "J"}, {"family": "Norin", "given": "Stefan", "initials": "S"}, {"family": "Buhl", "given": "Anne Mette", "initials": "AM"}, {"family": "Smedby", "given": "Karin Ekstr\u00f6m", "initials": "KE"}, {"family": "Hjalgrim", "given": "Henrik", "initials": "H"}, {"family": "Karlsson", "given": "Karin", "initials": "K"}, {"family": "Jurlander", "given": "Jesper", "initials": "J"}, {"family": "Geisler", "given": "Christian", "initials": "C"}, {"family": "Juliusson", "given": "Gunnar", "initials": "G"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}], "type": "journal article", "published": "2011-08-00", "journal": {"volume": "96", "issn": "1592-8721", "issue": "8", "pages": "1161-1169", "title": "Haematologica", "issn-l": "0390-6078"}, "abstract": "High-resolution genomic microarrays enable simultaneous detection of copy-number aberrations such as the known recurrent aberrations in chronic lymphocytic leukemia [del(11q), del(13q), del(17p) and trisomy 12], and copy-number neutral loss of heterozygosity. Moreover, comparison of genomic profiles from sequential patients' samples allows detection of clonal evolution.\n\nWe screened samples from 369 patients with newly diagnosed chronic lymphocytic leukemia from a population-based cohort using 250K single nucleotide polymorphism-arrays. Clonal evolution was evaluated in 59 follow-up samples obtained after 5-9 years.\n\nAt diagnosis, copy-number aberrations were identified in 90% of patients; 70% carried known recurrent alterations, including del(13q) (55%), trisomy 12 (10.5%), del(11q) (10%), and del(17p) (4%). Additional recurrent aberrations were detected on chromosomes 2 (1.9%), 4 (1.4%), 8 (1.6%) and 14 (1.6%). Thirteen patients (3.5%) displayed recurrent copy-number neutral loss of heterozygosity on 13q, of whom 11 had concurrent homozygous del(13q). Genomic complexity and large 13q deletions correlated with inferior outcome, while the former was linked to poor-prognostic aberrations. In the follow-up study, clonal evolution developed in 8/24 (33%) patients with unmutated IGHV, and in 4/25 (16%) IGHV-mutated and treated patients. In contrast, untreated patients with mutated IGHV (n=10) did not acquire additional aberrations. The most common secondary event, del(13q), was detected in 6/12 (50%) of all patients with acquired alterations. Interestingly, aberrations on, for example, chromosome 6q, 8p, 9p and 10q developed exclusively in patients with unmutated IGHV.\n\nWhole-genome screening revealed a high frequency of genomic aberrations in newly diagnosed chronic lymphocytic leukemia. Clonal evolution was associated with other markers of aggressive disease and commonly included the known recurrent aberrations.", "doi": "10.3324/haematol.2010.039768", "pmid": "21546498", "labels": {"National Genomics Infrastructure": null, "Array and Analysis Facility": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "haematol.2010.039768"}, {"db": "pmc", "key": "PMC3148910"}], "notes": [], "created": "2017-05-04T14:57:19.184Z", "modified": "2020-01-21T13:56:01.198Z"}, {"entity": "publication", "iuid": "f1e50163073f4091881a2166bd0efb59", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f1e50163073f4091881a2166bd0efb59.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f1e50163073f4091881a2166bd0efb59"}}, "title": "Antimicrobial susceptibility of Brachyspira spp. isolated from commercial laying hens and free-living wild mallards (Anas platyrhynchos).", "authors": [{"family": "Jansson", "given": "D\u00e9sir\u00e9e S", "initials": "DS"}, {"family": "Pringle", "given": "M\u00e4rit", "initials": "M"}], "type": "journal article", "published": "2011-08-00", "journal": {"volume": "40", "issn": "1465-3338", "issue": "4", "pages": "387-393", "title": "Avian Pathol.", "issn-l": "0307-9457"}, "abstract": "In vitro antimicrobial susceptibility to tylosin, valnemulin, tiamulin, doxycycline, lincomycin and ampicillin was investigated by broth dilution in 48 Brachyspira spp. isolates from commercial laying hens (n=30) and free-living wild mallards (Anas platyrhynchos) (n=18). Presumed pathogens (Brachyspira alvinipulli, Brachyspira intermedia, Brachyspira pilosicoli), commensals (Brachyspira murdochii, Brachyspira innocens, \"Brachyspira pulli\"), and isolates of undetermined species affiliation were included. The laying hens had not been exposed to therapeutic levels of antimicrobials for at least 50 weeks before sampling, and low levels of environmental antimicrobial exposure were presumed in mallards. No isolates with decreased susceptibility to tylosin, valnemulin, tiamulin or doxycycline were found. Decreased susceptibility to lincomycin (minimum inhibitory concentration 16 \u00b5g/ml) was detected in two isolates (Brachyspira sp.) from laying hens. Five isolates showed decreased susceptibility to ampicillin (minimum inhibitory concentration 16 to >32 \u00b5g/ml), including two \"B. pulli\" and one B. alvinipulli from laying hens, and isolates of B. pilosicoli and \"B. pulli\" from mallards. Decreased susceptibility to ampicillin was associated with \u03b2-lactamase activity in four isolates. A new variant of a class D \u03b2-lactamase gene designated bla (oxa-192) was identified in a B. pilosicoli isolate of mallard origin. This is the first time the genetic basis for antimicrobial resistance is described in Brachyspira spp. from a free-living wild bird. Isolates displaying decreased susceptibility to ampicillin were accompanied by fully susceptible isolates of the same species or other genotypes within three laying hen flocks. This underlines the need for performing antimicrobial susceptibility tests on single clones/genotypes, and to analyse multiple isolates from the same flock.", "doi": "10.1080/03079457.2011.588197", "pmid": "21812718", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:54.737Z", "modified": "2020-01-21T13:56:06.245Z"}, {"entity": "publication", "iuid": "ef4debf1b97940c2b233c98ac861e08f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef4debf1b97940c2b233c98ac861e08f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef4debf1b97940c2b233c98ac861e08f"}}, "title": "Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation.", "authors": [{"family": "Mild", "given": "Mattias", "initials": "M"}, {"family": "Hedskog", "given": "Charlotte", "initials": "C"}, {"family": "Jernberg", "given": "Johanna", "initials": "J"}, {"family": "Albert", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2011-07-25", "journal": {"volume": "6", "issn": "1932-6203", "issue": "7", "pages": "e22741", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Ultra-deep pyrosequencing (UDPS) has been used to detect minority variants within HIV-1 populations. Some aspects of the quality and reproducibility of UDPS have been previously evaluated, but comprehensive studies are still needed.\n\nIn this study the UDPS technology (FLX platform) was evaluated by analyzing a 120 base pair fragment of the HIV-1 pol gene from plasma samples from two patients and artificial mixtures of molecular clones. UDPS was performed using an optimized experimental protocol and an in-house data cleaning strategy. Nine samples and mixtures were analyzed and the average number of reads per sample was 19,404 (range 8,858-26,846). The two patient plasma samples were analyzed twice and quantification of viral variants was found to be highly repeatable for variants representing >0.27% of the virus population, whereas some variants representing 0.11-0.27% were detected in only one of the two UDPS runs. Bland-Altman analysis showed that a repeated measurement would have a 95% likelihood to lie approximately within \u00b10.5 log(10) of the initial estimate. A similar level of agreement was observed for variant frequency estimates in forward vs. reverse sequencing direction, but here the agreement was higher for common variants than for rare variants. UDPS following PCR amplification with alternative primers indicated that some variants may be incorrectly quantified due to primer-related selective amplification. Finally, the in vitro recombination rate during PCR was evaluated using artificial mixtures of clones and was found to be low. The most abundant in vitro recombinant represented 0.25% of all UDPS reads.\n\nThis study demonstrates that this UDPS protocol results in low experimental noise and high repeatability, which is relevant for future research and clinical use of the UDPS technology. The low rate of in vitro recombination suggests that this UDPS system can be used to study genetic variants and mutational linkage.", "doi": "10.1371/journal.pone.0022741", "pmid": "21799940", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-01646"}, {"db": "pmc", "key": "PMC3143174"}], "notes": [], "created": "2017-05-04T14:57:26.197Z", "modified": "2020-01-21T13:56:06.122Z"}, {"entity": "publication", "iuid": "32ab4f9a3a5c47ef9c53f6a734679b3a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/32ab4f9a3a5c47ef9c53f6a734679b3a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/32ab4f9a3a5c47ef9c53f6a734679b3a"}}, "title": "Structural alterations from multiple displacement amplification of a human genome revealed by mate-pair sequencing.", "authors": [{"family": "Jiao", "given": "Xiang", "initials": "X"}, {"family": "Rosenlund", "given": "Magnus", "initials": "M"}, {"family": "Hooper", "given": "Sean D", "initials": "SD"}, {"family": "Tellgren-Roth", "given": "Christian", "initials": "C"}, {"family": "He", "given": "Liqun", "initials": "L"}, {"family": "Fu", "given": "Yutao", "initials": "Y"}, {"family": "Mangion", "given": "Jonathan", "initials": "J"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}], "type": "journal article", "published": "2011-07-22", "journal": {"volume": "6", "issn": "1932-6203", "issue": "7", "pages": "e22250", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Comprehensive identification of the acquired mutations that cause common cancers will require genomic analyses of large sets of tumor samples. Typically, the tissue material available from tumor specimens is limited, which creates a demand for accurate template amplification. We therefore evaluated whether phi29-mediated whole genome amplification introduces false positive structural mutations by massive mate-pair sequencing of a normal human genome before and after such amplification. Multiple displacement amplification led to a decrease in clone coverage and an increase by two orders of magnitude in the prevalence of inversions, but did not increase the prevalence of translocations. While multiple strand displacement amplification may find uses in translocation analyses, it is likely that alternative amplification strategies need to be developed to meet the demands of cancer genomics.", "doi": "10.1371/journal.pone.0022250", "pmid": "21799804", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-06066"}, {"db": "pmc", "key": "PMC3142133"}], "notes": [], "created": "2017-05-04T15:02:02.657Z", "modified": "2020-01-21T13:56:01.424Z"}, {"entity": "publication", "iuid": "884ba280b10244048de9dd250b7257b9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/884ba280b10244048de9dd250b7257b9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/884ba280b10244048de9dd250b7257b9"}}, "title": "Low RBM3 protein expression correlates with tumour progression and poor prognosis in malignant melanoma: an analysis of 215 cases from the Malm\u00f6 Diet and Cancer Study.", "authors": [{"family": "Jonsson", "given": "Liv", "initials": "L"}, {"family": "Bergman", "given": "Julia", "initials": "J"}, {"family": "Nodin", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Manjer", "given": "Jonas", "initials": "J"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2011-07-21", "journal": {"volume": "9", "issn": "1479-5876", "issue": null, "pages": "114", "title": "J Transl Med", "issn-l": "1479-5876"}, "abstract": "We have previously reported that expression of the RNA- and DNA-binding protein RBM3 is associated with a good prognosis in breast cancer and ovarian cancer. In this study, the prognostic value of immunohistochemical RBM3 expression was assessed in incident cases of malignant melanoma from a prospective population-based cohort study.\n\nUntil Dec 31st 2008, 264 incident cases of primary invasive melanoma had been registered in the Malm\u00f6 Diet and Cancer Study. Histopathological and clinical information was obtained for available cases and tissue microarrays (TMAs) constructed from 226 (85.6%) suitable paraffin-embedded tumours and 31 metastases. RBM3 expression was analysed by immunohistochemistry on the TMAs and a subset of full-face sections. Chi-square and Mann-Whitney U tests were used for comparison of RBM3 expression and relevant clinicopathological characteristics. Kaplan Meier analysis and Cox proportional hazards modelling were used to assess the relationship between RBM3 and recurrence free survival (RFS) and overall survival (OS).\n\nRBM3 could be assessed in 215/226 (95.1%) of primary tumours and all metastases. Longitudinal analysis revealed that 16/31 (51.6%) of metastases lacked RBM3 expression, in contrast to the primary tumours in which RBM3 was absent in 3/215 (1.4%) cases and strongly expressed in 120/215 (55.8%) cases. Strong nuclear RBM3 expression in the primary tumour was significantly associated with favourable clinicopathological parameters; i.e. non-ulcerated tumours, lower depth of invasion, lower Clark level, less advanced clinical stage, low mitotic activity and non-nodular histological type, and a prolonged RFS (RR = 0.50; 95% CI = 0.27-0.91) and OS (RR = 0.36, 95%CI = 0.20-0.64). Multivariate analysis demonstrated that the beneficial prognostic value of RBM3 remained significant for OS (RR = 0.33; 95%CI = 0.18-0.61).\n\nIn line with previous in vitro data, we here show that RBM3 is down-regulated in metastatic melanoma and high nuclear RBM3 expression in the primary tumour is an independent marker of a prolonged OS. The potential utility of RBM3 in treatment stratification of patients with melanoma should be pursued in future studies.", "doi": "10.1186/1479-5876-9-114", "pmid": "21777469", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1479-5876-9-114"}, {"db": "pmc", "key": "PMC3156749"}], "notes": [], "created": "2017-05-04T14:55:48.238Z", "modified": "2021-07-08T13:44:33.391Z"}, {"entity": "publication", "iuid": "dc16b55f3b534d71ad478a06bb55ee88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dc16b55f3b534d71ad478a06bb55ee88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dc16b55f3b534d71ad478a06bb55ee88"}}, "title": "The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits.", "authors": [{"family": "Min", "given": "Josine L", "initials": "JL"}, {"family": "Taylor", "given": "Jennifer M", "initials": "JM"}, {"family": "Richards", "given": "J Brent", "initials": "JB"}, {"family": "Watts", "given": "Tim", "initials": "T"}, {"family": "Pettersson", "given": "Fredrik H", "initials": "FH"}, {"family": "Broxholme", "given": "John", "initials": "J"}, {"family": "Ahmadi", "given": "Kourosh R", "initials": "KR"}, {"family": "Surdulescu", "given": "Gabriela L", "initials": "GL"}, {"family": "Lowy", "given": "Ernesto", "initials": "E"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Newton-Cheh", "given": "Chris", "initials": "C"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "Ragoussis", "given": "Jiannis", "initials": "J"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Cardon", "given": "Lon R", "initials": "LR"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Zondervan", "given": "Krina T", "initials": "KT"}], "type": "journal article", "published": "2011-07-15", "journal": {"volume": "6", "issn": "1932-6203", "issue": "7", "pages": "e22070", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The integrated analysis of genotypic and expression data for association with complex traits could identify novel genetic pathways involved in complex traits. We profiled 19,573 expression probes in Epstein-Barr virus-transformed lymphoblastoid cell lines (LCLs) from 299 twins and correlated these with 44 quantitative traits (QTs). For 939 expressed probes correlating with more than one QT, we investigated the presence of eQTL associations in three datasets of 57 CEU HapMap founders and 86 unrelated twins. Genome-wide association analysis of these probes with 2.2 m SNPs revealed 131 potential eQTLs (1,989 eQTL SNPs) overlapping between the HapMap datasets, five of which were in cis (58 eQTL SNPs). We then tested 535 SNPs tagging the eQTL SNPs, for association with the relevant QT in 2,905 twins. We identified nine potential SNP-QT associations (P<0.01) but none significantly replicated in five large consortia of 1,097-16,129 subjects. We also failed to replicate previous reported eQTL associations with body mass index, plasma low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides levels derived from lymphocytes, adipose and liver tissue. Our results and additional power calculations suggest that proponents may have been overoptimistic in the power of LCLs in eQTL approaches to elucidate regulatory genetic effects on complex traits using the small datasets generated to date. Nevertheless, larger tissue-specific expression data sets relevant to specific traits are becoming available, and should enable the adoption of similar integrated analyses in the near future.", "doi": "10.1371/journal.pone.0022070", "pmid": "21789213", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-10-04087"}, {"db": "pmc", "key": "PMC3137612"}], "notes": [], "created": "2017-05-04T15:03:32.213Z", "modified": "2017-05-30T14:52:12.520Z"}, {"entity": "publication", "iuid": "09a4a465924d40dcb5efe40d27bef7f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/09a4a465924d40dcb5efe40d27bef7f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/09a4a465924d40dcb5efe40d27bef7f0"}}, "title": "Scalable transcriptome preparation for massive parallel sequencing.", "authors": [{"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Werne", "given": "Beata", "initials": "B"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2011-07-07", "journal": {"volume": "6", "issn": "1932-6203", "issue": "7", "pages": "e21910", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The tremendous output of massive parallel sequencing technologies requires automated robust and scalable sample preparation methods to fully exploit the new sequence capacity.\n\nIn this study, a method for automated library preparation of RNA prior to massively parallel sequencing is presented. The automated protocol uses precipitation onto carboxylic acid paramagnetic beads for purification and size selection of both RNA and DNA. The automated sample preparation was compared to the standard manual sample preparation.\n\nThe automated procedure was used to generate libraries for gene expression profiling on the Illumina HiSeq 2000 platform with the capacity of 12 samples per preparation with a significantly improved throughput compared to the standard manual preparation. The data analysis shows consistent gene expression profiles in terms of sensitivity and quantification of gene expression between the two library preparation methods.", "doi": "10.1371/journal.pone.0021910", "pmid": "21760920", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-00159"}, {"db": "pmc", "key": "PMC3131396"}], "notes": [], "created": "2017-05-04T14:57:26.789Z", "modified": "2021-07-08T13:26:08.080Z"}, {"entity": "publication", "iuid": "e43e7e015dec4e649c76420282600e5a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e43e7e015dec4e649c76420282600e5a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e43e7e015dec4e649c76420282600e5a"}}, "title": "Identification of noncoding transcripts from within CENP-A chromatin at fission yeast centromeres.", "authors": [{"family": "Choi", "given": "Eun Shik", "initials": "ES"}, {"family": "Str\u00e5lfors", "given": "Annelie", "initials": "A"}, {"family": "Castillo", "given": "Araceli G", "initials": "AG"}, {"family": "Durand-Dubief", "given": "Micka\u00ebl", "initials": "M"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Allshire", "given": "Robin C", "initials": "RC"}], "type": "journal article", "published": "2011-07-01", "journal": {"volume": "286", "issn": "1083-351X", "issue": "26", "pages": "23600-23607", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "The histone H3 variant CENP-A is the most favored candidate for an epigenetic mark that specifies the centromere. In fission yeast, adjacent heterochromatin can direct CENP-A(Cnp1) chromatin establishment, but the underlying features governing where CENP-A(Cnp1) chromatin assembles are unknown. We show that, in addition to centromeric regions, a low level of CENP-A(Cnp1) associates with gene promoters where histone H3 is depleted by the activity of the Hrp1(Chd1) chromatin-remodeling factor. Moreover, we demonstrate that noncoding RNAs are transcribed by RNA polymerase II (RNAPII) from CENP-A(Cnp1) chromatin at centromeres. These analyses reveal a similarity between centromeres and a subset of RNAPII genes and suggest a role for remodeling at RNAPII promoters within centromeres that influences the replacement of histone H3 with CENP-A(Cnp1).", "doi": "10.1074/jbc.M111.228510", "pmid": "21531710", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "M111.228510"}, {"db": "pmc", "key": "PMC3123123"}], "notes": [], "created": "2017-05-04T14:57:20.723Z", "modified": "2020-01-21T13:56:05.862Z"}, {"entity": "publication", "iuid": "22d4089c71f34aa89b07876b372edbe1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/22d4089c71f34aa89b07876b372edbe1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/22d4089c71f34aa89b07876b372edbe1"}}, "title": "Species sorting and neutral processes are both important during the initial assembly of bacterial communities.", "authors": [{"family": "Langenheder", "given": "Silke", "initials": "S"}, {"family": "Sz\u00e9kely", "given": "Anna J", "initials": "AJ"}], "type": "journal article", "published": "2011-07-00", "journal": {"volume": "5", "issn": "1751-7370", "issue": "7", "pages": "1086-1094", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "Many studies have shown that species sorting, that is, the selection by local environmental conditions is important for the composition and assembly of bacterial communities. On the other hand, there are other studies that could show that bacterial communities are neutrally assembled. In this study, we implemented a microcosm experiment with the aim to determine, at the same time, the importance of species sorting and neutral processes for bacterial community assembly during the colonisation of new, that is, sterile, habitats, by atmospheric bacteria. For this we used outdoor microcosms, which contained sterile medium from three different rock pools representing different environmental conditions, which were seeded by rainwater bacteria. We found some evidence for neutral assembly processes, as almost every 4th taxon growing in the microcosms was also detectable in the rainwater sample irrespective of the medium. Most of these taxa belonged to widespread families with opportunistic growth strategies, such as the Pseudomonadaceae and Comamonadaceae, indicating that neutrally assembled taxa may primarily be generalists. On the other hand, we also found evidence for species sorting, as one out of three media selected a differently composed bacterial community. Species sorting effects were relatively weak and established themselves via differences in relative abundance of generalists among the different media, as well as media-specific occurrences of a few specific taxa. In summary, our results suggest that neutral and species sorting processes interact during the assembly of bacterial communities and that their importance may differ depending on how many generalists and specialists are present in a community.", "doi": "10.1038/ismej.2010.207", "pmid": "21270841", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "ismej2010207"}, {"db": "pmc", "key": "PMC3146284"}], "notes": [], "created": "2017-05-04T14:57:20.126Z", "modified": "2020-01-21T13:56:01.082Z"}, {"entity": "publication", "iuid": "5303e6e8eb5743bb819fab14cfeb67b2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5303e6e8eb5743bb819fab14cfeb67b2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5303e6e8eb5743bb819fab14cfeb67b2"}}, "title": "SATB2 in combination with cytokeratin 20 identifies over 95% of all colorectal carcinomas.", "authors": [{"family": "Magnusson", "given": "Kristina", "initials": "K"}, {"family": "de Wit", "given": "Meike", "initials": "M"}, {"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Johnson", "given": "Louis B", "initials": "LB"}, {"family": "McGee", "given": "Sharon F", "initials": "SF"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Naicker", "given": "Kirsha", "initials": "K"}, {"family": "Klinger", "given": "Rut", "initials": "R"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Wester", "given": "Kenneth", "initials": "K"}, {"family": "Gry", "given": "Marcus", "initials": "M"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Gallagher", "given": "William M", "initials": "WM"}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Kilpinen", "given": "Sami", "initials": "S"}, {"family": "Kallioniemi", "given": "Olli-Pekka", "initials": "OP"}, {"family": "Belt", "given": "Eric", "initials": "E"}, {"family": "Goos", "given": "Jeroen", "initials": "J"}, {"family": "Meijer", "given": "Gerrit", "initials": "G"}, {"family": "Birgisson", "given": "Helgi", "initials": "H"}, {"family": "Glimelius", "given": "Bengt", "initials": "B"}, {"family": "Borrebaeck", "given": "Carl A K", "initials": "CA"}, {"family": "Navani", "given": "Sanjay", "initials": "S"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "O'Connor", "given": "Darran P", "initials": "DP"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}], "type": "comparative study", "published": "2011-07-00", "journal": {"volume": "35", "issn": "1532-0979", "issue": "7", "pages": "937-948", "title": "Am. J. Surg. Pathol.", "issn-l": "0147-5185"}, "abstract": "The special AT-rich sequence-binding protein 2 (SATB2), a nuclear matrix-associated transcription factor and epigenetic regulator, was identified as a tissue type-specific protein when screening protein expression patterns in human normal and cancer tissues using an antibody-based proteomics approach. In this respect, the SATB2 protein shows a selective pattern of expression and, within cells of epithelial lineages, SATB2 expression is restricted to glandular cells lining the lower gastrointestinal tract. The expression of SATB2 protein is primarily preserved in cancer cells of colorectal origin, indicating that SATB2 could function as a clinically useful diagnostic marker to distinguish colorectal cancer (CRC) from other types of cancer. The aim of this study was to further explore and validate the specific expression pattern of SATB2 as a clinical biomarker and to compare SATB2 with the well-known cytokeratin 20 (CK20). Immunohistochemistry was used to analyze the extent of SATB2 expression in tissue microarrays with tumors from 9 independent cohorts of patients with primary and metastatic CRCs (n=1882). Our results show that SATB2 is a sensitive and highly specific marker for CRC with distinct positivity in 85% of all CRCs, and that SATB2 and/or CK20 was positive in 97% of CRCs. In conclusion, the specific expression of SATB2 in a large majority of CRCs suggests that SATB2 can be used as an important complementary tool for the differential diagnosis of carcinoma of unknown primary origin.", "doi": "10.1097/PAS.0b013e31821c3dae", "pmid": "21677534", "labels": {"Tissue Profiling": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "00000478-201107000-00001"}], "notes": [], "created": "2017-05-04T14:55:08.363Z", "modified": "2021-07-08T13:44:33.256Z"}, {"entity": "publication", "iuid": "b1a7cb57f9a746f79b0040347a7e8970", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1a7cb57f9a746f79b0040347a7e8970.