{"entity": "publications", "timestamp": "2026-08-15T13:47:07.306Z", "year": "2010", "links": {"self": {"href": "https://publications.scilifelab.se/publications/2010.json"}, "display": {"href": "https://publications.scilifelab.se/publications/2010"}}, "publications_count": 139, "full": true, "publications": [{"entity": "publication", "iuid": "eb8fba97ca2b4824869e0e74714644a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/eb8fba97ca2b4824869e0e74714644a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/eb8fba97ca2b4824869e0e74714644a4"}}, "title": "Tryptophan hydroxylase gene 1 (TPH1) variants associated with cerebrospinal fluid 5-hydroxyindole acetic acid and homovanillic acid concentrations in healthy volunteers.", "authors": [{"family": "Andreou", "given": "Dimitrios", "initials": "D"}, {"family": "Saetre", "given": "Peter", "initials": "P"}, {"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": "2010-12-30", "journal": {"volume": "180", "issn": "1872-7123", "issue": "2-3", "pages": "63-67", "title": "Psychiatry Res", "issn-l": "0165-1781"}, "abstract": "Tryptophan hydroxylase (TPH) is the rate-limiting enzyme in serotonin synthesis. We investigated possible relationships between five TPH1 gene polymorphisms and cerebrospinal fluid (CSF) concentrations of the major serotonin metabolite 5-hydroxyindoleacetic acid (5-HIAA), the major dopamine metabolite homovanillic acid (HVA), and the major norepinephrine metabolite 3-methoxy-4-hydroxyphenylglycol (MHPG) in healthy volunteers (n=132). The G-allele of the TPH1 rs4537731 (A-6526G) polymorphism was associated with 5-HIAA and HVA, but not MHPG concentrations. None of the other four TPH1 polymorphisms (rs211105, rs1800532, rs1799913 and rs7933505) were significantly associated with any of the monoamine metabolite concentrations. Two (rs4537731G/rs211105T/rs1800532C/rs1799913C/rs7933505G and rs4537731A/rs211105T/rs1800532C/rs1799913C/rs7933505G) of five common TPH1 five-allele haplotypes were associated with 5-HIAA and HVA concentrations in opposite directions. None of the common haplotypes was associated with MHPG concentrations in the CSF. The results suggest that TPH1 gene variation participates in the regulation of serotonin and dopamine turnover rates in the central nervous system of healthy human subjects.", "doi": "10.1016/j.psychres.2009.11.018", "pmid": "20580984", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0165-1781(09)00434-X"}], "notes": [], "created": "2017-05-04T15:00:38.921Z", "modified": "2020-01-21T13:56:10.953Z"}, {"entity": "publication", "iuid": "8976e73062c743639011aea31322f5c4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8976e73062c743639011aea31322f5c4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8976e73062c743639011aea31322f5c4"}}, "title": "Defining the transcriptome and proteome in three functionally different human cell lines.", "authors": [{"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Matic", "given": "Ivan", "initials": "I"}, {"family": "Geiger", "given": "Tamar", "initials": "T"}, {"family": "Cox", "given": "Juergen", "initials": "J"}, {"family": "Algen\u00e4s", "given": "Cajsa", "initials": "C"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Mann", "given": "Matthias", "initials": "M"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal article", "published": "2010-12-21", "journal": {"title": "Mol. Syst. Biol.", "issn": "1744-4292", "issn-l": "1744-4292", "volume": "6", "issue": null, "pages": "450"}, "abstract": "An essential question in human biology is how cells and tissues differ in gene and protein expression and how these differences delineate specific biological function. Here, we have performed a global analysis of both mRNA and protein levels based on sequence-based transcriptome analysis (RNA-seq), SILAC-based mass spectrometry analysis and antibody-based confocal microscopy. The study was performed in three functionally different human cell lines and based on the global analysis, we estimated the fractions of mRNA and protein that are cell specific or expressed at similar/different levels in the cell lines. A highly ubiquitous RNA expression was found with >60% of the gene products detected in all cells. The changes of mRNA and protein levels in the cell lines using SILAC and RNA ratios show high correlations, even though the genome-wide dynamic range is substantially higher for the proteins as compared with the transcripts. Large general differences in abundance for proteins from various functional classes are observed and, in general, the cell-type specific proteins are low abundant and highly enriched for cell-surface proteins. Thus, this study shows a path to characterize the transcriptome and proteome in human cells from different origins.", "doi": "10.1038/msb.2010.106", "pmid": "21179022", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "msb2010106"}, {"db": "pmc", "key": "PMC3018165"}, {"db": "BioProject", "description": "Deep sequencing of the transcriptome of three human cell lines for the Human Protein Atlas", "key": "PRJNA79633"}, {"db": "SRA", "description": "Deep sequencing of the transcriptome of three human cell lines for the Human Protein Atlas (short read raw data)", "key": "SRP002338"}], "notes": [], "created": "2017-05-04T14:55:07.459Z", "modified": "2023-04-27T09:48:59.529Z"}, {"entity": "publication", "iuid": "13d3b764ad5e4bf282c6a1e3b541162d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/13d3b764ad5e4bf282c6a1e3b541162d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/13d3b764ad5e4bf282c6a1e3b541162d"}}, "title": "Unbalanced translocation 9;16 in two children with dysmorphic features, and severe developmental delay: Evidence of cross-over within derivative chromosome 9 in patient #1.", "authors": [{"family": "Zambrano", "given": "Regina M", "initials": "RM"}, {"family": "Wohler", "given": "Elizabeth", "initials": "E"}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Thuresson", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Cutting", "given": "Garry R", "initials": "GR"}, {"family": "Batista", "given": "Denise A", "initials": "DA"}], "type": "case reports", "published": "2010-12-07", "journal": {"volume": "54", "issn": "1878-0849", "issue": "2", "pages": "189-193", "title": "Eur J Med Genet", "issn-l": "1769-7212"}, "abstract": "We describe 2 children with dysmorphic features, and severe developmental delay presenting with overlapping unbalanced translocations of 9q34.3 and 16p13. Patient #1: A 4 year old African-American female with normal karyotype with a pericentric inversion on one chromosome 9 known to be a benign variant. Low resolution array CGH revealed a single BAC clone loss at 9q34.3 and a single BAC clone gain at 16p13.3, confirmed by FISH. Whole genome SNP array analysis refined these findings, identifying a terminal 1.28 Mb deletion (138,879,862-140,164,310) of 9q34.3 and a terminal 1.62 Mb duplication (45,320-1,621,753) of 16p13.3. Sub-telomeric FISH showed an unbalanced cryptic translocation involving the inverted chromosome 9 and chromosome 16. FISH of the father showed a balanced t(9;16)(q34.3;p13.3) involving the non-inverted chromosome 9, and a pericentric inversion on the normal 9 homologous chromosome. The presence of two rearrangements on chromosome 9, both an unbalanced translocation and a pericentric inversion, indicates recombination between the inverted and derivative 9 homologues from her father. Patient #2: A 1 year old Iraqi-Moroccan female with normal karyotype. Array-CGH identified a 0.56 Mb deletion of 9q34.3 (139,586,637-140,147,760) and an 11.31 Mb duplication of 16p13.3p13.13 (31,010-11,313,519). Maternal FISH showed a balanced t(9;16)(q34.3;p13.13). Both patients present with similar clinical phenotype.", "doi": "10.1016/j.ejmg.2010.11.008", "pmid": "21144914", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S1769-7212(10)00140-0"}], "notes": [], "created": "2017-05-04T15:01:57.557Z", "modified": "2020-01-21T13:56:00.839Z"}, {"entity": "publication", "iuid": "bbc4aa27752846dea221f0b103fdcdbf", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bbc4aa27752846dea221f0b103fdcdbf.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bbc4aa27752846dea221f0b103fdcdbf"}}, "title": "Analysis of transcript and protein overlap in a human osteosarcoma cell line.", "authors": [{"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Uhl\u00e9n", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.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": "2010-12-02", "journal": {"volume": "11", "issn": "1471-2164", "issue": null, "pages": "684", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "An interesting field of research in genomics and proteomics is to compare the overlap between the transcriptome and the proteome. Recently, the tools to analyse gene and protein expression on a whole-genome scale have been improved, including the availability of the new generation sequencing instruments and high-throughput antibody-based methods to analyze the presence and localization of proteins. In this study, we used massive transcriptome sequencing (RNA-seq) to investigate the transcriptome of a human osteosarcoma cell line and compared the expression levels with in situ protein data obtained in-situ from antibody-based immunohistochemistry (IHC) and immunofluorescence microscopy (IF).\r\n\r\nA large-scale analysis based on 2749 genes was performed, corresponding to approximately 13% of the protein coding genes in the human genome. We found the presence of both RNA and proteins to a large fraction of the analyzed genes with 60% of the analyzed human genes detected by all three methods. Only 34 genes (1.2%) were not detected on the transcriptional or protein level with any method. Our data suggest that the majority of the human genes are expressed at detectable transcript or protein levels in this cell line. Since the reliability of antibodies depends on possible cross-reactivity, we compared the RNA and protein data using antibodies with different reliability scores based on various criteria, including Western blot analysis. Gene products detected in all three platforms generally have good antibody validation scores, while those detected only by antibodies, but not by RNA sequencing, generally consist of more low-scoring antibodies.\r\n\r\nThis suggests that some antibodies are staining the cells in an unspecific manner, and that assessment of transcript presence by RNA-seq can provide guidance for validation of the corresponding antibodies.", "doi": "10.1186/1471-2164-11-684", "pmid": "21126332", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null, "Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-684"}, {"db": "pmc", "key": "PMC3014981"}, {"db": "BioProject", "description": "RNA-seq of human osteosarcoma cell line U2-OS", "key": "PRJNA79747"}, {"db": "SRA", "description": "RNA-seq of human osteosarcoma cell line U2-OS", "key": "SRP003405"}], "notes": [], "created": "2017-05-04T14:55:06.554Z", "modified": "2021-07-08T13:44:33.569Z"}, {"entity": "publication", "iuid": "d9d7334b5ed84f6997779557091c6c34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d9d7334b5ed84f6997779557091c6c34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d9d7334b5ed84f6997779557091c6c34"}}, "title": "Associations of gene sequence variation and serum levels of C-reactive protein and interleukin-6 with Alzheimer's disease and dementia.", "authors": [{"family": "Eriksson", "given": "Ulrika K", "initials": "UK"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Prince", "given": "Jonathan A", "initials": "JA"}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Dickman", "given": "Paul W", "initials": "PW"}, {"family": "Bennet", "given": "Anna M", "initials": "AM"}], "type": "journal article", "published": "2010-12-01", "journal": {"volume": "23", "issn": "1875-8908", "issue": "2", "pages": "361-369", "title": "J. Alzheimers Dis.", "issn-l": "1387-2877"}, "abstract": "Inflammatory mechanisms have been implicated in Alzheimer's disease (AD) and dementia. We therefore sought to study DNA sequence variation and serum levels of the potent inflammatory mediators Interleukin-6 (IL6) and C-reactive protein (CRP) in relation to AD and dementia. Tagging single nucleotide polymorphisms (tagSNPs) were chosen to capture most variation in and around CRP and IL6 in 3937 elderly Swedish men and women (1,265 AD cases). A sub-set of the population (n = 723) with serum measurements of CRP and IL6 was included in 1) a nested case-control study of incident dementia cases, and 2) a case-control study of prevalent dementia cases. None of the SNPs or haplotypes was significantly associated with AD or dementia after correcting for multiple testing nor were elevated baseline levels of hsCRP or IL6 (measured on average 4.3 years before dementia onset) significantly associated with risk of future AD or dementia. However, prevalent AD cases had higher levels of IL6 (measured on average 5.5 years after dementia onset) than age- and gender-matched controls, OR 2.24 (95% CI 1.27-3.95), p-value 0.006. In summary, this data suggests that AD patients have an altered immune profile with higher circulating levels of IL6 than age- and gender-matched controls. However, neither variation in the CRP and IL6 genes nor circulating levels of their respective protein products were associated with an increased risk of developing late-life dementias.", "doi": "10.3233/JAD-2010-101671", "pmid": "21116047", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "Q44555P141331367"}, {"db": "pmc", "key": "PMC3237048"}, {"db": "mid", "key": "NIHMS342086"}], "notes": [], "created": "2017-05-04T15:00:46.691Z", "modified": "2020-01-21T13:56:05.598Z"}, {"entity": "publication", "iuid": "fb446ca4d0534cbfab21de4404938c49", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb446ca4d0534cbfab21de4404938c49.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb446ca4d0534cbfab21de4404938c49"}}, "title": "Towards a knowledge-based Human Protein Atlas.", "authors": [{"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Fagerberg", "given": "Linn", "initials": "L"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Jonasson", "given": "Kalle", "initials": "K"}, {"family": "Forsberg", "given": "Mattias", "initials": "M"}, {"family": "Zwahlen", "given": "Martin", "initials": "M"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Wester", "given": "Kenneth", "initials": "K"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Wernerus", "given": "Henrik", "initials": "H"}, {"family": "Bj\u00f6rling", "given": "Lisa", "initials": "L"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}], "type": "letter", "published": "2010-12-00", "journal": {"title": "Nat. Biotechnol.", "issn": "1546-1696", "issn-l": "1087-0156", "volume": "28", "issue": "12", "pages": "1248-1250"}, "abstract": null, "doi": "10.1038/nbt1210-1248", "pmid": "21139605", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "nbt1210-1248"}], "notes": [], "created": "2017-05-04T14:55:07.757Z", "modified": "2021-07-08T13:44:33.767Z"}, {"entity": "publication", "iuid": "e338b78c45024a2896fdcaa1073fc3ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e338b78c45024a2896fdcaa1073fc3ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e338b78c45024a2896fdcaa1073fc3ee"}}, "title": "Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.", "authors": [{"family": "Elks", "given": "Cathy E", "initials": "CE"}, {"family": "Perry", "given": "John R B", "initials": "JR"}, {"family": "Sulem", "given": "Patrick", "initials": "P"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Franceschini", "given": "Nora", "initials": "N"}, {"family": "He", "given": "Chunyan", "initials": "C"}, {"family": "Lunetta", "given": "Kathryn L", "initials": "KL"}, {"family": "Visser", "given": "Jenny A", "initials": "JA"}, {"family": "Byrne", "given": "Enda M", "initials": "EM"}, {"family": "Cousminer", "given": "Diana L", "initials": "DL"}, {"family": "Gudbjartsson", "given": "Daniel F", "initials": "DF"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Feenstra", "given": "Bjarke", "initials": "B"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Koller", "given": "Daniel L", "initials": "DL"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Lin", "given": "Peng", "initials": "P"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Marongiu", "given": "Mara", "initials": "M"}, {"family": "McArdle", "given": "Patrick F", "initials": "PF"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Stolk", "given": "Lisette", "initials": "L"}, {"family": "van Wingerden", "given": "Sophie H", "initials": "SH"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Albrecht", "given": "Eva", "initials": "E"}, {"family": "Corre", "given": "Tanguy", "initials": "T"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Smith", "given": "Erin N", "initials": "EN"}, {"family": "Ulivi", "given": "Shelia", "initials": "S"}, {"family": "Warrington", "given": "Nicole M", "initials": "NM"}, {"family": "Zgaga", "given": "Lina", "initials": "L"}, {"family": "Alavere", "given": "Helen", "initials": "H"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Aspelund", "given": "Thor", "initials": "T"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Berenson", "given": "Gerald S", "initials": "GS"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Blackburn", "given": "Hannah", "initials": "H"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Buring", "given": "Julie E", "initials": "JE"}, {"family": "Busonero", "given": "Fabio", "initials": "F"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Chanock", "given": "Stephen J", "initials": "SJ"}, {"family": "Chen", "given": "Wei", "initials": "W"}, {"family": "Cornelis", "given": "Marilyn C", "initials": "MC"}, {"family": "Couper", "given": "David", "initials": "D"}, {"family": "Coviello", "given": "Andrea D", "initials": "AD"}, {"family": "d'Adamo", "given": "Pio", "initials": "P"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJ"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "D\u00f6ring", "given": "Angela", "initials": "A"}, {"family": "Smith", "given": "George Davey", "initials": "GD"}, {"family": "Easton", "given": "Douglas F", "initials": "DF"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Emilsson", "given": "Valur", "initials": "V"}, {"family": "Eriksson", "given": "Johan", "initials": "J"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Folsom", "given": "Aaron R", "initials": "AR"}, {"family": "Foroud", "given": "Tatiana", "initials": "T"}, {"family": "Garcia", "given": "Melissa", "initials": "M"}, {"family": "Gasparini", "given": "Paolo", "initials": "P"}, {"family": "Geller", "given": "Frank", "initials": "F"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "GIANT