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1a7cb57f9a746f79b0040347a7e8970"}}, "title": "Replication and explorations of high-order epistasis using a large advanced intercross line pedigree.", "authors": [{"family": "Pettersson", "given": "Mats", "initials": "M"}, {"family": "Besnier", "given": "Francois", "initials": "F"}, {"family": "Siegel", "given": "Paul B", "initials": "PB"}, {"family": "Carlborg", "given": "Orjan", "initials": "O"}], "type": "journal article", "published": "2011-07-00", "journal": {"volume": "7", "issn": "1553-7404", "issue": "7", "pages": "e1002180", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Dissection of the genetic architecture of complex traits persists as a major challenge in biology; despite considerable efforts, much remains unclear including the role and importance of genetic interactions. This study provides empirical evidence for a strong and persistent contribution of both second- and third-order epistatic interactions to long-term selection response for body weight in two divergently selected chicken lines. We earlier reported a network of interacting loci with large effects on body weight in an F(2) intercross between these high- and low-body weight lines. Here, most pair-wise interactions in the network are replicated in an independent eight-generation advanced intercross line (AIL). The original report showed an important contribution of capacitating epistasis to growth, meaning that the genotype at a hub in the network releases the effects of one or several peripheral loci. After fine-mapping of the loci in the AIL, we show that these interactions were persistent over time. The replication of five of six originally reported epistatic loci, as well as the capacitating epistasis, provides strong empirical evidence that the originally observed epistasis is of biological importance and is a contributor in the genetic architecture of this population. The stability of genetic interaction mechanisms over time indicates a non-transient role of epistasis on phenotypic change. Third-order epistasis was for the first time examined in this study and was shown to make an important contribution to growth, which suggests that the genetic architecture of growth is more complex than can be explained by two-locus interactions only. Our results illustrate the importance of designing studies that facilitate exploration of epistasis in populations for obtaining a comprehensive understanding of the genetics underlying a complex trait.", "doi": "10.1371/journal.pgen.1002180", "pmid": "21814519", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "PGENETICS-D-10-00335"}, {"db": "pmc", "key": "PMC3140984"}], "notes": [], "created": "2018-01-30T12:07:49.866Z", "modified": "2020-01-21T13:56:10.892Z"}, {"entity": "publication", "iuid": "e98203dd8dca4e79a329c847888f656d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e98203dd8dca4e79a329c847888f656d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e98203dd8dca4e79a329c847888f656d"}}, "title": "Prostasomal DNA characterization and transfer into human sperm.", "authors": [{"family": "Ronquist", "given": "G\u00f6ran K", "initials": "GK"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Ronquist", "given": "Gunnar", "initials": "G"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Hreinsson", "given": "Julius", "initials": "J"}, {"family": "Carlsson", "given": "Lena", "initials": "L"}, {"family": "Stavreus-Evers", "given": "Anneli", "initials": "A"}], "type": "journal article", "published": "2011-07-00", "journal": {"volume": "78", "issn": "1098-2795", "issue": "7", "pages": "467-476", "title": "Mol. Reprod. Dev.", "issn-l": "1040-452X"}, "abstract": "Human prostasomes, exosome-like microvesicles secreted by acinar cells of the prostate gland, contain chromosomal DNA. Agarose gel electrophoresis of DNA from seminal prostasomes displayed fragments of over 12 kb and smaller, with a distinct band around 1 kb that was excised, cloned, and sequenced. The sequences showed 8 out of 25 clones (32%) originating from genes. We elaborated the concept further by carrying out a genome-wide DNA copy number analysis of prostasomal DNA, hypothesizing that human prostasomes contain fragments of DNA randomly selected from the entire genome. Acridine orange-stained prostasomes were incubated with freshly prepared sperm for different times, and a transfer of acridine orange-stained prostasomal DNA to sperm (preferentially the head region) was observed. Fluorescence microscopy of slices in the center of 14 optical slides of the sperm head displayed an even fluorescence rather than a halo-like one, indicating DNA-uptake rather than just binding along the sperm head membrane.", "doi": "10.1002/mrd.21327", "pmid": "21638509", "labels": {"Array and Analysis Facility": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:53.033Z", "modified": "2017-05-30T12:35:58.608Z"}, {"entity": "publication", "iuid": "12cd8a04bec54421a735cd61bf6761fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/12cd8a04bec54421a735cd61bf6761fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/12cd8a04bec54421a735cd61bf6761fc"}}, "title": "Potential association of muscarinic receptor 3 gene variants with primary Sjogren's syndrome.", "authors": [{"family": "Appel", "given": "Silke", "initials": "S"}, {"family": "Le Hellard", "given": "Stephanie", "initials": "S"}, {"family": "Bruland", "given": "Ove", "initials": "O"}, {"family": "Brun", "given": "Johan G", "initials": "JG"}, {"family": "Omdal", "given": "Roald", "initials": "R"}, {"family": "Kristjansdottir", "given": "Gudlaug", "initials": "G"}, {"family": "Theander", "given": "Elke", "initials": "E"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Kvarnstr\u00f6m", "given": "Marika", "initials": "M"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Wahren-Herlenius", "given": "Marie", "initials": "M"}, {"family": "Jonsson", "given": "Roland", "initials": "R"}], "type": "journal article", "published": "2011-07-00", "journal": {"volume": "70", "issn": "1468-2060", "issue": "7", "pages": "1327-1329", "title": "Ann. Rheum. Dis.", "issn-l": "0003-4967"}, "abstract": "Primary Sj\u00f6gren's syndrome (pSS) is characterised by a chronic inflammation of exocrine glands. Salivary gland infiltrates, however, do not correlate well with disease symptoms, and a primary role for the salivary gland parenchyma in disease development has been suggested. Specifically, dysfunction of exocrine pathways involving the muscarinic receptor 3 (CHRM3) has been indicated.\n\nTo investigate possible genetic divergence in the CHRM3 gene in patients with pSS.\n\n530 patients with pSS and 532 controls from a combined Swedish and Norwegian cohort were genotyped for 84 single nucleotide polymorphisms (SNPs) distributed throughout CHRM3.\n\nGenetic association was observed with five SNPs localised in intron 3 and 4 of CHRM3, the strongest being rs7548522 (minor allele frequency = 0.06, OR=1.93, 95% CI (1.24 to 3.01); p=0.0033). In addition, clinical parameters, including focus score, abnormal Schirmer's test and presence of autoantibodies, were associated with different SNPs in CHRM3.\n\nThe study demonstrates a novel association of CHRM3 polymorphisms with pSS, suggesting a functional role for CHRM3 and the salivary gland parenchyma in the pathogenesis of pSS.", "doi": "10.1136/ard.2010.138966", "pmid": "21450750", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ard.2010.138966"}], "notes": [], "created": "2017-05-04T15:00:40.169Z", "modified": "2020-01-21T13:56:00.801Z"}, {"entity": "publication", "iuid": "2ac3ea9b6151417fa83ecfd62869be0e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ac3ea9b6151417fa83ecfd62869be0e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ac3ea9b6151417fa83ecfd62869be0e"}}, "title": "Genetic architecture of circulating lipid levels.", "authors": [{"family": "Demirkan", "given": "Ay\u015fe", "initials": "A"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Wichmann", "given": "Heinz-Erich", "initials": "HE"}, {"family": "Kyvik", "given": "Kirsten O H M", "initials": "KO"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Johansson", "given": "\u00c5sa", "initials": "\u00c5"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Smith", "given": "Johannes J", "initials": "JJ"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Witteman", "given": "Jacqueline", "initials": "J"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Pietil\u00e4inen", "given": "Kirsi H", "initials": "KH"}, {"family": "Rantanen", "given": "Taina", "initials": "T"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "D\u00f6ring", "given": "Angela", "initials": "A"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJ"}, {"family": "Penninx", "given": "Brenda W", "initials": "BW"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Rivadeneria", "given": "Fernando", "initials": "F"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Spector", "given": "Tim", "initials": "T"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Hoehne", "given": "Birgit", "initials": "B"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "McCarthy", "given": "Mark", "initials": "M"}, {"family": "Peltonen-Palotie", "given": "Leena", "initials": "L"}, {"family": "Aulchenko", "given": "Yurii", "initials": "Y"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Janssens", "given": "A Cecile J W", "initials": "AC"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "ENGAGE CONSORTIUM", "given": "", "initials": ""}], "type": "journal article", "published": "2011-07-00", "journal": {"volume": "19", "issn": "1476-5438", "issue": "7", "pages": "813-819", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "Serum concentrations of low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), triglycerides (TGs) and total cholesterol (TC) are important heritable risk factors for cardiovascular disease. Although genome-wide association studies (GWASs) of circulating lipid levels have identified numerous loci, a substantial portion of the heritability of these traits remains unexplained. Evidence of unexplained genetic variance can be detected by combining multiple independent markers into additive genetic risk scores. Such polygenic scores, constructed using results from the ENGAGE Consortium GWAS on serum lipids, were applied to predict lipid levels in an independent population-based study, the Rotterdam Study-II (RS-II). We additionally tested for evidence of a shared genetic basis for different lipid phenotypes. Finally, the polygenic score approach was used to identify an alternative genome-wide significance threshold before pathway analysis and those results were compared with those based on the classical genome-wide significance threshold. Our study provides evidence suggesting that many loci influencing circulating lipid levels remain undiscovered. Cross-prediction models suggested a small overlap between the polygenic backgrounds involved in determining LDL-C, HDL-C and TG levels. Pathway analysis utilizing the best polygenic score for TC uncovered extra information compared with using only genome-wide significant loci. These results suggest that the genetic architecture of circulating lipids involves a number of undiscovered variants with very small effects, and that increasing GWAS sample sizes will enable the identification of novel variants that regulate lipid levels.", "doi": "10.1038/ejhg.2011.21", "pmid": "21448234", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ejhg201121"}, {"db": "pmc", "key": "PMC3137496"}], "notes": [], "created": "2017-10-30T13:50:23.175Z", "modified": "2020-01-21T13:56:08.456Z"}, {"entity": "publication", "iuid": "873af7a6da5647ed84b11169c37b9cee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/873af7a6da5647ed84b11169c37b9cee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/873af7a6da5647ed84b11169c37b9cee"}}, "title": "Concomitant autoimmunity in myasthenia gravis--lack of association with IgA deficiency.", "authors": [{"family": "Ramanujam", "given": "Ryan", "initials": "R"}, {"family": "Piehl", "given": "Fredrik", "initials": "F"}, {"family": "Pirskanen", "given": "Ritva", "initials": "R"}, {"family": "Gregersen", "given": "Peter K", "initials": "PK"}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}], "type": "comparative study", "published": "2011-07-00", "journal": {"volume": "236", "issn": "1872-8421", "issue": "1-2", "pages": "118-122", "title": "J. Neuroimmunol.", "issn-l": "0165-5728"}, "abstract": "A marked increase in concomitant autoimmune diseases has previously been noted in patients with myasthenia gravis (MG). We show that these diseases occur both before and after the onset of MG and that the process is not influenced by thymectomy. IgA deficiency (IgAD), which is strongly associated with the same HLA haplotype as early onset MG, has recently been suggested to be an autoimmune disease. However, there was no increase in the prevalence of IgAD in a large cohort of Swedish MG patients.", "doi": "10.1016/j.jneuroim.2011.05.008", "pmid": "21669464", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "S0165-5728(11)00138-X"}, {"db": "pmc", "key": "PMC3230785"}, {"db": "mid", "key": "NIHMS305414"}], "notes": [], "created": "2017-05-04T15:03:31.560Z", "modified": "2017-05-30T12:44:37.980Z"}, {"entity": "publication", "iuid": "9cb0ff13b56a40bb90599a1156b7c3c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9cb0ff13b56a40bb90599a1156b7c3c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9cb0ff13b56a40bb90599a1156b7c3c8"}}, "title": "Genome wide association study identifies KCNMA1 contributing to human obesity.", "authors": [{"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Arner", "given": "Peter", "initials": "P"}, {"family": "Hoffstedt", "given": "Johan", "initials": "J"}, {"family": "Brodin", "given": "David", "initials": "D"}, {"family": "Dubern", "given": "Beatrice", "initials": "B"}, {"family": "Czernichow", "given": "S\u00e9bastien", "initials": "S"}, {"family": "van't Hooft", "given": "Ferdinand", "initials": "F"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "S\u00f8rensen", "given": "Thorkild I A", "initials": "TI"}, {"family": "Hebebrand", "given": "Johannes", "initials": "J"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Dahlman-Wright", "given": "Karin", "initials": "K"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Clement", "given": "Karine", "initials": "K"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}], "type": "journal article", "published": "2011-06-28", "journal": {"volume": "4", "issn": "1755-8794", "issue": null, "pages": "51", "title": "BMC Med Genomics", "issn-l": "1755-8794"}, "abstract": "Recent genome-wide association (GWA) analyses have identified common single nucleotide polymorphisms (SNPs) that are associated with obesity. However, the reported genetic variation in obesity explains only a minor fraction of the total genetic variation expected to be present in the population. Thus many genetic variants controlling obesity remain to be identified. The aim of this study was to use GWA followed by multiple stepwise validations to identify additional genes associated with obesity.\n\nWe performed a GWA analysis in 164 morbidly obese subjects (BMI:body mass index>40 kg/m2) and 163 Swedish subjects (>45 years) who had always been lean. The 700 SNPs displaying the strongest association with obesity in the GWA were analyzed in a second cohort comprising 460 morbidly obese subjects and 247 consistently lean Swedish adults. 23 SNPs remained significantly associated with obesity (nominal P<0.05) and were in a step-wise manner followed up in five additional cohorts from Sweden, France, and Germany together comprising 4214 obese and 5417 lean or population-based control individuals. Three samples, n=4133, were used to investigate the population-based associations with BMI. Gene expression in abdominal subcutaneous adipose tissue in relation to obesity was investigated for14 adults.\n\nPotassium channel, calcium activated, large conductance, subfamily M, alpha member (KCNMA1) rs2116830*G and BDNF rs988712*G were associated with obesity in five of six investigated case-control cohorts. In meta-analysis of 4838 obese and 5827 control subjects we obtained genome-wide significant allelic association with obesity for KCNMA1 rs2116830*G with P=2.82\u00d710(-10) and an odds ratio (OR) based on cases vs controls of 1.26 [95% C.I. 1.12-1.41] and for BDNF rs988712*G with P=5.2\u00d710(-17) and an OR of 1.36 [95% C.I. 1.20-1.55]. KCNMA1 rs2116830*G was not associated with BMI in the population-based samples. Adipose tissue (P=0.0001) and fat cell (P=0.04) expression of KCNMA1 was increased in obesity.\n\nWe have identified KCNMA1 as a new susceptibility locus for obesity, and confirmed the association of the BDNF locus at the genome-wide significant level.", "doi": "10.1186/1755-8794-4-51", "pmid": "21708048", "labels": {"National Genomics Infrastructure": null, "Mutation Analysis Facility (MAF)": null, "Bioinformatics and Expression Analysis (BEA)": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1755-8794-4-51"}, {"db": "pmc", "key": "PMC3148553"}], "notes": [], "created": "2017-05-04T15:00:41.084Z", "modified": "2020-01-21T13:56:04.059Z"}, {"entity": "publication", "iuid": "11efec5fca1f49c2bf42e294b282389c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/11efec5fca1f49c2bf42e294b282389c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/11efec5fca1f49c2bf42e294b282389c"}}, "title": "Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile.", "authors": [{"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Stan\u010d\u00e1kova", "given": "Alena", "initials": "A"}, {"family": "Finucane", "given": "Francis M", "initials": "FM"}, {"family": "Ried", "given": "Janina S", "initials": "JS"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Beckmann", "given": "Jacques S", "initials": "JS"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Vandenput", "given": "Liesbeth", "initials": "L"}, {"family": "Styrkarsdottir", "given": "Unnur", "initials": "U"}, {"family": "Zhou", "given": "Yanhua", "initials": "Y"}, {"family": "Smith", "given": "Albert Vernon", "initials": "AV"}, {"family": "Zhao", "given": "Jing-Hua", "initials": "JH"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Vedantam", "given": "Sailaja", "initials": "S"}, {"family": "Shin", "given": "So-Youn", "initials": "SY"}, {"family": "Haritunians", "given": "Talin", "initials": "T"}, {"family": "Fu", "given": "Mao", "initials": "M"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Halldorsson", "given": "Bjarni V", "initials": "BV"}, {"family": "Tikkanen", "given": "Emmi", "initials": "E"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Song", "given": "Ci", "initials": "C"}, {"family": "Arnold", "given": "Alice M", "initials": "AM"}, {"family": "Aulchenko", "given": "Yurii S", "initials": "YS"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Davis", "given": "Kathryn E", "initials": "KE"}, {"family": "D\u00f6ring", "given": "Angela", "initials": "A"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Estrada", "given": "Karol", "initials": "K"}, {"family": "Fern\u00e1ndez-Real", "given": "Jos\u00e9 Manuel", "initials": "JM"}, {"family": "Garcia", "given": "Melissa", "initials": "M"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Glazer", "given": "Nicole L", "initials": "NL"}, {"family": "Guiducci", "given": "Candace", "initials": "C"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Humphries", "given": "Steve E", "initials": "SE"}, {"family": "Isomaa", "given": "Bo", "initials": "B"}, {"family": "Jacobs", "given": "Leonie C", "initials": "LC"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Karasik", "given": "David", "initials": "D"}, {"family": "Karlsson", "given": "Magnus K", "initials": "MK"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "KT"}, {"family": "Kim", "given": "Lauren J", "initials": "LJ"}, {"family": "Kivim\u00e4ki", "given": "Mika", "initials": "M"}, {"family": "Klopp", "given": "Norman", "initials": "N"}, {"family": "K\u00fchnel", "given": "Brigitte", "initials": "B"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Ljunggren", "given": "Osten", "initials": "O"}, {"family": "Lorentzon", "given": "Mattias", "initials": "M"}, {"family": "Luben", "given": "Robert N", "initials": "RN"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Mellstr\u00f6m", "given": "Dan", "initials": "D"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Mooser", "given": "Vincent", "initials": "V"}, {"family": "Moreno", "given": "Jos\u00e9 Maria", "initials": "JM"}, {"family": "M\u00e4nnist\u00f6", "given": "Satu", "initials": "S"}, {"family": "O'Connell", "given": "Jeffery R", "initials": "JR"}, {"family": "Pascoe", "given": "Laura", "initials": "L"}, {"family": "Peltonen", "given": "Leena", "initials": "L"}, {"family": "Peral", "given": "Bel\u00e9n", "initials": "B"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Savage", "given": "David B", "initials": "DB"}, {"family": "Semple", "given": "Robert K", "initials": "RK"}, {"family": "Skaric-Juric", "given": "Tatjana", "initials": "T"}, {"family": "Sigurdsson", "given": "Gunnar", "initials": "G"}, {"family": "Song", "given": "Kijoung S", "initials": "KS"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Talmud", "given": "Philippa J", "initials": "PJ"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Vidal-Puig", "given": "Antonio", "initials": "A"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Clegg", "given": "Deborah J", "initials": "DJ"}, {"family": "Schadt", "given": "Eric", "initials": "E"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Jansson", "given": "John-Olov", "initials": "JO"}, {"family": "Kaplan", "given": "Robert C", "initials": "RC"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Kiel", "given": "Douglas P", "initials": "DP"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Waeber", "given": "G\u00e9rard", "initials": "G"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Wichmann", "given": "H-Erich", "initials": "HE"}, {"family": "Ohlsson", "given": "Claes", "initials": "C"}, {"family": "O'Rahilly", "given": "Stephen", "initials": "S"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Speliotes", "given": "Elizabeth K", "initials": "EK"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}], "type": "journal article", "published": "2011-06-26", "journal": {"volume": "43", "issn": "1546-1718", "issue": "8", "pages": "753-760", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Genome-wide association studies have identified 32 loci influencing body mass index, but this measure does not distinguish lean from fat mass. To identify adiposity loci, we meta-analyzed associations between \u223c2.5 million SNPs and body fat percentage from 36,626 individuals and followed up the 14 most significant (P < 10(-6)) independent loci in 39,576 individuals. We confirmed a previously established adiposity locus in FTO (P = 3 \u00d7 10(-26)) and identified two new loci associated with body fat percentage, one near IRS1 (P = 4 \u00d7 10(-11)) and one near SPRY2 (P = 3 \u00d7 10(-8)). Both loci contain genes with potential links to adipocyte physiology. Notably, the body-fat-decreasing allele near IRS1 is associated with decreased IRS1 expression and with an impaired metabolic profile, including an increased visceral to subcutaneous fat ratio, insulin resistance, dyslipidemia, risk of diabetes and coronary artery disease and decreased adiponectin levels. Our findings provide new insights into adiposity and insulin resistance.", "doi": "10.1038/ng.866", "pmid": "21706003", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.866"}, {"db": "pmc", "key": "PMC3262230"}, {"db": "mid", "key": "NIHMS329020"}], "notes": [], "created": "2017-05-04T15:00:48.656Z", "modified": "2021-07-07T15:11:02.289Z"}, {"entity": "publication", "iuid": "e20e1b8fb9db43a3bf9b732f96bd4303", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e20e1b8fb9db43a3bf9b732f96bd4303.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e20e1b8fb9db43a3bf9b732f96bd4303"}}, "title": "Specific syndecan-1 domains regulate mesenchymal tumor cell adhesion, motility and migration.", "authors": [{"family": "Zong", "given": "Fang", "initials": "F"}, {"family": "Fthenou", "given": "Eleni", "initials": "E"}, {"family": "Mundt", "given": "Filip", "initials": "F"}, {"family": "Szatm\u00e1ri", "given": "T\u00fcnde", "initials": "T"}, {"family": "Kovalszky", "given": "Ilona", "initials": "I"}, {"family": "Szil\u00e1k", "given": "L\u00e1szl\u00f3", "initials": "L"}, {"family": "Brodin", "given": "David", "initials": "D"}, {"family": "Tzanakakis", "given": "George", "initials": "G"}, {"family": "Hjerpe", "given": "Anders", "initials": "A"}, {"family": "Dobra", "given": "Katalin", "initials": "K"}], "type": "journal article", "published": "2011-06-23", "journal": {"volume": "6", "issn": "1932-6203", "issue": "6", "pages": "e14816", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Syndecans are proteoglycans whose core proteins have a short cytoplasmic domain, a transmembrane domain and a large N-terminal extracellular domain possessing glycosaminoglycan chains. Syndecans are involved in many important cellular processes. Our recent publications have demonstrated that syndecan-1 translocates into the nucleus and hampers tumor cell proliferation. In the present study, we aimed to investigate the role of syndecan-1 in tumor cell adhesion and migration, with special focus on the importance of its distinct protein domains, to better understand the structure-function relationship of syndecan-1 in tumor progression.\n\nWe utilized two mesenchymal tumor cell lines which were transfected to stably overexpress full-length syndecan-1 or truncated variants: the 78 which lacks the extracellular domain except the DRKE sequence proposed to be essential for oligomerization, the 77 which lacks the whole extracellular domain, and the RMKKK which serves as a nuclear localization signal. The deletion of the RMKKK motif from full-length syndecan-1 abolished the nuclear translocation of this proteoglycan. Various bioassays for cell adhesion, chemotaxis, random movement and wound healing were studied. Furthermore, we performed gene microarray to analyze the global gene expression pattern influenced by syndecan-1. Both full-length and truncated syndecan-1 constructs decrease tumor cell migration and motility, and affect cell adhesion. Distinct protein domains have differential effects, the extracellular domain is more important for promoting cell adhesion, while the transmembrane and cytoplasmic domains are sufficient for inhibition of cell migration. Cell behavior seems to depend also on the nuclear translocation of syndecan-1. Many genes are differentially regulated by syndecan-1 and a number of genes are actually involved in cell adhesion and migration.\n\nOur results demonstrate that syndecan-1 regulates mesenchymal tumor cell adhesion and migration, and different domains have differential effects. Our study provides new insights into better understanding of the role of syndecans in tumor progression.", "doi": "10.1371/journal.pone.0014816", "pmid": "21731601", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "10-PONE-RA-19265R1-CORRECTION"}, {"db": "pmc", "key": "PMC3121713"}], "notes": [], "created": "2017-05-04T15:03:11.317Z", "modified": "2017-05-30T14:50:48.508Z"}, {"entity": "publication", "iuid": "f4999c33ba544b25a7bc3636c70d4f15", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f4999c33ba544b25a7bc3636c70d4f15.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f4999c33ba544b25a7bc3636c70d4f15"}}, "title": "Translational database selection and multiplexed sequence capture for up front filtering of reliable breast cancer biomarker candidates.", "authors": [{"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Bjursell", "given": "Magnus K", "initials": "MK"}, {"family": "Mahdessian", "given": "Hovsep", "initials": "H"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2011-06-15", "journal": {"volume": "6", "issn": "1932-6203", "issue": "6", "pages": "e20794", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Biomarker identification is of utmost importance for the development of novel diagnostics and therapeutics. Here we make use of a translational database selection strategy, utilizing data from the Human Protein Atlas (HPA) on differentially expressed protein patterns in healthy and breast cancer tissues as a means to filter out potential biomarkers for underlying genetic causatives of the disease. DNA was isolated from ten breast cancer biopsies, and the protein coding and flanking non-coding genomic regions corresponding to the selected proteins were extracted in a multiplexed format from the samples using a single DNA sequence capture array. Deep sequencing revealed an even enrichment of the multiplexed samples and a great variation of genetic alterations in the tumors of the sampled individuals. Benefiting from the upstream filtering method, the final set of biomarker candidates could be completely verified through bidirectional Sanger sequencing, revealing a 40 percent false positive rate despite high read coverage. Of the variants encountered in translated regions, nine novel non-synonymous variations were identified and verified, two of which were present in more than one of the ten tumor samples.", "doi": "10.1371/journal.pone.0020794", "pmid": "21698250", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-04237"}, {"db": "pmc", "key": "PMC3115972"}], "notes": [], "created": "2017-05-04T14:57:27.086Z", "modified": "2021-07-08T13:26:08.411Z"}, {"entity": "publication", "iuid": "5ffcd103b6494ca686ab7b5dc8d1caee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5ffcd103b6494ca686ab7b5dc8d1caee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5ffcd103b6494ca686ab7b5dc8d1caee"}}, "title": "KIT pathway alterations in mucosal melanomas of the vulva and other sites.", "authors": [{"family": "Omholt", "given": "Katarina", "initials": "K"}, {"family": "Grafstr\u00f6m", "given": "Eva", "initials": "E"}, {"family": "Kanter-Lewensohn", "given": "Lena", "initials": "L"}, {"family": "Hansson", "given": "Johan", "initials": "J"}, {"family": "Ragnarsson-Olding", "given": "Boel K", "initials": "BK"}], "type": "journal article", "published": "2011-06-15", "journal": {"volume": "17", "issn": "1078-0432", "issue": "12", "pages": "3933-3942", "title": "Clin. Cancer Res.", "issn-l": null}, "abstract": "A significant proportion of mucosal melanomas contain alterations in KIT. The aim of this study was to characterize the pattern of KIT, NRAS, and BRAF mutations in mucosal melanomas at specific sites and to assess activation of the KIT downstream RAF/MEK/extracellular signal-regulated kinase (ERK) and phosphoinositide 3-kinase (PI3K)/AKT pathways in mucosal melanoma specimens.\n\nSeventy-one primary mucosal melanomas from various sites were studied. Mutation analysis was done by DNA sequencing. Expression of KIT, phosphorylated (p)-ERK, and p-AKT was evaluated by immunohistochemistry.\n\nKIT mutations were detected in 35% (8 of 23) of vulvar, 9% (2 of 22) of anorectal, 7% (1 of 14) of nasal cavity, and 20% (1 of 5) of penile melanomas. No KIT mutations were found in 7 vaginal melanomas. The difference in KIT mutation frequency between vulvar and nonvulvar cases was statistically significant (P = 0.014). The overall frequencies of NRAS and BRAF mutations were 10% and 6%, respectively. Notably, vaginal melanomas showed a NRAS mutation rate of 43%. KIT gene amplification (\u22654 copies), as assessed by quantitative real-time PCR, was observed in 19% of cases. KIT expression was associated with KIT mutation status (P < 0.001) and was more common in vulvar than nonvulvar tumors (P = 0.016). Expression of p-ERK and p-AKT was observed in 42% and 59% of tumors, respectively, and occurred irrespective of KIT/NRAS/BRAF mutation status. NRAS mutation was associated with worse overall survival in univariate analysis.