Consortium", "given": "", "initials": ""}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Hall", "given": "Per", "initials": "P"}, {"family": "Hankinson", "given": "Susan E", "initials": "SE"}, {"family": "Ferreli", "given": "Liana", "initials": "L"}, {"family": "Heath", "given": "Andrew C", "initials": "AC"}, {"family": "Hernandez", "given": "Dena G", "initials": "DG"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "J\u00e4rvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Karasik", "given": "David", "initials": "D"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "KT"}, {"family": "Kiel", "given": "Douglas P", "initials": "DP"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Kolcic", "given": "Ivana", "initials": "I"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Laven", "given": "Joop S E", "initials": "JS"}, {"family": "Li", "given": "Shengxu", "initials": "S"}, {"family": "Liu", "given": "Jianjun", "initials": "J"}, {"family": "Levy", "given": "Daniel", "initials": "D"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "McArdle", "given": "Wendy L", "initials": "WL"}, {"family": "Melbye", "given": "Mads", "initials": "M"}, {"family": "Mooser", "given": "Vincent", "initials": "V"}, {"family": "Murray", "given": "Jeffrey C", "initials": "JC"}, {"family": "Murray", "given": "Sarah S", "initials": "SS"}, {"family": "Nalls", "given": "Michael A", "initials": "MA"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "Nelis", "given": "Mari", "initials": "M"}, {"family": "Ness", "given": "Andrew R", "initials": "AR"}, {"family": "Northstone", "given": "Kate", "initials": "K"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "Peacock", "given": "Munro", "initials": "M"}, {"family": "Palmer", "given": "Lyle J", "initials": "LJ"}, {"family": "Palotie", "given": "Aarno", "initials": "A"}, {"family": "Par\u00e9", "given": "Guillaume", "initials": "G"}, {"family": "Parker", "given": "Alex N", "initials": "AN"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Peltonen", "given": "Leena", "initials": "L"}, {"family": "Pennell", "given": "Craig E", "initials": "CE"}, {"family": "Pharoah", "given": "Paul", "initials": "P"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Plump", "given": "Andrew S", "initials": "AS"}, {"family": "Pouta", "given": "Anneli", "initials": "A"}, {"family": "Porcu", "given": "Eleonora", "initials": "E"}, {"family": "Rafnar", "given": "Thorunn", "initials": "T"}, {"family": "Rice", "given": "John P", "initials": "JP"}, {"family": "Ring", "given": "Susan M", "initials": "SM"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Sala", "given": "Cinzia", "initials": "C"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Schork", "given": "Nicholas J", "initials": "NJ"}, {"family": "Scuteri", "given": "Angelo", "initials": "A"}, {"family": "Segr\u00e8", "given": "Ayellet V", "initials": "AV"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Sovio", "given": "Ulla", "initials": "U"}, {"family": "Srinivasan", "given": "Sathanur R", "initials": "SR"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Tammesoo", "given": "Mar-Liis", "initials": "ML"}, {"family": "Tikkanen", "given": "Emmi", "initials": "E"}, {"family": "Toniolo", "given": "Daniela", "initials": "D"}, {"family": "Tsui", "given": "Kim", "initials": "K"}, {"family": "Tryggvadottir", "given": "Laufey", "initials": "L"}, {"family": "Tyrer", "given": "Jonathon", "initials": "J"}, {"family": "Uda", "given": "Manuela", "initials": "M"}, {"family": "van Dam", "given": "Rob M", "initials": "RM"}, {"family": "van Meurs", "given": "Joyce B J", "initials": "JB"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Waeber", "given": "Gerard", "initials": "G"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Weedon", "given": "Michael N", "initials": "MN"}, {"family": "Wichmann", "given": "H Erich", "initials": "HE"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Young", "given": "Lauren", "initials": "L"}, {"family": "Zhai", "given": "Guangju", "initials": "G"}, {"family": "Zhuang", "given": "Wei Vivian", "initials": "WV"}, {"family": "Bierut", "given": "Laura J", "initials": "LJ"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Boyd", "given": "Heather A", "initials": "HA"}, {"family": "Crisponi", "given": "Laura", "initials": "L"}, {"family": "Demerath", "given": "Ellen W", "initials": "EW"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Econs", "given": "Michael J", "initials": "MJ"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Hunter", "given": "David J", "initials": "DJ"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Streeten", "given": "Elizabeth A", "initials": "EA"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Widen", "given": "Elisabeth", "initials": "E"}, {"family": "Murabito", "given": "Joanne M", "initials": "JM"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Murray", "given": "Anna", "initials": "A"}], "type": "journal article", "published": "2010-12-00", "journal": {"volume": "42", "issn": "1546-1718", "issue": "12", "pages": "1077-1085", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "To identify loci for age at menarche, we performed a meta-analysis of 32 genome-wide association studies in 87,802 women of European descent, with replication in up to 14,731 women. In addition to the known loci at LIN28B (P = 5.4 \u00d7 10\u207b\u2076\u2070) and 9q31.2 (P = 2.2 \u00d7 10\u207b\u00b3\u00b3), we identified 30 new menarche loci (all P < 5 \u00d7 10\u207b\u2078) and found suggestive evidence for a further 10 loci (P < 1.9 \u00d7 10\u207b\u2076). The new loci included four previously associated with body mass index (in or near FTO, SEC16B, TRA2B and TMEM18), three in or near other genes implicated in energy homeostasis (BSX, CRTC1 and MCHR2) and three in or near genes implicated in hormonal regulation (INHBA, PCSK2 and RXRG). Ingenuity and gene-set enrichment pathway analyses identified coenzyme A and fatty acid biosynthesis as biological processes related to menarche timing.", "doi": "10.1038/ng.714", "pmid": "21102462", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "ng.714"}, {"db": "pmc", "key": "PMC3140055"}, {"db": "mid", "key": "NIHMS306020"}], "notes": [], "created": "2017-10-30T13:50:29.374Z", "modified": "2020-01-21T13:56:08.463Z"}, {"entity": "publication", "iuid": "9286df46be4c4a84a0e04830876a3b84", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9286df46be4c4a84a0e04830876a3b84.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9286df46be4c4a84a0e04830876a3b84"}}, "title": "The genetic architecture of domestication in the chicken: effects of pleiotropy and linkage.", "authors": [{"family": "Wright", "given": "D", "initials": "D"}, {"family": "Rubin", "given": "C-J", "initials": "CJ"}, {"family": "Martinez Barrio", "given": "A", "initials": "A"}, {"family": "Sch\u00fctz", "given": "K", "initials": "K"}, {"family": "Kerje", "given": "S", "initials": "S", "orcid": "0000-0002-2944-9288", "researcher": {"href": "https://publications.scilifelab.se/researcher/078ca525f2cc4a68a430f2655e45efce.json"}}, {"family": "Br\u00e4ndstr\u00f6m", "given": "H", "initials": "H"}, {"family": "Kindmark", "given": "A", "initials": "A"}, {"family": "Jensen", "given": "P", "initials": "P"}, {"family": "Andersson", "given": "L", "initials": "L"}], "type": "journal article", "published": "2010-12-00", "journal": {"volume": "19", "issn": "1365-294X", "issue": "23", "pages": "5140-5156", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "The extent of pleiotropy and epistasis in quantitative traits remains equivocal. In the case of pleiotropy, multiple quantitative trait loci are often taken to be pleiotropic if their confidence intervals overlap, without formal statistical tests being used to ascertain if these overlapping loci are statistically significantly pleiotropic. Additionally, the degree to which the genetic correlations between phenotypic traits are reflected in these pleiotropic quantitative trait loci is often variable, especially in the case of antagonistic pleiotropy. Similarly, the extent of epistasis in various morphological, behavioural and life-history traits is also debated, with a general problem being the sample sizes required to detect such effects. Domestication involves a large number of trade-offs, which are reflected in numerous behavioural, morphological and life-history traits which have evolved as a consequence of adaptation to selective pressures exerted by humans and captivity. The comparison between wild and domestic animals allows the genetic analysis of the traits that differ between these population types, as well as being a general model of evolution. Using a large F(2) intercross between wild and domesticated chickens, in combination with a dense SNP and microsatellite marker map, both pleiotropy and epistasis were analysed. The majority of traits were found to segregate in 11 tight 'blocks' and reflected the trade-offs associated with domestication. These blocks were shown to have a pleiotropic 'core' surrounded by more loosely linked loci. In contrast, epistatic interactions were almost entirely absent, with only six pairs identified over all traits analysed. These results give insights both into the extent of such blocks in evolution and the development of domestication itself.", "doi": "10.1111/j.1365-294X.2010.04882.x", "pmid": "21040053", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:33.449Z", "modified": "2021-07-07T15:26:06.512Z"}, {"entity": "publication", "iuid": "78b877d735664093a8a37345d69d87c7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/78b877d735664093a8a37345d69d87c7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/78b877d735664093a8a37345d69d87c7"}}, "title": "SOX10 expression in superficial spreading and nodular malignant melanomas.", "authors": [{"family": "Agnarsd\u00f3ttir", "given": "Margr\u00e9t", "initials": "M"}, {"family": "Sooman", "given": "Linda", "initials": "L"}, {"family": "Bolander", "given": "Asa", "initials": "A"}, {"family": "Str\u00f6mberg", "given": "Sara", "initials": "S"}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Gallagher", "given": "William", "initials": "W"}, {"family": "Lennartsson", "given": "Johan", "initials": "J"}, {"family": "Ekman", "given": "Simon", "initials": "S"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Hedstrand", "given": "H\u00e5kan", "initials": "H"}], "type": "journal article", "published": "2010-12-00", "journal": {"volume": "20", "issn": "1473-5636", "issue": "6", "pages": "468-478", "title": "Melanoma Res.", "issn-l": "0960-8931"}, "abstract": "SOX10 is a transcription factor expressed in nerve cells and melanocytes. The aim of this study was to investigate the protein expression pattern of SOX10 in malignant melanoma tumors and to analyze whether the results correlated with clinical parameters and the proliferation marker Ki-67. Furthermore, proliferation and migration were analyzed in three different cell lines employing SOX10 small interfering RNA-mediated silencing. Expression patterns were determined in 106 primary tumors and 39 metastases in addition to 16 normal skin samples and six benign nevi employing immunohistochemistry and tissue microarrays. The immunohistochemical staining was evaluated manually and with an automated algorithm. SOX10 was strongly expressed in the benign tissues, but for the malignant tumors superficial spreading melanomas stained stronger than nodular malignant melanomas (P=0.008). The staining intensity was also inversely correlated with T-stage (Spearman's \u03c1=-0.261, P=0.008). Overall survival and time to recurrence were significantly correlated with SOX10 intensity, but not in multivariate analysis including T-stage. With the automated algorithm there was an inverse correlation between the SOX10 staining intensity and the proliferation marker, Ki-67 (\u03c1=-0.173, P=0.02) and a significant difference in the intensity signal between the benign tissues, the primary tumors and the metastases where the metastases stained the weakest (P\u22640.001). SOX10 downregulation resulted in variable effects on proliferation and migration rates in the melanoma cell lines. In conclusion, the SOX10 intensity level differed depending on the tissue studied and SOX10 might have a role in survival. No conclusion regarding the role of SOX10 for in-vitro proliferation and migration could be drawn.", "doi": "10.1097/CMR.0b013e3283403ccd", "pmid": "20890226", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:44.709Z", "modified": "2021-07-08T13:44:33.369Z"}, {"entity": "publication", "iuid": "daf02d7c1bf84c84a384d68131acfd2a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/daf02d7c1bf84c84a384d68131acfd2a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/daf02d7c1bf84c84a384d68131acfd2a"}}, "title": "SNPs in genes coding for ROS metabolism and signalling in association with docetaxel clearance.", "authors": [{"family": "Edvardsen", "given": "H", "initials": "H"}, {"family": "Brunsvig", "given": "P F", "initials": "PF"}, {"family": "Solvang", "given": "H", "initials": "H"}, {"family": "Tsalenko", "given": "A", "initials": "A"}, {"family": "Andersen", "given": "A", "initials": "A"}, {"family": "Syvanen", "given": "A-C", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Yakhini", "given": "Z", "initials": "Z"}, {"family": "B\u00f8rresen-Dale", "given": "A-L", "initials": "AL"}, {"family": "Olsen", "given": "H", "initials": "H"}, {"family": "Aamdal", "given": "S", "initials": "S"}, {"family": "Kristensen", "given": "V N", "initials": "VN"}], "type": "journal article", "published": "2010-12-00", "journal": {"volume": "10", "issn": "1473-1150", "issue": "6", "pages": "513-523", "title": "Pharmacogenomics J.", "issn-l": "1470-269X"}, "abstract": "The dose of docetaxel is currently calculated based on body surface area and does not reflect the pharmacokinetic, metabolic potential or genetic background of the patients. The influence of genetic variation on the clearance of docetaxel was analysed in a two-stage analysis. In step one, 583 single-nucleotide polymorphisms (SNPs) in 203 genes were genotyped on samples from 24 patients with locally advanced non-small cell lung cancer. We found that many of the genes harbour several SNPs associated with clearance of docetaxel. Most notably these were four SNPs in EGF, three SNPs in PRDX4 and XPC, and two SNPs in GSTA4, TGFBR2, TNFAIP2, BCL2, DPYD and EGFR. The multiple SNPs per gene suggested the existence of common haplotypes associated with clearance. These were confirmed with detailed haplotype analysis. On the basis of analysis of variance (ANOVA), quantitative mutual information score (QMIS) and Kruskal-Wallis (KW) analysis SNPs significantly associated with clearance of docetaxel were confirmed for GSTA4, PRDX4, TGFBR2 and XPC and additional putative markers were found in CYP2C8, EPHX1, IGF2, IL1R2, MAPK7, NDUFB4, TGFBR3, TPMT (2 SNPs), (P<0.05 or borderline significant for all three methods, 14 SNPs in total). In step two, these 14 SNPs were genotyped in additional 9 samples and the results combined with the genotyping results from the first step. For 7 of the 14 SNPs, the results are still significant/borderline significant by all three methods: ANOVA, QMIS and KW analysis strengthening our hypothesis that they are associated with the clearance of docetaxel.", "doi": "10.1038/tpj.2010.6", "pmid": "20157331", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "tpj20106"}], "notes": [], "created": "2017-05-04T15:00:37.078Z", "modified": "2021-07-07T15:11:02.271Z"}, {"entity": "publication", "iuid": "b7f29558b4af4c6f98335230b12d1dc2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7f29558b4af4c6f98335230b12d1dc2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7f29558b4af4c6f98335230b12d1dc2"}}, "title": "Interactions of dietary whole-grain intake with fasting glucose- and insulin-related genetic loci in individuals of European descent: a meta-analysis of 14 cohort studies.", "authors": [{"family": "Nettleton", "given": "Jennifer A", "initials": "JA"}, {"family": "McKeown", "given": "Nicola M", "initials": "NM"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Lemaitre", "given": "Rozenn N", "initials": "RN"}, {"family": "Hivert", "given": "Marie-France", "initials": "MF"}, {"family": "Ngwa", "given": "Julius", "initials": "J"}, {"family": "van Rooij", "given": "Frank J A", "initials": "FJ"}, {"family": "Sonestedt", "given": "Emily", "initials": "E"}, {"family": "Wojczynski", "given": "Mary K", "initials": "MK"}, {"family": "Ye", "given": "Zheng", "initials": "Z"}, {"family": "Tanaka", "given": "Tosh", "initials": "T"}, {"family": "Garcia", "given": "Melissa", "initials": "M"}, {"family": "Anderson", "given": "Jennifer S", "initials": "JS"}, {"family": "Follis", "given": "Jack L", "initials": "JL"}, {"family": "Djousse", "given": "Luc", "initials": "L"}, {"family": "Mukamal", "given": "Kenneth", "initials": "K"}, {"family": "Papoutsakis", "given": "Constantina", "initials": "C"}, {"family": "Mozaffarian", "given": "Dariush", "initials": "D"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Bennett", "given": "Amanda J", "initials": "AJ"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Forouhi", "given": "Nita G", "initials": "NG"}, {"family": "Groves", "given": "Christopher J", "initials": "CJ"}, {"family": "Hallmans", "given": "Goran", "initials": "G"}, {"family": "Harris", "given": "Tamara", "initials": "T"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Houston", "given": "Denise K", "initials": "DK"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Johansson", "given": "Ingegerd", "initials": "I"}, {"family": "Kritchevsky", "given": "Stephen B", "initials": "SB"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Launer", "given": "Lenore", "initials": "L"}, {"family": "Liu", "given": "Yongmei", "initials": "Y"}, {"family": "Loos", "given": "Ruth J", "initials": "RJ"}, {"family": "Nalls", "given": "Michael", "initials": "M"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Renstrom", "given": "Frida", "initials": "F"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Riserus", "given": "Ulf", "initials": "U"}, {"family": "Rolandsson", "given": "Olov", "initials": "O"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Saylor", "given": "Georgia", "initials": "G"}, {"family": "Sijbrands", "given": "Eric J G", "initials": "EJ"}, {"family": "Sjogren", "given": "Per", "initials": "P"}, {"family": "Smith", "given": "Albert", "initials": "A"}, {"family": "Steingr\u00edmsd\u00f3ttir", "given": "Laufey", "initials": "L"}, {"family": "Uitterlinden", "given": "Andr\u00e9 G", "initials": "AG"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "MAGIC Investigators", "given": null, "initials": null}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Dedoussis", "given": "George V", "initials": "GV"}, {"family": "Ordovas", "given": "Jose M", "initials": "JM"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Cupples", "given": "L Adrienne", "initials": "L"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Meigs", "given": "James B", "initials": "JB"}], "type": "journal article", "published": "2010-12-00", "journal": {"volume": "33", "issn": "1935-5548", "issue": "12", "pages": "2684-2691", "title": "Diabetes Care", "issn-l": "0149-5992"}, "abstract": "Whole-grain foods are touted for multiple health benefits, including enhancing insulin sensitivity and reducing type 2 diabetes risk. Recent genome-wide association studies (GWAS) have identified several single nucleotide polymorphisms (SNPs) associated with fasting glucose and insulin concentrations in individuals free of diabetes. We tested the hypothesis that whole-grain food intake and genetic variation interact to influence concentrations of fasting glucose and insulin.