\n\nResults show that KIT mutations are more common in vulvar melanomas than other types of mucosal melanomas and that both the RAF/MEK/ERK and PI3K/AKT pathways are activated in mucosal melanoma specimens.", "doi": "10.1158/1078-0432.CCR-10-2917", "pmid": "21680547", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "17/12/3933"}], "notes": [], "created": "2017-05-04T14:57:17.981Z", "modified": "2020-01-21T13:56:02.612Z"}, {"entity": "publication", "iuid": "878bb21721d54448b0b5ea8a9d65fb55", "links": {"self": {"href": "https://publications.scilifelab.se/publication/878bb21721d54448b0b5ea8a9d65fb55.json"}, "display": {"href": "https://publications.scilifelab.se/publication/878bb21721d54448b0b5ea8a9d65fb55"}}, "title": "The fat mass and obesity gene is linked to reduced verbal fluency in overweight and obese elderly men.", "authors": [{"family": "Benedict", "given": "Christian", "initials": "C"}, {"family": "Jacobsson", "given": "Josefin A", "initials": "JA"}, {"family": "R\u00f6nnemaa", "given": "Elina", "initials": "E"}, {"family": "S\u00e4llman-Alm\u00e9n", "given": "Markus", "initials": "M"}, {"family": "Brooks", "given": "Samantha", "initials": "S"}, {"family": "Schultes", "given": "Bernd", "initials": "B"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Kilander", "given": "Lena", "initials": "L"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2011-06-00", "journal": {"volume": "32", "issn": "1558-1497", "issue": "6", "pages": "1159.e1-1159.e5", "title": "Neurobiol. Aging", "issn-l": "0197-4580"}, "abstract": "Humans carrying the prevalent rs9939609 A allele of the fat mass and obesity-associated (FTO) gene are more susceptible to developing obesity than noncarries. Recently, polymorphisms in the FTO gene of elderly subjects have also been linked to a reduced volume in the frontal lobe as well as increased risk for incident Alzheimer disease. However, so far there is no evidence directly linking the FTO gene to functional cognitive processes. Here we examined whether the FTO rs9939609 A allele is associated with verbal fluency performance in 355 elderly men at the age of 82 years who have no clinically apparent cognitive impairment. Retrieval of verbal memory is a good surrogate measure reflecting frontal lobe functioning. Here we found that obese and overweight but not normal weight FTO A allele carriers showed a lower performance on verbal fluency than non-carriers (homozygous for rs9939609 T allele). This effect was not observed for a measure of general cognitive performance (i.e., Mini-Mental State Examination score), thereby indicating that the FTO gene primarily affects frontal lobe-dependent cognitive processes in elderly men.", "doi": "10.1016/j.neurobiolaging.2011.02.006", "pmid": "21458110", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0197-4580(11)00019-4"}], "notes": [], "created": "2017-05-04T15:00:49.853Z", "modified": "2020-01-21T13:56:03.449Z"}, {"entity": "publication", "iuid": "e416ac81a99a4283864d119c4bfdd9c0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e416ac81a99a4283864d119c4bfdd9c0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e416ac81a99a4283864d119c4bfdd9c0"}}, "title": "Tepidanaerobacter acetatoxydans sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from two ammonium-enriched mesophilic methanogenic processes.", "authors": [{"family": "Westerholm", "given": "Maria", "initials": "M"}, {"family": "Roos", "given": "Stefan", "initials": "S"}, {"family": "Schn\u00fcrer", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2011-06-00", "journal": {"volume": "34", "issn": "1618-0984", "issue": "4", "pages": "260-266", "title": "Syst. Appl. Microbiol.", "issn-l": "0723-2020"}, "abstract": "Four anaerobic syntrophic acetate-oxidizing bacteria, the thermotolerant strains Re1(T), Re2, T1 and T2, were isolated from two different mesophilic methanogenic systems. The strains originate from sludge of a continuously stirred laboratory-scale reactor containing high levels of ammonium and from a high ammonium enrichment culture. Comparative 16S rRNA gene sequence analysis confirmed that the strains belong to the Firmicutes-Clostridia class. The most closely related species to strains Re1(T), Re2, T1 and T2 was Tepidanaerobacter syntrophicus, with a 16S rRNA gene sequence identity of 96%. The DNA-DNA relatedness of strains Re2, T1 and T2 to strain Re1(T) was 92, 102, 81%, respectively. The gene encoding the acetogen key enzyme formyltetrahydrofolate synthetase (FTHFS) was detected and partly sequenced from the strains. In pure culture the bacteria used different organic compounds as carbon and energy source, such as organic acids, alcohols, sugars and amino acids. Furthermore, acetate-oxidizing ability was observed during co-cultivation with a hydrogen-consuming Methanoculleus sp. The bacteria were found to be spore-forming, rod-shaped and motile, and possessed Gram-positive cell walls. The four strains were thermotolerant and grew at temperatures between 25 and 55\u00b0C. Strain Re1(T) had a DNA G+C content of 38.4% and the major fatty acids were C(18:1) w7c, C(18:1) w9c, anteiso-C(17:0), C(16:1) w7c and C(18:0). The genetic and phenotypic properties of strains Re1(T), Re2, T1 and T2 suggest classification as representatives of a novel species of the genus Tepidanaerobacter; the name Tepidanaerobacter acetatoxydans sp. nov. is suggested. The type strain of T. acetatoxydans is Re1(T) (=DSM 21804(T)=JCM 16047(T)).", "doi": "10.1016/j.syapm.2010.11.018", "pmid": "21498020", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0723-2020(11)00014-2"}, {"db": "GENBANK", "key": "HQ290074"}, {"db": "GENBANK", "key": "HQ290075"}, {"db": "GENBANK", "key": "HQ290076"}, {"db": "GENBANK", "key": "HQ290077"}], "notes": [], "created": "2017-05-04T15:02:03.173Z", "modified": "2020-01-21T13:56:05.845Z"}, {"entity": "publication", "iuid": "6dae4cf24e97417fb0750005bffeca6c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6dae4cf24e97417fb0750005bffeca6c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6dae4cf24e97417fb0750005bffeca6c"}}, "title": "Genetic association and gene expression analysis identify FGFR1 as a new susceptibility gene for human obesity.", "authors": [{"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Arner", "given": "Peter", "initials": "P"}, {"family": "Dickson", "given": "Suzanne L", "initials": "SL"}, {"family": "Vidal", "given": "Hubert", "initials": "H"}, {"family": "Mejhert", "given": "Niklas", "initials": "N"}, {"family": "Henegar", "given": "Corneliu", "initials": "C"}, {"family": "Taube", "given": "Magdalena", "initials": "M"}, {"family": "Hansson", "given": "Caroline", "initials": "C"}, {"family": "Hinney", "given": "Anke", "initials": "A"}, {"family": "Galan", "given": "Pilar", "initials": "P"}, {"family": "Simon", "given": "Chantal", "initials": "C"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Benrick", "given": "Anna", "initials": "A"}, {"family": "Jansson", "given": "John-Olov", "initials": "JO"}, {"family": "Bouloumi\u00e9", "given": "Anne", "initials": "A"}, {"family": "Langin", "given": "Dominique", "initials": "D"}, {"family": "Laville", "given": "Martine", "initials": "M"}, {"family": "Debard", "given": "Cyrille", "initials": "C"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Ryd\u00e9n", "given": "Mikael", "initials": "M"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Dahlman-Wright", "given": "Karin", "initials": "K"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Clement", "given": "Karine", "initials": "K"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}], "type": "journal article", "published": "2011-06-00", "journal": {"volume": "96", "issn": "1945-7197", "issue": "6", "pages": "E962-E966", "title": "J. Clin. Endocrinol. Metab.", "issn-l": "0021-972X"}, "abstract": "Previous studies suggest a role for fibroblast growth factor receptor 1 (FGFR1) in the regulation of energy balance.\n\nOur objective was to investigate whether FGFR1 is an obesity gene by genetic association and functional studies.\n\nThe study was designed to genotype common FGFR1 single-nucleotide polymorphisms (SNP) in large cohorts, confirm significant results in additional cohorts, and measure FGFR1 expression in human adipose tissue and in rodent hypothalamus.\n\nGeneral community and referral centers for specialized care was the setting for the study.\n\nWe genotyped FGFR1 SNP in 2438 obese and 2115 lean adults and 985 obese and 532 population-based children. Results were confirmed in 928 obese and 2738 population-based adults and 487 obese and 441 lean children. Abdominal sc adipose tissue was investigated in 202 subjects. We also investigated diet-induced, obese fasting, and fed rats.\n\nWe analyzed the association between FGFR1 SNP and obesity. In secondary analyses, we related adipose FGFR1 expression to genotype, obesity, and degree of fat cell differentiation and related hypothalamic FGFR1 to energy balance.\n\nFGFR1 rs7012413*T was nominally associated with obesity in all four cohorts; metaanalysis odds ratio = 1.17 (95% confidence interval = 1.10-1.25), and P = 1.8 \u00d7 10(-6), which was P = 7.0 \u00d7 10(-8) in the recessive model. rs7012413*T was associated with FGFR1 expression in adipose tissue (P < 0.0001). In this organ, but not in skeletal muscle, FGFR1 mRNA (P < 0.0001) and protein (P < 0.05) were increased in obesity. In rats, hypothalamic expression of FGFR1 declined after fasting (P < ]0.001) and increased after diet-induced obesity (P < 0.05).\n\nFGFR1 is a novel obesity gene that may promote obesity by influencing adipose tissue and the hypothalamic control of appetite.", "doi": "10.1210/jc.2010-2639", "pmid": "21430024", "labels": {"National Genomics Infrastructure": null, "Mutation Analysis Facility (MAF)": null, "Bioinformatics and Expression Analysis (BEA)": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "jc.2010-2639"}], "notes": [], "created": "2017-05-04T15:00:47.347Z", "modified": "2020-01-21T13:56:02.867Z"}, {"entity": "publication", "iuid": "a0ffab842d724c6389fe4f2bdb882398", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a0ffab842d724c6389fe4f2bdb882398.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a0ffab842d724c6389fe4f2bdb882398"}}, "title": "Feather pecking behavior in laying hens: hypothalamic gene expression in birds performing and receiving pecks.", "authors": [{"family": "Brunberg", "given": "E", "initials": "E"}, {"family": "Jensen", "given": "P", "initials": "P"}, {"family": "Isaksson", "given": "A", "initials": "A"}, {"family": "Keeling", "given": "L", "initials": "L"}], "type": "journal article", "published": "2011-06-00", "journal": {"volume": "90", "issn": "0032-5791", "issue": "6", "pages": "1145-1152", "title": "Poult. Sci.", "issn-l": null}, "abstract": "Feather pecking (FP) is a welfare and economic problem in the egg production sector. Beak trimming, the current method used to reduce FP, is also criticized. The present study used gene expression to explore the biological mechanisms underlying this behavior, which could lead to a greater understanding of the cause and a tool to mitigate the problem. White Leghorn hens performing and receiving FP, as well as neutral control birds, were identified on a commercial farm. Hypothalamic RNA from 11 peckers, 10 victims, and 10 controls was hybridized onto GeneChip Chicken Genome Arrays (Affymetrix Inc., Santa Clara, CA) to compare gene expression profiles in the different groups. Eleven transcripts corresponding to 10 genes differed significantly between the 3 groups (adjusted P < 0.05). Eight of these transcripts differed in the peckers compared with the controls, 1 was upregulated in the victims compared with the controls, and 6 differed significantly in the peckers compared with the victims. Additionally, 5 transcripts showed a trend (adjusted P < 0.1) to differ in the pecker-victim comparison. Some of the products of the differently expressed genes are involved in disorders, such as intestinal inflammation and insulin resistance, which fit well with the previously proposed hypothesis that FP is an abnormal foraging behavior. Other findings may also support the proposal that FP is linked to immune mechanisms and may serve as an animal model for obsessive compulsive disorder in humans. In conclusion, this study provides a gene list that may be useful in further research on the mechanisms behind FP.", "doi": "10.3382/ps.2010-00961", "pmid": "21597052", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "90/6/1145"}], "notes": [], "created": "2017-05-04T15:02:54.148Z", "modified": "2017-05-30T12:36:17.012Z"}, {"entity": "publication", "iuid": "99278e30eee946ffb0a4d48f21609360", "links": {"self": {"href": "https://publications.scilifelab.se/publication/99278e30eee946ffb0a4d48f21609360.json"}, "display": {"href": "https://publications.scilifelab.se/publication/99278e30eee946ffb0a4d48f21609360"}}, "title": "Cytochrome P450 1A, 1B, and 1C mRNA induction patterns in three-spined stickleback exposed to a transient and a persistent inducer.", "authors": [{"family": "Gao", "given": "Kai", "initials": "K"}, {"family": "Brandt", "given": "Ingvar", "initials": "I"}, {"family": "Goldstone", "given": "Jared V", "initials": "JV"}, {"family": "J\u00f6nsson", "given": "Maria E", "initials": "ME"}], "type": "journal article", "published": "2011-06-00", "journal": {"volume": "154", "issn": "1532-0456", "issue": "1", "pages": "42-55", "title": "Comp. Biochem. Physiol. C Toxicol. Pharmacol.", "issn-l": null}, "abstract": "Cytochrome P450 1 (CYP1) mRNA induction patterns in three-spined stickleback (Gasterosteus aculeatus) were explored for use in environmental monitoring of aryl hydrocarbon receptor (AHR) agonists. The cDNAs of stickleback CYP1A, CYP1B1, CYP1C1, and CYP1C2 were cloned and their basal and induced expression patterns were determined in the brain, gill, liver and kidney. Also, their induction time courses were compared after waterborne exposure to a transient (indigo) or a persistent (3,3',4,4',5-pentacholorbiphenyl PCB 126) AHR agonist. The cloned stickleback CYP1s exhibited a high amino acid sequence identity compared with their zebrafish orthologs and their constitutive tissue distribution patterns largely agreed with those reported in other species. PCB 126 (100 nM) induced different CYP1 expression patterns in the four tissues, suggesting tissue-specific regulation. Both indigo (1 nM) and PCB 126 (10 nM) induced a strong CYP1 expression in gills. However, while PCB 126 gave rise to a high and persistent induction in gills and liver, induction by indigo was transient in both organs. The number of putative dioxin response elements found in each CYP1 gene promoter roughly reflected the induction levels of the genes. The high responsiveness of CYP1A, CYP1B1, and CYP1C1 observed in several organs suggests that three-spined stickleback is suitable for monitoring of pollution with AHR agonists.", "doi": "10.1016/j.cbpc.2011.02.005", "pmid": "21354474", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S1532-0456(11)00021-4"}, {"db": "pmc", "key": "PMC3560405"}, {"db": "mid", "key": "NIHMS278245"}], "notes": [], "created": "2017-05-04T15:01:55.759Z", "modified": "2020-01-21T13:56:03.929Z"}, {"entity": "publication", "iuid": "ac81ab74ad174de68d6d87c006d8c50f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ac81ab74ad174de68d6d87c006d8c50f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ac81ab74ad174de68d6d87c006d8c50f"}}, "title": "Co-occurring SHOC2 and PTPN11 mutations in a patient with severe/complex Noonan syndrome-like phenotype.", "authors": [{"family": "Ekvall", "given": "Sara", "initials": "S"}, {"family": "Hagen\u00e4s", "given": "Lars", "initials": "L"}, {"family": "Allanson", "given": "Judith", "initials": "J"}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "ML"}], "type": "case reports", "published": "2011-06-00", "journal": {"volume": "155A", "issn": "1552-4833", "issue": "6", "pages": "1217-1224", "title": "Am. J. Med. Genet. A", "issn-l": "1552-4825"}, "abstract": "Noonan syndrome (NS) is a heterogeneous disorder caused by activating mutations in the RAS-MAPK signaling pathway. It is associated with variable clinical expression including short stature, congenital heart defect, unusual pectus deformity, and typical facial features and the inheritance is autosomal dominant. Here, we present a clinical and molecular characterization of a patient with Noonan-like syndrome with loose anagen hair phenotype and additional features including mild psychomotor developmental delay, osteoporosis, gingival hyperplasia, spinal neuroblastoma, intrathoracic extramedullary hematopoiesis, and liver hemangioma. Mutation analysis of PTPN11, SOS1, RAF1, KRAS, BRAF, MEK1, MEK2, NRAS, and SHOC2 was conducted, revealing a co-occurrence of two heterozygous previously identified mutations in the index patient. The mutation SHOC2 c.4A > G; p.Ser2Gly represents a de novo mutation, whereas, PTPN11 c.1226G > C; p.Gly409Ala was inherited from the mother and also identified in the brother. The mother and the brother present with some NS manifestations, such as short stature, delayed puberty, keratosis pilaris, caf\u00e9-au-lait spots, refraction error (mother), and undescended testis (brother), but no NS facial features, supporting the notion that the PTPN11 p.Gly409Ala mutation leads to a relatively mild phenotype. We propose that, the atypical phenotype of the young woman with NS reported here is an additive effect, where the PTPN11 mutation acts as a modifier. Interestingly, co-occurrence of RAS-MAPK mutations has been previously identified in a few patients with variable NS or neurofibromatosis-NS phenotypes. Taken together, the results suggest that co-occurrence of mutations or modifying loci in the RAS-MAPK pathway may contribute to the clinical variability observed among NS patients.", "doi": "10.1002/ajmg.a.33987", "pmid": "21548061", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:53.833Z", "modified": "2020-01-21T13:56:04.530Z"}, {"entity": "publication", "iuid": "37b2076f6fb04f7d99d7e81e9b576ada", "links": {"self": {"href": "https://publications.scilifelab.se/publication/37b2076f6fb04f7d99d7e81e9b576ada.json"}, "display": {"href": "https://publications.scilifelab.se/publication/37b2076f6fb04f7d99d7e81e9b576ada"}}, "title": "(R,S)-dichlorprop herbicide in agricultural soil induces proliferation and expression of multiple dioxygenase-encoding genes in the indigenous microbial community.", "authors": [{"family": "Paulin", "given": "M\u00e9lanie M", "initials": "MM"}, {"family": "Nicolaisen", "given": "Mette H", "initials": "MH"}, {"family": "S\u00f8rensen", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2011-06-00", "journal": {"volume": "13", "issn": "1462-2920", "issue": "6", "pages": "1513-1523", "title": "Environ. Microbiol.", "issn-l": "1462-2912"}, "abstract": "We investigated the effect of (R,S)-dichlorprop herbicide addition to soil microcosms on the degrading indigenous microbial community by targeting multiple \u03b1-ketoglutarate-dependent (\u03b1-KG) dioxygenase-encoding genes (rdpA, sdpA and tfdA group I) at both gene and transcript level. The soil microbial community responded with high growth of potential degraders as measured by the abundance of dioxygenase-encoding genes using quantitative real-time PCR (qPCR). rdpA DNA was not detectable in unamended soil but reached over 10\u2076 copies g\u207b\u00b9 soil after amendment. sdpA and tfdA were both present prior to amendment at levels of ~5 \u00d7 10\u2074 and ~ 10\u00b2 copies g\u207b\u00b9 soil, respectively, and both reached over 10\u2075copies g\u207b\u00b9 soil. While expression of all three target genes was detected during two cycles of herbicide degradation, a time-shift occurred between maximum expression of each gene. Gene diversity by denaturing gradient gel electrophoresis (DGGE) uncovered a diversity of sdpA and tfdA genes at the DNA level while rdpA remained highly conserved. However, mRNA profiles indicated that all transcribed tfdA sequences were class III genes while rdpA transcripts shared 100% identity to rdpA of Delftia acidovorans MC1 and sdpA transcripts shared 100% identity to sdpA from Sphingomonas herbicidovorans MH. This is the first report to describe expression dynamics of multiple \u03b1-KG dioxygenase-encoding genes in the indigenous microbial community as related to degradation of a phenoxypropionate herbicide in soil.", "doi": "10.1111/j.1462-2920.2011.02456.x", "pmid": "21418495", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "GENBANK", "key": "HQ009355"}, {"db": "GENBANK", "key": "HQ009356"}, {"db": "GENBANK", "key": "HQ009357"}, {"db": "GENBANK", "key": "HQ009358"}, {"db": "GENBANK", "key": "HQ009359"}, {"db": "GENBANK", "key": "HQ009360"}, {"db": "GENBANK", "key": "HQ009361"}, {"db": "GENBANK", "key": "HQ009362"}, {"db": "GENBANK", "key": "HQ009363"}, {"db": "GENBANK", "key": "HQ009364"}, {"db": "GENBANK", "key": "HQ009365"}, {"db": "GENBANK", "key": "HQ009366"}, {"db": "GENBANK", "key": "HQ009367"}, {"db": "GENBANK", "key": "HQ009368"}, {"db": "GENBANK", "key": "HQ009369"}, {"db": "GENBANK", "key": "HQ009370"}, {"db": "GENBANK", "key": "HQ009371"}, {"db": "GENBANK", "key": "HQ009372"}, {"db": "GENBANK", "key": "HQ009373"}, {"db": "GENBANK", "key": "HQ009374"}, {"db": "GENBANK", "key": "HQ009375"}, {"db": "GENBANK", "key": "HQ009376"}, {"db": "GENBANK", "key": "HQ009377"}, {"db": "GENBANK", "key": "HQ009378"}, {"db": "GENBANK", "key": "HQ009379"}, {"db": "GENBANK", "key": "HQ009380"}, {"db": "GENBANK", "key": "HQ009381"}, {"db": "GENBANK", "key": "HQ009382"}, {"db": "GENBANK", "key": "HQ009383"}, {"db": "GENBANK", "key": "HQ009384"}, {"db": "GENBANK", "key": "HQ009385"}, {"db": "GENBANK", "key": "HQ009386"}, {"db": "GENBANK", "key": "HQ009387"}, {"db": "GENBANK", "key": "HQ009388"}, {"db": "GENBANK", "key": "HQ009389"}, {"db": "GENBANK", "key": "HQ009390"}, {"db": "GENBANK", "key": "HQ009391"}, {"db": "GENBANK", "key": "HQ009392"}, {"db": "GENBANK", "key": "HQ009393"}, {"db": "GENBANK", "key": "HQ009394"}, {"db": "GENBANK", "key": "HQ009395"}, {"db": "GENBANK", "key": "HQ009396"}, {"db": "GENBANK", "key": "HQ009397"}, {"db": "GENBANK", "key": "HQ009398"}], "notes": [], "created": "2017-05-04T15:01:56.357Z", "modified": "2020-01-21T13:56:01.582Z"}, {"entity": "publication", "iuid": "1f7ff751e78f4fdc8765d7930824da83", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1f7ff751e78f4fdc8765d7930824da83.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1f7ff751e78f4fdc8765d7930824da83"}}, "title": "Detailed analysis of variants in FTO in association with body composition in a cohort of 70-year-olds suggests a weakened effect among elderly.", "authors": [{"family": "Jacobsson", "given": "Josefin A", "initials": "JA"}, {"family": "Alm\u00e9n", "given": "Markus S\u00e4llman", "initials": "MS"}, {"family": "Benedict", "given": "Christian", "initials": "C"}, {"family": "Hedberg", "given": "Lilia A", "initials": "LA"}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}, {"family": "Brooks", "given": "Samantha", "initials": "S"}, {"family": "Kullberg", "given": "Joel", "initials": "J"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Johansson", "given": "Lars", "initials": "L"}, {"family": "Ahlstr\u00f6m", "given": "H\u00e5kan", "initials": "H"}, {"family": "Fredriksson", "given": "Robert", "initials": "R"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2011-05-27", "journal": {"volume": "6", "issn": "1932-6203", "issue": "5", "pages": "e20158", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The rs9939609 single-nucleotide polymorphism (SNP) in the fat mass and obesity (FTO) gene has previously been associated with higher BMI levels in children and young adults. In contrast, this association was not found in elderly men. BMI is a measure of overweight in relation to the individuals' height, but offers no insight into the regional body fat composition or distribution.\n\nTo examine whether the FTO gene is associated with overweight and body composition-related phenotypes rather than BMI, we measured waist circumference, total fat mass, trunk fat mass, leg fat mass, visceral and subcutaneous adipose tissue, and daily energy intake in 985 humans (493 women) at the age of 70 years. In total, 733 SNPs located in the FTO gene were genotyped in order to examine whether rs9939609 alone or the other SNPs, or their combinations, are linked to obesity-related measures in elderly humans.\n\nCross-sectional analysis of the Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) cohort.\n\nNeither a single SNP, such as rs9939609, nor a SNP combination was significantly linked to overweight, body composition-related measures, or daily energy intake in elderly humans. Of note, these observations hold both among men and women.\n\nDue to the diversity of measurements included in the study, our findings strengthen the view that the effect of FTO on body composition appears to be less profound in later life compared to younger ages and that this is seemingly independent of gender.", "doi": "10.1371/journal.pone.0020158", "pmid": "21637715", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-00770"}, {"db": "pmc", "key": "PMC3103532"}], "notes": [], "created": "2017-05-04T15:00:51.035Z", "modified": "2020-01-21T13:56:01.015Z"}, {"entity": "publication", "iuid": "6e2abacd4b6143b0ba0221414eba6648", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6e2abacd4b6143b0ba0221414eba6648.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6e2abacd4b6143b0ba0221414eba6648"}}, "title": "Multiple recognition assay reveals prostasomes as promising plasma biomarkers for prostate cancer.", "authors": [{"family": "Tavoosidana", "given": "Gholamreza", "initials": "G"}, {"family": "Ronquist", "given": "Gunnar", "initials": "G"}, {"family": "Darmanis", "given": "Spyros", "initials": "S"}, {"family": "Yan", "given": "Junhong", "initials": "J"}, {"family": "Carlsson", "given": "Lena", "initials": "L"}, {"family": "Wu", "given": "Di", "initials": "D"}, {"family": "Conze", "given": "Tim", "initials": "T"}, {"family": "Ek", "given": "Pia", "initials": "P"}, {"family": "Semjonow", "given": "Axel", "initials": "A"}, {"family": "Eltze", "given": "Elke", "initials": "E"}, {"family": "Larsson", "given": "Anders", "initials": "A"}, {"family": "Landegren", "given": "Ulf D", "initials": "UD"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "evaluation studies", "published": "2011-05-24", "journal": {"volume": "108", "issn": "1091-6490", "issue": "21", "pages": "8809-8814", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Prostasomes are microvesicles (mean diameter, 150 nm) that are produced and secreted by normal and malignant prostate acinar cells. It has been hypothesized that invasive growth of malignant prostate cells may cause these microvesicles, normally released into seminal fluid, to appear in interstitial space and therewith into peripheral circulation. The suitability of prostasomes as blood biomarkers in patients with prostate cancer was tested by using an expanded variant of the proximity ligation assay (PLA). We developed an extremely sensitive and specific assay (4PLA) for detection of complex target structures such as microvesicles in which the target is first captured via an immobilized antibody and subsequently detected by using four other antibodies with attached DNA strands. The requirement for coincident binding by five antibodies to generate an amplifiable reporter results in both increased specificity and sensitivity. The assay successfully detected significantly elevated levels of prostasomes in blood samples from patients with prostate cancer before radical prostatectomy, compared with controls and men with benign biopsy results. The medians for prostasome levels in blood plasma of patients with prostate cancer were 2.5 to sevenfold higher compared with control samples in two independent studies, and the assay also distinguished patients with high and medium prostatectomy Gleason scores (8/9 and 7, respectively) from those with low score (\u2264 6), thus reflecting disease aggressiveness. This approach that enables detection of prostasomes in peripheral blood may be useful for early diagnosis and assessment of prognosis in organ-confined prostate cancer.", "doi": "10.1073/pnas.1019330108", "pmid": "21555566", "labels": {"Clinical Biomarkers": "", "PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "1019330108"}, {"db": "pmc", "key": "PMC3102389"}], "notes": [], "created": "2017-05-04T14:55:21.963Z", "modified": "2023-04-14T13:56:31.738Z"}, {"entity": "publication", "iuid": "3288a254cd004acaac77dcacd80433e1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3288a254cd004acaac77dcacd80433e1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3288a254cd004acaac77dcacd80433e1"}}, "title": "Sequence and generation of mature ribosomal RNA transcripts in Dictyostelium discoideum.", "authors": [{"family": "Boesler", "given": "Carsten", "initials": "C"}, {"family": "Kruse", "given": "Janis", "initials": "J"}, {"family": "S\u00f6derbom", "given": "Fredrik", "initials": "F"}, {"family": "Hammann", "given": "Christian", "initials": "C"}], "type": "journal article", "published": "2011-05-20", "journal": {"volume": "286", "issn": "1083-351X", "issue": "20", "pages": "17693-17703", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "The amoeba Dictyostelium discoideum is a well established model organism for studying numerous aspects of cellular and developmental functions. Its ribosomal RNA (rRNA) is encoded in an extrachromosomal palindrome that exists in \u223c100 copies in the cell. In this study, we have set out to investigate the sequence of the expressed rRNA. For this, we have ligated the rRNA ends and performed RT-PCR on these circular RNAs. Sequencing revealed that the mature 26 S, 17 S, 5.8 S, and 5 S rRNAs have sizes of 3741, 1871, 162, and 112 nucleotides, respectively. Unlike the published data, all mature rRNAs of the same type uniformly display the same start and end nucleotides in the analyzed AX2 strain. We show the existence of a short lived primary transcript covering the rRNA transcription unit of 17 S, 5.8 S, and 26 S rRNA. Northern blots and RT-PCR reveal that from this primary transcript two precursor molecules of the 17 S and two precursors of the 26 S rRNA are generated. We have also determined the sequences of these precursor molecules, and based on these data, we propose a model for the maturation of the rRNAs in Dictyostelium discoideum that we compare with the processing of the rRNA transcription unit of Saccharomyces cerevisiae.", "doi": "10.1074/jbc.M110.208306", "pmid": "21454536", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "M110.208306"}, {"db": "pmc", "key": "PMC3093845"}, {"db": "GENBANK", "key": "FR733593"}, {"db": "GENBANK", "key": "FR733594"}, {"db": "GENBANK", "key": "FR733595"}, {"db": "GENBANK", "key": "FR733596"}, {"db": "GENBANK", "key": "FR733598"}, {"db": "GENBANK", "key": "FR733599"}, {"db": "GENBANK", "key": "FR733600"}], "notes": [], "created": "2017-05-04T14:57:20.426Z", "modified": "2020-01-21T13:56:01.411Z"}, {"entity": "publication", "iuid": "65371185f539415c8309e4853d37ed2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/65371185f539415c8309e4853d37ed2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/65371185f539415c8309e4853d37ed2a"}}, "title": "Cardio-facio-cutaneous syndrome: does genotype predict phenotype?", "authors": [{"family": "Allanson", "given": "Judith E", "initials": "JE"}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Aoki", "given": "Yoki", "initials": "Y"}, {"family": "Armour", "given": "Christine M", "initials": "CM"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "ML"}, {"family": "Cave", "given": "Helene", "initials": "H"}, {"family": "Gripp", "given": "Karen W", "initials": "KW"}, {"family": "Kerr", "given": "Bronwyn", "initials": "B"}, {"family": "Nystrom", "given": "Anna-Maja", "initials": "AM"}, {"family": "Sol-Church", "given": "Katia", "initials": "K"}, {"family": "Verloes", "given": "Alain", "initials": "A"}, {"family": "Zenker", "given": "Martin", "initials": "M"}], "type": "comparative study", "published": "2011-05-15", "journal": {"volume": "157C", "issn": "1552-4876", "issue": "2", "pages": "129-135", "title": "Am J Med Genet C Semin Med Genet", "issn-l": "1552-4868"}, "abstract": "Cardio-facio-cutaneous (CFC) syndrome is a sporadic multiple congenital anomalies/mental retardation condition principally caused by mutations in BRAF, MEK1, and MEK2. Mutations in KRAS and SHOC2 lead to a phenotype with overlapping features. In approximately 10\u201330% of individuals with a clinical diagnosis of CFC, a mutation in one of these causative genes is not found. Cardinal features of CFC include congenital heart defects, a characteristic facial appearance, and ectodermal abnormalities. Additional features include failure to thrive with severe feeding problems, moderate to severe intellectual disability and short stature with relative macrocephaly. First described in 1986, more than 100 affected individuals are reported. Following the discovery of the causative genes, more information has emerged on the breadth of clinical features. Little, however, has been published on genotype\u2013phenotype correlations. This clinical study of 186 children and young adults with mutation-proven CFC syndrome is the largest reported to date. BRAF mutations are documented in 140 individuals (approximately 75%), while 46 (approximately 25%) have a mutation in MEK 1 or MEK 2. The age range is 6 months to 32 years, the oldest individual being a female from the original report [Reynolds et al. (1986); Am J Med Genet 25:413\u2013427]. While some clinical data on 136 are in the literature, 50 are not previously published. We provide new details of the breadth of phenotype and discuss the frequency of particular features in each genotypic group. Pulmonary stenosis is the only anomaly that demonstrates a statistically significant genotype\u2013phenotype correlation, being more common in individuals with a BRAF mutation.", "doi": "10.1002/ajmg.c.30295", "pmid": "21495173", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pmc", "key": "PMC3086095"}, {"db": "mid", "key": "NIHMS282899"}], "notes": [], "created": "2017-05-04T15:01:54.139Z", "modified": "2020-01-21T13:56:02.754Z"}, {"entity": "publication", "iuid": "4f647b0a384344e581a7383c15fa9006", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4f647b0a384344e581a7383c15fa9006.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4f647b0a384344e581a7383c15fa9006"}}, "title": "A roadmap to generate renewable protein binders to the human proteome.", "authors": [{"family": "Colwill", "given": "Karen", "initials": "K"}, {"family": "Renewable Protein Binder Working Group", "given": "", "initials": ""}, {"family": "Gr\u00e4slund", "given": "Susanne", "initials": "S"}], "type": "journal article", "published": "2011-05-15", "journal": {"volume": "8", "issn": "1548-7105", "issue": "7", "pages": "551-558", "title": "Nat. Methods", "issn-l": "1548-7091"}, "abstract": "Despite the wealth of commercially available antibodies to human proteins, research is often hindered by their inconsistent validation, their poor performance and the inadequate coverage of the proteome. These issues could be addressed by systematic, genome-wide efforts to generate and validate renewable protein binders. We report a multicenter study to assess the potential of hybridoma and phage-display technologies in a coordinated large-scale antibody generation and validation effort. We produced over 1,000 antibodies targeting 20 SH2 domain proteins and evaluated them for potency and specificity by enzyme-linked immunosorbent assay (ELISA), protein microarray and surface plasmon resonance (SPR). We also tested selected antibodies in immunoprecipitation, immunoblotting and immunofluorescence assays. Our results show that high-affinity, high-specificity renewable antibodies generated by different technologies can be produced quickly and efficiently. We believe that this work serves as a foundation and template for future larger-scale studies to create renewable protein binders.", "doi": "10.1038/nmeth.1607", "pmid": "21572409", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "nmeth.1607"}], "notes": [], "created": "2017-10-30T10:38:36.549Z", "modified": "2021-05-24T15:27:28.238Z"}, {"entity": "publication", "iuid": "b53086961f1e45b0b13944910d3c1dc4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b53086961f1e45b0b13944910d3c1dc4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b53086961f1e45b0b13944910d3c1dc4"}}, "title": "Experimental evidence supports a sex-specific selective sieve in mitochondrial genome evolution.", "authors": [{"family": "Innocenti", "given": "Paolo", "initials": "P"}, {"family": "Morrow", "given": "Edward H", "initials": "EH"}, {"family": "Dowling", "given": "Damian K", "initials": "DK"}], "type": "journal article", "published": "2011-05-13", "journal": {"volume": "332", "issn": "1095-9203", "issue": "6031", "pages": "845-848", "title": "Science", "issn-l": "0036-8075"}, "abstract": "Mitochondria are maternally transmitted; hence, their genome can only make a direct and adaptive response to selection through females, whereas males represent an evolutionary dead end. In theory, this creates a sex-specific selective sieve, enabling deleterious mutations to accumulate in mitochondrial genomes if they exert male-specific effects. We tested this hypothesis, expressing five mitochondrial variants alongside a standard nuclear genome in Drosophila melanogaster, and found striking sexual asymmetry in patterns of nuclear gene expression. Mitochondrial polymorphism had few effects on nuclear gene expression in females but major effects in males, modifying nearly 10% of transcripts. These were mostly male-biased in expression, with enrichment hotspots in the testes and accessory glands. Our results suggest an evolutionary mechanism that results in mitochondrial genomes harboring male-specific mutation loads.", "doi": "10.1126/science.1201157", "pmid": "21566193", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "332/6031/845"}, {"db": "GEO", "key": "GSE24729"}], "notes": [], "created": "2017-05-04T15:02:54.449Z", "modified": "2017-05-31T08:17:00.513Z"}, {"entity": "publication", "iuid": "c78777ade0d647c8bb89f2dbabcd3ba7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c78777ade0d647c8bb89f2dbabcd3ba7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c78777ade0d647c8bb89f2dbabcd3ba7"}}, "title": "Cys-X scanning for expansion of active-site residues and modulation of catalytic functions in a glutathione transferase.", "authors": [{"family": "Norrg\u00e5rd", "given": "Malena A", "initials": "MA"}, {"family": "Hellman", "given": "Ulf", "initials": "U"}, {"family": "Mannervik", "given": "Bengt", "initials": "B"}], "type": "journal article", "published": "2011-05-13", "journal": {"volume": "286", "issn": "1083-351X", "issue": "19", "pages": "16871-16878", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "We propose Cys-X scanning as a semisynthetic approach to engineer the functional properties of recombinant proteins. As in the case of Ala scanning, key residues in the primary structure are identified, and one of them is replaced by Cys via site-directed mutagenesis. The thiol of the residue introduced is subsequently modified by alternative chemical reagents to yield diverse Cys-X mutants of the protein. This chemical approach is orthogonal to Ala or Cys scanning and allows the expansion of the repertoire of amino acid side chains far beyond those present in natural proteins. In its present application, we have introduced Cys-X residues in human glutathione transferase (GST) M2-2, replacing Met-212 in the substrate-binding site. To achieve selectivity of the modifications, the Cys residues in the wild-type enzyme were replaced by Ala. A suite of simple substitutions resulted in a set of homologous Met derivatives ranging from normethionine to S-heptyl-cysteine. The chemical modifications were validated by HPLC and mass spectrometry. The derivatized mutant enzymes were assayed with alternative GST substrates representing diverse chemical reactions: aromatic substitution, epoxide opening, transnitrosylation, and addition to an ortho-quinone. The Cys substitutions had different effects on the alternative substrates and differentially enhanced or suppressed catalytic activities depending on both the Cys-X substitution and the substrate assayed. As a consequence, the enzyme specificity profile could be changed among the alternative substrates. The procedure lends itself to large-scale production of Cys-X modified protein variants.", "doi": "10.1074/jbc.M111.230078", "pmid": "21454564", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "M111.230078"}, {"db": "pmc", "key": "PMC3089530"}], "notes": [], "created": "2017-05-04T15:01:58.898Z", "modified": "2020-01-21T13:56:05.144Z"}, {"entity": "publication", "iuid": "ca045d3361f44f1c9dd7e9248c4c1e98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ca045d3361f44f1c9dd7e9248c4c1e98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ca045d3361f44f1c9dd7e9248c4c1e98"}}, "title": "Methods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro.", "authors": [{"family": "Jolma", "given": "Arttu", "initials": "A"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2011-05-11", "journal": {"volume": "52", "issn": "0306-0225", "issue": null, "pages": "155-173", "title": "Subcell. Biochem.", "issn-l": null}, "abstract": "Transcription of genes during development and in response to environmental stimuli is determined by genomic DNA sequence. The DNA sequences regulating transcription are read by sequence-specific transcription factors (TFs) that recognize relatively short sequences, generally between four and twenty base pairs in length. Transcriptional regulation generally requires binding of multiple TFs in close proximity to each other. Mechanistic understanding of transcription in an organism thus requires detailed knowledge of binding affinities of all its TFs to all possible DNA sequences, and the co-operative interactions between the TFs. However, very little is known about such co-operative binding interactions, and even the simple TF-DNA binding information exists only for a very small proportion of all TFs - for example, mammals have approximately 1,300-2,000 TFs [1, 2], yet the largest public databases for TF binding specificity, Jaspar and Uniprobe [3, 4] currently list only approximately 500 moderate to high resolution profiles for human or mouse. This lack of knowledge is in part due to the fact that analysis of TF DNA binding has been laborious and expensive. In this chapter, we review methods that can be used to determine binding specificity of TFs to DNA, mainly focusing on recently developed assays that allow high-resolution analysis of TF binding specificity in relatively high throughput.", "doi": "10.1007/978-90-481-9069-0_7", "pmid": "21557082", "labels": {"Karolinska High Throughput Center (KHTC)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:03.967Z", "modified": "2017-05-30T11:43:59.054Z"}, {"entity": "publication", "iuid": "bc15673d6bcc443a91b105cd85fb16bd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bc15673d6bcc443a91b105cd85fb16bd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bc15673d6bcc443a91b105cd85fb16bd"}}, "title": "Growth differentiation factor 15: a prognostic marker for recurrence in colorectal cancer.", "authors": [{"family": "Wallin", "given": "U", "initials": "U"}, {"family": "Glimelius", "given": "B", "initials": "B"}, {"family": "Jirstr\u00f6m", "given": "K", "initials": "K"}, {"family": "Darmanis", "given": "S", "initials": "S"}, {"family": "Nong", "given": "R Y", "initials": "RY"}, {"family": "Pont\u00e9n", "given": "F", "initials": "F"}, {"family": "Johansson", "given": "C", "initials": "C"}, {"family": "P\u00e5hlman", "given": "L", "initials": "L"}, {"family": "Birgisson", "given": "H", "initials": "H"}], "type": "journal article", "published": "2011-05-10", "journal": {"volume": "104", "issn": "1532-1827", "issue": "10", "pages": "1619-1627", "title": "Br. J. Cancer", "issn-l": "0007-0920"}, "abstract": "Growth differentiation factor 15 (GDF15) belongs to the transforming growth factor beta superfamily and has been associated with activation of the p53 pathway in human cancer. The aim of this study was to assess the prognostic value of GDF15 in patients with colorectal cancer (CRC).\n\nImmunohistochemistry and tissue microarrays were used to analyse GDF15 protein expression in 320 patients with CRC. In a subgroup of 60 patients, the level of GDF15 protein in plasma was also measured using a solid-phase proximity ligation assay.\n\nPatients with CRC with moderate to high intensity of GDF15 immunostaining had a higher recurrence rate compared with patients with no or low intensity in all stages (stages I-III) (HR, 3.9; 95% CI, 1.16-13.15) and in stage III (HR, 10.32; 95% CI, 1.15-92.51). Patients with high plasma levels of GDF15 had statistically shorter time to recurrence (P=0.041) and reduced overall survival (P=0.002).\n\nGrowth differentiation factor 15 serves as a negative prognostic marker in CRC. High expression of GDF15 in tumour tissue and high plasma levels correlate with an increased risk of recurrence and reduced overall survival.", "doi": "10.1038/bjc.2011.112", "pmid": "21468045", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "bjc2011112"}, {"db": "pmc", "key": "PMC3101900"}], "notes": [], "created": "2017-05-04T14:55:45.827Z", "modified": "2017-05-30T12:56:35.167Z"}, {"entity": "publication", "iuid": "2542fca589754fc69c85633b9604f02c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2542fca589754fc69c85633b9604f02c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2542fca589754fc69c85633b9604f02c"}}, "title": "Melanoma cells produce multiple laminin isoforms and strongly migrate on \u03b15 laminin(s) via several integrin receptors.", "authors": [{"family": "Oikawa", "given": "Yuko", "initials": "Y"}, {"family": "Hansson", "given": "Johan", "initials": "J"}, {"family": "Sasaki", "given": "Takako", "initials": "T"}, {"family": "Rousselle", "given": "Patricia", "initials": "P"}, {"family": "Domogatskaya", "given": "Anna", "initials": "A"}, {"family": "Rodin", "given": "Sergey", "initials": "S"}, {"family": "Tryggvason", "given": "Karl", "initials": "K"}, {"family": "Patarroyo", "given": "Manuel", "initials": "M"}], "type": "journal article", "published": "2011-05-01", "journal": {"volume": "317", "issn": "1090-2422", "issue": "8", "pages": "1119-1133", "title": "Exp. Cell Res.", "issn-l": "0014-4827"}, "abstract": "Melanoma cells express and interact with laminins (LMs) and other basement membrane components during invasion and metastasis. In the present study we have investigated the production and migration-promoting activity of laminin isoforms in melanoma. Immunohistochemistry of melanoma specimens and immunoprecipitation/western blotting of melanoma cell lines indicated expression of laminin-111/121, laminin-211, laminin-411/421, and laminin-511/521. Laminin-332 was not detected. In functional assays, laminin-111, laminin-332, and laminin-511, but not laminin-211 and laminin-411, strongly promoted haptotactic cell migration either constitutively or following stimulation with insulin-like growth factors. Both placenta and recombinant laminin-511 preparations were highly active, and the isolated recombinant IVa domain of LM\u03b15 also promoted cell migration. Function-blocking antibodies in cell migration assays revealed \u03b16\u03b21 integrin as the major receptor for laminin-111, and both \u03b13\u03b21 and \u03b16\u03b21 integrins for laminin-332 and laminin-511. In contrast, isolated LM\u03b15 IVa domain-promoted melanoma cell migration was largely mediated via \u03b1V\u03b23 integrin and inhibited by RGD peptides. Given the ubiquitous expression of \u03b15 laminins in melanoma cells and in melanoma-target tissues/anatomical structures, as well as the strong migration-promoting activity of these laminin isoforms, the \u03b15 laminins emerge as putative primary extracellular matrix mediators of melanoma invasion and metastasis via \u03b13\u03b21 and other integrin receptors.", "doi": "10.1016/j.yexcr.2010.12.019", "pmid": "21195710", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0014-4827(10)00577-X"}], "notes": [], "created": "2017-05-04T14:57:18.577Z", "modified": "2020-01-21T13:56:01.105Z"}, {"entity": "publication", "iuid": "2af340190511436e870f8637d5f43f89", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2af340190511436e870f8637d5f43f89.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2af340190511436e870f8637d5f43f89"}}, "title": "Characterization of NPY Y2 receptor protein expression in the mouse brain. II. Coexistence with NPY, the Y1 receptor, and other neurotransmitter-related molecules.", "authors": [{"family": "Stani\u0107", "given": "Davor", "initials": "D"}, {"family": "Mulder", "given": "Jan", "initials": "J"}, {"family": "Watanabe", "given": "Masahiko", "initials": "M"}, {"family": "H\u00f6kfelt", "given": "Tomas", "initials": "T"}], "type": "journal article", "published": "2011-05-01", "journal": {"volume": "519", "issn": "1096-9861", "issue": "7", "pages": "1219-1257", "title": "J. Comp. Neurol.", "issn-l": "0021-9967"}, "abstract": "Neuropeptide Y (NPY) is widely expressed in the brain and its biological effects are mediated through a variety of receptors. We examined, using immunohistochemistry, expression of the Y2 receptor (R) protein in the adult mouse brain and its association with NPY and the Y1R, as well as a range of additional neurotransmitters and signaling-related molecules, which previously have not been defined. Our main focus was on the hippocampal formation (HiFo), amygdaloid complex, and hypothalamus, considering the known functions of NPY and the wide expression of NPY, Y1R, and Y2R in these regions. Y2R-like immunoreactivity (-LI) was distributed in nerve fibers/terminal endings throughout the brain axis, without apparent colocalization with NPY or the Y1R. Occasional coexistence between NPY- and Y1R-LI was found in the HiFo. Following colchicine treatment, Y2R-LI accumulated in cell bodies that coexpressed \u03b3-aminobutyric acid (GABA) in a population of cells in the amygdaloid complex and lateral septal nucleus, but not in the HiFo. Instead, Y2R-positive nerve terminals appeared to surround GABA-immunoreactive (ir) cells in the HiFo and other neuronal populations, e.g., NPY-ir cells in HiFo and tyrosine hydroxylase-ir cells in the hypothalamus. In the HiFo, Y2R-ir mossy fibers coexpressed GABA, glutamic acid decarboxylase 67 and calbindin, and Y2R-LI was found in the same fibers that contained the presynaptic metabotropic glutamate receptor 2, but not together with any of the three vesicular glutamate transporters. Our findings provide further support that Y2R is mostly presynaptic, and that Y2Rs thus have a modulatory role in mediating presynaptic neurotransmitter release.", "doi": "10.1002/cne.22608", "pmid": "21452195", "labels": {"Fluorescence Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:17.733Z", "modified": "2017-05-30T11:33:33.894Z"}, {"entity": "publication", "iuid": "3c311d033f2f4e079d7daf1f85bbb354", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3c311d033f2f4e079d7daf1f85bbb354.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3c311d033f2f4e079d7daf1f85bbb354"}}, "title": "The 12q14 microdeletion syndrome: six new cases confirming the role of HMGA2 in growth.", "authors": [{"family": "Lynch", "given": "Sally Ann", "initials": "SA"}, {"family": "Foulds", "given": "Nicola", "initials": "N"}, {"family": "Thuresson", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Collins", "given": "Amanda L", "initials": "AL"}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Hedberg", "given": "Bernt-Oves", "initials": "BO"}, {"family": "Delaney", "given": "Carol A", "initials": "CA"}, {"family": "Iremonger", "given": "James", "initials": "J"}, {"family": "Murray", "given": "Caroline M", "initials": "CM"}, {"family": "Crolla", "given": "John A", "initials": "JA"}, {"family": "Costigan", "given": "Colm", "initials": "C"}, {"family": "Lam", "given": "Wayne", "initials": "W"}, {"family": "Fitzpatrick", "given": "David R", "initials": "DR"}, {"family": "Regan", "given": "Regina", "initials": "R"}, {"family": "Ennis", "given": "Sean", "initials": "S"}, {"family": "Sharkey", "given": "Freddie", "initials": "F"}], "type": "journal article", "published": "2011-05-00", "journal": {"volume": "19", "issn": "1476-5438", "issue": "5", "pages": "534-539", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "We report six patients with array deletions encompassing 12q14. Out of a total of 2538 array investigations carried out on children with developmental delay and dysmorphism in three diagnostic testing centres, six positive cases yielded a frequency of 1 in 423 for this deletion syndrome. The deleted region in each of the six cases overlaps significantly with previously reported cases with microdeletions of this region. The chromosomal range of the deletions extends from 12q13.3q15. In the current study, we report overlapping deletions of variable extent and size but primarily comprising chromosomal bands 12q13.3q14.1. Four of the six deletions were confirmed as de novo events. Two cases had deletions that included HMGA2, and both children had significant short stature. Neither case had osteopoikilosis despite both being deleted for LEMD3. Four cases had deletions that ended proximal to HMGA2 and all of these had much better growth. Five cases had congenital heart defects, including two with atrial septal defects, one each with pulmonary stenosis, sub-aortic stenosis and a patent ductus. Four cases had moderate delay, two had severe developmental delay and a further two had a diagnosis of autism. All six cases had significant speech delay with subtle facial dysmorphism.", "doi": "10.1038/ejhg.2010.215", "pmid": "21267005", "labels": {"National Genomics Infrastructure": null, "Array and Analysis Facility": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "ejhg2010215"}, {"db": "pmc", "key": "PMC3083609"}], "notes": [], "created": "2017-05-04T15:01:56.658Z", "modified": "2020-01-21T13:56:01.699Z"}, {"entity": "publication", "iuid": "c4d3e805f38848189e13204dcfd51b1a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c4d3e805f38848189e13204dcfd51b1a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c4d3e805f38848189e13204dcfd51b1a"}}, "title": "Parental criticism and externalizing behavior problems in adolescents: the role of environment and genotype-environment correlation.", "authors": [{"family": "Narusyte", "given": "Jurgita", "initials": "J"}, {"family": "Neiderhiser", "given": "Jenae M", "initials": "JM"}, {"family": "Andershed", "given": "Anna-Karin", "initials": "AK"}, {"family": "D'Onofrio", "given": "Brian M", "initials": "BM"}, {"family": "Reiss", "given": "David", "initials": "D"}, {"family": "Spotts", "given": "Erica", "initials": "E"}, {"family": "Ganiban", "given": "Jody", "initials": "J"}, {"family": "Lichtenstein", "given": "Paul", "initials": "P"}], "type": "journal article", "published": "2011-05-00", "journal": {"volume": "120", "issn": "1939-1846", "issue": "2", "pages": "365-376", "title": "J Abnorm Psychol", "issn-l": "0021-843X"}, "abstract": "Genetic factors are important for the association between parental negativity and child problem behavior, but it is not clear whether this is due to passive or evocative genotype-environment correlation (rGE). In this study, we applied the extended children-of-twins model to directly examine the presence of passive and evocative rGE as well as direct environmental effects in the association between parental criticism and adolescent externalizing problem behavior. The cross-sectional data come from the Twin and Offspring Study in Sweden (N = 909 pairs of adult twins) and from the Twin Study of Child and Adolescent Development (N = 915 pairs of twin children). The results revealed that maternal criticism was primarily due to evocative rGE emanating from their adolescent's externalizing behavior. On the other hand, fathers' critical remarks tended to affect adolescent problem behavior in a direct environmental way. This suggests that previously reported differences in caretaking between mothers and fathers also are reflected in differences in why parenting is associated with externalizing behavior in offspring.", "doi": "10.1037/a0021815", "pmid": "21280930", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "2011-01600-001"}, {"db": "pmc", "key": "PMC3093313"}, {"db": "mid", "key": "NIHMS289298"}], "notes": [], "created": "2017-05-04T15:03:30.403Z", "modified": "2017-05-30T12:44:19.342Z"}, {"entity": "publication", "iuid": "33d391ea923b4bf38faba4133d79ba7e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33d391ea923b4bf38faba4133d79ba7e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33d391ea923b4bf38faba4133d79ba7e"}}, "title": "Directional genetic selection by pulp mill effluent on multiple natural populations of three-spined stickleback (Gasterosteus aculeatus).", "authors": [{"family": "Lind", "given": "Emma E", "initials": "EE"}, {"family": "Grahn", "given": "Mats", "initials": "M"}], "type": "journal article", "published": "2011-05-00", "journal": {"volume": "20", "issn": "1573-3017", "issue": "3", "pages": "503-512", "title": "Ecotoxicology", "issn-l": "0963-9292"}, "abstract": "Contamination can cause a rapid environmental change which may require populations to respond with evolutionary changes. To evaluate the effects of pulp mill effluents on population genetics, we sampled three-spined sticklebacks (Gasterosteus aculeatus) near four pulp mills and four adjacent reference sites and analyzed Amplified Fragment Length Polymorphism (AFLP) to compare genetic variability. A fine scale genetic structure was detected and samples from polluted sites separated from reference sites in multidimensional scaling plots (P<0.005, 1000 permutations) and locus-by-locus Analysis of Molecular Variance (AMOVA) further confirmed that habitats are significantly separated (F(ST)=0.021, P<0.01, 1023 permutations). The amount of genetic variation between populations did not differ between habitats, and populations from both habitats had similar levels of heterozygosity (polluted sites Nei's Hs=0.11, reference sites Nei's Hs=0.11). Still, pairwise F(ST): s between three, out of four, pairs of polluted-reference sites were significant. A F(ST)-outlier analysis showed that 21 (8.4%) loci were statistically different from a neutral distribution at the P<0.05 level and therefore indicated to be under divergent selection. When removing 13 F(ST)-outlier loci, significant at the P<0.01 level, differentiation between habitats disappeared in a multidimensional scaling plot. In conclusion, pulp mill effluence has acted as a selective agent on natural populations of G. aculeatus, causing a convergence in genotype composition change at multiple sites in an open environment.", "doi": "10.1007/s10646-011-0639-8", "pmid": "21455608", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pmc", "key": "PMC3081435"}], "notes": [], "created": "2017-05-04T15:01:56.059Z", "modified": "2020-01-21T13:56:01.461Z"}, {"entity": "publication", "iuid": "a46d60b67e3c4ad1931e3df667e27017", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a46d60b67e3c4ad1931e3df667e27017.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a46d60b67e3c4ad1931e3df667e27017"}}, "title": "Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria.", "authors": [{"family": "Farnelid", "given": "Hanna", "initials": "H"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Bertilsson", "given": "Stefan", "initials": "S"}, {"family": "Al-Soud", "given": "Waleed Abu", "initials": "WA"}, {"family": "Hansen", "given": "Lars H", "initials": "LH"}, {"family": "S\u00f8rensen", "given": "S\u00f8ren", "initials": "S"}, {"family": "Steward", "given": "Grieg F", "initials": "GF"}, {"family": "Hagstr\u00f6m", "given": "\u00c5ke", "initials": "\u00c5"}, {"family": "Riemann", "given": "Lasse", "initials": "L"}], "type": "journal article", "published": "2011-04-29", "journal": {"volume": "6", "issn": "1932-6203", "issue": "4", "pages": "e19223", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Cyanobacteria are thought to be the main N(2)-fixing organisms (diazotrophs) in marine pelagic waters, but recent molecular analyses indicate that non-cyanobacterial diazotrophs are also present and active. Existing data are, however, restricted geographically and by limited sequencing depths. Our analysis of 79,090 nitrogenase (nifH) PCR amplicons encoding 7,468 unique proteins from surface samples (ten DNA samples and two RNA samples) collected at ten marine locations world-wide provides the first in-depth survey of a functional bacterial gene and yield insights into the composition and diversity of the nifH gene pool in marine waters. Great divergence in nifH composition was observed between sites. Cyanobacteria-like genes were most frequent among amplicons from the warmest waters, but overall the data set was dominated by nifH sequences most closely related to non-cyanobacteria. Clusters related to Alpha-, Beta-, Gamma-, and Delta-Proteobacteria were most common and showed distinct geographic distributions. Sequences related to anaerobic bacteria (nifH Cluster III) were generally rare, but preponderant in cold waters, especially in the Arctic. Although the two transcript samples were dominated by unicellular cyanobacteria, 42% of the identified non-cyanobacterial nifH clusters from the corresponding DNA samples were also detected in cDNA. The study indicates that non-cyanobacteria account for a substantial part of the nifH gene pool in marine surface waters and that these genes are at least occasionally expressed. The contribution of non-cyanobacterial diazotrophs to the global N(2) fixation budget cannot be inferred from sequence data alone, but the prevalence of non-cyanobacterial nifH genes and transcripts suggest that these bacteria are ecologically significant.", "doi": "10.1371/journal.pone.0019223", "pmid": "21559425", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-11-00451"}, {"db": "pmc", "key": "PMC3084785"}], "notes": [], "created": "2017-05-04T14:57:25.899Z", "modified": "2020-01-21T13:56:04.237Z"}, {"entity": "publication", "iuid": "c29aadb8392f487487302b27fddcc407", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c29aadb8392f487487302b27fddcc407.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c29aadb8392f487487302b27fddcc407"}}, "title": "Large scale library generation for high throughput sequencing.", "authors": [{"family": "Borgstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2011-04-27", "journal": {"volume": "6", "issn": "1932-6203", "issue": "4", "pages": "e19119", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Large efforts have recently been made to automate the sample preparation protocols for massively parallel sequencing in order to match the increasing instrument throughput. Still, the size selection through agarose gel electrophoresis separation is a labor-intensive bottleneck of these protocols.\n\nIn this study a method for automatic library preparation and size selection on a liquid handling robot is presented. The method utilizes selective precipitation of certain sizes of DNA molecules on to paramagnetic beads for cleanup and selection after standard enzymatic reactions.