\n\nVia meta-analysis of data from 14 cohorts comprising \u223c 48,000 participants of European descent, we studied interactions of whole-grain intake with loci previously associated in GWAS with fasting glucose (16 loci) and/or insulin (2 loci) concentrations. For tests of interaction, we considered a P value <0.0028 (0.05 of 18 tests) as statistically significant.\n\nGreater whole-grain food intake was associated with lower fasting glucose and insulin concentrations independent of demographics, other dietary and lifestyle factors, and BMI (\u03b2 [95% CI] per 1-serving-greater whole-grain intake: -0.009 mmol/l glucose [-0.013 to -0.005], P < 0.0001 and -0.011 pmol/l [ln] insulin [-0.015 to -0.007], P = 0.0003). No interactions met our multiple testing-adjusted statistical significance threshold. The strongest SNP interaction with whole-grain intake was rs780094 (GCKR) for fasting insulin (P = 0.006), where greater whole-grain intake was associated with a smaller reduction in fasting insulin concentrations in those with the insulin-raising allele.\n\nOur results support the favorable association of whole-grain intake with fasting glucose and insulin and suggest a potential interaction between variation in GCKR and whole-grain intake in influencing fasting insulin concentrations.", "doi": "10.2337/dc10-1150", "pmid": "20693352", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "dc10-1150"}, {"db": "pmc", "key": "PMC2992213"}], "notes": [], "created": "2017-05-04T15:00:29.536Z", "modified": "2020-01-21T13:56:04.814Z"}, {"entity": "publication", "iuid": "ace41dfd8e0840279e4ac0c774e367a0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ace41dfd8e0840279e4ac0c774e367a0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ace41dfd8e0840279e4ac0c774e367a0"}}, "title": "High frequency of p16(INK4A) promoter methylation in NRAS-mutated cutaneous melanoma.", "authors": [{"family": "Jonsson", "given": "Anders", "initials": "A"}, {"family": "Tuominen", "given": "Rainer", "initials": "R"}, {"family": "Grafstr\u00f6m", "given": "Eva", "initials": "E"}, {"family": "Hansson", "given": "Johan", "initials": "J"}, {"family": "Egyhazi", "given": "Suzanne", "initials": "S"}], "type": "journal article", "published": "2010-12-00", "journal": {"volume": "130", "issn": "1523-1747", "issue": "12", "pages": "2809-2817", "title": "J. Invest. Dermatol.", "issn-l": "0022-202X"}, "abstract": "The p16(INK4A) tumor suppressor is often deleted, or otherwise inactivated, in malignant melanoma. To investigate the loss of p16(INK4A) in greater detail, we analyzed 77 cutaneous melanoma metastases. Of these 56 retained at least one p16(INK4A) allele, and 21 had biallelic deletions. Using methylation-specific PCR, direct sequencing, and immunohistochemical methods, we analyzed p16(INK4A) promoter methylation, mutations, and protein expression, respectively. In addition, 14 corresponding primary tumors were analyzed for protein expression. Results were compared to clinicopathological parameters and previously obtained data regarding mutations in proto-oncogenes NRAS and BRAF. Results revealed that p16(INK4A) promoter methylation was present in 15 of 59 (25%) metastases; nonsynonymous mutations in 9 of 56 (16%) metastases; and protein expression in 12 of 67 (18%) metastases. Protein expression was lost during progression from primary to metastatic tumors, 71% (10 of 14) and 43% (6 of 14) being positive, respectively. However, the genetic and epigenetic alterations of p16(INK4A) observed could not explain the lack of p16(INK4A) protein in 27 metastases, indicating the presence of additional inactivating mechanisms for p16(INK4A). Interestingly, p16(INK4A) promoter methylation was significantly overrepresented in NRAS-mutated samples compared to NRAS wild-type samples (P=0.0004), indicating an association between these two events.", "doi": "10.1038/jid.2010.216", "pmid": "20703244", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0022-202X(15)34650-9"}], "notes": [], "created": "2017-05-04T14:57:11.657Z", "modified": "2020-01-21T13:56:04.547Z"}, {"entity": "publication", "iuid": "49de0859712c408eabd80917a59f2310", "links": {"self": {"href": "https://publications.scilifelab.se/publication/49de0859712c408eabd80917a59f2310.json"}, "display": {"href": "https://publications.scilifelab.se/publication/49de0859712c408eabd80917a59f2310"}}, "title": "Distinct gene expression profiles in subsets of chronic lymphocytic leukemia expressing stereotyped IGHV4-34 B-cell receptors.", "authors": [{"family": "Marincevic", "given": "Millaray", "initials": "M"}, {"family": "Mansouri", "given": "Mahmoud", "initials": "M"}, {"family": "Kanduri", "given": "Meena", "initials": "M"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "G\u00f6ransson", "given": "Hanna", "initials": "H"}, {"family": "Smedby", "given": "Karin Ekstr\u00f6m", "initials": "KE"}, {"family": "Jurlander", "given": "Jesper", "initials": "J"}, {"family": "Juliusson", "given": "Gunnar", "initials": "G"}, {"family": "Davi", "given": "Fred", "initials": "F"}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}], "type": "journal article", "published": "2010-12-00", "journal": {"volume": "95", "issn": "1592-8721", "issue": "12", "pages": "2072-2079", "title": "Haematologica", "issn-l": "0390-6078"}, "abstract": "Numerous subsets of patients with chronic lymphocytic leukemia display similar immunoglobulin gene usage with almost identical complementarity determining region 3 sequences. Among IGHV4-34 cases, two such subsets with \"stereotyped\" B-cell receptors were recently identified, i.e. subset #4 (IGHV4-34/IGKV2-30) and subset #16 (IGHV4-34/IGKV3-20). Subset #4 patients appear to share biological and clinical features, e.g. young age at diagnosis and indolent disease, whereas little is known about subset #16 at a clinical level.\r\n\r\nWe investigated the global gene expression pattern in sorted chronic lymphocytic leukemia cells from 25 subset/non-subset IGHV4-34 patients using Affymetrix gene expression arrays.\r\n\r\nAlthough generally few differences were found when comparing subset to non-subset 4/16 IGHV4-34 cases, distinct gene expression profiles were revealed for subset #4 versus subset #16. The differentially expressed genes, predominantly with lower expression in subset #4 patients, are involved in important cell regulatory pathways including cell-cycle control, proliferation and immune response, which may partly explain the low-proliferative disease observed in subset #4 patients.\r\n\r\nOur novel data demonstrate distinct gene expression profiles among patients with stereotyped IGHV4-34 B-cell receptors, providing further evidence for biological differences in the pathogenesis of these subsets and underscoring the functional relevance of subset assignment based on B-cell receptor sequence features.", "doi": "10.3324/haematol.2010.028639", "pmid": "20801898", "labels": {"National Genomics Infrastructure": null, "Array and Analysis Facility": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "haematol.2010.028639"}, {"db": "pmc", "key": "PMC2995565"}], "notes": [], "created": "2017-05-04T14:57:11.356Z", "modified": "2020-01-21T13:56:10.375Z"}, {"entity": "publication", "iuid": "10110364b86746baa129d44062770482", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10110364b86746baa129d44062770482.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10110364b86746baa129d44062770482"}}, "title": "Common variants at 10 genomic loci influence hemoglobin A\u2081(C) levels via glycemic and nonglycemic pathways.", "authors": [{"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Wheeler", "given": "Eleanor", "initials": "E"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Radke", "given": "D\u00f6rte", "initials": "D"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Stolerman", "given": "Elliot", "initials": "E"}, {"family": "Sandhu", "given": "Manjinder S", "initials": "MS"}, {"family": "Heeney", "given": "Matthew M", "initials": "MM"}, {"family": "Devaney", "given": "Joseph M", "initials": "JM"}, {"family": "Reilly", "given": "Muredach P", "initials": "MP"}, {"family": "Ricketts", "given": "Sally L", "initials": "SL"}, {"family": "Stewart", "given": "Alexandre F R", "initials": "AF"}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Willenborg", "given": "Christina", "initials": "C"}, {"family": "Wright", "given": "Benjamin", "initials": "B"}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "Arking", "given": "Dan", "initials": "D"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Barnes", "given": "Daniel", "initials": "D"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "B\u00f6hm", "given": "Bernhard", "initials": "B"}, {"family": "Bonnefond", "given": "Am\u00e9lie", "initials": "A"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Bornstein", "given": "Stefan R", "initials": "SR"}, {"family": "B\u00f6ttcher", "given": "Yvonne", "initials": "Y"}, {"family": "Bumpstead", "given": "Suzannah", "initials": "S"}, {"family": "Burnett-Miller", "given": "Mary Susan", "initials": "MS"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Cao", "given": "Antonio", "initials": "A"}, {"family": "Chambers", "given": "John", "initials": "J"}, {"family": "Clark", "given": "Robert", "initials": "R"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Coresh", "given": "Josef", "initials": "J"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJ"}, {"family": "Dei", "given": "Mariano", "initials": "M"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "D\u00f6ring", "given": "Angela", "initials": "A"}, {"family": "Egan", "given": "Josephine M", "initials": "JM"}, {"family": "Elosua", "given": "Roberto", "initials": "R"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Forouhi", "given": "Nita", "initials": "N"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Franklin", "given": "Christopher", "initials": "C"}, {"family": "Franzosi", "given": "Maria Grazia", "initials": "MG"}, {"family": "Gallina", "given": "Sophie", "initials": "S"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Graessler", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Greinacher", "given": "Andreas", "initials": "A"}, {"family": "Hadley", "given": "David", "initials": "D"}, {"family": "Hall", "given": "Alistair", "initials": "A"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Heath", "given": "Simon", "initials": "S"}, {"family": "Herder", "given": "Christian", "initials": "C"}, {"family": "Homuth", "given": "Georg", "initials": "G"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Hunter-Merrill", "given": "Rachel", "initials": "R"}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Jula", "given": "Antti", "initials": "A"}, {"family": "Kleber", "given": "Marcus", "initials": "M"}, {"family": "Knouff", "given": "Christopher W", "initials": "CW"}, {"family": "Kong", "given": "Augustine", "initials": "A"}, {"family": "Kooner", "given": "Jaspal", "initials": "J"}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Krohn", "given": "Knut", "initials": "K"}, {"family": "K\u00fchnel", "given": "Brigitte", "initials": "B"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Lathrop", "given": "Mark", "initials": "M"}, {"family": "Lecoeur", "given": "C\u00e9cile", "initials": "C"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Li", "given": "Mingyao", "initials": "M"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Mart\u00ednez-Larrad", "given": "Mar\u00eda Teresa", "initials": "MT"}, {"family": "M\u00e4rz", "given": "Winfried", "initials": "W"}, {"family": "McArdle", "given": "Wendy L", "initials": "WL"}, {"family": "McPherson", "given": "Ruth", "initials": "R"}, {"family": "Meisinger", "given": "Christa", "initials": "C"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Mooser", "given": "Vincent E", "initials": "VE"}, {"family": "Morken", "given": "Mario A", "initials": "MA"}, {"family": "Narisu", "given": "Narisu", "initials": "N"}, {"family": "Nathan", "given": "David M", "initials": "DM"}, {"family": "Nauck", "given": "Matthias", "initials": "M"}, {"family": "O'Donnell", "given": "Chris", "initials": "C"}, {"family": "Oexle", "given": "Konrad", "initials": "K"}, {"family": "Olla", "given": "Nazario", "initials": "N"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Payne", "given": "Felicity", "initials": "F"}, {"family": "Peden", "given": "John F", "initials": "JF"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Peltonen", "given": "Leena", "initials": "L"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Porcu", "given": "Eleonora", "initials": "E"}, {"family": "Rader", "given": "Daniel J", "initials": "DJ"}, {"family": "Rathmann", "given": "Wolfgang", "initials": "W"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Rocheleau", "given": "Ghislain", "initials": "G"}, {"family": "Roden", "given": "Michael", "initials": "M"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Saxena", "given": "Richa", "initials": "R"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Schwarz", "given": "Peter", "initials": "P"}, {"family": "Seedorf", "given": "Udo", "initials": "U"}, {"family": "Selvin", "given": "Elizabeth", "initials": "E"}, {"family": "Serrano-R\u00edos", "given": "Manuel", "initials": "M"}, {"family": "Shrader", "given": "Peter", "initials": "P"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "Siscovick", "given": "David", "initials": "D"}, {"family": "Song", "given": "Kjioung", "initials": "K"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Strawbridge", "given": "Rona", "initials": "R"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Swift", "given": "Amy J", "initials": "AJ"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Usala", "given": "Gianluca", "initials": "G"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Wallaschofski", "given": "Henri", "initials": "H"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Watkins", "given": "Hugh", "initials": "H"}, {"family": "Wichmann", "given": "H-Erich", "initials": "HE"}, {"family": "Wild", "given": "Sarah H", "initials": "SH"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Williams", "given": "Gordon H", "initials": "GH"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Winkelmann", "given": "Juliane", "initials": "J"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "WTCCC", "given": "", "initials": ""}, {"family": "Zabena", "given": "Carina", "initials": "C"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Epstein", "given": "Stephen E", "initials": "SE"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Hakonarson", "given": "Hakon H", "initials": "HH"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "KT"}, {"family": "Roberts", "given": "Robert", "initials": "R"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Fleming", "given": "Mark D", "initials": "MD"}, {"family": "Sladek", "given": "Robert", "initials": "R"}, {"family": "Abecasis", "given": "Gon\u00e7alo", "initials": "G"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Kao", "given": "W H Linda", "initials": "WH"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Uda", "given": "Manuela", "initials": "M"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Meigs", "given": "James B", "initials": "JB"}], "type": "journal article", "published": "2010-12-00", "journal": {"volume": "59", "issn": "1939-327X", "issue": "12", "pages": "3229-3239", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": "Glycated hemoglobin (HbA\u2081(c)), used to monitor and diagnose diabetes, is influenced by average glycemia over a 2- to 3-month period. Genetic factors affecting expression, turnover, and abnormal glycation of hemoglobin could also be associated with increased levels of HbA\u2081(c). We aimed to identify such genetic factors and investigate the extent to which they influence diabetes classification based on HbA\u2081(c) levels.\n\nWe studied associations with HbA\u2081(c) in up to 46,368 nondiabetic adults of European descent from 23 genome-wide association studies (GWAS) and 8 cohorts with de novo genotyped single nucleotide polymorphisms (SNPs). We combined studies using inverse-variance meta-analysis and tested mediation by glycemia using conditional analyses. We estimated the global effect of HbA\u2081(c) loci using a multilocus risk score, and used net reclassification to estimate genetic effects on diabetes screening.\n\nTen loci reached genome-wide significant association with HbA(1c), including six new loci near FN3K (lead SNP/P value, rs1046896/P = 1.6 \u00d7 10\u207b\u00b2\u2076), HFE (rs1800562/P = 2.6 \u00d7 10\u207b\u00b2\u2070), TMPRSS6 (rs855791/P = 2.7 \u00d7 10\u207b\u00b9\u2074), ANK1 (rs4737009/P = 6.1 \u00d7 10\u207b\u00b9\u00b2), SPTA1 (rs2779116/P = 2.8 \u00d7 10\u207b\u2079) and ATP11A/TUBGCP3 (rs7998202/P = 5.2 \u00d7 10\u207b\u2079), and four known HbA\u2081(c) loci: HK1 (rs16926246/P = 3.1 \u00d7 10\u207b\u2075\u2074), MTNR1B (rs1387153/P = 4.0 \u00d7 10\u207b\u00b9\u00b9), GCK (rs1799884/P = 1.5 \u00d7 10\u207b\u00b2\u2070) and G6PC2/ABCB11 (rs552976/P = 8.2 \u00d7 10\u207b\u00b9\u2078). We show that associations with HbA\u2081(c) are partly a function of hyperglycemia associated with 3 of the 10 loci (GCK, G6PC2 and MTNR1B). The seven nonglycemic loci accounted for a 0.19 (% HbA\u2081(c)) difference between the extreme 10% tails of the risk score, and would reclassify \u223c2% of a general white population screened for diabetes with HbA\u2081(c).