\n\nThe method is used to generate libraries for de novo and re-sequencing on the Illumina HiSeq 2000 instrument with a throughput of 12 samples per instrument in approximately 4 hours. The resulting output data show quality scores and pass filter rates comparable to manually prepared samples. The sample size distribution can be adjusted for each application, and are suitable for all high throughput DNA processing protocols seeking to control size intervals.", "doi": "10.1371/journal.pone.0019119", "pmid": "21589638", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "PONE-D-10-05646"}, {"db": "pmc", "key": "PMC3083417"}], "notes": [], "created": "2017-05-04T14:57:25.602Z", "modified": "2021-07-08T13:26:08.325Z"}, {"entity": "publication", "iuid": "dbe52e1f133d4beb8fd0c3a4cc18ef06", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbe52e1f133d4beb8fd0c3a4cc18ef06.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbe52e1f133d4beb8fd0c3a4cc18ef06"}}, "title": "Structure and assembly-disassembly properties of wild-type transthyretin amyloid protofibrils observed with atomic force microscopy.", "authors": [{"family": "Pires", "given": "Ricardo H", "initials": "RH"}, {"family": "Saraiva", "given": "Maria J", "initials": "MJ"}, {"family": "Damas", "given": "Ana M", "initials": "AM"}, {"family": "Kellermayer", "given": "Mikl\u00f3s S Z", "initials": "MS"}], "type": "journal article", "published": "2011-04-20", "journal": {"volume": "24", "issn": "1099-1352", "issue": "3", "pages": "467-476", "title": "J. Mol. Recognit.", "issn-l": "0952-3499"}, "abstract": "Transthyretin (TTR) is an important human transport protein present in the serum and the cerebrospinal fluid. Aggregation of TTR in the form of amyloid fibrils is associated with neurodegeneration, but the mechanisms of cytotoxicity are likely to stem from the presence of intermediate assembly states. Characterization of these intermediate species is therefore essential to understand the etiology and pathogenesis of TTR-related amyloidoses. In the present work we used atomic force microscopy to investigate the morphological features of wild-type (WT) TTR amyloid protofibrils that appear in the early stages of aggregation. TTR protofibrils obtained by mild acidification appeared as flexible filaments with variable length and were able to bind amyloid markers (thioflavin T and Congo red). Surface topology and contour-length distribution displayed a periodic pattern of \u223c 15 nm, suggesting that the protofibrils assemble via an end-binding oligomer fusion mechanism. The average height and periodic substructure found in protofibrils is compatible with the double-helical model of the TTR amyloid protofilament. Over time protofibrils aggregated into bundles and did not form mature amyloid-like fibrils. Unlike amyloid fibrils that are typically stable under physiological conditions, the bundles dissociated into component protofibrils with axially compacted and radially dilated structure when exposed to phosphate-buffered saline solution. Thus, WT TTR can form metastable filamentous aggregates that may represent an important transient state along the pathway towards the formation of cytotoxic TTR species.", "doi": "10.1002/jmr.1112", "pmid": "21504025", "labels": {"Mass Spectrometry-based Proteomics, Uppsala": null}, "xrefs": [], "notes": [], "created": "2017-05-02T12:57:55.227Z", "modified": "2017-05-30T13:13:09.485Z"}, {"entity": "publication", "iuid": "686f536c265a43c5be5d03c143d4c835", "links": {"self": {"href": "https://publications.scilifelab.se/publication/686f536c265a43c5be5d03c143d4c835.json"}, "display": {"href": "https://publications.scilifelab.se/publication/686f536c265a43c5be5d03c143d4c835"}}, "title": "Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods.", "authors": [{"family": "Jakobsen", "given": "Lis", "initials": "L"}, {"family": "Vanselow", "given": "Katja", "initials": "K"}, {"family": "Skogs", "given": "Marie", "initials": "M"}, {"family": "Toyoda", "given": "Yusuke", "initials": "Y"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Poser", "given": "Ina", "initials": "I"}, {"family": "Falkenby", "given": "Lasse G", "initials": "LG"}, {"family": "Bennetzen", "given": "Martin", "initials": "M"}, {"family": "Westendorf", "given": "Jens", "initials": "J"}, {"family": "Nigg", "given": "Erich A", "initials": "EA"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Hyman", "given": "Anthony A", "initials": "AA"}, {"family": "Andersen", "given": "Jens S", "initials": "JS"}], "type": "journal article", "published": "2011-04-20", "journal": {"volume": "30", "issn": "1460-2075", "issue": "8", "pages": "1520-1535", "title": "EMBO J.", "issn-l": "0261-4189"}, "abstract": "Centrosomes in animal cells are dynamic organelles with a proteinaceous matrix of pericentriolar material assembled around a pair of centrioles. They organize the microtubule cytoskeleton and the mitotic spindle apparatus. Mature centrioles are essential for biogenesis of primary cilia that mediate key signalling events. Despite recent advances, the molecular basis for the plethora of processes coordinated by centrosomes is not fully understood. We have combined protein identification and localization, using PCP-SILAC mass spectrometry, BAC transgeneOmics, and antibodies to define the constituents of human centrosomes. From a background of non-specific proteins, we distinguished 126 known and 40 candidate centrosomal proteins, of which 22 were confirmed as novel components. An antibody screen covering 4000 genes revealed an additional 113 candidates. We illustrate the power of our methods by identifying a novel set of five proteins preferentially associated with mother or daughter centrioles, comprising genes implicated in cell polarity. Pulsed labelling demonstrates a remarkable variation in the stability of centrosomal protein complexes. These spatiotemporal proteomics data provide leads to the further functional characterization of centrosomal proteins.", "doi": "10.1038/emboj.2011.63", "pmid": "21399614", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "emboj201163"}, {"db": "pmc", "key": "PMC3102290"}], "notes": [], "created": "2017-05-04T14:55:08.671Z", "modified": "2021-07-08T13:44:33.329Z"}, {"entity": "publication", "iuid": "6020ba73a1074d6781fddb32a0955729", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6020ba73a1074d6781fddb32a0955729.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6020ba73a1074d6781fddb32a0955729"}}, "title": "Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements.", "authors": [{"family": "Skarin", "given": "Hanna", "initials": "H"}, {"family": "H\u00e5fstr\u00f6m", "given": "Therese", "initials": "T"}, {"family": "Westerberg", "given": "Josefina", "initials": "J"}, {"family": "Segerman", "given": "Bo", "initials": "B"}], "type": "journal article", "published": "2011-04-12", "journal": {"volume": "12", "issn": "1471-2164", "issue": null, "pages": "185", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Clostridium botulinum strains can be divided into four physiological groups that are sufficiently diverged to be considered as separate species. Here we present the first complete genome of a C. botulinum strain from physiological group III, causing animal botulism. We also compare the sequence to three new draft genomes from the same physiological group.\n\nThe 2.77 Mb chromosome was highly conserved between the isolates and also closely related to that of C. novyi. However, the sequence was very different from the human C. botulinum group genomes. Replication-directed translocations were rare and conservation of synteny was high. The largest difference between C. botulinum group III isolates occurred within their surprisingly large plasmidomes and in the pattern of mobile elements insertions. Five plasmids, constituting 13.5% of the total genetic material, were present in the completed genome. Interestingly, the set of plasmids differed compared to other isolates. The largest plasmid, the botulinum-neurotoxin carrying prophage, was conserved at a level similar to that of the chromosome while the medium-sized plasmids seemed to be undergoing faster genetic drift. These plasmids also contained more mobile elements than other replicons. Several toxins and resistance genes were identified, many of which were located on the plasmids.\n\nThe completion of the genome of C. botulinum group III has revealed it to be a genome with dual identity. It belongs to the pathogenic species C. botulinum, but as a genotypic species it should also include C. novyi and C. haemolyticum. The genotypic species share a conserved chromosomal core that can be transformed into various pathogenic variants by modulation of the highly plastic plasmidome.", "doi": "10.1186/1471-2164-12-185", "pmid": "21486474", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-12-185"}, {"db": "pmc", "key": "PMC3098183"}], "notes": [], "created": "2017-05-04T14:57:16.786Z", "modified": "2020-01-21T13:56:02.619Z"}, {"entity": "publication", "iuid": "f0314f8754d14b05883ff8e1db48007a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f0314f8754d14b05883ff8e1db48007a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f0314f8754d14b05883ff8e1db48007a"}}, "title": "Utilizing twins concordance rates to infer the predisposition to myasthenia gravis.", "authors": [{"family": "Ramanujam", "given": "Ryan", "initials": "R"}, {"family": "Pirskanen", "given": "Ritva", "initials": "R"}, {"family": "Ramanujam", "given": "S", "initials": "S"}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}], "type": "journal article", "published": "2011-04-00", "journal": {"volume": "14", "issn": "1832-4274", "issue": "2", "pages": "129-136", "title": "Twin Res Hum Genet", "issn-l": null}, "abstract": "Myasthenia gravis (MG) is an autoimmune disorder in which patients experience muscular fatigability due to the presence of anti-acetylcholine receptor (AChR) antibodies which inhibit signal transduction across the neuro-muscular junction. Like all complex disorders, disease is caused by an interaction between genetic and environmental factors. Although several genes have been identified which appear to be associated with MG, both classic twin studies and current multi-gene models are insufficient to explain either disease pathogenesis or inheritance. We examined the literature on MG to determine both mono- and dizygotic twin concordance rates, and used this data to (1) estimate the proportion of the population with underlying genetic predisposition to MG and the frequency of the environmental component and (2) derive the number of inherited genetic regions that are required to confer predisposition to MG. Using a MZ twin concordance rate of 35.5%, and a dizygotic rate of approximately 4-5% (based on family data), the probability of encountering environmental components necessary to develop MG in an individual with genetic predisposition is approximately 52.4%, making the frequency of predisposition (1:5240) roughly twice the rate of incidence. Furthermore, the number of genetic regions co-inherited between affected individuals is between two and four, which may be large haplotypes with interacting activity. Determining these haplotypes, by fully sequencing associated regions in cases and controls to identify mutations present, may therefore be a practically step toward the understanding of complex disease.", "doi": "10.1375/twin.14.2.129", "pmid": "21425894", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "10.1375/twin.14.2.129"}], "notes": [], "created": "2017-05-04T15:03:32.845Z", "modified": "2017-05-30T12:44:56.599Z"}, {"entity": "publication", "iuid": "1c2920749c0e4106a3ec98ce2a1bca13", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1c2920749c0e4106a3ec98ce2a1bca13.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1c2920749c0e4106a3ec98ce2a1bca13"}}, "title": "Synthesis and application of a bromomethyl substituted scaffold to be used for efficient optimization of anti-virulence activity.", "authors": [{"family": "Chorell", "given": "Erik", "initials": "E", "orcid": "0000-0003-2523-1940", "researcher": {"href": "https://publications.scilifelab.se/researcher/ada783ae0a824621a3b8e1024aae13a4.json"}}, {"family": "Bengtsson", "given": "Christoffer", "initials": "C"}, {"family": "Sainte-Luce Banchelin", "given": "Thomas", "initials": "T"}, {"family": "Das", "given": "Pralay", "initials": "P"}, {"family": "Uvell", "given": "Hanna", "initials": "H"}, {"family": "Sinha", "given": "Arun K", "initials": "AK"}, {"family": "Pinkner", "given": "Jerome S", "initials": "JS"}, {"family": "Hultgren", "given": "Scott J", "initials": "SJ"}, {"family": "Almqvist", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2011-04-00", "journal": {"volume": "46", "issn": "1768-3254", "issue": "4", "pages": "1103-1116", "title": "Eur J Med Chem", "issn-l": "0223-5234"}, "abstract": "Pilicides are a class of compounds that attenuate virulence in Gram negative bacteria by blocking the chaperone/usher pathway in Escherichia coli. It has also been shown that compounds derived from the peptidomimetic scaffold that the pilicides are based on can prevent both A\u03b2 aggregation and curli formation. To facilitate optimizations towards the different targets, a new synthetic platform has been developed that enables fast and simple introduction of various substituents in position C-7 on the peptidomimetic scaffold. Importantly, this strategy also enables introduction of previously unattainable heteroatoms in this position. Pivotal to the synthetic strategy is the synthesis of a C-7 bromomethyl substituted derivative of the ring-fused dihydrothiazolo 2-pyridone pilicide scaffold. From this versatile and reactive intermediate various heteroatom-linked substituents could be introduced on the scaffold including amines, ethers, amides and sulfonamides. In addition, carbon-carbon bonds could be introduced to the sp(3)-hybridized bromomethyl substituted scaffold by Suzuki-Miyaura cross couplings. Evaluation of the 24 C-7 substituted compounds in whole-bacterial assays provided important structure-activity data and resulted in the identification of a number of new pilicides with activity as good or better than those developed previously.", "doi": "10.1016/j.ejmech.2011.01.025", "pmid": "21316127", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "S0223-5234(11)00045-6"}, {"db": "pmc", "key": "PMC3694777"}, {"db": "mid", "key": "NIHMS295032"}], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:36.418Z", "modified": "2025-10-17T13:04:30.792Z"}, {"entity": "publication", "iuid": "abe1b0f948cc41378846035fee301ed7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/abe1b0f948cc41378846035fee301ed7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/abe1b0f948cc41378846035fee301ed7"}}, "title": "Kynurenine 3-monooxygenase (KMO) polymorphisms in schizophrenia: An association study", "authors": [{"family": "Holtze", "given": "Maria", "initials": "M"}, {"family": "Saetre", "given": "Peter", "initials": "P"}, {"family": "Erhardt", "given": "Sophie", "initials": "S"}, {"family": "Schwieler", "given": "Lilly", "initials": "L"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Hansen", "given": "Thomas", "initials": "T"}, {"family": "Nielsen", "given": "Jimmi", "initials": "J"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Hall", "given": "H\u00e5kan", "initials": "H"}, {"family": "Terenius", "given": "Lars", "initials": "L"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Engberg", "given": "G\u00f6ran", "initials": "G"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}, {"family": "Schalling", "given": "Martin", "initials": "M"}], "type": "journal-article", "published": "2011-04-00", "journal": {"volume": "127", "issn": "0920-9964", "issue": "1-3", "pages": "270-272", "title": "Schizophr. Res.", "issn-l": null}, "abstract": null, "doi": "10.1016/j.schres.2010.10.002", "pmid": "21030213", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0920-9964(10)01575-6"}], "notes": [], "created": "2017-05-04T15:11:19.211Z", "modified": "2021-07-05T13:04:59.791Z"}, {"entity": "publication", "iuid": "748a3d45ec0e4674b8121c28a2cb233f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/748a3d45ec0e4674b8121c28a2cb233f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/748a3d45ec0e4674b8121c28a2cb233f"}}, "title": "A candidate gene study of the type I interferon pathway implicates IKBKE and IL8 as risk loci for SLE.", "authors": [{"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Garnier", "given": "Sophie", "initials": "S"}, {"family": "Sigurdsson", "given": "Snaevar", "initials": "S"}, {"family": "Wang", "given": "Chuan", "initials": "C"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Sturfelt", "given": "Gunnar", "initials": "G"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Truedsson", "given": "Lennart", "initials": "L"}, {"family": "Eriksson", "given": "Catharina", "initials": "C"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A"}, {"family": "Strawbridge", "given": "Rona J", "initials": "RJ"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Criswell", "given": "Lindsey A", "initials": "LA"}, {"family": "Graham", "given": "Robert R", "initials": "RR"}, {"family": "Behrens", "given": "Timothy W", "initials": "TW"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Alm", "given": "Gunnar", "initials": "G"}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2011-04-00", "journal": {"volume": "19", "issn": "1476-5438", "issue": "4", "pages": "479-484", "title": "Eur. J. Hum. Genet.", "issn-l": "1018-4813"}, "abstract": "Systemic Lupus Erythematosus (SLE) is a systemic autoimmune disease in which the type I interferon pathway has a crucial role. We have previously shown that three genes in this pathway, IRF5, TYK2 and STAT4, are strongly associated with risk for SLE. Here, we investigated 78 genes involved in the type I interferon pathway to identify additional SLE susceptibility loci. First, we genotyped 896 single-nucleotide polymorphisms in these 78 genes and 14 other candidate genes in 482 Swedish SLE patients and 536 controls. Genes with P<0.01 in the initial screen were then followed up in 344 additional Swedish patients and 1299 controls. SNPs in the IKBKE, TANK, STAT1, IL8 and TRAF6 genes gave nominal signals of association with SLE in this extended Swedish cohort. To replicate these findings we extracted data from a genomewide association study on SLE performed in a US cohort. Combined analysis of the Swedish and US data, comprising a total of 2136 cases and 9694 controls, implicates IKBKE and IL8 as SLE susceptibility loci (P(meta)=0.00010 and P(meta)=0.00040, respectively). STAT1 was also associated with SLE in this cohort (P(meta)=3.3 \u00d7 10\u207b\u2075), but this association signal appears to be dependent of that previously reported for the neighbouring STAT4 gene. Our study suggests additional genes from the type I interferon system in SLE, and highlights genes in this pathway for further functional analysis.", "doi": "10.1038/ejhg.2010.197", "pmid": "21179067", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ejhg2010197"}, {"db": "pmc", "key": "PMC3060320"}], "notes": [], "created": "2017-05-04T15:00:43.036Z", "modified": "2021-07-07T15:11:02.525Z"}, {"entity": "publication", "iuid": "a8022e2181c949ed840b4aae04ff21a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8022e2181c949ed840b4aae04ff21a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8022e2181c949ed840b4aae04ff21a4"}}, "title": "FATP4 missense and nonsense mutations cause similar features in Ichthyosis Prematurity Syndrome.", "authors": [{"family": "Sobol", "given": "Maria", "initials": "M"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Klar", "given": "Joakim", "initials": "J"}], "type": "journal article", "published": "2011-03-30", "journal": {"volume": "4", "issn": "1756-0500", "issue": null, "pages": "90", "title": "BMC Res Notes", "issn-l": "1756-0500"}, "abstract": "Ichthyosis Prematurity Syndrome (IPS) is an autosomal recessive disorder characterized by premature birth, non-scaly ichthyosis and atopic manifestations. The disease was recently shown to be caused by mutations in the gene encoding the fatty acid transport protein 4 (FATP4) and a specific reduction in the incorporation of very long chain fatty acids (VLCFA) into cellular lipids.\r\n\r\nWe screened probands from five families segregating IPS for mutations in the FATP4 gene. Four probands were compound heterozygous for four different mutations of which three are novel. Four patients were heterozygous and one patient homozygous for the previously reported non-sense mutation p.C168X (c.504c > a). All patients had clinical characteristics of IPS and a similar clinical course.\r\n\r\nMissense mutations and non-sense mutations in FATP4 are associated with similar clinical features suggesting that missense mutations have a severe impact on FATP4 function. The results broaden the mutational spectrum in FATP4 associated with IPS for molecular diagnosis of and further functional analysis of FATP4.", "doi": "10.1186/1756-0500-4-90", "pmid": "21450060", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1756-0500-4-90"}, {"db": "pmc", "key": "PMC3072334"}], "notes": [], "created": "2017-05-04T14:57:17.378Z", "modified": "2020-01-21T13:56:10.420Z"}, {"entity": "publication", "iuid": "4d3f09c6a5b6444abc9f2514f6c1f3e9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4d3f09c6a5b6444abc9f2514f6c1f3e9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4d3f09c6a5b6444abc9f2514f6c1f3e9"}}, "title": "Human oral, gut, and plaque microbiota in patients with atherosclerosis.", "authors": [{"family": "Koren", "given": "Omry", "initials": "O"}, {"family": "Spor", "given": "Aym\u00e9", "initials": "A"}, {"family": "Felin", "given": "Jenny", "initials": "J"}, {"family": "F\u00e5k", "given": "Frida", "initials": "F"}, {"family": "Stombaugh", "given": "Jesse", "initials": "J"}, {"family": "Tremaroli", "given": "Valentina", "initials": "V"}, {"family": "Behre", "given": "Carl Johan", "initials": "CJ"}, {"family": "Knight", "given": "Rob", "initials": "R"}, {"family": "Fagerberg", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Ley", "given": "Ruth E", "initials": "RE"}, {"family": "B\u00e4ckhed", "given": "Fredrik", "initials": "F"}], "type": "journal article", "published": "2011-03-15", "journal": {"volume": "108 Suppl 1", "issn": "1091-6490", "issue": null, "pages": "4592-4598", "title": "Proc. Natl. Acad. Sci. U.S.A.", "issn-l": "0027-8424"}, "abstract": "Periodontal disease has been associated with atherosclerosis, suggesting that bacteria from the oral cavity may contribute to the development of atherosclerosis and cardiovascular disease. Furthermore, the gut microbiota may affect obesity, which is associated with atherosclerosis. Using qPCR, we show that bacterial DNA was present in the atherosclerotic plaque and that the amount of DNA correlated with the amount of leukocytes in the atherosclerotic plaque. To investigate the microbial composition of atherosclerotic plaques and test the hypothesis that the oral or gut microbiota may contribute to atherosclerosis in humans, we used 454 pyrosequencing of 16S rRNA genes to survey the bacterial diversity of atherosclerotic plaque, oral, and gut samples of 15 patients with atherosclerosis, and oral and gut samples of healthy controls. We identified Chryseomonas in all atherosclerotic plaque samples, and Veillonella and Streptococcus in the majority. Interestingly, the combined abundances of Veillonella and Streptococcus in atherosclerotic plaques correlated with their abundance in the oral cavity. Moreover, several additional bacterial phylotypes were common to the atherosclerotic plaque and oral or gut samples within the same individual. Interestingly, several bacterial taxa in the oral cavity and the gut correlated with plasma cholesterol levels. Taken together, our findings suggest that bacteria from the oral cavity, and perhaps even the gut, may correlate with disease markers of atherosclerosis.", "doi": "10.1073/pnas.1011383107", "pmid": "20937873", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1011383107"}, {"db": "pmc", "key": "PMC3063583"}], "notes": [], "created": "2017-05-04T14:57:23.767Z", "modified": "2020-01-21T13:56:02.215Z"}, {"entity": "publication", "iuid": "4b2162ad67b4445ebf3fa76db2933919", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4b2162ad67b4445ebf3fa76db2933919.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4b2162ad67b4445ebf3fa76db2933919"}}, "title": "Molecular characterization of acquired tolerance of tumor cells to picropodophyllin (PPP).", "authors": [{"family": "Hashemi", "given": "Jamileh", "initials": "J"}, {"family": "Worrall", "given": "Claire", "initials": "C"}, {"family": "Vasilcanu", "given": "Daiana", "initials": "D"}, {"family": "Frykn\u00e4s", "given": "M\u00e5rten", "initials": "M"}, {"family": "Sulaiman", "given": "Luqman", "initials": "L"}, {"family": "Karimi", "given": "Mohsen", "initials": "M"}, {"family": "Weng", "given": "Wen-Hui", "initials": "WH"}, {"family": "Lui", "given": "Weng-Onn", "initials": "WO"}, {"family": "Rudduck", "given": "Christina", "initials": "C"}, {"family": "Axelson", "given": "Magnus", "initials": "M"}, {"family": "Jernberg-Wiklund", "given": "Helena", "initials": "H"}, {"family": "Girnita", "given": "Leonard", "initials": "L"}, {"family": "Larsson", "given": "Olle", "initials": "O"}, {"family": "Larsson", "given": "Catharina", "initials": "C"}], "type": "journal article", "published": "2011-03-14", "journal": {"volume": "6", "issn": "1932-6203", "issue": "3", "pages": "e14757", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Picropodophyllin (PPP) is a promising novel anti-neoplastic agent that efficiently kills tumor cells in vitro and causes tumor regression and increased survival in vivo. We have previously reported that PPP treatment induced moderate tolerance in two out of 10 cell lines only, and here report the acquired genomic and expression alterations associated with PPP selection over 1.5 years of treatment.\n\nCopy number alterations monitored using metaphase and array-based comparative genomic hybridization analyses revealed largely overlapping alterations in parental and maximally tolerant cells. Gain/amplification of the MYC and PVT1 loci in 8q24.21 were verified on the chromosome level. Abnormalities observed in connection to PPP treatment included regular gains and losses, as well as homozygous losses in 10q24.1-q24.2 and 12p12.3-p13.2 in one of the lines and amplification at 5q11.2 in the other. Abnormalities observed in both tolerant derivatives include amplification/gain of 5q11.2, gain of 11q12.1-q14.3 and gain of 13q33.3-qter. Using Nexus software analysis we combined the array-CGH data with data from gene expression profilings and identified genes that were altered in both inputs. A subset of genes identified as downregulated (ALDH1A3, ANXA1, TLR4 and RAB5A) or upregulated (COX6A1, NFIX, ME1, MAPK and TAP2) were validated by siRNA in the tolerant or parental cells to alter sensitivity to PPP and confirmed to alter sensitivity to PPP in further cell lines.\n\nLong-term PPP selection lead to altered gene expression in PPP tolerant cells with increase as well as decrease of genes involved in cell death such as PTEN and BCL2. In addition, acquired genomic copy number alterations were observed that were often reflected by altered mRNA expression levels for genes in the same regions.", "doi": "10.1371/journal.pone.0014757", "pmid": "21423728", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pmc", "key": "PMC3056661"}], "notes": [], "created": "2017-05-04T15:03:32.540Z", "modified": "2017-05-30T14:52:18.133Z"}, {"entity": "publication", "iuid": "4a704b5db6174a42974b0988a638573d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4a704b5db6174a42974b0988a638573d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4a704b5db6174a42974b0988a638573d"}}, "title": "An assessment of CETP sequence variation in relation to cognitive decline and dementia risk.", "authors": [{"family": "Reynolds", "given": "Chandra A", "initials": "CA", "orcid": "0000-0001-6502-7173", "researcher": {"href": "https://publications.scilifelab.se/researcher/6b7cd2b82d81463c8dd3f13c4d75ab6f.json"}}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL", "orcid": "0000-0001-8057-3543", "researcher": {"href": "https://publications.scilifelab.se/researcher/cbee4e5f6d10460cac50f00ee92d5bdf.json"}}, {"family": "Prince", "given": "Jonathan A", "initials": "JA"}], "type": "journal article", "published": "2011-03-10", "journal": {"volume": "2", "issn": "1948-1756", "issue": "2", "pages": "122-129", "title": "Int J Mol Epidemiol Genet", "issn-l": "1948-1756"}, "abstract": "The gene encoding the cholesteryl ester transfer protein (CETP) plays an integral role in lipid metabolism. We evaluated common genetic variation spanning CETP for association with cognitive decline as well as incident and prevalent dementia and Alzheimer disease risk. Data from four population-based twin studies and a case-control sample were included, encompassing an analysis sample of 1513 dementia cases and 2137 controls with available CETP genotypes and covariates. Memory and perceptual speed performance was assessed over 16 years in up to 1540 participants. Only sporadic associations were observed across 26 markers and were largely consistent with statistical noise. Polymorphism in CETP is unlikely to contribute to cognitive change or dementia risk.", "doi": null, "pmid": "21686126", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pmc", "key": "PMC3110386"}], "notes": [], "created": "2017-05-04T15:00:45.785Z", "modified": "2025-11-17T09:37:12.519Z"}, {"entity": "publication", "iuid": "8f5f30934878425b800b2dbf5ce56342", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8f5f30934878425b800b2dbf5ce56342.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8f5f30934878425b800b2dbf5ce56342"}}, "title": "Decoding a substantial set of samples in parallel by massive sequencing.", "authors": [{"family": "Neiman", "given": "M\u00e5rten", "initials": "M"}, {"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Savolainen", "given": "Peter", "initials": "P"}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}], "type": "journal article", "published": "2011-03-09", "journal": {"volume": "6", "issn": "1932-6203", "issue": "3", "pages": "e17785", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "There has been a dramatic increase of throughput of sequenced bases in the last years but sequencing a multitude of samples in parallel has not yet developed equally. Here we present a novel strategy where the combination of two tags is used to link sequencing reads back to their origins from a pool of samples. By incorporating the tags in two steps sample-handling complexity is lowered by nearly 100 times compared to conventional indexing protocols. In addition, the method described here enables accurate identification and typing of thousands of samples in parallel. In this study the system was designed to test 4992 samples using only 122 tags. To prove the concept of the two-tagging method, the highly polymorphic 2(nd) exon of DLA-DRB1 in dogs and wolves was sequenced using the 454 GS FLX Titanium Chemistry. By requiring a minimum sequence depth of 20 reads per sample, 94% of the successfully amplified samples were genotyped. In addition, the method allowed digital detection of chimeric fragments. These results demonstrate that it is possible to sequence thousands of samples in parallel without complex pooling patterns or primer combinations. Furthermore, the method is highly scalable as only a limited number of additional tags leads to substantial increase of the sample size.", "doi": "10.1371/journal.pone.0017785", "pmid": "21408018", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC3052374"}], "notes": [], "created": "2017-05-04T14:57:26.493Z", "modified": "2020-01-21T13:56:03.696Z"}, {"entity": "publication", "iuid": "c3a4ef6ee1004e53936a995f425ee3da", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3a4ef6ee1004e53936a995f425ee3da.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3a4ef6ee1004e53936a995f425ee3da"}}, "title": "A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease.", "authors": [{"family": "Coronary Artery Disease (C4D) Genetics Consortium", "given": null, "initials": null}], "type": "journal article", "published": "2011-03-06", "journal": {"volume": "43", "issn": "1546-1718", "issue": "4", "pages": "339-344", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Genome-wide association studies have identified 11 common variants convincingly associated with coronary artery disease (CAD)\u00b9\u207b\u2077, a modest number considering the apparent heritability of CAD\u2078. All of these variants have been discovered in European populations. We report a meta-analysis of four large genome-wide association studies of CAD, with \u223c575,000 genotyped SNPs in a discovery dataset comprising 15,420 individuals with CAD (cases) (8,424 Europeans and 6,996 South Asians) and 15,062 controls. There was little evidence for ancestry-specific associations, supporting the use of combined analyses. Replication in an independent sample of 21,408 cases and 19,185 controls identified five loci newly associated with CAD (P < 5 \u00d7 10\u207b\u2078 in the combined discovery and replication analysis): LIPA on 10q23, PDGFD on 11q22, ADAMTS7-MORF4L1 on 15q25, a gene rich locus on 7q22 and KIAA1462 on 10p11. The CAD-associated SNP in the PDGFD locus showed tissue-specific cis expression quantitative trait locus effects. These findings implicate new pathways for CAD susceptibility.", "doi": "10.1038/ng.782", "pmid": "21378988", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.782"}], "notes": [], "created": "2017-05-04T15:00:48.966Z", "modified": "2020-01-21T13:56:05.086Z"}, {"entity": "publication", "iuid": "2759f61b2b44435d8c551e4ed8476e7b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2759f61b2b44435d8c551e4ed8476e7b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2759f61b2b44435d8c551e4ed8476e7b"}}, "title": "Antibody suspension bead arrays.", "authors": [{"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2011-03-04", "journal": {"volume": "723", "issn": "1940-6029", "issue": null, "pages": "29-36", "title": "Methods Mol. Biol.", "issn-l": "1064-3745"}, "abstract": "Alongside the increasing availability of affinity reagents, antibody microarrays have been developed to become a powerful tool to screen for target proteins in complex samples. Besides multiplexed sandwich immunoassays, the application of directly applying labeled sample onto arrays with immobilized capture reagents offers an approach to facilitate a systematic, high-throughput analysis of body fluids such as serum or plasma. An alternative to commonly used planar arrays has become available in form of a system based on color-coded beads for the creation of antibody arrays in suspension. The assay procedure offers an uncomplicated option to screen larger numbers of serum or plasma samples with variable sets of capture reagents. In addition, the established procedure of whole sample biotinylation circumvents the purification steps, which are generally required to remove excess labeling substance. We have shown that this assay system allows detecting proteins down into lower pico-molar and higher picogram per milliliter levels with dynamic ranges over three orders of magnitude. Presently, this workflow enables the profiling of 384 clinical samples for up to 100 proteins per assay.", "doi": "10.1007/978-1-61779-043-0_3", "pmid": "21370057", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-10-30T10:37:50.048Z", "modified": "2021-07-08T12:07:34.021Z"}, {"entity": "publication", "iuid": "6295ee8d911c4628865b4228aa2fcc16", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6295ee8d911c4628865b4228aa2fcc16.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6295ee8d911c4628865b4228aa2fcc16"}}, "title": "Bioinformatic tools for using whole genome sequencing as a rapid high resolution diagnostic typing tool when tracing bioterror organisms in the food and feed chain.", "authors": [{"family": "Segerman", "given": "Bo", "initials": "B"}, {"family": "De Medici", "given": "Dario", "initials": "D"}, {"family": "Ehling Schulz", "given": "Monika", "initials": "M"}, {"family": "Fach", "given": "Patrick", "initials": "P"}, {"family": "Fenicia", "given": "Lucia", "initials": "L"}, {"family": "Fricker", "given": "Martina", "initials": "M"}, {"family": "Wielinga", "given": "Peter", "initials": "P"}, {"family": "Van Rotterdam", "given": "Bart", "initials": "B"}, {"family": "Knutsson", "given": "Rickard", "initials": "R"}], "type": "journal article", "published": "2011-03-01", "journal": {"volume": "145 Suppl 1", "issn": "1879-3460", "issue": null, "pages": "S167-S176", "title": "Int. J. Food Microbiol.", "issn-l": "0168-1605"}, "abstract": "The rapid technological development in the field of parallel sequencing offers new opportunities when tracing and tracking microorganisms in the food and feed chain. If a bioterror organism is deliberately spread it is of crucial importance to get as much information as possible regarding the strain as fast as possible to aid the decision process and select suitable controls, tracing and tracking tools. A lot of efforts have been made to sequence multiple strains of potential bioterror organisms so there is a relatively large set of reference genomes available. This study is focused on how to use parallel sequencing for rapid phylogenomic analysis and screen for genetic modifications. A bioinformatic methodology has been developed to rapidly analyze sequence data with minimal post-processing. Instead of assembling the genome, defining genes, defining orthologous relations and calculating distances, the present method can achieve a similar high resolution directly from the raw sequence data. The method defines orthologous sequence reads instead of orthologous genes and the average similarity of the core genome (ASC) is calculated. The sequence reads from the core and from the non-conserved genomic regions can also be separated for further analysis. Finally, the comparison algorithm is used to visualize the phylogenomic diversity of the bacterial bioterror organisms Bacillus anthracis and Clostridium botulinum using heat plot diagrams.", "doi": "10.1016/j.ijfoodmicro.2010.06.027", "pmid": "20826036", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0168-1605(10)00369-7"}], "notes": [], "created": "2017-05-04T14:57:19.825Z", "modified": "2020-01-21T13:56:02.651Z"}, {"entity": "publication", "iuid": "44ff17fa893645fda398ce68c707b6d8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/44ff17fa893645fda398ce68c707b6d8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/44ff17fa893645fda398ce68c707b6d8"}}, "title": "Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins.", "authors": [{"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Stewart", "given": "James B", "initials": "JB"}, {"family": "Freyer", "given": "Christoph", "initials": "C"}, {"family": "Hagstr\u00f6m", "given": "Erik", "initials": "E"}, {"family": "Ingman", "given": "Max", "initials": "M"}, {"family": "Larsson", "given": "Nils-G\u00f6ran", "initials": "NG"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2011-03-00", "journal": {"volume": "7", "issn": "1553-7404", "issue": "3", "pages": "e1002028", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Somatic mutations of mtDNA are implicated in the aging process, but there is no universally accepted method for their accurate quantification. We have used ultra-deep sequencing to study genome-wide mtDNA mutation load in the liver of normally- and prematurely-aging mice. Mice that are homozygous for an allele expressing a proof-reading-deficient mtDNA polymerase (mtDNA mutator mice) have 10-times-higher point mutation loads than their wildtype siblings. In addition, the mtDNA mutator mice have increased levels of a truncated linear mtDNA molecule, resulting in decreased sequence coverage in the deleted region. In contrast, circular mtDNA molecules with large deletions occur at extremely low frequencies in mtDNA mutator mice and can therefore not drive the premature aging phenotype. Sequence analysis shows that the main proportion of the mutation load in heterozygous mtDNA mutator mice and their wildtype siblings is inherited from their heterozygous mothers consistent with germline transmission. We found no increase in levels of point mutations or deletions in wildtype C57Bl/6N mice with increasing age, thus questioning the causative role of these changes in aging. In addition, there was no increased frequency of transversion mutations with time in any of the studied genotypes, arguing against oxidative damage as a major cause of mtDNA mutations. Our results from studies of mice thus indicate that most somatic mtDNA mutations occur as replication errors during development and do not result from damage accumulation in adult life.", "doi": "10.1371/journal.pgen.1002028", "pmid": "21455489", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pmc", "key": "PMC3063763"}], "notes": [], "created": "2017-05-04T14:57:24.082Z", "modified": "2021-07-07T14:37:06.431Z"}, {"entity": "publication", "iuid": "afa95f4100dc4c0da07afa5c8d24a1b6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/afa95f4100dc4c0da07afa5c8d24a1b6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/afa95f4100dc4c0da07afa5c8d24a1b6"}}, "title": "Systematic antibody and antigen-based proteomic profiling with microarrays.", "authors": [{"family": "Ayoglu", "given": "Burcu", "initials": "B"}, {"family": "H\u00e4ggmark", "given": "Anna", "initials": "A"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "journal article", "published": "2011-03-00", "journal": {"volume": "11", "issn": "1744-8352", "issue": "2", "pages": "219-234", "title": "Expert Rev. Mol. Diagn.", "issn-l": "1473-7159"}, "abstract": "Current approaches within affinity-based proteomics are driven both by the accessibility and availability of antigens and capture reagents, and by suitable multiplexed technologies onto which these are implemented. By combining planar microarrays and other multiparallel systems with sets of reagents, possibilities to discover new and unpredicted protein-disease associations, either via directed hypothesis-driven or via undirected hypothesis-generating target selection, can be created. In the following stages, the discoveries made during these screening phases have to be verified for potential clinical relevance based on both technical and biological aspects. The use of affinity tools throughout discovery and verification has the potential to streamline the introduction of new markers, as transition into clinically required assay formats appears straightforward. In this article, we summarize some of the current building blocks within array- and affinity-based proteomic profiling with a focus on body fluids, by giving a perspective on how current and upcoming developments in this bioscience could enable a path of pursuit for biomarker discovery.", "doi": "10.1586/erm.10.110", "pmid": "21405972", "labels": {"Autoimmunity and Serology Profiling": "Technology development", "Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:29.977Z", "modified": "2021-07-08T13:44:33.525Z"}, {"entity": "publication", "iuid": "a3efa561874145b4b41e3df3ac114ab9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3efa561874145b4b41e3df3ac114ab9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3efa561874145b4b41e3df3ac114ab9"}}, "title": "Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.", "authors": [{"family": "Speliotes", "given": "Elizabeth K", "initials": "EK"}, {"family": "Yerges-Armstrong", "given": "Laura M", "initials": "LM"}, {"family": "Wu", "given": "Jun", "initials": "J"}, {"family": "Hernaez", "given": "Ruben", "initials": "R"}, {"family": "Kim", "given": "Lauren J", "initials": "LJ"}, {"family": "Palmer", "given": "Cameron D", "initials": "CD"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Garcia", "given": "Melissa E", "initials": "ME"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Nalls", "given": "Michael A", "initials": "MA"}, {"family": "Clark", "given": "Jeanne M", "initials": "JM"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Butler", "given": "Johannah L", "initials": "JL"}, {"family": "Tomas", "given": "Marta", "initials": "M"}, {"family": "Hoffmann", "given": "Udo", "initials": "U"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ"}, {"family": "Massaro", "given": "Joseph M", "initials": "JM"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Sahani", "given": "Dushyant V", "initials": "DV"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Schwartz", "given": "Stephen M", "initials": "SM"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "NASH CRN", "given": null, "initials": null}, {"family": "GIANT Consortium", "given": null, "initials": null}, {"family": "MAGIC Investigators", "given": null, "initials": null}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Carr", "given": "J Jeffrey", "initials": "JJ"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Kao", "given": "W H Linda", "initials": "WH"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "GOLD Consortium", "given": null, "initials": null}], "type": "journal article", "published": "2011-03-00", "journal": {"volume": "7", "issn": "1553-7404", "issue": "3", "pages": "e1001324", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Nonalcoholic fatty liver disease (NAFLD) clusters in families, but the only known common genetic variants influencing risk are near PNPLA3. We sought to identify additional genetic variants influencing NAFLD using genome-wide association (GWA) analysis of computed tomography (CT) measured hepatic steatosis, a non-invasive measure of NAFLD, in large population based samples. Using variance components methods, we show that CT hepatic steatosis is heritable (\u223c26%-27%) in family-based Amish, Family Heart, and Framingham Heart Studies (n\u200a=\u200a880 to 3,070). By carrying out a fixed-effects meta-analysis of genome-wide association (GWA) results between CT hepatic steatosis and \u223c2.4 million imputed or genotyped SNPs in 7,176 individuals from the Old Order Amish, Age, Gene/Environment Susceptibility-Reykjavik study (AGES), Family Heart, and Framingham Heart Studies, we identify variants associated at genome-wide significant levels (p<5\u00d710(-8)) in or near PNPLA3, NCAN, and PPP1R3B. We genotype these and 42 other top CT hepatic steatosis-associated SNPs in 592 subjects with biopsy-proven NAFLD from the NASH Clinical Research Network (NASH CRN). In comparisons with 1,405 healthy controls from the Myocardial Genetics Consortium (MIGen), we observe significant associations with histologic NAFLD at variants in or near NCAN, GCKR, LYPLAL1, and PNPLA3, but not PPP1R3B. Variants at these five loci exhibit distinct patterns of association with serum lipids, as well as glycemic and anthropometric traits. We identify common genetic variants influencing CT-assessed steatosis and risk of NAFLD. Hepatic steatosis associated variants are not uniformly associated with NASH/fibrosis or result in abnormalities in serum lipids or glycemic and anthropometric traits, suggesting genetic heterogeneity in the pathways influencing these traits.", "doi": "10.1371/journal.pgen.1001324", "pmid": "21423719", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pmc", "key": "PMC3053321"}], "notes": [], "created": "2017-05-04T15:00:50.188Z", "modified": "2020-01-21T13:56:04.220Z"}, {"entity": "publication", "iuid": "6aa7f8f98e21473694890d64d59fcfb4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6aa7f8f98e21473694890d64d59fcfb4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6aa7f8f98e21473694890d64d59fcfb4"}}, "title": "CUBN is a gene locus for albuminuria.", "authors": [{"family": "B\u00f6ger", "given": "Carsten A", "initials": "CA"}, {"family": "Chen", "given": "Ming-Huei", "initials": "MH"}, {"family": "Tin", "given": "Adrienne", "initials": "A"}, {"family": "Olden", "given": "Matthias", "initials": "M"}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A"}, {"family": "de Boer", "given": "Ian H", "initials": "IH"}, {"family": "Fuchsberger", "given": "Christian", "initials": "C"}, {"family": "O'Seaghdha", "given": "Conall M", "initials": "CM"}, {"family": "Pattaro", "given": "Cristian", "initials": "C"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Liu", "given": "Ching-Ti", "initials": "CT"}, {"family": "Glazer", "given": "Nicole L", "initials": "NL"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "O'Connell", "given": "Jeffrey R", "initials": "JR"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Peralta", "given": "Carmen A", "initials": "CA"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Hwang", "given": "Shih-Jen", "initials": "SJ"}, {"family": "Akylbekova", "given": "Ermeg", "initials": "E"}, {"family": "Kramer", "given": "Holly", "initials": "H"}, {"family": "van der Harst", "given": "Pim", "initials": "P"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Lohman", "given": "Kurt", "initials": "K"}, {"family": "de Andrade", "given": "Mariza", "initials": "M"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Kollerits", "given": "Barbara", "initials": "B"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Aspelund", "given": "Thor", "initials": "T"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Arking", "given": "Dan E", "initials": "DE"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Egan", "given": "Josephine", "initials": "J"}, {"family": "Hernandez", "given": "Dena", "initials": "D"}, {"family": "Reilly", "given": "Muredach", "initials": "M"}, {"family": "Townsend", "given": "Raymond R", "initials": "RR"}, {"family": "Lumley", "given": "Thomas", "initials": "T"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Kestenbaum", "given": "Bryan", "initials": "B"}, {"family": "Haritunians", "given": "Talin", "initials": "T"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Waeber", "given": "Gerard", "initials": "G"}, {"family": "Mooser", "given": "Vincent", "initials": "V"}, {"family": "Waterworth", "given": "Dawn", "initials": "D"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Lu", "given": "Xiaoning", "initials": "X"}, {"family": "Turner", "given": "Stephen T", "initials": "ST"}, {"family": "Atkinson", "given": "Elizabeth J", "initials": "EJ"}, {"family": "Leak", "given": "Tennille S", "initials": "TS"}, {"family": "Aasar\u00f8d", "given": "Knut", "initials": "K"}, {"family": "Skorpen", "given": "Frank", "initials": "F"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Baumert", "given": "Jens", "initials": "J"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Kr\u00e4mer", "given": "Bernhard K", "initials": "BK"}, {"family": "Devuyst", "given": "Olivier", "initials": "O"}, {"family": "Mychaleckyj", "given": "Josyf C", "initials": "JC"}, {"family": "Minelli", "given": "Cosetta", "initials": "C"}, {"family": "Bakker", "given": "Stephan J L", "initials": "SJ"}, {"family": "Kedenko", "given": "Lyudmyla", "initials": "L"}, {"family": "Paulweber", "given": "Bernhard", "initials": "B"}, {"family": "Coassin", "given": "Stefan", "initials": "S"}, {"family": "Endlich", "given": "Karlhans", "initials": "K"}, {"family": "Kroemer", "given": "Heyo K", "initials": "HK"}, {"family": "Biffar", "given": "Reiner", "initials": "R"}, {"family": "Stracke", "given": "Sylvia", "initials": "S"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Hastie", "given": "Nicholas D", "initials": "ND"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Kardia", "given": "Sharon L R", "initials": "SL"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Curhan", "given": "Gary", "initials": "G"}, {"family": "Kronenberg", "given": "Florian", "initials": "F"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Arnl\u00f6v", "given": "Johan", "initials": "J"}, {"family": "Hallan", "given": "Stein", "initials": "S"}, {"family": "Navis", "given": "Gerjan", "initials": "G"}, {"family": "CKDGen Consortium", "given": null, "initials": null}, {"family": "Parsa", "given": "Afshin", "initials": "A"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Coresh", "given": "Josef", "initials": "J"}, {"family": "Shlipak", "given": "Michael G", "initials": "MG"}, {"family": "Bull", "given": "Shelley B", "initials": "SB"}, {"family": "Paterson", "given": "Nicholas J", "initials": "NJ"}, {"family": "Wichmann", "given": "H-Erich", "initials": "HE"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Beckmann", "given": "Jacques S", "initials": "JS"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Rettig", "given": "Rainer", "initials": "R"}, {"family": "Dreisbach", "given": "Albert W", "initials": "AW"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Kao", "given": "W H L", "initials": "WH"}], "type": "journal article", "published": "2011-03-00", "journal": {"volume": "22", "issn": "1533-3450", "issue": "3", "pages": "555-570", "title": "J. Am. Soc. Nephrol.", "issn-l": "1046-6673"}, "abstract": "Identification of genetic risk factors for albuminuria may alter strategies for early prevention of CKD progression, particularly among patients with diabetes. Little is known about the influence of common genetic variants on albuminuria in both general and diabetic populations. We performed a meta-analysis of data from 63,153 individuals of European ancestry with genotype information from genome-wide association studies (CKDGen Consortium) and from a large candidate gene study (CARe Consortium) to identify susceptibility loci for the quantitative trait urinary albumin-to-creatinine ratio (UACR) and the clinical diagnosis microalbuminuria. We identified an association between a missense variant (I2984V) in the CUBN gene, which encodes cubilin, and both UACR (P = 1.1 \u00d7 10(-11)) and microalbuminuria (P = 0.001). We observed similar associations among 6981 African Americans in the CARe Consortium. The associations between this variant and both UACR and microalbuminuria were significant in individuals of European ancestry regardless of diabetes status. Finally, this variant associated with a 41% increased risk for the development of persistent microalbuminuria during 20 years of follow-up among 1304 participants with type 1 diabetes in the prospective DCCT/EDIC Study. In summary, we identified a missense CUBN variant that associates with levels of albuminuria in both the general population and in individuals with diabetes.", "doi": "10.1681/ASN.2010060598", "pmid": "21355061", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ASN.2010060598"}, {"db": "pmc", "key": "PMC3060449"}], "notes": [], "created": "2017-05-04T15:00:47.014Z", "modified": "2021-07-07T15:11:02.497Z"}, {"entity": "publication", "iuid": "360adb2100cc47fdb8d5f1cb573f8f70", "links": {"self": {"href": "https://publications.scilifelab.se/publication/360adb2100cc47fdb8d5f1cb573f8f70.json"}, "display": {"href": "https://publications.scilifelab.se/publication/360adb2100cc47fdb8d5f1cb573f8f70"}}, "title": "Association of EBF1, FAM167A(C8orf13)-BLK and TNFSF4 gene variants with primary Sj\u00f6gren's syndrome.", "authors": [{"family": "Nordmark", "given": "G", "initials": "G"}, {"family": "Kristjansdottir", "given": "G", "initials": "G"}, {"family": "Theander", "given": "E", "initials": "E"}, {"family": "Appel", "given": "S", "initials": "S"}, {"family": "Eriksson", "given": "P", "initials": "P"}, {"family": "Vasaitis", "given": "L", "initials": "L"}, {"family": "Kvarnstr\u00f6m", "given": "M", "initials": "M"}, {"family": "Delaleu", "given": "N", "initials": "N"}, {"family": "Lundmark", "given": "P", "initials": "P"}, {"family": "Lundmark", "given": "A", "initials": "A"}, {"family": "Sj\u00f6wall", "given": "C", "initials": "C"}, {"family": "Brun", "given": "J G", "initials": "JG"}, {"family": "Jonsson", "given": "M V", "initials": "MV"}, {"family": "Harboe", "given": "E", "initials": "E"}, {"family": "G\u00f8ransson", "given": "L G", "initials": "LG"}, {"family": "Johnsen", "given": "S J", "initials": "SJ"}, {"family": "S\u00f6derkvist", "given": "P", "initials": "P", "orcid": "0000-0001-9867-8706", "researcher": {"href": "https://publications.scilifelab.se/researcher/c1fc163b9a08421180f7f235af3897f4.json"}}, {"family": "Eloranta", "given": "M-L", "initials": "ML"}, {"family": "Alm", "given": "G", "initials": "G"}, {"family": "Baecklund", "given": "E", "initials": "E"}, {"family": "Wahren-Herlenius", "given": "M", "initials": "M"}, {"family": "Omdal", "given": "R", "initials": "R"}, {"family": "R\u00f6nnblom", "given": "L", "initials": "L"}, {"family": "Jonsson", "given": "R", "initials": "R"}, {"family": "Syv\u00e4nen", "given": "A-C", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2011-03-00", "journal": {"volume": "12", "issn": "1476-5470", "issue": "2", "pages": "100-109", "title": "Genes Immun.", "issn-l": "1466-4879"}, "abstract": "We performed a candidate gene association study in 540 patients with primary Sj\u00f6gren's Syndrome (SS) from Sweden (n=344) and Norway (n=196) and 532 controls (n=319 Swedish, n=213 Norwegian). A total of 1139 single-nucleotide polymorphisms (SNPs) in 84 genes were analyzed. In the meta-analysis of the Swedish and Norwegian cohorts, we found high signals for association between primary SS and SNPs in three gene loci, not previously associated with primary SS. These are the early B-cell factor 1 (EBF1) gene, P=9.9 \u00d7 10(-5), OR 1.68, the family with sequence similarity 167 member A-B-lymphoid tyrosine kinase (FAM167A-BLK) locus, P=4.7 \u00d7 10(-4), OR 1.37 and the tumor necrosis factor superfamily (TNFSF4=Ox40L) gene, P=7.4 \u00d7 10(-4), OR 1.34. We also confirmed the association between primary SS and the IRF5/TNPO3 locus and the STAT4 gene. We found no association between the SNPs in these five genes and the presence of anti-SSA/anti-SSB antibodies. EBF1, BLK and TNFSF4 are all involved in B-cell differentiation and activation, and we conclude that polymorphisms in several susceptibility genes in the immune system contribute to the pathogenesis of primary SS.", "doi": "10.1038/gene.2010.44", "pmid": "20861858", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "gene201044"}], "notes": [], "created": "2017-05-04T15:00:44.878Z", "modified": "2021-07-07T15:11:02.247Z"}, {"entity": "publication", "iuid": "9e240ec071d04bc6a6782376703f9f72", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e240ec071d04bc6a6782376703f9f72.