\n\nGWAS identified 10 genetic loci reproducibly associated with HbA\u2081(c). Six are novel and seven map to loci where rarer variants cause hereditary anemias and iron storage disorders. Common variants at these loci likely influence HbA\u2081(c) levels via erythrocyte biology, and confer a small but detectable reclassification of diabetes diagnosis by HbA\u2081(c).", "doi": "10.2337/db10-0502", "pmid": "20858683", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "db10-0502"}, {"db": "pmc", "key": "PMC2992787"}], "notes": [], "created": "2017-10-30T13:50:30.358Z", "modified": "2020-01-21T13:56:08.474Z"}, {"entity": "publication", "iuid": "3943cafd8d924224afc0aedc6b4c267e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3943cafd8d924224afc0aedc6b4c267e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3943cafd8d924224afc0aedc6b4c267e"}}, "title": "A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes.", "authors": [{"family": "Willing", "given": "Ben P", "initials": "BP"}, {"family": "Dicksved", "given": "Johan", "initials": "J"}, {"family": "Halfvarson", "given": "Jonas", "initials": "J"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Lucio", "given": "Marianna", "initials": "M"}, {"family": "Zheng", "given": "Zongli", "initials": "Z"}, {"family": "J\u00e4rnerot", "given": "Gunnar", "initials": "G"}, {"family": "Tysk", "given": "Curt", "initials": "C"}, {"family": "Jansson", "given": "Janet K", "initials": "JK"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2010-12-00", "journal": {"volume": "139", "issn": "1528-0012", "issue": "6", "pages": "1844-1854.e1", "title": "Gastroenterology", "issn-l": "0016-5085"}, "abstract": "The composition of the gastrointestinal microbiota is thought to have an important role in the etiology of inflammatory bowel diseases (IBDs) such as Crohn's disease (CD) and ulcerative colitis (UC). Interindividual variation and an inability to detect less abundant bacteria have made it difficult to correlate specific bacteria with disease.\n\nWe used 454 pyrotag sequencing to determine the compositions of microbial communities in feces samples collected from a cohort of 40 twin pairs who were concordant or discordant for CD or UC, and in mucosal samples from a subset of the cohort. The cohort primarily comprised patients who were in remission, but also some with active disease.\n\nThe profiles of the microbial community differed with disease phenotypes; relative amounts of bacterial populations correlated with IBD phenotypes. The microbial compositions of individuals with CD differed from those of healthy individuals, but were similar between healthy individuals and individuals with UC. Profiles from individuals with CD that predominantly involved the ileum differed from those with CD that predominantly involved the colon; several bacterial populations increased or decreased with disease type. Changes specific to patients with ileal CD included the disappearance of core bacteria, such as Faecalibacterium and Roseburia, and increased amounts of Enterobacteriaceae and Ruminococcus gnavus.\n\nBacterial populations differ in abundance among individuals with different phenotypes of CD. Specific species of bacteria are associated with ileal CD; further studies should investigate their role in pathogenesis.", "doi": "10.1053/j.gastro.2010.08.049", "pmid": "20816835", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "S0016-5085(10)01299-0"}], "notes": [], "created": "2017-05-04T14:57:10.454Z", "modified": "2020-01-21T13:56:01.605Z"}, {"entity": "publication", "iuid": "cb52173bbf4a4f1481c7e14d19e92f04", "links": {"self": {"href": "https://publications.scilifelab.se/publication/cb52173bbf4a4f1481c7e14d19e92f04.json"}, "display": {"href": "https://publications.scilifelab.se/publication/cb52173bbf4a4f1481c7e14d19e92f04"}}, "title": "A high-density scan of the Z chromosome in Ficedula flycatchers reveals candidate loci for diversifying selection.", "authors": [{"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}, {"family": "Lindell", "given": "Johan", "initials": "J"}, {"family": "Zhang", "given": "Yu", "initials": "Y"}, {"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "Qvarnstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Saetre", "given": "Glenn-Peter", "initials": "GP"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2010-12-00", "journal": {"volume": "64", "issn": "1558-5646", "issue": "12", "pages": "3461-3475", "title": "Evolution", "issn-l": "0014-3820"}, "abstract": "Theoretical and empirical data suggest that genes located on sex chromosomes may play an important role both for sexually selected traits and for traits involved in the build-up of hybrid incompatibilities. We investigated patterns of genetic variation in 73 genes located on the Z chromosomes of two species of the flycatcher genus Ficedula, the pied flycatcher and the collared flycatcher. Sequence data were evaluated for signs of selection potentially related to genomic differentiation in these young sister species, which hybridize despite reduced fitness of hybrids. Seven loci were significantly more divergent between the two species than expected under neutrality and they also displayed reduced nucleotide diversity, consistent with having been influenced by directional selection. Two of the detected candidate regions contain genes that are associated with plumage coloration in birds. Plumage characteristics play an important role in species recognition in these flycatchers suggesting that the detected genes may have been involved in the evolution of sexual isolation between the species.", "doi": "10.1111/j.1558-5646.2010.01082.x", "pmid": "20629730", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "EVO1082"}], "notes": [], "created": "2017-05-04T15:00:30.153Z", "modified": "2020-01-21T13:56:05.193Z"}, {"entity": "publication", "iuid": "a3360f0bfa004bea9ca37b6b64c086dd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a3360f0bfa004bea9ca37b6b64c086dd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a3360f0bfa004bea9ca37b6b64c086dd"}}, "title": "The obesity related gene, FTO, interacts with APOE, and is associated with Alzheimer's disease risk: a prospective cohort study.", "authors": [{"family": "Keller", "given": "Lina", "initials": "L"}, {"family": "Xu", "given": "Weili", "initials": "W"}, {"family": "Wang", "given": "Hui-Xin", "initials": "HX"}, {"family": "Winblad", "given": "Bengt", "initials": "B"}, {"family": "Fratiglioni", "given": "Laura", "initials": "L"}, {"family": "Graff", "given": "Caroline", "initials": "C"}], "type": "comparative study", "published": "2010-11-26", "journal": {"volume": "23", "issn": "1875-8908", "issue": "3", "pages": "461-469", "title": "J. Alzheimers Dis.", "issn-l": "1387-2877"}, "abstract": "The FTO gene has been shown to have a small but robust effect on body mass index (BMI) and to increase the risk for diabetes. Both high BMI and diabetes are vascular risk factors that might play a role in the development of Alzheimer's disease (AD) and dementia. Thus, our aim was to explore the impact of FTO on AD and dementia risk. Nine years of follow-up data was gathered from the Kungsholmen project, a prospective population-based study on 1,003 persons without dementia. Cox-regression models were used to assess the relative risks of developing AD and dementia (DSM-III-R criteria) according to FTO genotypes (rs9939609), taking into account APOE, physical inactivity, BMI, diabetes, and cardiovascular disease (CVD). Compared to carriers of the FTO TT-genotype, AA-carriers had a higher risk for AD (RR 1.58, 95% CI: 1.11-2.24) and for dementia (RR 1.48, 95% CI: 1.09-2.02) after adjustment for age, gender, education, and APOE genotype. This effect remained after additional adjustment for physical inactivity, BMI, diabetes, and CVD. An interaction between FTO and APOE was found, with increased risk for dementia for those carrying both FTO AA and APOE \u03f54. Importantly, the effect of the AA-genotype on dementia/AD risk seems to act mostly through the interaction with APOE \u03f54. Our findings suggest that the FTO AA-genotype increases the risk for dementia, and in particular AD, independently of physical inactivity, BMI, diabetes, and CVD measured at baseline. Our results are in line with the recently reported association between FTO and reduced brain volume in cognitively healthy subjects.", "doi": "10.3233/JAD-2010-101068", "pmid": "21098976", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "K2785TXG42873L62"}], "notes": [], "created": "2017-05-04T15:03:31.037Z", "modified": "2017-05-30T12:44:28.640Z"}, {"entity": "publication", "iuid": "95602e2c69144b29be43c990a4c55b8d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/95602e2c69144b29be43c990a4c55b8d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/95602e2c69144b29be43c990a4c55b8d"}}, "title": "SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools.", "authors": [{"family": "Marklund", "given": "Stefan", "initials": "S"}, {"family": "Carlborg", "given": "Orjan", "initials": "O"}], "type": "journal article", "published": "2010-11-25", "journal": {"volume": "11", "issn": "1471-2164", "issue": null, "pages": "665", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Next-generation sequencing technologies are widely used for detection of millions of Single Nucleotide Polymorphisms (SNPs) and also provide a means of assessing their variation. This information is useful for composing subsets of highly informative SNPs for region-specific or genome-wide analysis and to identify mutations regulating phenotypic differences within or between populations. In this study, we investigated the sensitivity of SNP detection and introduced the flanking SNPs value (FSV) as a novel measure for predicting SNP-variability using ~5X genome resequencing with ABI SOLID and DNA pools from two chicken lines divergently selected for juvenile bodyweight.\n\nGenotyping with a 60 K SNP chip revealed polymorphisms within or between two divergently selected chicken lines for 31 363 SNPs, 48% of which were also detected using resequencing of DNA pools. SNP detection using resequencing was more powerful for positions with larger differences in allele frequency between the lines. About 50% of the SNPs with non-reference allele frequencies in the range 0.5-0.6 and 67% of those with frequencies > 0.9 could be detected. On average, ~3.7 SNPs/kb were detected by resequencing, with about 5% lower density on microchromosomes than on macrochromosomes. There was a positive correlation between the observed between-line SNP variation from the 60 K chip analysis and our proposed FSV score computed from the genome resequencing data. The strongest correlations on macrochromosomes and microchromosomes were observed when the FSV was calculated with total flanking regions of 62 kb (correlation 0.55) and 38 kb (correlation 0.45), respectively.\n\nGenome resequencing with limited coverage (~5X) using pooled DNA samples and three non-reference reads as a threshold for SNP detection, identified 50 - 67% of the 60 K SNPs with a non-reference allele frequency larger than 0.5. The SNP density was around 5% lower on the microchromosomes, most likely because of their higher gene content. Our proposed method to estimate the SNP variation (FSV) uses additional sequence information to better predict SNP informativity. The FSV scores showed higher correlations for SNPs with a larger difference in allele frequency between the populations. The correlation was strongest on macrochromosomes, probably due to a lower recombination rate.", "doi": "10.1186/1471-2164-11-665", "pmid": "21108801", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-665"}, {"db": "pmc", "key": "PMC3091782"}], "notes": [], "created": "2017-05-04T15:01:50.437Z", "modified": "2020-01-21T13:56:03.840Z"}, {"entity": "publication", "iuid": "329341749ed544ad9028d36d8972f6a4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/329341749ed544ad9028d36d8972f6a4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/329341749ed544ad9028d36d8972f6a4"}}, "title": "Gene expression profiling and chromatin immunoprecipitation identify DBN1, SETMAR and HIG2 as direct targets of SOX11 in mantle cell lymphoma.", "authors": [{"family": "Wang", "given": "Xiao", "initials": "X"}, {"family": "Bj\u00f6rklund", "given": "Stefan", "initials": "S"}, {"family": "Wasik", "given": "Agata M", "initials": "AM"}, {"family": "Grandien", "given": "Alf", "initials": "A"}, {"family": "Andersson", "given": "Patrik", "initials": "P"}, {"family": "Kimby", "given": "Eva", "initials": "E"}, {"family": "Dahlman-Wright", "given": "Karin", "initials": "K"}, {"family": "Zhao", "given": "Chunyan", "initials": "C"}, {"family": "Christensson", "given": "Birger", "initials": "B"}, {"family": "Sander", "given": "Birgitta", "initials": "B"}], "type": "journal article", "published": "2010-11-22", "journal": {"volume": "5", "issn": "1932-6203", "issue": "11", "pages": "e14085", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "The SRY (sex determining region Y)-box 11 (SOX11) gene, located on chromosome 2p25, encodes for a transcription factor that is involved in tissue remodeling during embryogenesis and is crucial for neurogenesis. The role for SOX11 in hematopoiesis has not yet been defined. Two genes under direct control of SOX11 are the class- III \u03b2-tubulin gene (TUBB3) in neural cells and the transcription factor TEA domain family member 2 (TEAD2) in neural and mesenchymal progenitor cells. Normal, mature lymphocytes lack SOX11 but express SOX4, another member of the same group of SOX transcription factors. We and others recently identified SOX11 as aberrantly expressed in mantle cell lymphoma (MCL). Since SOX11 is variably expressed in MCL it may not be essential for tumorigenesis, but may carry prognostic information. Currently, no specific functional effects have been linked to SOX11 expression in MCL and it is not known which genes are under influence of SOX11 in lymphoma. In this study we found variable expression of SOX11, SOX4 and SOX12 mRNA in mantle cell lymphoma cell lines. Downregulation of SOX11 expression by siRNA verified that SOX11 controlled the expression of the gene TUBB3 in the MCL cell line Granta 519. Furthermore we identified, by global gene expression analysis, 26 new target genes influenced by siRNA SOX11 downmodulation. Among these genes, DBN1, SETMAR and HIG2 were found to be significantly correlated to SOX11 expression in two cohorts of primary mantle cell lymphomas. Chromatin immunoprecipitation (ChIP) analysis showed that these genes are direct targets of the SOX11 protein. In spite of almost complete downregulation of the SOX11 protein no significant effects on Granta 519 cell proliferation or survival in short term in vitro experiments was found. In summary we have identified a number of genes influenced by SOX11 expression in MCL cell lines and primary MCL. Among these genes, DBN1, SETMAR and HIG2 are direct transcriptional targets of the SOX11 protein.", "doi": "10.1371/journal.pone.0014085", "pmid": "21124928", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pmc", "key": "PMC2989913"}], "notes": [], "created": "2017-05-04T15:03:09.031Z", "modified": "2017-05-30T14:50:39.168Z"}, {"entity": "publication", "iuid": "9972459d788b4187a2c11c60c744ce88", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9972459d788b4187a2c11c60c744ce88.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9972459d788b4187a2c11c60c744ce88"}}, "title": "Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays.", "authors": [{"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Neiman", "given": "Maja", "initials": "M"}, {"family": "Langen", "given": "Hanno", "initials": "H"}, {"family": "Becker", "given": "Charlotte", "initials": "C"}, {"family": "Bjartell", "given": "Anders", "initials": "A"}, {"family": "Ponten", "given": "Fredrik", "initials": "F"}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "evaluation studies", "published": "2010-11-00", "journal": {"volume": "9", "issn": "1535-9484", "issue": "11", "pages": "2497-2507", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "There is a need for high throughput methods for screening patient samples in the quest for potential biomarkers for diagnostics and patient care. Here, we used a combination of undirected target selection, antibody suspension bead arrays, and heat-induced epitope retrieval to allow for protein profiling of human plasma in a novel and systematic manner. Several antibodies were found to reveal altered protein profiles upon epitope retrieval at elevated temperatures with limits of detection improving into lower ng/ml ranges. In a study based on prostate cancer patients, several proteins with differential profiles were discovered and subsequently validated in an independent cohort. For one of the potential biomarkers, the human carnosine dipeptidase 1 protein (CNDP1), the differences were determined to be related to the glycosylation status of the targeted protein. The study shows a path of pursuit for large scale screening of biobank repositories in a flexible and proteome-wide fashion by utilizing heat-induced epitope retrieval and using an antibody suspension bead array format.", "doi": "10.1074/mcp.M110.001560", "pmid": "20682762", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [{"db": "pii", "key": "M110.001560"}, {"db": "pmc", "key": "PMC2984230"}], "notes": [], "created": "2017-05-04T14:55:29.167Z", "modified": "2021-07-08T13:44:33.459Z"}, {"entity": "publication", "iuid": "20c3b2a3f89c4415ba5d2cffcf699165", "links": {"self": {"href": "https://publications.scilifelab.se/publication/20c3b2a3f89c4415ba5d2cffcf699165.json"}, "display": {"href": "https://publications.scilifelab.se/publication/20c3b2a3f89c4415ba5d2cffcf699165"}}, "title": "Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.", "authors": [{"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Randall", "given": "Joshua C", "initials": "JC"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Zillikens", "given": "M Carola", "initials": "MC"}, {"family": "Speliotes", "given": "Elizabeth K", "initials": "EK"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Workalemahu", "given": "Tsegaselassie", "initials": "T"}, {"family": "White", "given": "Charles C", "initials": "CC"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Berndt", "given": "Sonja I", "initials": "SI"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Weedon", "given": "Michael N", "initials": "MN"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Vedantam", "given": "Sailaja", "initials": "S"}, {"family": "Esko", "given": "T\u00f5nu", "initials": "T"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Kutalik", "given": "Zolt\u00e1n", "initials": "Z"}, {"family": "Li", "given": "Shengxu", "initials": "S"}, {"family": "Monda", "given": "Keri