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e240ec071d04bc6a6782376703f9f72"}}, "title": "A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs.", "authors": [{"family": "Olsson", "given": "Mia", "initials": "M"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Truv\u00e9", "given": "Katarina", "initials": "K"}, {"family": "Rosengren Pielberg", "given": "Gerli", "initials": "G"}, {"family": "Puppo", "given": "Francesca", "initials": "F"}, {"family": "Mauceli", "given": "Evan", "initials": "E"}, {"family": "Quilez", "given": "Javier", "initials": "J"}, {"family": "Tonomura", "given": "Noriko", "initials": "N"}, {"family": "Zanna", "given": "Giordana", "initials": "G"}, {"family": "Docampo", "given": "Maria Jos\u00e9", "initials": "MJ"}, {"family": "Bassols", "given": "Anna", "initials": "A"}, {"family": "Avery", "given": "Anne C", "initials": "AC"}, {"family": "Karlsson", "given": "Elinor K", "initials": "EK"}, {"family": "Thomas", "given": "Anne", "initials": "A"}, {"family": "Kastner", "given": "Daniel L", "initials": "DL"}, {"family": "Bongcam-Rudloff", "given": "Erik", "initials": "E"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Sanchez", "given": "Armand", "initials": "A"}, {"family": "Hedhammar", "given": "Ake", "initials": "A"}, {"family": "Remmers", "given": "Elaine F", "initials": "EF"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Ferrer", "given": "Lluis", "initials": "L"}, {"family": "Tintle", "given": "Linda", "initials": "L"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}], "type": "journal article", "published": "2011-03-00", "journal": {"volume": "7", "issn": "1553-7404", "issue": "3", "pages": "e1001332", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "Hereditary periodic fever syndromes are characterized by recurrent episodes of fever and inflammation with no known pathogenic or autoimmune cause. In humans, several genes have been implicated in this group of diseases, but the majority of cases remain unexplained. A similar periodic fever syndrome is relatively frequent in the Chinese Shar-Pei breed of dogs. In the western world, Shar-Pei have been strongly selected for a distinctive thick and heavily folded skin. In this study, a mutation affecting both these traits was identified. Using genome-wide SNP analysis of Shar-Pei and other breeds, the strongest signal of a breed-specific selective sweep was located on chromosome 13. The same region also harbored the strongest genome-wide association (GWA) signal for susceptibility to the periodic fever syndrome (p(raw)\u200a= 2.3 \u00d7 10\u207b\u2076, p(genome)\u200a= 0.01). Dense targeted resequencing revealed two partially overlapping duplications, 14.3 Kb and 16.1 Kb in size, unique to Shar-Pei and upstream of the Hyaluronic Acid Synthase 2 (HAS2) gene. HAS2 encodes the rate-limiting enzyme synthesizing hyaluronan (HA), a major component of the skin. HA is up-regulated and accumulates in the thickened skin of Shar-Pei. A high copy number of the 16.1 Kb duplication was associated with an increased expression of HAS2 as well as the periodic fever syndrome (p < 0.0001). When fragmented, HA can act as a trigger of the innate immune system and stimulate sterile fever and inflammation. The strong selection for the skin phenotype therefore appears to enrich for a pleiotropic mutation predisposing these dogs to a periodic fever syndrome. The identification of HA as a major risk factor for this canine disease raises the potential of this glycosaminoglycan as a risk factor for human periodic fevers and as an important driver of chronic inflammation.", "doi": "10.1371/journal.pgen.1001332", "pmid": "21437276", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pmc", "key": "PMC3060080"}], "notes": [], "created": "2017-05-04T14:57:24.688Z", "modified": "2021-06-16T10:19:26.594Z"}, {"entity": "publication", "iuid": "50da86899be74ae69cd43af9a226fbaa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/50da86899be74ae69cd43af9a226fbaa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/50da86899be74ae69cd43af9a226fbaa"}}, "title": "Expression of 5,8-LDS of Aspergillus fumigatus and its dioxygenase domain. A comparison with 7,8-LDS, 10-dioxygenase, and cyclooxygenase.", "authors": [{"family": "Hoffmann", "given": "Inga", "initials": "I"}, {"family": "Jerner\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Garscha", "given": "Ulrike", "initials": "U"}, {"family": "Oliw", "given": "Ernst H", "initials": "EH"}], "type": "comparative study", "published": "2011-02-15", "journal": {"volume": "506", "issn": "1096-0384", "issue": "2", "pages": "216-222", "title": "Arch. Biochem. Biophys.", "issn-l": "0003-9861"}, "abstract": "5,8-Linoleate diol synthase (5,8-LDS) of Aspergillus fumigatus was cloned, expressed, and compared with 7,8-LDS of the Take-all fungus. Replacements of Tyr and Cys in the conserved YRWH and FXXGPHXCLG sequences abolished 8R-dioxygenase (8-DOX) and hydroperoxide isomerase activities, respectively. The predicted \u03b1-helices of LDS were aligned with \u03b1-helices of cyclooxygenase-1 (COX-1) to identify the 8-DOX domains. N-terminal expression constructs of 5,8- and 7,8-LDS (674 of 1079, and 673 of 1165 residues), containing one additional \u03b1-helix compared to cyclooxygenase-1, yielded prominent 8R-DOX activities with apparently unchanged or slightly lower substrate affinities, respectively. Val-328 of 5,8-LDS did not influence the position of oxygenation in contrast to the homologous residues Val-349 of COX-1 and Leu-384 of 10R-dioxygenase. We conclude that ~675 amino acids are sufficient to support 8-DOX activity.", "doi": "10.1016/j.abb.2010.11.022", "pmid": "21130068", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0003-9861(10)00495-9"}], "notes": [], "created": "2017-05-04T15:01:54.437Z", "modified": "2020-01-21T13:56:02.280Z"}, {"entity": "publication", "iuid": "63edf630527848e0b6ac076a603afb2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63edf630527848e0b6ac076a603afb2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63edf630527848e0b6ac076a603afb2a"}}, "title": "Identification of epigenetically regulated genes that predict patient outcome in neuroblastoma.", "authors": [{"family": "Car\u00e9n", "given": "Helena", "initials": "H"}, {"family": "Djos", "given": "Anna", "initials": "A"}, {"family": "Nethander", "given": "Maria", "initials": "M"}, {"family": "Sj\u00f6berg", "given": "Rose-Marie", "initials": "RM", "orcid": "0000-0003-1363-5796", "researcher": {"href": "https://publications.scilifelab.se/researcher/d08326da26da422ab445a26563843e79.json"}}, {"family": "Kogner", "given": "Per", "initials": "P"}, {"family": "Enstr\u00f6m", "given": "Camilla", "initials": "C"}, {"family": "Nilsson", "given": "Staffan", "initials": "S"}, {"family": "Martinsson", "given": "Tommy", "initials": "T"}], "type": "journal article", "published": "2011-02-11", "journal": {"volume": "11", "issn": "1471-2407", "issue": null, "pages": "66", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "Epigenetic mechanisms such as DNA methylation and histone modifications are important regulators of gene expression and are frequently involved in silencing tumor suppressor genes.\n\nIn order to identify genes that are epigenetically regulated in neuroblastoma tumors, we treated four neuroblastoma cell lines with the demethylating agent 5-Aza-2'-deoxycytidine (5-Aza-dC) either separately or in conjunction with the histone deacetylase inhibitor trichostatin A (TSA). Expression was analyzed using whole-genome expression arrays to identify genes activated by the treatment. These data were then combined with data from genome-wide DNA methylation arrays to identify candidate genes silenced in neuroblastoma due to DNA methylation.\n\nWe present eight genes (KRT19, PRKCDBP, SCNN1A, POU2F2, TGFBI, COL1A2, DHRS3 and DUSP23) that are methylated in neuroblastoma, most of them not previously reported as such, some of which also distinguish between biological subsets of neuroblastoma tumors. Differential methylation was observed for the genes SCNN1A (p < 0.001), PRKCDBP (p < 0.001) and KRT19 (p < 0.01). Among these, the mRNA expression of KRT19 and PRKCDBP was significantly lower in patients that have died from the disease compared with patients with no evidence of disease (fold change -8.3, p = 0.01 for KRT19 and fold change -2.4, p = 0.04 for PRKCDBP).\n\nIn our study, a low methylation frequency of SCNN1A, PRKCDBP and KRT19 is significantly associated with favorable outcome in neuroblastoma. It is likely that analysis of specific DNA methylation will be one of several methods in future patient therapy stratification protocols for treatment of childhood neuroblastomas.", "doi": "10.1186/1471-2407-11-66", "pmid": "21314941", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1471-2407-11-66"}, {"db": "pmc", "key": "PMC3045360"}], "notes": [], "created": "2017-05-04T15:00:40.779Z", "modified": "2021-07-07T15:55:21.173Z"}, {"entity": "publication", "iuid": "b1de501af0ef45cdb57e2b3fe76e2f31", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1de501af0ef45cdb57e2b3fe76e2f31.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1de501af0ef45cdb57e2b3fe76e2f31"}}, "title": "Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery.", "authors": [{"family": "Kiialainen", "given": "Anna", "initials": "A"}, {"family": "Karlberg", "given": "Olof", "initials": "O"}, {"family": "Ahlford", "given": "Annika", "initials": "A"}, {"family": "Sigurdsson", "given": "Snaevar", "initials": "S"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}], "type": "journal article", "published": "2011-02-09", "journal": {"volume": "6", "issn": "1932-6203", "issue": "2", "pages": "e16486", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Targeted sequencing is a cost-efficient way to obtain answers to biological questions in many projects, but the choice of the enrichment method to use can be difficult. In this study we compared two hybridization methods for target enrichment for massively parallel sequencing and single nucleotide polymorphism (SNP) discovery, namely Nimblegen sequence capture arrays and the SureSelect liquid-based hybrid capture system. We prepared sequencing libraries from three HapMap samples using both methods, sequenced the libraries on the Illumina Genome Analyzer, mapped the sequencing reads back to the genome, and called variants in the sequences. 74-75% of the sequence reads originated from the targeted region in the SureSelect libraries and 41-67% in the Nimblegen libraries. We could sequence up to 99.9% and 99.5% of the regions targeted by capture probes from the SureSelect libraries and from the Nimblegen libraries, respectively. The Nimblegen probes covered 0.6 Mb more of the original 3.1 Mb target region than the SureSelect probes. In each sample, we called more SNPs and detected more novel SNPs from the libraries that were prepared using the Nimblegen method. Thus the Nimblegen method gave better results when judged by the number of SNPs called, but this came at the cost of more over-sampling.", "doi": "10.1371/journal.pone.0016486", "pmid": "21347407", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pmc", "key": "PMC3036585"}], "notes": [], "created": "2017-05-04T15:00:51.347Z", "modified": "2021-07-07T15:11:02.682Z"}, {"entity": "publication", "iuid": "c21e6e471d4f4261aa043808a081e4df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c21e6e471d4f4261aa043808a081e4df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c21e6e471d4f4261aa043808a081e4df"}}, "title": "Genetic association of sequence variants near AGER/NOTCH4 and dementia.", "authors": [{"family": "Bennet", "given": "Anna M", "initials": "AM"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Eriksson", "given": "Ulrika K", "initials": "UK"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Prince", "given": "Jonathan A", "initials": "JA"}], "type": "journal article", "published": "2011-02-08", "journal": {"volume": "24", "issn": "1875-8908", "issue": "3", "pages": "475-484", "title": "J. Alzheimers Dis.", "issn-l": "1387-2877"}, "abstract": "We performed a survey of sequence variation in a series of 20 genes involved in inflammation-related pathways for association with dementia risk in twin and unrelated case-control samples consisting in total of 1462 Swedish dementia casesand 1929 controls. For a total of 218 tested genetic markers, strong evidence was obtained implicating a region near AGER and NOTCH4 on chromosome 6p with replication across both samples and maximum combined significance at marker rs1800625 (OR = 1.37, 95% CI 1.19\u20131.56, p = 1.36\u00d710(\u20136)). Imputation of the associated genomic interval provided an improved signal atrs8365, near the 3UTR of AGER (p = 7.34\u00d710(\u20137)). The associated region extends 120 kb encompassing 11 candidate genes.While AGER encodes a key receptor for amyloid-\u03b2 protein, an analysis of network context based upon genes now confirmed to contribute to dementia risk (A\u03b2PP, PSEN1, PSEN2, CR1, CLU, PICALM, and APOE) suggested strong functional coupling to NOTCH4, with no significant coupling to the remaining candidates. The implicated region occurs in the broad HLA locus on chromosome 6p, but associated markers were not in strong LD with known variants that regulate HLA gene function, suggesting that this may represent a signal distinct from immune-system pathways.", "doi": "10.3233/JAD-2011-101848", "pmid": "21297263", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "JRM32751N8163TL3"}, {"db": "pmc", "key": "PMC3477600"}, {"db": "mid", "key": "NIHMS404211"}], "notes": [], "created": "2017-05-04T15:00:46.388Z", "modified": "2020-01-21T13:56:05.040Z"}, {"entity": "publication", "iuid": "516b7d86ac29495cb3a9c713a3be0ae8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/516b7d86ac29495cb3a9c713a3be0ae8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/516b7d86ac29495cb3a9c713a3be0ae8"}}, "title": "The Swedish new variant of Chlamydia trachomatis.", "authors": [{"family": "Unemo", "given": "Magnus", "initials": "M"}, {"family": "Clarke", "given": "Ian N", "initials": "IN"}], "type": "journal article", "published": "2011-02-00", "journal": {"volume": "24", "issn": "1473-6527", "issue": "1", "pages": "62-69", "title": "Curr. Opin. Infect. Dis.", "issn-l": "0951-7375"}, "abstract": "This review focuses on the anatomy of the Swedish new variant of Chlamydia trachomatis (nvCT). This information provides an interesting insight into the emergence of new strains (how, where, and when), and the important lessons learned are discussed.\n\nIn late 2006, the nvCT was first reported in Sweden; it carries a 377 bp deletion within its plasmid which covers the single targets originally used by Roche and Abbott diagnostic systems. The nvCT spread rapidly with thousands of falsely negative diagnoses. Genome sequencing and phenotypic characterization showed that the biological fitness of nvCT when compared with wild-type CT in vitro is unaltered. Therefore, the rapid transmission of nvCT was due to the selective advantage gained from failed diagnosis and the introduction of nvCT into a high-frequency transmitting population. The proportions of nvCT cases are now converging toward equilibrium with the wild-type CT strains. Interestingly, the nvCT remains rarely reported beyond the Nordic countries.\n\nThe spread of nvCT had a substantial impact on C. trachomatis identification, epidemiology, and public health in Sweden. Lessons learned from this experience include the importance of investigating the incidence and epidemiology of infection in detail, the frequent participation in appropriate quality assurance schemes, and the careful design of diagnostic assays. The nvCT presents a unique opportunity to study the spread of a single C. trachomatis strain within both the human and bacterial populations; this may substantially increase our knowledge of epidemiology and transmission of chlamydial infections, and other sexually transmitted infections.", "doi": "10.1097/QCO.0b013e32834204d5", "pmid": "21157332", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:18.280Z", "modified": "2020-01-21T13:56:02.293Z"}, {"entity": "publication", "iuid": "cc8b30d9114545e3824d54880a0cd264", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cc8b30d9114545e3824d54880a0cd264.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cc8b30d9114545e3824d54880a0cd264"}}, "title": "Sun-induced nonsynonymous p53 mutations are extensively accumulated and tolerated in normal appearing human skin.", "authors": [{"family": "St\u00e5hl", "given": "Patrik L", "initials": "PL"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Berglund", "given": "Lisa", "initials": "L"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "comparative study", "published": "2011-02-00", "journal": {"volume": "131", "issn": "1523-1747", "issue": "2", "pages": "504-508", "title": "J. Invest. Dermatol.", "issn-l": "0022-202X"}, "abstract": "Here we demonstrate that intermittently sun-exposed human skin contains an extensive number of phenotypically intact cell compartments bearing missense and nonsense mutations in the p53 tumor suppressor gene. Deep sequencing of sun-exposed and shielded microdissected skin from mid-life individuals revealed that persistent p53 mutations had accumulated in 14% of all epidermal cells, with no apparent signs of a growth advantage of the affected cell compartments. Furthermore, 6% of the mutated epidermal cells encoded a truncated protein. The abundance of these events, not taking into account intron mutations and mutations in other genes that also may have functional implications, suggests an extensive tolerance of human cells to severe genetic alterations caused by UV light, with an estimated annual rate of accumulation of \u223c35,000 new persistent protein-altering p53 mutations in sun-exposed skin of a human individual.", "doi": "10.1038/jid.2010.302", "pmid": "20944651", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0022-202X(15)35132-0"}], "notes": [], "created": "2017-05-04T14:57:21.029Z", "modified": "2021-07-08T13:26:08.355Z"}, {"entity": "publication", "iuid": "e196eff556fd47aa9db69794a88a5c31", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e196eff556fd47aa9db69794a88a5c31.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e196eff556fd47aa9db69794a88a5c31"}}, "title": "Reactive astrocytes and Wnt/\u03b2-catenin signaling link nigrostriatal injury to repair in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine model of Parkinson's disease.", "authors": [{"family": "L'Episcopo", "given": "F", "initials": "F"}, {"family": "Tirolo", "given": "C", "initials": "C"}, {"family": "Testa", "given": "N", "initials": "N"}, {"family": "Caniglia", "given": "S", "initials": "S"}, {"family": "Morale", "given": "M C", "initials": "MC"}, {"family": "Cossetti", "given": "C", "initials": "C"}, {"family": "D'Adamo", "given": "P", "initials": "P"}, {"family": "Zardini", "given": "E", "initials": "E"}, {"family": "Andreoni", "given": "L", "initials": "L"}, {"family": "Ihekwaba", "given": "A E C", "initials": "AE"}, {"family": "Serra", "given": "P A", "initials": "PA"}, {"family": "Franciotta", "given": "D", "initials": "D"}, {"family": "Martino", "given": "G", "initials": "G"}, {"family": "Pluchino", "given": "S", "initials": "S"}, {"family": "Marchetti", "given": "B", "initials": "B"}], "type": "journal article", "published": "2011-02-00", "journal": {"volume": "41", "issn": "1095-953X", "issue": "2", "pages": "508-527", "title": "Neurobiol. Dis.", "issn-l": "0969-9961"}, "abstract": "Emerging evidence points to reactive glia as a pivotal factor in Parkinson's disease (PD) and 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-lesioned mouse model of basal ganglia injury, but whether astrocytes and microglia activation may exacerbate dopaminergic (DAergic) neuron demise and/or contribute to DAergic repair is presently the subject of much debate. Here, we have correlated the loss and recovery of the nigrostriatal DAergic functionality upon acute MPTP exposure with extensive gene expression analysis at the level of the ventral midbrain (VM) and striata (Str) and found a major upregulation of pro-inflammatory chemokines and wingless-type MMTV integration site1 (Wnt1), a key transcript involved in midbrain DAergic neurodevelopment. Wnt signaling components (including Frizzled-1 [Fzd-1] and \u03b2-catenin) were dynamically regulated during MPTP-induced DAergic degeneration and reactive glial activation. Activated astrocytes of the ventral midbrain were identified as candidate source of Wnt1 by in situ hybridization and real-time PCR in vitro. Blocking Wnt/Fzd signaling with Dickkopf-1 (Dkk1) counteracted astrocyte-induced neuroprotection against MPP(+) toxicity in primary mesencephalic astrocyte-neuron cultures, in vitro. Moreover, astroglial-derived factors, including Wnt1, promoted neurogenesis and DAergic neurogenesis from adult midbrain stem/neuroprogenitor cells, in vitro. Conversely, lack of Wnt1 transcription in response to MPTP in middle-aged mice and failure of DAergic neurons to recover were reversed by pharmacological activation of Wnt/\u03b2-catenin signaling, in vivo, thus suggesting MPTP-reactive astrocytes in situ and Wnt1 as candidate components of neuroprotective/neurorescue pathways in MPTP-induced nigrostriatal DAergic plasticity.", "doi": "10.1016/j.nbd.2010.10.023", "pmid": "21056667", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "S0969-9961(10)00366-9"}, {"db": "pmc", "key": "PMC3558878"}, {"db": "mid", "key": "EMS51159"}], "notes": [], "created": "2017-05-04T15:03:10.673Z", "modified": "2017-05-30T12:40:16.423Z"}, {"entity": "publication", "iuid": "ef0fa515e7784205b0174e14717300cd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ef0fa515e7784205b0174e14717300cd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ef0fa515e7784205b0174e14717300cd"}}, "title": "High-resolution genomic screening in mantle cell lymphoma--specific changes correlate with genomic complexity, the proliferation signature and survival.", "authors": [{"family": "Halld\u00f3rsd\u00f3ttir", "given": "Anna M", "initials": "AM"}, {"family": "Sander", "given": "Birgitta", "initials": "B"}, {"family": "G\u00f6ransson", "given": "Hanna", "initials": "H"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Kimby", "given": "Eva", "initials": "E"}, {"family": "Mansouri", "given": "Mahmoud", "initials": "M"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}, {"family": "Ehrencrona", "given": "Hans", "initials": "H"}], "type": "comparative study", "published": "2011-02-00", "journal": {"volume": "50", "issn": "1098-2264", "issue": "2", "pages": "113-121", "title": "Genes Chromosomes Cancer", "issn-l": "1045-2257"}, "abstract": "Mantle cell lymphoma (MCL) is characterized by the t(11;14)(q13;q32) and numerous copy number aberrations (CNAs). Recently, gene expression profiling defined a proliferation gene expression signature in MCL where high scores predict shorter survival. We investigated 31 MCL cases using high-density single nucleotide polymorphism arrays and correlated CNA patterns with the proliferation signature and with clinical data. Many recurrent CNAs typical of MCL were detected, including losses at 1p (55%), 8p (29%), 9q (29%), 11q (55%), 13q (42%) and 17p (32%), and gains at 3q (39%), 8q (26%), 15q (23%) and 18q (23%). A novel deleted region at 20q (16%) contained only one candidate gene, ZFP64, a putative tumor suppressor. Unsupervised clustering identified subgroups with different patterns of CNAs, including a subset (19%) characterized by the presence of 11q loss in all cases and by the absence of 13q loss, and 3q and 7p gains. Losses at 1p, 8p, 13q and 17p were associated with increased genomic complexity. High proliferation signature scores correlated with increased number of large (>15 Mbp) CNAs (P = 0.03) as well as copy number gains at 7p (P = 0.02) and losses at 9q (P = 0.04). Furthermore, large/complex 13q losses were associated with improved survival (P < 0.05) as were losses/copy number neutral LOH at 19p13 (P = 0.01). In summary, this high-resolution genomic analysis identified novel aberrations and revealed that several CNAs correlated with genomic complexity, the proliferation status and survival.", "doi": "10.1002/gcc.20836", "pmid": "21117067", "labels": {"National Genomics Infrastructure": null, "Array and Analysis Facility": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:18.877Z", "modified": "2020-01-21T13:56:06.110Z"}, {"entity": "publication", "iuid": "ffda3b19c8eb4e6c84f82b2ef8d35ffb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ffda3b19c8eb4e6c84f82b2ef8d35ffb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ffda3b19c8eb4e6c84f82b2ef8d35ffb"}}, "title": "Genetic variation on chromosome 9p21 shows association with the ischaemic stroke subtype large-vessel disease in a Swedish sample aged \u2264 70.", "authors": [{"family": "Olsson", "given": "S", "initials": "S"}, {"family": "Jood", "given": "K", "initials": "K"}, {"family": "Blomstrand", "given": "C", "initials": "C"}, {"family": "Jern", "given": "C", "initials": "C"}], "type": "journal article", "published": "2011-02-00", "journal": {"volume": "18", "issn": "1468-1331", "issue": "2", "pages": "365-367", "title": "Eur. J. Neurol.", "issn-l": "1351-5101"}, "abstract": "The aim of this study was to investigate whether we could replicate a recent finding of an association between genetic variants on chromosome 9p21 and the ischaemic stroke (IS) subtype large-vessel disease (LVD).\n\nThe Sahlgrenska Academy Study on Ischemic Stroke comprises 844 patients with IS, who suffered IS before reaching the age of 70, and 668 healthy controls. IS subtype was defined according to the TOAST criteria, and 111 patients were categorized as LVD. Seven single-nucleotide polymorphisms (SNPs) on 9p21 were analyzed. Functional outcome was assessed 3 months after IS using the modified Rankin scale.\n\nThe SNP rs7857345 showed a significant association with the subtype LVD independent of traditional vascular risk factors. In addition, an association between rs7857345 and functional outcome after LVD was observed.\n\nIn this relatively young sample of patients with IS, genetic variation on 9p21 is associated with LVD.", "doi": "10.1111/j.1468-1331.2010.03096.x", "pmid": "20500804", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ENE3096"}], "notes": [], "created": "2017-05-04T15:00:43.345Z", "modified": "2020-01-21T13:56:06.549Z"}, {"entity": "publication", "iuid": "c756e9bf06874f469f0cd521ed6dca65", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c756e9bf06874f469f0cd521ed6dca65.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c756e9bf06874f469f0cd521ed6dca65"}}, "title": "GAD1 is a biomarker for benign and malignant prostatic tissue.", "authors": [{"family": "Jaraj", "given": "Sara Jonmarker", "initials": "SJ"}, {"family": "Augsten", "given": "Martin", "initials": "M"}, {"family": "H\u00e4ggarth", "given": "Lars", "initials": "L"}, {"family": "Wester", "given": "Kenneth", "initials": "K"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Ostman", "given": "Arne", "initials": "A"}, {"family": "Egevad", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2011-02-00", "journal": {"volume": "45", "issn": "1651-2065", "issue": "1", "pages": "39-45", "title": "Scand. J. Urol. Nephrol.", "issn-l": "0036-5599"}, "abstract": "Tissue-specific markers are useful for identification of tumour type in advanced cancers of unknown origin. This study investigated the expression of glutamate decarboxylase 1 (GAD1) in prostate and control tissue compared with the established prostate-specific markers prostate-specific antigen (PSA) and prostate-specific membrane antigen (PSMA).\n\nA tissue microarray was constructed of 36 prostate adenocarcinomas, eight benign prostate samples and benign and malignant control tissues from urinary bladder, lung and rectum. Immunohistochemistry for GAD1, PSA and PSMA was performed. The products of staining intensity and extent were analysed. The GAD1 antibody was validated by Western blot. Real-time polymerase chain reaction (RT-PCR) was performed on malignant and benign samples from each tissue type.\n\nGAD1 and PSA immunostains were significantly stronger in malignant and benign prostatic tissue than in controls. PSMA was stronger in prostate cancer than in urothelial and rectal cancer but had a lower specificity than GAD1 and PSA. GAD1 expression decreased with increasing Gleason score. RT-PCR confirmed the presence of mRNA for GAD1, PSA and PSMA in prostate samples.\n\nGAD1 is expressed in benign and malignant prostatic tissue and may serve as a highly prostate-specific tissue biomarker.", "doi": "10.3109/00365599.2010.521189", "pmid": "21091088", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:49.137Z", "modified": "2017-05-30T12:57:12.425Z"}, {"entity": "publication", "iuid": "1835f6705e4e47bba1905ab6a0871ae8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1835f6705e4e47bba1905ab6a0871ae8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1835f6705e4e47bba1905ab6a0871ae8"}}, "title": "Diagnostic biomarkers of prostate cancer.", "authors": [{"family": "H\u00e4ggarth", "given": "Lars", "initials": "L"}, {"family": "H\u00e4ggl\u00f6f", "given": "Christina", "initials": "C"}, {"family": "Jaraj", "given": "Sara Jonmarker", "initials": "SJ"}, {"family": "Wester", "given": "Kenneth", "initials": "K"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Ostman", "given": "Arne", "initials": "A"}, {"family": "Egevad", "given": "Lars", "initials": "L"}], "type": "comparative study", "published": "2011-02-00", "journal": {"volume": "45", "issn": "1651-2065", "issue": "1", "pages": "60-67", "title": "Scand. J. Urol. Nephrol.", "issn-l": "0036-5599"}, "abstract": "Diagnostic tissue biomarkers for prostate cancer (PC) include basal cell markers and \u03b1-methylacyl-coenzyme A-racemase (AMACR), often used in combination. Their sensitivity and specificity are not perfect and there is a need for additional diagnostic biomarkers for PC in cases that are difficult to diagnose on routine stained sections.\n\nThis study investigated the diagnostic accuracy of three novel tissue biomarkers for PC found through a search in the Human Protein Atlas database ( www.proteinatlas.com ): somatic cytochrome c (CYCS), intestinal cell kinase (ICK) and inhibitor of nuclear factor-\u03baB kinase subunit beta (IKBKB), and compared the results with AMACR. A tissue microarray was constructed from 40 consecutive radical prostatectomy (RP) specimens including benign prostatic tissue, atrophy, high-grade prostatic intraepithelial neoplasia (HGPIN) and PC. Immunoreactivity was scored based on staining intensity and extent. Real-time polymerase chain reaction (PCR) was performed on malignant and benign frozen tissue samples from 32 RP specimens.\n\nAll four biomarkers showed a stronger expression in PC and HGPIN than in benign tissue (p < 0.001). The highest diagnostic accuracy for PC was achieved with ICK and AMACR at 97%. The area under the curve for CYCS, ICK, IKBKB and AMACR was 0.859, 0.997, 0.865 and 0.983, respectively. The presence of mRNA transcripts of the genes was confirmed by real-time PCR in benign and malignant prostatic tissue.\n\nAMACR is an accurate diagnostic tissue marker for PC. However, in some PCs AMACR is false negative and a panel of CYCS, ICK and IKBKB may serve as ancillary diagnostic tool.", "doi": "10.3109/00365599.2010.526141", "pmid": "21034352", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:48.837Z", "modified": "2017-05-30T12:51:43.860Z"}, {"entity": "publication", "iuid": "d3b47082bad348deb853a4cbb821a2dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d3b47082bad348deb853a4cbb821a2dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d3b47082bad348deb853a4cbb821a2dc"}}, "title": "Common pathogenetic mechanism involving human chromosome 18 in familial and sporadic ileal carcinoid tumors.", "authors": [{"family": "Cunningham", "given": "Janet L", "initials": "JL"}, {"family": "D\u00edaz de St\u00e5hl", "given": "Teresita", "initials": "T"}, {"family": "Sj\u00f6blom", "given": "Tobias", "initials": "T"}, {"family": "Westin", "given": "Gunnar", "initials": "G"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}, {"family": "Janson", "given": "Eva T", "initials": "ET"}], "type": "journal article", "published": "2011-02-00", "journal": {"volume": "50", "issn": "1098-2264", "issue": "2", "pages": "82-94", "title": "Genes Chromosomes Cancer", "issn-l": "1045-2257"}, "abstract": "Serotonin producing endocrine carcinoma of small intestine (ileal carcinoid) is a clinically distinct endocrine tumor. It is generally considered as a sporadic disease and its molecular etiology is poorly understood. We report comprehensive clinical and molecular studies of 55 sporadic and familial patients diagnosed with this condition. Nine pedigrees encompassing 23 affected subjects were established, consistent with autosomal dominant mode of inheritance. Familial and sporadic patients demonstrated indistinguishable clinical pictures. Molecular analyses of 61 tumors from 45 individuals, including eight familial and 37 sporadic patients, aimed at determination of global copy number aberrations using BAC and Illumina SNP arrays and gene expression profiling by Affymetrix chips. Chromosome 18 aberrations were identified in both sporadic and in familial tumors; 100% vs. 38%, respectively. Other, less frequent aberrations were also common for both groups. Global expression profiles revealed no differentially expressed genes. Frequent gain of chromosome 7 was exclusively observed in metastases, when patient matched primary tumors and metastases were compared. Notably, the latter aberration correlated with solid growth pattern morphology (P < 0.01), a histopathological feature that has previously been related to worse prognosis. The clinical and molecular similarities identified between sporadic and familial cases suggest a common pathogenetic mechanism involved in tumor initiation. The familial variant of ileal carcinoid represents a previously unrecognized autosomal dominant inherited tumor disease, which we propose to call Familial Ileal Endocrine Carcinoma (FIEC). Our findings indicate the location of a FIEC tumor suppressor gene near the telomere of 18q, involved in development of inherited and sporadic tumors.", "doi": "10.1002/gcc.20834", "pmid": "21104784", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:44.277Z", "modified": "2020-01-21T13:56:05.408Z"}, {"entity": "publication", "iuid": "2554eb3b0bec43aebf752978fa30a3c1", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2554eb3b0bec43aebf752978fa30a3c1.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2554eb3b0bec43aebf752978fa30a3c1"}}, "title": "Tumor-specific HMG-CoA reductase expression in primary premenopausal breast cancer predicts response to tamoxifen.", "authors": [{"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Laursen", "given": "Henriette", "initials": "H"}, {"family": "O'Connor", "given": "Darran P", "initials": "DP"}, {"family": "Borgquist", "given": "Signe", "initials": "S"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Gallagher", "given": "William M", "initials": "WM"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Millikan", "given": "Robert C", "initials": "RC"}, {"family": "Ryd\u00e9n", "given": "Lisa", "initials": "L"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2011-01-31", "journal": {"volume": "13", "issn": "1465-542X", "issue": "1", "pages": "R12", "title": "Breast Cancer Res.", "issn-l": "1465-5411"}, "abstract": "We previously reported an association between tumor-specific 3-hydroxy-3-methylglutharyl-coenzyme A reductase (HMG-CoAR) expression and a good prognosis in breast cancer. Here, the predictive value of HMG-CoAR expression in relation to tamoxifen response was examined.\n\nHMG-CoAR protein and RNA expression was analyzed in a cell line model of tamoxifen resistance using western blotting and PCR. HMG-CoAR mRNA expression was examined in 155 tamoxifen-treated breast tumors obtained from a previously published gene expression study (Cohort I). HMG-CoAR protein expression was examined in 422 stage II premenopausal breast cancer patients, who had previously participated in a randomized control trial comparing 2 years of tamoxifen with no systemic adjuvant treatment (Cohort II). Kaplan-Meier analysis and Cox proportional hazards modeling were used to estimate the risk of recurrence-free survival (RFS) and the effect of HMG-CoAR expression on tamoxifen response.\n\nHMG-CoAR protein and RNA expression were decreased in tamoxifen-resistant MCF7-LCC9 cells compared with their tamoxifen-sensitive parental cell line. HMG-CoAR mRNA expression was decreased in tumors that recurred following tamoxifen treatment (P < 0.001) and was an independent predictor of RFS in Cohort I (hazard ratio = 0.63, P = 0.009). In Cohort II, adjuvant tamoxifen increased RFS in HMG-CoAR-positive tumors (P = 0.008). Multivariate Cox regression analysis demonstrated that HMG-CoAR was an independent predictor of improved RFS in Cohort II (hazard ratio = 0.67, P = 0.010), and subset analysis revealed that this was maintained in estrogen receptor (ER)-positive patients (hazard ratio = 0.65, P = 0.029). Multivariate interaction analysis demonstrated a difference in tamoxifen efficacy relative to HMG-CoAR expression (P = 0.05). Analysis of tamoxifen response revealed that patients with ER-positive/HMG-CoAR tumors had a significant response to tamoxifen (P = 0.010) as well as patients with ER-positive or HMG-CoAR-positive tumors (P = 0.035). Stratification according to ER and HMG-CoAR status demonstrated that ER-positive/HMG-CoAR-positive tumors had an improved RFS compared with ER-positive/HMG-CoAR-negative tumors in the treatment arm (P = 0.033); this effect was lost in the control arm (P = 0.138), however, suggesting that HMG-CoAR predicts tamoxifen response.\n\nHMG-CoAR expression is a predictor of response to tamoxifen in both ER-positive and ER-negative disease. Premenopausal patients with tumors that express ER or HMG-CoAR respond to adjuvant tamoxifen.", "doi": "10.1186/bcr2820", "pmid": "21281480", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "bcr2820"}, {"db": "pmc", "key": "PMC3109580"}], "notes": [], "created": "2017-05-04T14:55:45.527Z", "modified": "2021-07-08T13:44:33.095Z"}, {"entity": "publication", "iuid": "a858146d2f1f4fcf8b7a42b0fe4ab1dc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a858146d2f1f4fcf8b7a42b0fe4ab1dc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a858146d2f1f4fcf8b7a42b0fe4ab1dc"}}, "title": "HRG inhibits tumor growth and metastasis by inducing macrophage polarization and vessel normalization through downregulation of PlGF.", "authors": [{"family": "Rolny", "given": "Charlotte", "initials": "C"}, {"family": "Mazzone", "given": "Massimiliano", "initials": "M"}, {"family": "Tugues", "given": "S\u00f2nia", "initials": "S"}, {"family": "Laoui", "given": "Damya", "initials": "D"}, {"family": "Johansson", "given": "Irja", "initials": "I"}, {"family": "Coulon", "given": "Cathy", "initials": "C"}, {"family": "Squadrito", "given": "Mario Leonardo", "initials": "ML"}, {"family": "Segura", "given": "Inmaculada", "initials": "I"}, {"family": "Li", "given": "Xiujuan", "initials": "X"}, {"family": "Knevels", "given": "Ellen", "initials": "E"}, {"family": "Costa", "given": "Sandra", "initials": "S"}, {"family": "Vinckier", "given": "Stefan", "initials": "S"}, {"family": "Dresselaer", "given": "Tom", "initials": "T"}, {"family": "\u00c5kerud", "given": "Peter", "initials": "P"}, {"family": "De Mol", "given": "Maria", "initials": "M"}, {"family": "Salom\u00e4ki", "given": "Henriikka", "initials": "H"}, {"family": "Phillipson", "given": "Mia", "initials": "M"}, {"family": "Wyns", "given": "Sabine", "initials": "S"}, {"family": "Larsson", "given": "Erik", "initials": "E"}, {"family": "Buysschaert", "given": "Ian", "initials": "I"}, {"family": "Botling", "given": "Johan", "initials": "J"}, {"family": "Himmelreich", "given": "Uwe", "initials": "U"}, {"family": "Van Ginderachter", "given": "Jo A", "initials": "JA"}, {"family": "De Palma", "given": "Michele", "initials": "M"}, {"family": "Dewerchin", "given": "Mieke", "initials": "M"}, {"family": "Claesson-Welsh", "given": "Lena", "initials": "L"}, {"family": "Carmeliet", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2011-01-18", "journal": {"volume": "19", "issn": "1878-3686", "issue": "1", "pages": "31-44", "title": "Cancer Cell", "issn-l": "1535-6108"}, "abstract": "Polarization of tumor-associated macrophages (TAMs) to a proangiogenic/immune-suppressive (M2-like) phenotype and abnormal, hypoperfused vessels are hallmarks of malignancy, but their molecular basis and interrelationship remains enigmatic. We report that the host-produced histidine-rich glycoprotein (HRG) inhibits tumor growth and metastasis, while improving chemotherapy. By skewing TAM polarization away from the M2- to a tumor-inhibiting M1-like phenotype, HRG promotes antitumor immune responses and vessel normalization, effects known to decrease tumor growth and metastasis and to enhance chemotherapy. Skewing of TAM polarization by HRG relies substantially on downregulation of placental growth factor (PlGF). Besides unveiling an important role for TAM polarization in tumor vessel abnormalization, and its regulation by HRG/PlGF, these findings offer therapeutic opportunities for anticancer and antiangiogenic treatment.", "doi": "10.1016/j.ccr.2010.11.009", "pmid": "21215706", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "S1535-6108(10)00474-5"}], "notes": [], "created": "2017-05-04T14:55:46.430Z", "modified": "2017-05-30T12:56:02.593Z"}, {"entity": "publication", "iuid": "71e5d91b32b54cc9a55b920ee4f979c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/71e5d91b32b54cc9a55b920ee4f979c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/71e5d91b32b54cc9a55b920ee4f979c8"}}, "title": "Fine mapping and replication of QTL in outbred chicken advanced intercross lines.", "authors": [{"family": "Besnier", "given": "Francois", "initials": "F"}, {"family": "Wahlberg", "given": "Per", "initials": "P"}, {"family": "R\u00f6nneg\u00e5rd", "given": "Lars", "initials": "L"}, {"family": "Ek", "given": "Weronica", "initials": "W"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Siegel", "given": "Paul B", "initials": "PB"}, {"family": "Carlborg", "given": "Orjan", "initials": "O"}], "type": "journal article", "published": "2011-01-17", "journal": {"volume": "43", "issn": "1297-9686", "issue": "1", "pages": "3", "title": "Genet. Sel. Evol.", "issn-l": "0999-193X"}, "abstract": "Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F(2) populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F(2) animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature.\n\nWe have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F(2) population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight.\n\nFive of the nine QTL detected with the original F(2) population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL.\n\nOur results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.", "doi": "10.1186/1297-9686-43-3", "pmid": "21241486", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1297-9686-43-3"}, {"db": "pmc", "key": "PMC3034666"}], "notes": [], "created": "2017-05-04T15:00:45.182Z", "modified": "2020-01-21T13:56:02.993Z"}, {"entity": "publication", "iuid": "75f63960003d4fa5891b0ceb7f08a7fc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/75f63960003d4fa5891b0ceb7f08a7fc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/75f63960003d4fa5891b0ceb7f08a7fc"}}, "title": "New CYP1 genes in the frog Xenopus (Silurana) tropicalis: induction patterns and effects of AHR agonists during development.", "authors": [{"family": "J\u00f6nsson", "given": "Maria E", "initials": "ME"}, {"family": "Berg", "given": "Cecilia", "initials": "C"}, {"family": "Goldstone", "given": "Jared V", "initials": "JV"}, {"family": "Stegeman", "given": "John J", "initials": "JJ"}], "type": "comparative study", "published": "2011-01-15", "journal": {"volume": "250", "issn": "1096-0333", "issue": "2", "pages": "170-183", "title": "Toxicol. Appl. Pharmacol.", "issn-l": "0041-008X"}, "abstract": "The Xenopus tropicalis genome shows a single gene in each of the four cytochrome P450 1 (CYP1) subfamilies that occur in vertebrates, designated as CYP1A, CYP1B1, CYP1C1, and CYP1D1. We cloned the cDNAs of these genes and examined their expression in untreated tadpoles and in tadpoles exposed to waterborne aryl hydrocarbon receptor agonists, 3,3',4,4',5-pentachlorobiphenyl (PCB126), \u03b2-naphthoflavone (\u03b2NF), or indigo. We also examined the effects of PCB126 on expression of genes involved in stress response, cell proliferation, thyroid homeostasis, and prostaglandin synthesis. PCB126 induced CYP1A, CYP1B1, and CYP1C1 but had little effect on CYP1D1 (77-, 1.7-, 4.6- and 1.4-fold induction versus the control, respectively). \u03b2NF induced CYP1A and CYP1C1 (26- and 2.5-fold), while, under conditions used, indigo tended to induce only CYP1A (1.9-fold). The extent of CYP1 induction by PCB126 and \u03b2NF was positively correlated to the number of putative dioxin response elements 0-20 kb upstream of the start codons. No morphological effect was observed in tadpoles exposed to 1 nM-10 \u03bcM PCB126 at two days post-fertilization (dpf) and screened 20 days later. However, in 14-dpf tadpoles a slight up-regulation of the genes for PCNA, transthyretin, HSC70, Cu-Zn SOD, and Cox-2 was observed two days after exposure to 1 \u03bcM PCB126. This study of the full suite of CYP1 genes in an amphibian species reveals gene- and AHR agonist-specific differences in response, as well as a much lower sensitivity to CYP1 induction and short-term toxicity by PCB126 compared with in fish larvae. The single genes in each CYP1 subfamily may make X. tropicalis a useful model for mechanistic studies of CYP1 functions.", "doi": "10.1016/j.taap.2010.10.010", "pmid": "20965207", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0041-008X(10)00395-9"}, {"db": "pmc", "key": "PMC3014448"}, {"db": "mid", "key": "NIHMS247860"}], "notes": [], "created": "2017-05-04T15:02:03.475Z", "modified": "2020-01-21T13:56:03.084Z"}, {"entity": "publication", "iuid": "7f0890af177f4d7d92a156e717f31f13", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f0890af177f4d7d92a156e717f31f13.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f0890af177f4d7d92a156e717f31f13"}}, "title": "A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation.", "authors": [{"family": "Street", "given": "Nathaniel Robert", "initials": "NR"}, {"family": "Jansson", "given": "Stefan", "initials": "S"}, {"family": "Hvidsten", "given": "Torgeir R", "initials": "TR"}], "type": "journal article", "published": "2011-01-13", "journal": {"volume": "11", "issn": "1471-2229", "issue": null, "pages": "13", "title": "BMC Plant Biol.", "issn-l": "1471-2229"}, "abstract": "Green plant leaves have always fascinated biologists as hosts for photosynthesis and providers of basic energy to many food webs. Today, comprehensive databases of gene expression data enable us to apply increasingly more advanced computational methods for reverse-engineering the regulatory network of leaves, and to begin to understand the gene interactions underlying complex emergent properties related to stress-response and development. These new systems biology methods are now also being applied to organisms such as Populus, a woody perennial tree, in order to understand the specific characteristics of these species.\n\nWe present a systems biology model of the regulatory network of Populus leaves. The network is reverse-engineered from promoter information and expression profiles of leaf-specific genes measured over a large set of conditions related to stress and developmental. The network model incorporates interactions between regulators, such as synergistic and competitive relationships, by evaluating increasingly more complex regulatory mechanisms, and is therefore able to identify new regulators of leaf development not found by traditional genomics methods based on pair-wise expression similarity. The approach is shown to explain available gene function information and to provide robust prediction of expression levels in new data. We also use the predictive capability of the model to identify condition-specific regulation as well as conserved regulation between Populus and Arabidopsis.\n\nWe outline a computationally inferred model of the regulatory network of Populus leaves, and show how treating genes as interacting, rather than individual, entities identifies new regulators compared to traditional genomics analysis. Although systems biology models should be used with care considering the complexity of regulatory programs and the limitations of current genomics data, methods describing interactions can provide hypotheses about the underlying cause of emergent properties and are needed if we are to identify target genes other than those constituting the \"low hanging fruit\" of genomic analysis.", "doi": "10.1186/1471-2229-11-13", "pmid": "21232107", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1471-2229-11-13"}, {"db": "pmc", "key": "PMC3030533"}], "notes": [], "created": "2017-05-04T14:57:17.082Z", "modified": "2020-01-21T13:56:03.294Z"}, {"entity": "publication", "iuid": "573cf957fd0d4486a6cf314387222a31", "links": {"self": {"href": "https://publications.scilifelab.se/publication/573cf957fd0d4486a6cf314387222a31.json"}, "display": {"href": "https://publications.scilifelab.se/publication/573cf957fd0d4486a6cf314387222a31"}}, "title": "Vitamin D receptor genotypes, ultraviolet radiation exposure, and risk of non-Hodgkin lymphoma.", "authors": [{"family": "Smedby", "given": "Karin Ekstr\u00f6m", "initials": "KE"}, {"family": "Eloranta", "given": "Sandra", "initials": "S"}, {"family": "Duvefelt", "given": "Kristina", "initials": "K"}, {"family": "Melbye", "given": "Mads", "initials": "M"}, {"family": "Humphreys", "given": "Keith", "initials": "K"}, {"family": "Hjalgrim", "given": "Henrik", "initials": "H"}, {"family": "Chang", "given": "Ellen T", "initials": "ET"}], "type": "comparative study", "published": "2011-01-01", "journal": {"volume": "173", "issn": "1476-6256", "issue": "1", "pages": "48-54", "title": "Am. J. Epidemiol.", "issn-l": "0002-9262"}, "abstract": "Ultraviolet radiation (UVR) exposure may influence risk of non-Hodgkin lymphoma (NHL) through vitamin D, with antineoplastic effects mediated through the vitamin D receptor (VDR). To explore the role of vitamin D in NHL risk and the potential interaction with UVR, the authors genotyped 10 VDR polymorphisms in 2,448 NHL patients and 1,981 controls from Denmark and Sweden who were recruited in 1999-2002. Odds ratios and 95% confidence intervals were computed with logistic regression. P values were 2-sided. Most VDR variants (e.g., rs731236/TaqI, rs15444410/BsmI) were not associated with overall risk of NHL, but there was some evidence of a positive association between rs4760655 and follicular lymphoma risk (nominal P(trend) = 0.004, corrected P(trend) = 0.24). There was no support for an effect of interaction between VDR variants and UVR exposure on risk of overall NHL or B-cell lymphoma subtypes. However, there was some evidence that rs731236 altered associations between UVR and T-cell NHL risk; while increasing UVR frequency lowered T-cell NHL risk among rs731236 TT carriers, an elevated risk was observed among rs731236 CC carriers (nominal P(interaction) \u2264 0.008, corrected P(interaction) \u2265 0.12). VDR does not appear to harbor major determinants of NHL risk, except perhaps for follicular lymphoma. Possible heterogeneity in effects of UVR exposure on T-cell lymphoma risk by VDR rs731236 genotype merits further investigation.", "doi": "10.1093/aje/kwq340", "pmid": "21076051", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "kwq340"}], "notes": [], "created": "2017-05-04T15:03:29.237Z", "modified": "2017-05-30T12:44:00.304Z"}, {"entity": "publication", "iuid": "c078a6e6ac5a41028569854b10862c18", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c078a6e6ac5a41028569854b10862c18.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c078a6e6ac5a41028569854b10862c18"}}, "title": "Targeted resequencing of candidate genes using selector probes.", "authors": [{"family": "Johansson", "given": "H", "initials": "H"}, {"family": "Isaksson", "given": "M", "initials": "M"}, {"family": "S\u00f6rqvist", "given": "E Falk", "initials": "EF"}, {"family": "Roos", "given": "F", "initials": "F"}, {"family": "Stenberg", "given": "J", "initials": "J"}, {"family": "Sj\u00f6blom", "given": "T", "initials": "T"}, {"family": "Botling", "given": "J", "initials": "J"}, {"family": "Micke", "given": "P", "initials": "P"}, {"family": "Edlund", "given": "K", "initials": "K"}, {"family": "Fredriksson", "given": "S", "initials": "S"}, {"family": "Kultima", "given": "H G\u00f6ransson", "initials": "HG"}, {"family": "Ericsson", "given": "Olle", "initials": "O"}, {"family": "Nilsson", "given": "Mats", "initials": "M", "orcid": "0000-0001-9985-0387", "researcher": {"href": "https://publications.scilifelab.se/researcher/197cf8ba83ba430f9712b2f4d94dc3e5.json"}}], "type": "evaluation study", "published": "2011-01-00", "journal": {"volume": "39", "issn": "1362-4962", "issue": "2", "pages": "e8", "title": "Nucleic Acids Res.", "issn-l": "0305-1048"}, "abstract": "Targeted genome enrichment is a powerful tool for making use of the massive throughput of novel DNA-sequencing instruments. We herein present a simple and scalable protocol for multiplex amplification of target regions based on the Selector technique. The updated version exhibits improved coverage and compatibility with next-generation-sequencing (NGS) library-construction procedures for shotgun sequencing with NGS platforms. To demonstrate the performance of the technique, all 501 exons from 28 genes frequently involved in cancer were enriched for and sequenced in specimens derived from cell lines and tumor biopsies. DNA from both fresh frozen and formalin-fixed paraffin-embedded biopsies were analyzed and 94% specificity and 98% coverage of the targeted region was achieved. Reproducibility between replicates was high (R(2) = 0, 98) and readily enabled detection of copy-number variations. The procedure can be carried out in <24 h and does not require any dedicated instrumentation.", "doi": "10.1093/nar/gkq1005", "pmid": "21059679", "labels": {"National Genomics Infrastructure": null, "Array and Analysis Facility": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "gkq1005"}, {"db": "pmc", "key": "PMC3025563"}], "notes": [], "created": "2017-05-04T14:57:23.142Z", "modified": "2021-07-07T13:54:46.136Z"}, {"entity": "publication", "iuid": "cf3c5bf195f441879b931b11fa1f9d4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cf3c5bf195f441879b931b11fa1f9d4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cf3c5bf195f441879b931b11fa1f9d4a"}}, "title": "Structure and etiology of co-occurring internalizing and externalizing disorders in adolescents.", "authors": [{"family": "Cosgrove", "given": "Victoria E", "initials": "VE"}, {"family": "Rhee", "given": "Soo H", "initials": "SH"}, {"family": "Gelhorn", "given": "Heather L", "initials": "HL"}, {"family": "Boeldt", "given": "Debra", "initials": "D"}, {"family": "Corley", "given": "Robin C", "initials": "RC"}, {"family": "Ehringer", "given": "Marissa A", "initials": "MA"}, {"family": "Young", "given": "Susan E", "initials": "SE"}, {"family": "Hewitt", "given": "John K", "initials": "JK"}], "type": "journal article", "published": "2011-01-00", "journal": {"volume": "39", "issn": "1573-2835", "issue": "1", "pages": "109-123", "title": "J Abnorm Child Psychol", "issn-l": "0091-0627"}, "abstract": "Several studies suggest that a two-factor model positing internalizing and externalizing factors explains the interrelationships among psychiatric disorders. However, it is unclear whether the covariation between internalizing and externalizing disorders is due to common genetic or environmental influences. We examined whether a model positing two latent factors, internalizing and externalizing, explained the interrelationships among six psychiatric disorders (major depressive disorder, generalized anxiety disorder, separation anxiety disorder, attention-deficit/hyperactivity disorder, oppositional defiant disorder, and conduct disorder) in adolescents, and whether there are common genetic and environmental influences on internalizing and externalizing latent factors. Multivariate behavior genetic analyses of data from 1162 twin pairs and 426 siblings ascertained from the general population via the Colorado Center for Antisocial Drug Dependence (CADD) were conducted. We found support for a model positing two latent factors (internalizing and externalizing). These factors were moderately heritable and influenced by significant common genetic and nonshared environmental influences. These findings suggest that co-occurrence of internalizing and externalizing psychopathology in adolescents results from both genetic and environmental influences.", "doi": "10.1007/s10802-010-9444-8", "pmid": "20683651", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pmc", "key": "PMC3036783"}, {"db": "mid", "key": "NIHMS243833"}], "notes": [], "created": "2017-05-04T15:03:30.708Z", "modified": "2017-05-30T12:44:23.976Z"}, {"entity": "publication", "iuid": "e19f2db4827945808629a3442e82d077", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e19f2db4827945808629a3442e82d077.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e19f2db4827945808629a3442e82d077"}}, "title": "Meta-analysis of the association between variants in SORL1 and Alzheimer disease.", "authors": [{"family": "Reitz", "given": "Christiane", "initials": "C"}, {"family": "Cheng", "given": "Rong", "initials": "R"}, {"family": "Rogaeva", "given": "Ekaterina", "initials": "E"}, {"family": "Lee", "given": "Joseph H", "initials": "JH"}, {"family": "Tokuhiro", "given": "Shinya", "initials": "S"}, {"family": "Zou", "given": "Fanggeng", "initials": "F"}, {"family": "Bettens", "given": "Karolien", "initials": "K"}, {"family": "Sleegers", "given": "Kristel", "initials": "K"}, {"family": "Tan", "given": "Eng King", "initials": "EK"}, {"family": "Kimura", "given": "Ryo", "initials": "R"}, {"family": "Shibata", "given": "Nobuto", "initials": "N"}, {"family": "Arai", "given": "Heii", "initials": "H"}, {"family": "Kamboh", "given": "M Ilyas", "initials": "MI"}, {"family": "Prince", "given": "Jonathan A", "initials": "JA"}, {"family": "Maier", "given": "Wolfgang", "initials": "W"}, {"family": "Riemenschneider", "given": "Matthias", "initials": "M"}, {"family": "Owen", "given": "Michael", "initials": "M"}, {"family": "Harold", "given": "Denise", "initials": "D"}, {"family": "Hollingworth", "given": "Paul", "initials": "P"}, {"family": "Cellini", "given": "Elena", "initials": "E"}, {"family": "Sorbi", "given": "Sandro", "initials": "S"}, {"family": "Nacmias", "given": "Benedetta", "initials": "B"}, {"family": "Takeda", "given": "Masatoshi", "initials": "M"}, {"family": "Pericak-Vance", "given": "Margaret A", "initials": "MA"}, {"family": "Haines", "given": "Jonathan L", "initials": "JL"}, {"family": "Younkin", "given": "Steven", "initials": "S"}, {"family": "Williams", "given": "Julie", "initials": "J"}, {"family": "van Broeckhoven", "given": "Christine", "initials": "C"}, {"family": "Farrer", "given": "Lindsay A", "initials": "LA"}, {"family": "St George-Hyslop", "given": "Peter H", "initials": "PH"}, {"family": "Mayeux", "given": "Richard", "initials": "R"}, {"family": "Genetic and Environmental Risk in Alzheimer Disease 1 Consortium", "given": null, "initials": null}], "type": "comparative study", "published": "2011-01-00", "journal": {"volume": "68", "issn": "1538-3687", "issue": "1", "pages": "99-106", "title": "Arch. Neurol.", "issn-l": "0003-9942"}, "abstract": "To reexamine the association between the neuronal sortilin-related receptor gene (SORL1) and Alzheimer disease (AD).\n\nComprehensive and unbiased meta-analysis of all published and unpublished data from case-control studies for the SORL1 single-nucleotide polymorphisms (SNPs) that had been repeatedly assessed across studies.\n\nAcademic research institutions in the United States, the Netherlands, Canada, Belgium, the United Kingdom, Singapore, Japan, Sweden, Germany, France, and Italy.\n\nAll published white and Asian case-control data sets, which included a total of 12,464 cases and 17,929 controls.\n\nAlzheimer disease according to the Diagnostic and Statistical Manual of Mental Disorders (Fourth Edition) and the National Institute of Neurological and Communicative Disorders and Stroke and the Alzheimer's Disease and Related Disorders Association (now known as the Alzheimer's Association).\n\nIn the white data sets, several markers were associated with AD after correction for multiple testing, including previously reported SNPs 8, 9, and 10 (P < .001). In addition, the C-G-C haplotype at SNPs 8 through 10 was associated with AD risk (P < .001). In the combined Asian data sets, SNPs 19 and 23 through 25 were associated with AD risk (P < .001). The disease-associated alleles at SNPs 8, 9, and 10 (120,873,131-120,886,175 base pairs [bp]; C-G-C alleles), at SNP 19 (120,953,300 bp; G allele), and at SNPs 24 through 25 (120,988,611 bp; T and C alleles) were the same previously reported alleles. The SNPs 4 through 5, 8 through 10, 12, and 19 through 25 belong to distinct linkage disequilibrium blocks. The same alleles at SNPs 8 through 10 (C-G-C), 19 (G), and 24 and 25 (T and C) have also been associated with AD endophenotypes, including white matter hyperintensities and hippocampal atrophy on magnetic resonance imaging, cerebrospinal fluid measures of amyloid \u03b2-peptide 42, and full-length SORL1 expression in the human brain.\n\nThis comprehensive meta-analysis provides confirmatory evidence that multiple SORL1 variants in distinct linkage disequilibrium blocks are associated with AD.", "doi": "10.1001/archneurol.2010.346", "pmid": "21220680", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "68/1/99"}, {"db": "pmc", "key": "PMC3086666"}, {"db": "mid", "key": "NIHMS284155"}], "notes": [], "created": "2017-05-04T15:00:40.473Z", "modified": "2020-01-21T13:56:05.791Z"}, {"entity": "publication", "iuid": "16ac87c2a4b447b882f321708a5dc6e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/16ac87c2a4b447b882f321708a5dc6e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/16ac87c2a4b447b882f321708a5dc6e5"}}, "title": "Mechanisms of blast induced brain injuries, experimental studies in rats.", "authors": [{"family": "Risling", "given": "M", "initials": "M"}, {"family": "Plantman", "given": "S", "initials": "S"}, {"family": "Angeria", "given": "M", "initials": "M"}, {"family": "Rostami", "given": "E", "initials": "E"}, {"family": "Bellander", "given": "B-M", "initials": "BM"}, {"family": "Kirkegaard", "given": "M", "initials": "M"}, {"family": "Arborelius", "given": "U", "initials": "U"}, {"family": "Davidsson", "given": "J", "initials": "J"}], "type": "journal article", "published": "2011-01-00", "journal": {"volume": "54 Suppl 1", "issn": "1095-9572", "issue": null, "pages": "S89-S97", "title": "Neuroimage", "issn-l": "1053-8119"}, "abstract": "Traumatic brain injuries (TBI) potentially induced by blast waves from detonations result in significant diagnostic problems. It may be assumed that several mechanisms contribute to the injury. This study is an attempt to characterize the presumed components of the blast induced TBI. Our experimental models include a blast tube in which an anesthetized rat can be exposed to controlled detonations of explosives that result in a pressure wave with a magnitude between 130 and 260 kPa. In this model, the animal is fixed with a metal net to avoid head acceleration forces. The second model is a controlled penetration of a 2mm thick needle. In the third model the animal is subjected to a high-speed sagittal rotation angular acceleration. Immunohistochemical labeling for amyloid precursor protein revealed signs of diffuse axonal injury (DAI) in the penetration and rotation models. Signs of punctuate inflammation were observed after focal and rotation injury. Exposure in the blast tube did not induce DAI or detectable cell death, but functional changes. Affymetrix Gene arrays showed changes in the expression in a large number of gene families including cell death, inflammation and neurotransmitters in the hippocampus after both acceleration and penetration injuries. Exposure to the primary blast wave induced limited shifts in gene expression in the hippocampus. The most interesting findings were a downregulation of genes involved in neurogenesis and synaptic transmission. These experiments indicate that rotational acceleration may be a critical factor for DAI and other acute changes after blast TBI. The further exploration of the mechanisms of blast TBI will have to include a search for long-term effects.", "doi": "10.1016/j.neuroimage.2010.05.031", "pmid": "20493951", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "S1053-8119(10)00763-9"}], "notes": [], "created": "2017-05-04T15:03:08.730Z", "modified": "2017-05-30T12:39:53.130Z"}]}