L", "initials": "KL"}, {"family": "Dixon", "given": "Anna L", "initials": "AL"}, {"family": "Holmes", "given": "Christopher C", "initials": "CC"}, {"family": "Kaplan", "given": "Lee M", "initials": "LM"}, {"family": "Liang", "given": "Liming", "initials": "L"}, {"family": "Min", "given": "Josine L", "initials": "JL"}, {"family": "Moffatt", "given": "Miriam F", "initials": "MF"}, {"family": "Molony", "given": "Cliona", "initials": "C"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Zondervan", "given": "Krina T", "initials": "KT"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Ferreira", "given": "Teresa", "initials": "T"}, {"family": "Lango Allen", "given": "Hana", "initials": "H"}, {"family": "Weyant", "given": "Robert J", "initials": "RJ"}, {"family": "Wheeler", "given": "Eleanor", "initials": "E"}, {"family": "Wood", "given": "Andrew R", "initials": "AR"}, {"family": "MAGIC", "given": null, "initials": null}, {"family": "Estrada", "given": "Karol", "initials": "K"}, {"family": "Goddard", "given": "Michael E", "initials": "ME"}, {"family": "Lettre", "given": "Guillaume", "initials": "G"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Nyholt", "given": "Dale R", "initials": "DR"}, {"family": "Purcell", "given": "Shaun", "initials": "S"}, {"family": "Smith", "given": "Albert Vernon", "initials": "AV"}, {"family": "Visscher", "given": "Peter M", "initials": "PM"}, {"family": "Yang", "given": "Jian", "initials": "J"}, {"family": "McCarroll", "given": "Steven A", "initials": "SA"}, {"family": "Nemesh", "given": "James", "initials": "J"}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Absher", "given": "Devin", "initials": "D"}, {"family": "Amin", "given": "Najaf", "initials": "N"}, {"family": "Aspelund", "given": "Thor", "initials": "T"}, {"family": "Coin", "given": "Lachlan", "initials": "L"}, {"family": "Glazer", "given": "Nicole L", "initials": "NL"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Heard-Costa", "given": "Nancy L", "initials": "NL"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Johansson", "given": "Asa", "initials": "A"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Kaakinen", "given": "Marika", "initials": "M"}, {"family": "Kapur", "given": "Karen", "initials": "K"}, {"family": "Ketkar", "given": "Shamika", "initials": "S"}, {"family": "Knowles", "given": "Joshua W", "initials": "JW"}, {"family": "Kraft", "given": "Peter", "initials": "P"}, {"family": "Kraja", "given": "Aldi T", "initials": "AT"}, {"family": "Lamina", "given": "Claudia", "initials": "C"}, {"family": "Leitzmann", "given": "Michael F", "initials": "MF"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Perry", "given": "John R B", "initials": "JR"}, {"family": "Peters", "given": "Marjolein J", "initials": "MJ"}, {"family": "Polasek", "given": "Ozren", "initials": "O"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Rayner", "given": "Nigel W", "initials": "NW"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Robertson", "given": "Neil R", "initials": "NR"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Sovio", "given": "Ulla", "initials": "U"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Teumer", "given": "Alexander", "initials": "A"}, {"family": "van Wingerden", "given": "Sophie", "initials": "S"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "Cavalcanti-Proen\u00e7a", "given": "Christine", "initials": "C"}, {"family": "Chines", "given": "Peter S", "initials": "PS"}, {"family": "Fisher", "given": "Eva", "initials": "E"}, {"family": "Kulzer", "given": "Jennifer R", "initials": "JR"}, {"family": "Lecoeur", "given": "Cecile", "initials": "C"}, {"family": "Narisu", "given": "Narisu", "initials": "N"}, {"family": "Sandholt", "given": "Camilla", "initials": "C"}, {"family": "Scott", "given": "Laura J", "initials": "LJ"}, {"family": "Silander", "given": "Kaisa", "initials": "K"}, {"family": "Stark", 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"Tuomi", "given": "Tiinamaija", "initials": "T"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Valle", "given": "Timo T", "initials": "TT"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Arnold", "given": "Alice M", "initials": "AM"}, {"family": "Beckmann", "given": "Jacques S", "initials": "JS"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Hattersley", "given": "Andrew T", "initials": "AT"}, {"family": "Hofman", 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{"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Syvanen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Uda", "given": "Manuela", "initials": "M"}, {"family": "Uitterlinden", "given": "Andr\u00e9", "initials": "A"}, {"family": "V\u00f6lzke", "given": "Henry", "initials": "H"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Witteman", "given": "Jacqueline C", "initials": "JC"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Abecasis", "given": "Gon\u00e7alo R", "initials": "GR"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Groop", "given": "Leif C", "initials": "LC"}, {"family": "Haritunians", "given": "Talin", "initials": "T"}, {"family": "Hunter", "given": "David J", "initials": "DJ"}, {"family": "Kaplan", "given": "Robert C", "initials": "RC"}, {"family": "North", "given": "Kari E", "initials": "KE"}, {"family": "O'Connell", "given": "Jeffrey R", "initials": "JR"}, {"family": "Peltonen", "given": "Leena", "initials": "L"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Hirschhorn", "given": "Joel N", "initials": "JN"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Wichmann", "given": "H-Erich", "initials": "HE"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}], "type": "journal article", "published": "2010-11-00", "journal": {"volume": "42", "issn": "1546-1718", "issue": "11", "pages": "949-960", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Waist-hip ratio (WHR) is a measure of body fat distribution and a predictor of metabolic consequences independent of overall adiposity. WHR is heritable, but few genetic variants influencing this trait have been identified. We conducted a meta-analysis of 32 genome-wide association studies for WHR adjusted for body mass index (comprising up to 77,167 participants), following up 16 loci in an additional 29 studies (comprising up to 113,636 subjects). We identified 13 new loci in or near RSPO3, VEGFA, TBX15-WARS2, NFE2L3, GRB14, DNM3-PIGC, ITPR2-SSPN, LY86, HOXC13, ADAMTS9, ZNRF3-KREMEN1, NISCH-STAB1 and CPEB4 (P = 1.9 \u00d7 10\u207b\u2079 to P = 1.8 \u00d7 10\u207b\u2074\u2070) and the known signal at LYPLAL1. Seven of these loci exhibited marked sexual dimorphism, all with a stronger effect on WHR in women than men (P for sex difference = 1.9 \u00d7 10\u207b\u00b3 to P = 1.2 \u00d7 10\u207b\u00b9\u00b3). These findings provide evidence for multiple loci that modulate body fat distribution independent of overall adiposity and reveal strong gene-by-sex interactions.", "doi": "10.1038/ng.685", "pmid": "20935629", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.685"}, {"db": "pmc", "key": "PMC3000924"}, {"db": "mid", "key": "UKMS33585"}], "notes": [], "created": "2017-05-04T15:00:35.152Z", "modified": "2021-07-07T15:11:02.313Z"}, {"entity": "publication", "iuid": "34111be2048f4625a193b2667af88a69", "links": {"self": {"href": "https://publications.scilifelab.se/publication/34111be2048f4625a193b2667af88a69.json"}, "display": {"href": "https://publications.scilifelab.se/publication/34111be2048f4625a193b2667af88a69"}}, "title": "Meiofauna reduces bacterial mineralization of naphthalene in marine sediment.", "authors": [{"family": "N\u00e4slund", "given": "Johan", "initials": "J"}, {"family": "Nascimento", "given": "Francisco J A", "initials": "FJ"}, {"family": "Gunnarsson", "given": "Jonas S", "initials": "JS"}], "type": "journal article", "published": "2010-11-00", "journal": {"volume": "4", "issn": "1751-7370", "issue": "11", "pages": "1421-1430", "title": "ISME J", "issn-l": "1751-7362"}, "abstract": "The role of sediment-living meiofauna, benthic invertebrates smaller than 1000\u2009\u03bcm such as nematodes and ostracods, on the mineralization of naphthalene, a common polycyclic aromatic hydrocarbon (PAH) in marine sediments, was studied in microcosms using radiorespirometry. A method to extract live meiofauna was developed and used in order to experimentally manipulate meiofauna abundance and group diversity. Higher abundances of meiofauna were found to significantly decrease naphthalene mineralization. Furthermore, a change in the bacterial community composition (studied using terminal restriction fragment length polymorphism) was also observed in presence of higher meiofauna abundance, as well as a lower number of cultivable naphthalene-degrading bacteria. The reduced mineralization of naphthalene and the altered bacterial community composition in the presence of increased meiofauna abundance is likely the result of top-down control by meiofauna. This study shows that higher abundances of meiofauna can significantly decrease the microbial mineralization of PAHs such as naphthalene and also significantly modify the bacterial community composition in natural marine sediments.", "doi": "10.1038/ismej.2010.63", "pmid": "20463764", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "ismej201063"}, {"db": "GENBANK", "key": "FN555293"}, {"db": "GENBANK", "key": "FN555294"}, {"db": "GENBANK", "key": "FN555295"}, {"db": "GENBANK", "key": "FN555296"}, {"db": "GENBANK", "key": "FN555297"}, {"db": "GENBANK", "key": "FN555298"}, {"db": "GENBANK", "key": "FN555299"}, {"db": "GENBANK", "key": "FN555300"}, {"db": "GENBANK", "key": "FN641887"}, {"db": "GENBANK", "key": "FN641888"}, {"db": "GENBANK", "key": "FN641889"}], "notes": [], "created": "2017-05-04T15:01:51.681Z", "modified": "2020-01-21T13:56:01.486Z"}, {"entity": "publication", "iuid": "64c09e829c5b4b38acb0651cdc56bed7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/64c09e829c5b4b38acb0651cdc56bed7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/64c09e829c5b4b38acb0651cdc56bed7"}}, "title": "Creation of an antibody-based subcellular protein atlas.", "authors": [{"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"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": "2010-11-00", "journal": {"volume": "10", "issn": "1615-9861", "issue": "22", "pages": "3984-3996", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "An important part for understanding the complex machinery of living cells is to know the spatial distribution of proteins all the way from organ to organelle levels. An equally important part of proteomics is to map the subcellular distribution of all human proteins. Here, we discuss methodologies for systematic subcellular profiling with emphasis on the antibody-based approach performed as a part of the Human Protein Atlas project. The considerations made when creating the subcellular protein atlas and critical parameters of this approach are discussed.", "doi": "10.1002/pmic.201000125", "pmid": "20648481", "labels": {"Spatial Proteomics": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:08.056Z", "modified": "2021-07-08T13:44:33.324Z"}, {"entity": "publication", "iuid": "c8638d1f82e04f4882ccfde795629a50", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c8638d1f82e04f4882ccfde795629a50.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c8638d1f82e04f4882ccfde795629a50"}}, "title": "Common variants in the ATP2B1 gene are associated with susceptibility to hypertension: the Japanese Millennium Genome Project.", "authors": [{"family": "Tabara", "given": "Yasuharu", "initials": "Y"}, {"family": "Kohara", "given": "Katsuhiko", "initials": "K"}, {"family": "Kita", "given": "Yoshikuni", "initials": "Y"}, {"family": "Hirawa", "given": "Nobuhito", "initials": "N"}, {"family": "Katsuya", "given": "Tomohiro", "initials": "T"}, {"family": "Ohkubo", "given": "Takayoshi", "initials": "T"}, {"family": "Hiura", "given": "Yumiko", "initials": "Y"}, {"family": "Tajima", "given": "Atsushi", "initials": "A"}, {"family": "Morisaki", "given": "Takayuki", "initials": "T"}, {"family": "Miyata", "given": "Toshiyuki", "initials": "T"}, {"family": "Nakayama", "given": "Tomohiro", "initials": "T"}, {"family": "Takashima", "given": "Naoyuki", "initials": "N"}, {"family": "Nakura", "given": "Jun", "initials": "J"}, {"family": "Kawamoto", "given": "Ryuichi", "initials": "R"}, {"family": "Takahashi", "given": "Norio", "initials": "N"}, {"family": "Hata", "given": "Akira", "initials": "A"}, {"family": "Soma", "given": "Masayoshi", "initials": "M"}, {"family": "Imai", "given": "Yutaka", "initials": "Y"}, {"family": "Kokubo", "given": "Yoshihiro", "initials": "Y"}, {"family": "Okamura", "given": "Tomonori", "initials": "T"}, {"family": "Tomoike", "given": "Hitonobu", "initials": "H"}, {"family": "Iwai", "given": "Naoharu", "initials": "N"}, {"family": "Ogihara", "given": "Toshio", "initials": "T"}, {"family": "Inoue", "given": "Itsuro", "initials": "I"}, {"family": "Tokunaga", "given": "Katsushi", "initials": "K"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Caulfield", "given": "Mark", "initials": "M"}, {"family": "Munroe", "given": "Patricia", "initials": "P"}, {"family": "Global Blood Pressure Genetics Consortium", "given": null, "initials": null}, {"family": "Umemura", "given": "Satoshi", "initials": "S"}, {"family": "Ueshima", "given": "Hirotsugu", "initials": "H"}, {"family": "Miki", "given": "Tetsuro", "initials": "T"}], "type": "journal article", "published": "2010-11-00", "journal": {"volume": "56", "issn": "1524-4563", "issue": "5", "pages": "973-980", "title": "Hypertension", "issn-l": "0194-911X"}, "abstract": "Hypertension is one of the most common complex genetic disorders. We have described previously 38 single nucleotide polymorphisms (SNPs) with suggestive association with hypertension in Japanese individuals. In this study we extend our previous findings by analyzing a large sample of Japanese individuals (n=14 105) for the most associated SNPs. We also conducted replication analyses in Japanese of susceptibility loci for hypertension identified recently from genome-wide association studies of European ancestries. Association analysis revealed significant association of the ATP2B1 rs2070759 polymorphism with hypertension (P=5.3\u00d710(-5); allelic odds ratio: 1.17 [95% CI: 1.09 to 1.26]). Additional SNPs in ATP2B1 were subsequently genotyped, and the most significant association was with rs11105378 (odds ratio: 1.31 [95% CI: 1.21 to 1.42]; P=4.1\u00d710(-11)). Association of rs11105378 with hypertension was cross-validated by replication analysis with the Global Blood Pressure Genetics consortium data set (odds ratio: 1.13 [95% CI: 1.05 to 1.21]; P=5.9\u00d710(-4)). Mean adjusted systolic blood pressure was highly significantly associated with the same SNP in a meta-analysis with individuals of European descent (P=1.4\u00d710(-18)). ATP2B1 mRNA expression levels in umbilical artery smooth muscle cells were found to be significantly different among rs11105378 genotypes. Seven SNPs discovered in published genome-wide association studies were also genotyped in the Japanese population. In the combined analysis with replicated 3 genes, FGF5 rs1458038, CYP17A1, rs1004467, and CSK rs1378942, odds ratio of the highest risk group was 2.27 (95% CI: 1.65 to 3.12; P=4.6\u00d710(-7)) compared with the lower risk group. In summary, this study confirmed common genetic variation in ATP2B1, as well as FGF5, CYP17A1, and CSK, to be associated with blood pressure levels and risk of hypertension.", "doi": "10.1161/HYPERTENSIONAHA.110.153429", "pmid": "20921432", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "HYPERTENSIONAHA.110.153429"}, {"db": "pmc", "key": "PMC5003412"}, {"db": "mid", "key": "NIHMS810751"}], "notes": [], "created": "2017-05-04T15:00:31.913Z", "modified": "2020-01-21T13:56:05.152Z"}, {"entity": "publication", "iuid": "d4773352acbe426596ee187edad66e52", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d4773352acbe426596ee187edad66e52.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d4773352acbe426596ee187edad66e52"}}, "title": "Four novel Loci (19q13, 6q24, 12q24, and 5q14) influence the microcirculation in vivo.", "authors": [{"family": "Ikram", "given": "M Kamran", "initials": "MK"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Xueling", "given": "Sim", "initials": "S"}, {"family": "Jensen", "given": "Richard A", "initials": "RA"}, {"family": "Cotch", "given": "Mary Frances", "initials": "MF"}, {"family": "Hewitt", "given": "Alex W", "initials": "AW"}, {"family": "Ikram", "given": "M Arfan", "initials": "MA"}, {"family": "Wang", "given": "Jie Jin", "initials": "JJ"}, {"family": "Klein", "given": "Ronald", "initials": "R"}, {"family": "Klein", "given": "Barbara E K", "initials": "BE"}, {"family": "Breteler", "given": "Monique M B", "initials": "MM"}, {"family": "Cheung", "given": "Ning", "initials": "N"}, {"family": "Liew", "given": "Gerald", "initials": "G"}, {"family": "Mitchell", "given": "Paul", "initials": "P"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Rivadeneira", "given": "Fernando", "initials": "F"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "de Jong", "given": "Paulus T V M", "initials": "PT"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Kao", "given": "Linda", "initials": "L"}, {"family": "Cheng", "given": "Ching-Yu", "initials": "CY"}, {"family": "Smith", "given": "Albert Vernon", "initials": "AV"}, {"family": "Glazer", "given": "Nicole L", "initials": "NL"}, {"family": "Lumley", "given": "Thomas", "initials": "T"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Jonasson", "given": "Fridbert", "initials": "F"}, {"family": "Eiriksdottir", "given": "Gudny", "initials": "G"}, {"family": "Aspelund", "given": "Thor", "initials": "T"}, {"family": "Global BPgen Consortium", "given": null, "initials": null}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Taylor", "given": "Kent D", "initials": "KD"}, {"family": "Li", "given": "Xiaohui", "initials": "X"}, {"family": "Iyengar", "given": "Sudha K", "initials": "SK"}, {"family": "Xi", "given": "Quansheng", "initials": "Q"}, {"family": "Sivakumaran", "given": "Theru A", "initials": "TA"}, {"family": "Mackey", "given": "David A", "initials": "DA"}, {"family": "Macgregor", "given": "Stuart", "initials": "S"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Young", "given": "Terri L", "initials": "TL"}, {"family": "Bis", "given": "Josh C", "initials": "JC"}, {"family": "Wiggins", "given": "Kerri L", "initials": "KL"}, {"family": "Heckbert", "given": "Susan R", "initials": "SR"}, {"family": "Hammond", "given": "Christopher J", "initials": "CJ"}, {"family": "Andrew", "given": "Toby", "initials": "T"}, {"family": "Fahy", "given": "Samantha", "initials": "S"}, {"family": "Attia", "given": "John", "initials": "J"}, {"family": "Holliday", "given": "Elizabeth G", "initials": "EG"}, {"family": "Scott", "given": "Rodney J", "initials": "RJ"}, {"family": "Islam", "given": "F M Amirul", "initials": "FM"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "McAuley", "given": "Annie K", "initials": "AK"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Vingerling", "given": "Johannes R", "initials": "JR"}, {"family": "Wong", "given": "Tien Y", "initials": "TY"}], "type": "journal article", "published": "2010-10-28", "journal": {"volume": "6", "issn": "1553-7404", "issue": "10", "pages": "e1001184", "title": "PLoS Genet.", "issn-l": "1553-7390"}, "abstract": "There is increasing evidence that the microcirculation plays an important role in the pathogenesis of cardiovascular diseases. Changes in retinal vascular caliber reflect early microvascular disease and predict incident cardiovascular events. We performed a genome-wide association study to identify genetic variants associated with retinal vascular caliber. We analyzed data from four population-based discovery cohorts with 15,358 unrelated Caucasian individuals, who are members of the Cohort for Heart and Aging Research in Genomic Epidemiology (CHARGE) consortium, and replicated findings in four independent Caucasian cohorts (n \u200a= \u200a6,652). All participants had retinal photography and retinal arteriolar and venular caliber measured from computer software. In the discovery cohorts, 179 single nucleotide polymorphisms (SNP) spread across five loci were significantly associated (p<5.0\u00d710(-8)) with retinal venular caliber, but none showed association with arteriolar caliber. Collectively, these five loci explain 1.0%-3.2% of the variation in retinal venular caliber. Four out of these five loci were confirmed in independent replication samples. In the combined analyses, the top SNPs at each locus were: rs2287921 (19q13; p\u200a =\u200a 1.61\u00d710(-25), within the RASIP1 locus), rs225717 (6q24; p\u200a=\u200a1.25\u00d710(-16), adjacent to the VTA1 and NMBR loci), rs10774625 (12q24; p \u200a=\u200a 2.15\u00d710(-13), in the region of ATXN2,SH2B3 and PTPN11 loci), and rs17421627 (5q14; p\u200a=\u200a7.32\u00d710(-16), adjacent to the MEF2C locus). In two independent samples, locus 12q24 was also associated with coronary heart disease and hypertension. Our population-based genome-wide association study demonstrates four novel loci associated with retinal venular caliber, an endophenotype of the microcirculation associated with clinical cardiovascular disease. These data provide further insights into the contribution and biological mechanisms of microcirculatory changes that underlie cardiovascular disease.", "doi": "10.1371/journal.pgen.1001184", "pmid": "21060863", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pmc", "key": "PMC2965750"}], "notes": [], "created": "2017-05-04T15:00:37.997Z", "modified": "2020-01-21T13:56:05.414Z"}, {"entity": "publication", "iuid": "5edf0feb4623412fa93023e2c4e35990", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5edf0feb4623412fa93023e2c4e35990.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5edf0feb4623412fa93023e2c4e35990"}}, "title": "Sensitive detection of A\u03b2 protofibrils by proximity ligation--relevance for Alzheimer's disease.", "authors": [{"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Pettersson", "given": "Frida Ekholm", "initials": "FE"}, {"family": "Wu", "given": "Di", "initials": "D"}, {"family": "Englund", "given": "Hillevi", "initials": "H"}, {"family": "Darmanis", "given": "Spyros", "initials": "S"}, {"family": "Lord", "given": "Anna", "initials": "A"}, {"family": "Tavoosidana", "given": "Gholamreza", "initials": "G"}, {"family": "Sehlin", "given": "Dag", "initials": "D"}, {"family": "Gustafsdottir", "given": "Sigrun", "initials": "S"}, {"family": "Nilsson", "given": "Lars N G", "initials": "LN"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2010-10-05", "journal": {"volume": "11", "issn": "1471-2202", "issue": null, "pages": "124", "title": "BMC Neurosci", "issn-l": "1471-2202"}, "abstract": "Protein aggregation plays important roles in several neurodegenerative disorders. For instance, insoluble aggregates of phosphorylated tau and of A\u03b2 peptides are cornerstones in the pathology of Alzheimer's disease. Soluble protein aggregates are therefore potential diagnostic and prognostic biomarkers for their cognate disorders. Detection of the aggregated species requires sensitive tools that efficiently discriminate them from monomers of the same proteins. Here we have established a proximity ligation assay (PLA) for specific and sensitive detection of A\u03b2 protofibrils via simultaneous recognition of three identical determinants present in the aggregates. PLA is a versatile technology in which the requirement for multiple target recognitions is combined with the ability to translate signals from detected target molecules to amplifiable DNA strands, providing very high specificity and sensitivity.\n\nFor specific detection of A\u03b2 protofibrils we have used a monoclonal antibody, mAb158, selective for A\u03b2 protofibrils in a modified PLA, where the same monoclonal antibody was used for the three classes of affinity reagents required in the assay. These reagents were used for detection of soluble A\u03b2 aggregates in solid-phase reactions, allowing detection of just 0.1 pg/ml A\u03b2 protofibrils, and with a dynamic range greater than six orders of magnitude. Compared to a sandwich ELISA setup of the same antibody the PLA increases the sensitivity of the A\u03b2 protofibril detection by up to 25-fold. The assay was used to measure soluble A\u03b2 aggregates in brain homogenates from mice transgenic for a human allele predisposing to A\u03b2 aggregation.\n\nThe proximity ligation assay is a versatile analytical technology for proteins, which can provide highly sensitive and specific detection of A\u03b2 aggregates - and by implication other protein aggregates of relevance in Alzheimer's disease and other neurodegenerative disorders.", "doi": "10.1186/1471-2202-11-124", "pmid": "20923550", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "1471-2202-11-124"}, {"db": "pmc", "key": "PMC2959092"}], "notes": [], "created": "2017-05-04T14:55:20.462Z", "modified": "2023-04-14T13:56:31.926Z"}, {"entity": "publication", "iuid": "0c492751e0eb47a2b3ff1ae2cdda416d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0c492751e0eb47a2b3ff1ae2cdda416d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0c492751e0eb47a2b3ff1ae2cdda416d"}}, "title": "Association analysis of PALB2 and BRCA2 in bipolar disorder and schizophrenia in a scandinavian case-control sample.", "authors": [{"family": "Tesli", "given": "Martin", "initials": "M"}, {"family": "Athanasiu", "given": "Lavinia", "initials": "L"}, {"family": "Mattingsdal", "given": "Morten", "initials": "M"}, {"family": "K\u00e4hler", "given": "Anna K", "initials": "AK"}, {"family": "Gustafsson", "given": "Omar", "initials": "O"}, {"family": "Andreassen", "given": "Bettina K", "initials": "BK"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Hansen", "given": "Thomas", "initials": "T"}, {"family": "Mors", "given": "Ole", "initials": "O"}, {"family": "Mellerup", "given": "Erling", "initials": "E"}, {"family": "Koefoed", "given": "Pernille", "initials": "P"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Morken", "given": "Gunnar", "initials": "G"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}], "type": "journal article", "published": "2010-10-05", "journal": {"volume": "153B", "issn": "1552-485X", "issue": "7", "pages": "1276-1282", "title": "Am. J. Med. Genet. B Neuropsychiatr. Genet.", "issn-l": "1552-4841"}, "abstract": "A recent genome-wide association study (GWAS) found significant association between the PALB2 SNP rs420259 and bipolar disorder (BD). The intracellular functions of the expressed proteins from the breast cancer risk genes PALB2 and BRCA2 are closely related. Therefore, we investigated the relation between genetic variants in PALB2 and BRCA2 and BD. Due to increasing evidence of genetic overlap between BD and schizophrenia (SCZ), we also investigated association with SCZ. In a Scandinavian case-control sample (n\u2009=\u2009686/2,538) we found the BRCA2 SNP rs9567552 to be significantly associated with BD (Nominal P\u2009=\u20090.00043). Additionally, we replicated the association between PALB2 SNP rs420259 and BD (Nominal P\u2009=\u20090.025). We then combined our sample with another Nordic case-control sample (n\u2009=\u2009435/11,491) from Iceland, and added results from the Wellcome Trust Case Control Consortium (WTCCC) (n\u2009=\u20091,868/2,938) and the STEP-UCL/ED-DUB-STEP2 study (n\u2009=\u20092,558/3,274) in a meta-analysis which revealed a P-value of 1.2\u2009\u00d7\u200910(-5) for association between PALB2 SNP rs420259 and BD (n\u2009=\u20095,547/20,241). Neither the PALB2 SNP rs420259 nor the BRCA2 SNP rs9567552 were nominally significantly associated with the SCZ phenotype in our Scandinavian sample (n\u2009=\u2009781/2,839). Our findings support PALB2 and BRCA2 as risk genes specifically for BD, and suggest that altered DNA repair related to neurogenesis may be involved in BD pathophysiology. \u00a9 2010 Wiley-Liss, Inc.", "doi": "10.1002/ajmg.b.31098", "pmid": "20872766", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:25.818Z", "modified": "2020-01-21T13:56:00.657Z"}, {"entity": "publication", "iuid": "bd499c90dfdc4a7aafef90aece3db764", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bd499c90dfdc4a7aafef90aece3db764.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bd499c90dfdc4a7aafef90aece3db764"}}, "title": "An exploratory model for G x E interaction on hippocampal volume in schizophrenia; obstetric complications and hypoxia-related genes.", "authors": [{"family": "Haukvik", "given": "Unn Kristin", "initials": "UK"}, {"family": "Saetre", "given": "Peter", "initials": "P"}, {"family": "McNeil", "given": "Thomas", "initials": "T"}, {"family": "Bjerkan", "given": "Petr S", "initials": "PS"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}], "type": "journal article", "published": "2010-10-01", "journal": {"volume": "34", "issn": "1878-4216", "issue": "7", "pages": "1259-1265", "title": "Prog. Neuropsychopharmacol. Biol. Psychiatry", "issn-l": "0278-5846"}, "abstract": "Smaller hippocampal volume has repeatedly been reported in schizophrenia patients. Obstetric complications (OCs) and single nucleotide polymorphism (SNP) variation in schizophrenia susceptibility genes have independently been related to hippocampal volume. We investigated putative independent and interaction effects of severe hypoxia-related OCs and variation in four hypoxia-regulated schizophrenia susceptibility genes (BDNF, DTNBP1, GRM3 and NRG1) on hippocampal volume in schizophrenia patients and healthy controls.\n\nClinical assessment, structural MRI scans, and blood samples for genotyping of 32 SNPs were obtained from 54 schizophrenia patients and 53 control subjects. Information on obstetric complications was collected from original birth records.\n\nSevere OCs were related to hippocampal volume in both patients with schizophrenia and healthy control subjects. Of the 32 SNPs studied, effects of severe OCs on hippocampal volume were associated with allele variation in GRM3 rs13242038, but the interaction effect was not specific for schizophrenia. SNP variation in any of the four investigated genes alone did not significantly affect hippocampal volume.\n\nThe findings suggest a gene-environment (G x E) interaction between GRM3 gene variants and severe obstetric complications on hippocampus volume, independent of a diagnosis of schizophrenia. Due to the modest sample size, the results must be considered preliminary and require replication in independent samples.", "doi": "10.1016/j.pnpbp.2010.07.001", "pmid": "20638435", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0278-5846(10)00249-6"}], "notes": [], "created": "2017-05-04T15:00:38.621Z", "modified": "2020-01-21T13:56:04.950Z"}, {"entity": "publication", "iuid": "6c43855fe1b34aa19a4270c80ba62ebc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c43855fe1b34aa19a4270c80ba62ebc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c43855fe1b34aa19a4270c80ba62ebc"}}, "title": "Somatic mosaicism for chromosome X and Y aneuploidies in monozygotic twins heterozygous for sickle cell disease mutation.", "authors": [{"family": "Razzaghian", "given": "Hamid Reza", "initials": "HR"}, {"family": "Shahi", "given": "Mehdi Hayat", "initials": "MH"}, {"family": "Forsberg", "given": "Lars A", "initials": "LA"}, {"family": "de St\u00e5hl", "given": "Teresita Diaz", "initials": "TD"}, {"family": "Absher", "given": "Devin", "initials": "D"}, {"family": "Dahl", "given": "Niklas", "initials": "N"}, {"family": "Westerman", "given": "Maxwell P", "initials": "MP"}, {"family": "Dumanski", "given": "Jan P", "initials": "JP"}], "type": "journal article", "published": "2010-10-00", "journal": {"volume": "152A", "issn": "1552-4833", "issue": "10", "pages": "2595-2598", "title": "Am. J. Med. Genet. A", "issn-l": "1552-4825"}, "abstract": "Somatic genetic variation in health and disease is poorly explored. Monozygotic (MZ) twins are a suitable model for studies of somatic mosaicism since genetic differences in twins derived from the same zygote represent an irrefutable example of somatic variation. We report the analysis of a pair of generally healthy female MZ twins, discordant for somatic mosaicism for aneuploidy of chromosomes X and Y. Both twins are heterozygous carriers of sickle cell disease mutation. Genotyping of blood DNA from both twins using Illumina Human 610 SNP array revealed a copy number imbalance for chromosome X in a proportion of cells in one twin. Fluorescent in situ hybridization (FISH) analysis confirmed monosomy X (45,X) in 7% of proband nucleated blood cells. Unexpectedly, FISH analysis of cells from the other twin revealed 45,X and 46,XY lineages, both present in 1% of cells. The mechanism behind formation of these aneuploidies suggests several aberrant chromosome segregation events in meiosis and mitoses following conception. Our report contributes to the delineation of the frequency of somatic structural genomic variation in normal MZ twins. These results also illustrate the plasticity of the human genome for tolerating large copy number changes in healthy subjects and show the sensitivity of the Illumina platform for detection of aberrations that are present in a minority of the studied cells.", "doi": "10.1002/ajmg.a.33604", "pmid": "20734341", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:24.905Z", "modified": "2020-01-21T13:56:02.841Z"}, {"entity": "publication", "iuid": "7c03d2f20d3a4ee4ae7fdc85329037ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c03d2f20d3a4ee4ae7fdc85329037ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c03d2f20d3a4ee4ae7fdc85329037ed"}}, "title": "Lycosid spiders and alternative food: Feeding behavior and implications for biological control", "authors": [{"family": "Kuusk", "given": "Anna Karin", "initials": "AK"}, {"family": "Ekbom", "given": "Barbara", "initials": "B"}], "type": "journal-article", "published": "2010-10-00", "journal": {"volume": "55", "issn": "1049-9644", "issue": "1", "pages": "20-26", "title": "Biological Control", "issn-l": null}, "abstract": null, "doi": "10.1016/j.biocontrol.2010.06.009", "pmid": null, "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:01:49.755Z", "modified": "2021-06-22T12:07:49.031Z"}, {"entity": "publication", "iuid": "7c48ea382df744929db00a07b357b296", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7c48ea382df744929db00a07b357b296.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7c48ea382df744929db00a07b357b296"}}, "title": "Linkage to 20p13 including the ANGPT4 gene in families with mixed Alzheimer's disease and vascular dementia.", "authors": [{"family": "Sill\u00e9n", "given": "Anna", "initials": "A"}, {"family": "Brohede", "given": "Jesper", "initials": "J"}, {"family": "Lilius", "given": "Lena", "initials": "L"}, {"family": "Forsell", "given": "Charlotte", "initials": "C"}, {"family": "Andrade", "given": "Jorge", "initials": "J"}, {"family": "Odeberg", "given": "Jacob", "initials": "J"}, {"family": "Ebise", "given": "Hayao", "initials": "H"}, {"family": "Winblad", "given": "Bengt", "initials": "B"}, {"family": "Graff", "given": "Caroline", "initials": "C"}], "type": "journal article", "published": "2010-10-00", "journal": {"volume": "55", "issn": "1435-232X", "issue": "10", "pages": "649-655", "title": "J. Hum. Genet.", "issn-l": "1434-5161"}, "abstract": "This study aimed at identifying novel susceptibility genes for a mixed phenotype of Alzheimer's disease and vascular dementia. Results from a genome scan showed strongest linkage to 20p13 in 18 families, and subsequent fine mapping was performed with both microsatellites and single-nucleotide polymorphisms in 18 selected candidate transcripts in an extended sample set of 30 families. The multipoint linkage peak was located at marker rs2144151 in the ANGPT4 gene, which is a strong candidate gene for vascular disease because of its involvement in angiogenesis. Although the significance of the linkage decreased, we find this result intriguing, considering that we included additional families, and thus the reduced linkage signal may be caused by genetic heterogeneity.", "doi": "10.1038/jhg.2010.79", "pmid": "20596041", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "jhg201079"}], "notes": [], "created": "2017-05-04T15:03:28.282Z", "modified": "2017-05-30T12:43:46.331Z"}, {"entity": "publication", "iuid": "5a675f987fd0410ea0e9f5cec5be6c1b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5a675f987fd0410ea0e9f5cec5be6c1b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5a675f987fd0410ea0e9f5cec5be6c1b"}}, "title": "Brain gene expression in relation to fearfulness in female red junglefowl (Gallus gallus).", "authors": [{"family": "J\u00f6ngren", "given": "M", "initials": "M"}, {"family": "Westander", "given": "J", "initials": "J"}, {"family": "N\u00e4tt", "given": "D", "initials": "D"}, {"family": "Jensen", "given": "P", "initials": "P"}], "type": "journal article", "published": "2010-10-00", "journal": {"volume": "9", "issn": "1601-183X", "issue": "7", "pages": "751-758", "title": "Genes Brain Behav.", "issn-l": null}, "abstract": "The biology of fear is central to animal welfare and has been a major target for selection during domestication. Fear responses were studied in female red junglefowl (RJF), the ancestor of domesticated chickens. A total of 31 females were tested in a ground predator test, an aerial predator test and a tonic immobility (TI) test, in order to assess their level of fearfulness across different situations. Two to six variables from each test were entered into a principal component (PC) analysis, which showed one major fearfulness component (explaining 27% of the variance). Based on the PC scores, four high- and four low-fearful birds were then selected for gene expression analysis. From each of these birds, the midbrain region (including thalamus, hypothalamus, pituitary, mesencephalon, pons, nucleus tractus solitarii and medulla oblongata), was collected and global gene expression compared between groups using a 14k chicken cDNA microarray. There were 13 significantly differentially expressed (DE) genes (based on M > 1 and B > 0; FDR-adjusted P < 0.05) between the fearful and non-fearful females. Among the DE genes, we identified the neuroprotein Axin1, two potential DNA/RNA regulating proteins and a retrotransposon transcript situated in a well-studied quantitative trait loci (QTL) region on chromosome 1, known to affect several domestication-related traits. The differentially expressed genes may be part of a possible molecular mechanism controlling fear responses in fowl.", "doi": "10.1111/j.1601-183X.2010.00612.x", "pmid": "20597989", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "GBB612"}], "notes": [], "created": "2017-05-04T15:01:50.737Z", "modified": "2020-01-21T13:56:02.476Z"}, {"entity": "publication", "iuid": "2053235d85a7403f82a48f1034ca4dac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2053235d85a7403f82a48f1034ca4dac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2053235d85a7403f82a48f1034ca4dac"}}, "title": "A chromatin-remodeling protein is a component of fission yeast mediator.", "authors": [{"family": "Khorosjutina", "given": "Olga", "initials": "O"}, {"family": "Wanrooij", "given": "Paulina H", "initials": "PH"}, {"family": "Walfridsson", "given": "Julian", "initials": "J"}, {"family": "Szilagyi", "given": "Zsolt", "initials": "Z"}, {"family": "Zhu", "given": "Xuefeng", "initials": "X"}, {"family": "Baraznenok", "given": "Vera", "initials": "V"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Gustafsson", "given": "Claes M", "initials": "CM"}], "type": "journal article", "published": "2010-09-24", "journal": {"volume": "285", "issn": "1083-351X", "issue": "39", "pages": "29729-29737", "title": "J. Biol. Chem.", "issn-l": "0021-9258"}, "abstract": "The multiprotein Mediator complex is an important regulator of RNA polymerase II-dependent genes in eukaryotic cells. In contrast to the situation in many other eukaryotes, the conserved Med15 protein is not a stable component of Mediator isolated from fission yeast. We here demonstrate that Med15 exists in a protein complex together with Hrp1, a CHD1 ATP-dependent chromatin-remodeling protein. The Med15-Hrp1 subcomplex is not a component of the core Mediator complex but can interact with the L-Mediator conformation. Deletion of med15(+) and hrp1(+) causes very similar effects on global steady-state levels of mRNA, and genome-wide analyses demonstrate that Med15 associates with a distinct subset of Hrp1-bound gene promoters. Our findings therefore indicate that Mediator may directly influence histone density at regulated promoters.", "doi": "10.1074/jbc.M110.153858", "pmid": "20622008", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "M110.153858"}, {"db": "pmc", "key": "PMC2943280"}], "notes": [], "created": "2017-05-04T15:03:06.026Z", "modified": "2017-05-30T12:39:09.916Z"}, {"entity": "publication", "iuid": "6482892af4c9466ba4c123bb6376350b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6482892af4c9466ba4c123bb6376350b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6482892af4c9466ba4c123bb6376350b"}}, "title": "A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.", "authors": [{"family": "Heinig", "given": "Matthias", "initials": "M"}, {"family": "Petretto", "given": "Enrico", "initials": "E"}, {"family": "Wallace", "given": "Chris", "initials": "C"}, {"family": "Bottolo", "given": "Leonardo", "initials": "L"}, {"family": "Rotival", "given": "Maxime", "initials": "M"}, {"family": "Lu", "given": "Han", "initials": "H"}, {"family": "Li", "given": "Yoyo", "initials": "Y"}, {"family": "Sarwar", "given": "Rizwan", "initials": "R"}, {"family": "Langley", "given": "Sarah R", "initials": "SR"}, {"family": "Bauerfeind", "given": "Anja", "initials": "A"}, {"family": "Hummel", "given": "Oliver", "initials": "O"}, {"family": "Lee", "given": "Young-Ae", "initials": "YA"}, {"family": "Paskas", "given": "Svetlana", "initials": "S"}, {"family": "Rintisch", "given": "Carola", "initials": "C"}, {"family": "Saar", "given": "Kathrin", "initials": "K"}, {"family": "Cooper", "given": "Jason", "initials": "J"}, {"family": "Buchan", "given": "Rachel", "initials": "R"}, {"family": "Gray", "given": "Elizabeth E", "initials": "EE"}, {"family": "Cyster", "given": "Jason G", "initials": "JG"}, {"family": "Cardiogenics Consortium", "given": null, "initials": null}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Hengstenberg", "given": "Christian", "initials": "C"}, {"family": "Maouche", "given": "Seraya", "initials": "S"}, {"family": "Ouwehand", "given": "Willem H", "initials": "WH"}, {"family": "Rice", "given": "Catherine M", "initials": "CM"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Goodall", "given": "Alison H", "initials": "AH"}, {"family": "Schulz", "given": "Herbert", "initials": "H"}, {"family": "Roider", "given": "Helge G", "initials": "HG"}, {"family": "Vingron", "given": "Martin", "initials": "M"}, {"family": "Blankenberg", "given": "Stefan", "initials": "S"}, {"family": "M\u00fcnzel", "given": "Thomas", "initials": "T"}, {"family": "Zeller", "given": "Tanja", "initials": "T"}, {"family": "Szymczak", "given": "Silke", "initials": "S"}, {"family": "Ziegler", "given": "Andreas", "initials": "A"}, {"family": "Tiret", "given": "Laurence", "initials": "L"}, {"family": "Smyth", "given": "Deborah J", "initials": "DJ"}, {"family": "Pravenec", "given": "Michal", "initials": "M"}, {"family": "Aitman", "given": "Timothy J", "initials": "TJ"}, {"family": "Cambien", "given": "Francois", "initials": "F"}, {"family": "Clayton", "given": "David", "initials": "D"}, {"family": "Todd", "given": "John A", "initials": "JA"}, {"family": "Hubner", "given": "Norbert", "initials": "N"}, {"family": "Cook", "given": "Stuart A", "initials": "SA"}], "type": "journal article", "published": "2010-09-23", "journal": {"volume": "467", "issn": "1476-4687", "issue": "7314", "pages": "460-464", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Combined analyses of gene networks and DNA sequence variation can provide new insights into the aetiology of common diseases that may not be apparent from genome-wide association studies alone. Recent advances in rat genomics are facilitating systems-genetics approaches. Here we report the use of integrated genome-wide approaches across seven rat tissues to identify gene networks and the loci underlying their regulation. We defined an interferon regulatory factor 7 (IRF7)-driven inflammatory network (IDIN) enriched for viral response genes, which represents a molecular biomarker for macrophages and which was regulated in multiple tissues by a locus on rat chromosome 15q25. We show that Epstein-Barr virus induced gene 2 (Ebi2, also known as Gpr183), which lies at this locus and controls B lymphocyte migration, is expressed in macrophages and regulates the IDIN. The human orthologous locus on chromosome 13q32 controlled the human equivalent of the IDIN, which was conserved in monocytes. IDIN genes were more likely to associate with susceptibility to type 1 diabetes (T1D)-a macrophage-associated autoimmune disease-than randomly selected immune response genes (P = 8.85\u2009\u00d7\u200910(-6)). The human locus controlling the IDIN was associated with the risk of T1D at single nucleotide polymorphism rs9585056 (P = 7.0\u2009\u00d7\u200910(-10); odds ratio, 1.15), which was one of five single nucleotide polymorphisms in this region associated with EBI2 (GPR183) expression. These data implicate IRF7 network genes and their regulatory locus in the pathogenesis of T1D.", "doi": "10.1038/nature09386", "pmid": "20827270", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "nature09386"}, {"db": "pmc", "key": "PMC3657719"}, {"db": "mid", "key": "EMS49281"}], "notes": [], "created": "2017-05-04T15:00:35.858Z", "modified": "2020-01-21T13:56:02.734Z"}, {"entity": "publication", "iuid": "02a89d31328a4bc681053d56186048cc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/02a89d31328a4bc681053d56186048cc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/02a89d31328a4bc681053d56186048cc"}}, "title": "Pleiotropy in the presence of allelic heterogeneity: alternative genetic models for the influence of APOE on serum LDL, CSF amyloid-\u03b242, and dementia.", "authors": [{"family": "Bennet", "given": "Anna M", "initials": "AM"}, {"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Prince", "given": "Jonathan A", "initials": "JA"}], "type": "comparative study", "published": "2010-09-18", "journal": {"volume": "22", "issn": "1875-8908", "issue": "1", "pages": "129-134", "title": "J. Alzheimers Dis.", "issn-l": "1387-2877"}, "abstract": "The two genetic polymorphisms, rs7412 and rs429358, that collectively form the e2, e3, and e4 alleles of apolipoprotein E (APOE) are among the most widely studied sequence variants in the genome. The predominant model for testing APOE involves the haplotype combinations of e2, e3, and e4 and has been basis of associations with dementia, atherosclerosis, and serum lipid levels. Here, we demonstrate the functional independence of these two component sites, with rs7412 contributing to the majority of variance in serum LDL (p=10-20), whereas rs429358 alone influences variance in CSF amyloid-\u00df42 (A\u00df42) (p=10(-17)). This latter relationship is also reflected in the association of APOE with dementia, where rs429358 strongly influences disease (p=10(-67)), but rs7412 does not. Models based upon e2, e3, and e4 explained less variance for both dementia risk and CSF A\u00df42 than did rs429358 alone. When adjusted for CSF A\u00df42, the association of rs429358 with dementia is greatly reduced but remains significant indicating that APOE polymorphism influences disease by additional mechanisms distinct from A\u00df42 metabolism. We reach four principal conclusion from this study: 1) rs429358 alone is responsible for the association of APOE with dementia; 2) The association of APOE with dementia is substantially mediated by its effect on CNS A\u00df42 levels; 3) The association of APOE with dementia is not mediated by its impact on peripheral lipid metabolism; and 4) The dichotomy of effects of rs429358 and rs7412 represents one of the best examples of genetic pleiotropy for complex traits known and illustrates the importance of allelic heterogeneity in APOE.", "doi": "10.3233/JAD-2010-100864", "pmid": "20847432", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "8053337K12207242"}, {"db": "pmc", "key": "PMC3547982"}, {"db": "mid", "key": "NIHMS404207"}], "notes": [], "created": "2017-05-04T15:00:32.543Z", "modified": "2020-01-21T13:56:00.523Z"}, {"entity": "publication", "iuid": "779f19440cf34645bca610a012f6bacc", "links": {"self": {"href": "https://publications.scilifelab.se/publication/779f19440cf34645bca610a012f6bacc.json"}, "display": {"href": "https://publications.scilifelab.se/publication/779f19440cf34645bca610a012f6bacc"}}, "title": "Trisomy and triploidy are sources of embryo mortality in the zebra finch.", "authors": [{"family": "Forstmeier", "given": "Wolfgang", "initials": "W"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2010-09-07", "journal": {"volume": "277", "issn": "1471-2954", "issue": "1694", "pages": "2655-2660", "title": "Proc. Biol. Sci.", "issn-l": "0962-8452"}, "abstract": "Hatching failure is a surprisingly common phenomenon given that natural selection constantly works against it. In birds, an average of about 10 per cent of eggs across species fail to hatch, often owing to the death of embryos. While embryo mortality owing to inbreeding is both well-documented and evolutionarily plausible, this is not true for other sources of mortality. In fact, the basis for hatching failure in natural populations remains largely unexplained. Here, we demonstrate that embryo mortality in captive zebra finches (Taeniopygia guttata) follows from chromosomal aneuploidy or polyploidy. As part of microsatellite genotyping of a captive breeding population, we found 12 individuals (3.6%) with three alleles among 331 embryos that had died during development, while there were no such cases observed among 1210 adult birds. Subsequent genotyping of 1920 single nucleotide polymorphism markers distributed across the genome in birds with three alleles at microsatellite loci, and in greater than 1000 normal birds, revealed that the aberrant karyotypes involved cases of both trisomies and triploidy. Cases of both maternally and paternally inherited trisomies resulted from non-disjunction during meiosis. Maternally inherited cases of triploidy were attributable to failure of meiosis leading to diploid eggs, while paternally inherited triploidy could have arisen either from diploid sperm or from dispermy. Our initial microsatellite screening set only had the power to detect less than 10 per cent of trisomies and by extrapolation, our data therefore tentatively suggest that trisomy might be a major cause of embryo mortality in zebra finches.", "doi": "10.1098/rspb.2010.0394", "pmid": "20444723", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "rspb.2010.0394"}, {"db": "pmc", "key": "PMC2982043"}], "notes": [], "created": "2017-05-04T15:00:36.777Z", "modified": "2020-01-21T13:56:03.112Z"}, {"entity": "publication", "iuid": "8ee4600e144f43e38d5812d0b02725f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ee4600e144f43e38d5812d0b02725f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ee4600e144f43e38d5812d0b02725f0"}}, "title": "Small-molecule screening using a whole-cell viral replication reporter gene assay identifies 2-{[2-(benzoylamino)benzoyl]amino}-benzoic acid as a novel antiadenoviral compound.", "authors": [{"family": "Andersson", "given": "Emma K", "initials": "EK"}, {"family": "Strand", "given": "M\u00e5rten", "initials": "M"}, {"family": "Edlund", "given": "Karin", "initials": "K"}, {"family": "Lindman", "given": "Kristina", "initials": "K"}, {"family": "Enquist", "given": "Per-Anders", "initials": "P"}, {"family": "Spjut", "given": "Sara", "initials": "S"}, {"family": "Allard", "given": "Annika", "initials": "A"}, {"family": "Elofsson", "given": "Mikael", "initials": "M"}, {"family": "Mei", "given": "Ya-Fang", "initials": "Y"}, {"family": "Wadell", "given": "G\u00f6ran", "initials": "G"}], "type": "journal article", "published": "2010-09-00", "journal": {"volume": "54", "issn": "1098-6596", "issue": "9", "pages": "3871-3877", "title": "Antimicrob. Agents Chemother.", "issn-l": "0066-4804"}, "abstract": "Adenovirus infections are widespread in society and are occasionally associated with severe, but rarely with life-threatening, disease in otherwise healthy individuals. In contrast, adenovirus infections present a real threat to immunocompromised individuals and can result in disseminated and fatal disease. The number of patients undergoing immunosuppressive therapy for solid organ or hematopoietic stem cell transplantation is steadily increasing, as is the number of AIDS patients, and this makes the problem of adenovirus infections even more urgent to solve. There is no formally approved treatment of adenovirus infections today, and existing antiviral agents evaluated for their antiadenoviral effect give inconsistent results. We have developed a whole cell-based assay for high-throughput screening of potential antiadenoviral compounds. The assay is unique in that it is based on a replication-competent adenovirus type 11p green fluorescent protein (GFP)-expressing vector (RCAd11pGFP). This allows measurement of fluorescence changes as a direct result of RCAd11pGFP genome expression. Using this assay, we have screened 9,800 commercially available small organic compounds. Initially, we observed approximately 400 compounds that inhibited adenovirus expression in vitro by > or = 80%, but only 24 were later confirmed as dose-dependent inhibitors of adenovirus. One compound in particular, 2-{[2-(benzoylamino)benzoyl]amino}-benzoic acid, turned out to be a potent inhibitor of adenovirus replication.", "doi": "10.1128/AAC.00203-10", "pmid": "20585112", "labels": {"Chemical Biology Consortium Sweden": "Collaborative"}, "xrefs": [{"db": "pii", "key": "AAC.00203-10"}, {"db": "pmc", "key": "PMC2935025"}], "notes": "Laboratories for Chemical Biology Ume\u00e5 (LCBU)", "created": "2017-05-04T14:56:36.118Z", "modified": "2025-10-17T13:04:30.833Z"}, {"entity": "publication", "iuid": "8b975fdad1da4f849d445f32fd8883c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8b975fdad1da4f849d445f32fd8883c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8b975fdad1da4f849d445f32fd8883c8"}}, "title": "Profiling protein expression and interactions: proximity ligation as a tool for personalized medicine.", "authors": [{"family": "Blokzijl", "given": "A", "initials": "A"}, {"family": "Friedman", "given": "M", "initials": "M"}, {"family": "Pont\u00e9n", "given": "F", "initials": "F"}, {"family": "Landegren", "given": "U", "initials": "U"}], "type": "journal article", "published": "2010-09-00", "journal": {"volume": "268", "issn": "1365-2796", "issue": "3", "pages": "232-245", "title": "J. Intern. Med.", "issn-l": "0954-6820"}, "abstract": "The ability to detect very low levels of expressed proteins has enormous potential for early diagnostics and intervention at curable stages of disease. An extended range of targets such as interacting or post-translationally modified proteins can further improve the potential for diagnostics and patient stratification, and for monitoring response to treatment. These are critical building blocks for personalized treatment strategies to manage disease. The past few decades have seen a remarkably improved understanding of the molecular basis of disease in general, and of tumour formation and progression in particular. This accumulated knowledge creates opportunities to develop drugs that specifically target molecules or molecular complexes critical for survival and expansion of tumour cells. However, tumours are highly variable between patients, necessitating the development of diagnostic tools to individualize treatment through parallel analysis of sets of biomarkers. The proximity ligation assay (PLA) can address many of the requirements for advanced molecular analysis. The method builds on the principle that recognition of target proteins by two, three or more antibodies can bring in proximity DNA strands attached to the antibodies. The DNA strands can then participate in ligation reactions, giving rise to molecules that are amplified for highly sensitive detection. PLA is particularly well suited for sensitive, specific and multiplexed analysis of protein expression, post-translational modifications and protein-protein interactions. The analysis of this extended range of biomarkers will prove critical for the development and implementation of personalized medicine.", "doi": "10.1111/j.1365-2796.2010.02256.x", "pmid": "20695973", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "JIM2256"}], "notes": [], "created": "2017-05-04T14:55:20.761Z", "modified": "2023-04-14T13:56:32.097Z"}, {"entity": "publication", "iuid": "dbdc49d5da184ad19afdce0efd321237", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dbdc49d5da184ad19afdce0efd321237.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dbdc49d5da184ad19afdce0efd321237"}}, "title": "Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests.", "authors": [{"family": "Wallander", "given": "H\u00e5kan", "initials": "H"}, {"family": "Johansson", "given": "Ulf", "initials": "U"}, {"family": "Sterkenburg", "given": "Erica", "initials": "E"}, {"family": "Brandstr\u00f6m Durling", "given": "Mikael", "initials": "M"}, {"family": "Lindahl", "given": "Bj\u00f6rn D", "initials": "BD"}], "type": "journal article", "published": "2010-09-00", "journal": {"volume": "187", "issn": "1469-8137", "issue": "4", "pages": "1124-1134", "title": "New Phytol.", "issn-l": "0028-646X"}, "abstract": "*Here, species composition and biomass production of actively growing ectomycorrhizal (EM) mycelia were studied over the rotation period of managed Norway spruce (Picea abies) stands in south-western Sweden. *The EM mycelia were collected using ingrowth mesh bags incubated in the forest soil during one growing season. Fungal biomass was estimated by ergosterol analysis and the EM species were identified by 454 sequencing of internal transcribed spacer (ITS) amplicons. Nutrient availability and the fungal biomass in soil samples were also estimated. *Biomass production peaked in young stands (10-30 yr old) before the first thinning phase. Tylospora fibrillosa dominated the EM community, especially in these young stands, where it constituted 80% of the EM amplicons derived from the mesh bags. Species richness increased in older stands. *The establishment of EM mycelial networks in young Norway spruce stands requires large amounts of carbon, while much less is needed to sustain the EM community in older stands. The variation in EM biomass production over the rotation period has implications for carbon sequestration rates in forest soils.", "doi": "10.1111/j.1469-8137.2010.03324.x", "pmid": "20561206", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "NPH3324"}], "notes": [], "created": "2017-05-04T14:57:13.449Z", "modified": "2020-01-21T13:56:05.624Z"}, {"entity": "publication", "iuid": "a343b5d7ca1f49f7a9dad4764c15835f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a343b5d7ca1f49f7a9dad4764c15835f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a343b5d7ca1f49f7a9dad4764c15835f"}}, "title": "High-density screening reveals a different spectrum of genomic aberrations in chronic lymphocytic leukemia patients with 'stereotyped' IGHV3-21 and IGHV4-34 B-cell receptors.", "authors": [{"family": "Marincevic", "given": "Millaray", "initials": "M"}, {"family": "Cahill", "given": "Nicola", "initials": "N"}, {"family": "Gunnarsson", "given": "Rebeqa", "initials": "R"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Mansouri", "given": "Mahmoud", "initials": "M"}, {"family": "G\u00f6ransson", "given": "Hanna", "initials": "H"}, {"family": "Rasmussen", "given": "Markus", "initials": "M"}, {"family": "Jansson", "given": "Mattias", "initials": "M"}, {"family": "Ryan", "given": "Fergus", "initials": "F"}, {"family": "Karlsson", "given": "Karin", "initials": "K"}, {"family": "Adami", "given": "Hans-Olov", "initials": "HO"}, {"family": "Davi", "given": "Fred", "initials": "F"}, {"family": "Jurlander", "given": "Jesper", "initials": "J"}, {"family": "Juliusson", "given": "Gunnar", "initials": "G"}, {"family": "Stamatopoulos", "given": "Kostas", "initials": "K"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}], "type": "journal article", "published": "2010-09-00", "journal": {"volume": "95", "issn": "1592-8721", "issue": "9", "pages": "1519-1525", "title": "Haematologica", "issn-l": "0390-6078"}, "abstract": "The existence of multiple subsets of chronic lymphocytic leukemia expressing 'stereotyped' B-cell receptors implies the involvement of antigen(s) in leukemogenesis. Studies also indicate that 'stereotypy' may influence the clinical course of patients with chronic lymphocytic leukemia, for example, in subsets with stereotyped IGHV3-21 and IGHV4-34 B-cell receptors; however, little is known regarding the genomic profile of patients in these subsets.\n\nWe applied 250K single nucleotide polymorphism-arrays to study copy-number aberrations and copy-number neutral loss-of-heterozygosity in patients with stereotyped IGHV3-21 (subset #2, n=29), stereotyped IGHV4-34 (subset #4, n=17; subset #16, n=8) and non-subset #2 IGHV3-21 (n=13) and non-subset #4/16 IGHV4-34 (n=34) patients.\n\nOver 90% of patients in subset #2 and non-subset #2 carried copy-number aberrations, whereas 75-76% of patients in subset #4 and subset #16 showed copy-number aberrations. Subset #2 and non-subset #2 patients also displayed a higher average number of aberrations compared to patients in subset #4. Deletion of 13q was the only known recurrent aberration detected in subset #4 (35%); this aberration was even more frequent in subset #2 (79%). del(11q) was more frequent in subset #2 and non-subset #2 (31% and 23%) patients than in subset #4 and non-subset #4/16 patients. Recurrent copy-number neutral loss-of-heterozygosity was mainly detected on chromosome 13q, independently of B-cell receptor stereotypy.\n\nGenomic aberrations were more common in subset #2 and non-subset #2 than in subset #4. The particularly high frequency of del(11q) in subset #2 may be linked to the adverse outcome reported for patients in this subset. Conversely, the lower prevalence of copy-number aberrations and the absence of poor-prognostic aberrations in subset #4 may reflect an inherently low-proliferative disease, which would prevent accumulation of genomic alterations.", "doi": "10.3324/haematol.2009.021014", "pmid": "20421269", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "haematol.2009.021014"}, {"db": "pmc", "key": "PMC2930953"}], "notes": [], "created": "2017-05-04T15:02:49.751Z", "modified": "2017-05-30T12:35:02.795Z"}, {"entity": "publication", "iuid": "5b63dc3ea73541608890047d4c582417", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5b63dc3ea73541608890047d4c582417.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5b63dc3ea73541608890047d4c582417"}}, "title": "Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency.", "authors": [{"family": "Ferreira", "given": "Ricardo C", "initials": "RC"}, {"family": "Pan-Hammarstr\u00f6m", "given": "Qiang", "initials": "Q"}, {"family": "Graham", "given": "Robert R", "initials": "RR"}, {"family": "Gateva", "given": "Vesela", "initials": "V"}, {"family": "Font\u00e1n", "given": "Gumersindo", "initials": "G"}, {"family": "Lee", "given": "Annette T", "initials": "AT"}, {"family": "Ortmann", "given": "Ward", "initials": "W"}, {"family": "Urcelay", "given": "Elena", "initials": "E"}, {"family": "Fern\u00e1ndez-Arquero", "given": "Miguel", "initials": "M"}, {"family": "N\u00fa\u00f1ez", "given": "Concepci\u00f3n", "initials": "C"}, {"family": "Jorgensen", "given": "Gudmundur", "initials": "G"}, {"family": "Ludviksson", "given": "Bj\u00f6rn R", "initials": "BR"}, {"family": "Koskinen", "given": "Sinikka", "initials": "S"}, {"family": "Haimila", "given": "Katri", "initials": "K"}, {"family": "Clark", "given": "Hilary F", "initials": "HF"}, {"family": "Klareskog", "given": "Lars", "initials": "L"}, {"family": "Gregersen", "given": "Peter K", "initials": "PK"}, {"family": "Behrens", "given": "Timothy W", "initials": "TW"}, {"family": "Hammarstr\u00f6m", "given": "Lennart", "initials": "L"}], "type": "journal article", "published": "2010-09-00", "journal": {"volume": "42", "issn": "1546-1718", "issue": "9", "pages": "777-780", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "To understand the genetic predisposition to selective immunoglobulin A deficiency (IgAD), we performed a genome-wide association study in 430 affected individuals (cases) from Sweden and Iceland and 1,090 ethnically matched controls, and we performed replication studies in two independent European cohorts. In addition to the known association of HLA with IgAD, we identified association with a nonsynonymous variant in IFIH1 (rs1990760G>A, P = 7.3 x 10(-10)) which was previously associated with type 1 diabetes and systemic lupus erythematosus. Variants in CLEC16A, another known autoimmunity locus, showed suggestive evidence for association (rs6498142C>G, P = 1.8 x 10(-7)), and 29 additional loci were identified with P < 5 x 10(-5). A survey in IgAD of 118 validated non-HLA autoimmunity loci indicated a significant enrichment for association with autoimmunity loci as compared to non-autoimmunity loci (P = 9.0 x 10(-4)) or random SNPs across the genome (P < 0.0001). These findings support the hypothesis that autoimmune mechanisms may contribute to the pathogenesis of IgAD.", "doi": "10.1038/ng.644", "pmid": "20694011", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "ng.644"}], "notes": [], "created": "2017-05-04T15:03:28.615Z", "modified": "2017-05-30T12:43:51.041Z"}, {"entity": "publication", "iuid": "48f20361419045e3bacde5fd8576433b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/48f20361419045e3bacde5fd8576433b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/48f20361419045e3bacde5fd8576433b"}}, "title": "Expression of the RNA-binding protein RBM3 is associated with a favourable prognosis and cisplatin sensitivity in epithelial ovarian cancer.", "authors": [{"family": "Ehl\u00e9n", "given": "Asa", "initials": "A"}, {"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Nodin", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "O'Connor", "given": "Darran P", "initials": "DP"}, {"family": "Eberhard", "given": "Jakob", "initials": "J"}, {"family": "Alvarado-Kristensson", "given": "Maria", "initials": "M"}, {"family": "Jeffrey", "given": "Ian B", "initials": "IB"}, {"family": "Manjer", "given": "Jonas", "initials": "J"}, {"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": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Jirstr\u00f6m", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2010-08-20", "journal": {"volume": "8", "issn": "1479-5876", "issue": null, "pages": "78", "title": "J Transl Med", "issn-l": "1479-5876"}, "abstract": "We recently demonstrated that increased expression of the RNA-binding protein RBM3 is associated with a favourable prognosis in breast cancer. The aim of this study was to examine the prognostic value of RBM3 mRNA and protein expression in epithelial ovarian cancer (EOC) and the cisplatin response upon RBM3 depletion in a cisplatin-sensitive ovarian cancer cell line.\n\nRBM3 mRNA expression was analysed in tumors from a cohort of 267 EOC cases (Cohort I) and RBM3 protein expression was analysed using immunohistochemistry (IHC) in an independent cohort of 154 prospectively collected EOC cases (Cohort II). Kaplan Meier analysis and Cox proportional hazards modelling were applied to assess the relationship between RBM3 and recurrence free survival (RFS) and overall survival (OS). Immunoblotting and IHC were used to examine the expression of RBM3 in a cisplatin-resistant ovarian cancer cell line A2780-Cp70 and its cisplatin-responsive parental cell line A2780. The impact of RBM3 on cisplatin response in EOC was assessed using siRNA-mediated silencing of RBM3 in A2780 cells followed by cell viability assay and cell cycle analysis.\n\nIncreased RBM3 mRNA expression was associated with a prolonged RFS (HR = 0.64, 95% CI = 0.47-0.86, p = 0.003) and OS (HR = 0.64, 95% CI = 0.44-0.95, p = 0.024) in Cohort I. Multivariate analysis confirmed that RBM3 mRNA expression was an independent predictor of a prolonged RFS, (HR = 0.61, 95% CI = 0.44-0.84, p = 0.003) and OS (HR = 0.62, 95% CI = 0.41-0.95; p = 0.028) in Cohort I. In Cohort II, RBM3 protein expression was associated with a prolonged OS (HR = 0.53, 95% CI = 0.35-0.79, p = 0.002) confirmed by multivariate analysis (HR = 0.61, 95% CI = 0.40-0.92, p = 0.017). RBM3 mRNA and protein expression levels were significantly higher in the cisplatin sensitive A2780 cell line compared to the cisplatin resistant A2780-Cp70 derivative. siRNA-mediated silencing of RBM3 expression in the A2780 cells resulted in a decreased sensitivity to cisplatin as demonstrated by increased cell viability and reduced proportion of cells arrested in the G2/M-phase.\n\nThese data demonstrate that RBM3 expression is associated with cisplatin sensitivity in vitro and with a good prognosis in EOC. Taken together these findings suggest that RBM3 may be a useful prognostic and treatment predictive marker in EOC.", "doi": "10.1186/1479-5876-8-78", "pmid": "20727170", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1479-5876-8-78"}, {"db": "pmc", "key": "PMC2936876"}], "notes": [], "created": "2017-05-04T14:55:44.411Z", "modified": "2021-07-08T13:44:33.212Z"}, {"entity": "publication", "iuid": "6e72f003dd044238899adec74a9c8680", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6e72f003dd044238899adec74a9c8680.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6e72f003dd044238899adec74a9c8680"}}, "title": "Familial cutaneous melanoma.", "authors": [{"family": "Hansson", "given": "Johan", "initials": "J"}], "type": "journal article", "published": "2010-08-07", "journal": {"volume": "685", "issn": "0065-2598", "issue": null, "pages": "134-145", "title": "Adv. Exp. Med. Biol.", "issn-l": null}, "abstract": "Approximately 5-10 % of all cutaneous melanomas occur in families with hereditary melanoma predisposition. Worldwide, approximately 20-40% of kindreds with familial elanoma harbor germline mutations in the CDKN2A gene, located on chromosome 9p21, which encodes two different proteins, p16INK4 and p14ARF, both involved in regulation of cell cycle progression and induction of senescence. In different populations several recurring CDKN2A founder mutations have been described. The risk of melanoma in CDKN2A mutations carriers varies between populations and is higher in regions with high sun exposure and high incidence of melanoma in the general population. Some CDKN2A mutations have been associated not only with melanoma but also with increased risk of other malignancies--most notably pancreatic carcinoma. A much smaller number of families have germline mutations in the CDK4 gene on chromosome 12q14, encoding a cyclin dependent kinase which normally interacts with p16INK4A. The management of families with hereditary melanoma is discussed.", "doi": "10.1007/978-1-4419-6448-9_13", "pmid": "20687502", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:57:09.045Z", "modified": "2020-01-21T13:56:09.194Z"}, {"entity": "publication", "iuid": "a10e1b676335416d8f4800f5965390c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a10e1b676335416d8f4800f5965390c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a10e1b676335416d8f4800f5965390c5"}}, "title": "Biological, clinical and population relevance of 95 loci for blood lipids.", "authors": [{"family": "Teslovich", "given": "Tanya M", "initials": "TM"}, {"family": "Musunuru", "given": "Kiran", "initials": "K"}, {"family": "Smith", "given": "Albert V", "initials": "AV"}, {"family": "Edmondson", "given": "Andrew C", "initials": "AC"}, {"family": "Stylianou", "given": "Ioannis M", "initials": "IM"}, {"family": "Koseki", "given": "Masahiro", "initials": "M"}, {"family": "Pirruccello", "given": "James P", "initials": "JP"}, {"family": "Ripatti", "given": "Samuli", "initials": "S"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Willer", "given": "Cristen J", "initials": "CJ"}, {"family": "Johansen", "given": "Christopher T", "initials": "CT"}, {"family": "Fouchier", "given": "Sigrid W", "initials": "SW"}, {"family": "Isaacs", "given": "Aaron", "initials": "A"}, {"family": "Peloso", "given": "Gina M", "initials": "GM"}, {"family": "Barbalic", "given": "Maja", "initials": "M"}, {"family": "Ricketts", "given": "Sally L", "initials": "SL"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "Aulchenko", "given": "Yurii S", "initials": "YS"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Feitosa", "given": "Mary F", "initials": "MF"}, {"family": "Chambers", "given": "John", "initials": "J"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Li", "given": "Xiaohui", "initials": "X"}, {"family": "Guo", "given": "Xiuqing", "initials": "X"}, {"family": "Li", "given": "Mingyao", "initials": "M"}, {"family": "Shin Cho", "given": "Yoon", "initials": "Y"}, {"family": "Jin Go", "given": "Min", "initials": "M"}, {"family": "Jin Kim", "given": "Young", "initials": "Y"}, {"family": "Lee", "given": "Jong-Young", "initials": "JY"}, {"family": "Park", "given": "Taesung", "initials": "T"}, {"family": "Kim", "given": "Kyunga", "initials": "K"}, {"family": "Sim", "given": "Xueling", "initials": "X"}, {"family": "Twee-Hee Ong", "given": "Rick", "initials": "R"}, {"family": "Croteau-Chonka", "given": "Damien C", "initials": "DC"}, {"family": "Lange", "given": "Leslie A", "initials": "LA"}, {"family": "Smith", "given": "Joshua D", "initials": "JD"}, {"family": "Song", "given": "Kijoung", "initials": "K"}, {"family": "Hua Zhao", "given": "Jing", "initials": "J"}, {"family": "Yuan", "given": "Xin", "initials": "X"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Lamina", "given": "Claudia", "initials": "C"}, {"family": "Ziegler", "given": "Andreas", "initials": "A"}, {"family": "Zhang", "given": "Weihua", "initials": "W"}, {"family": "Zee", "given": "Robert Y L", "initials": "RY"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Willemsen", "given": "Gonneke", "initials": "G"}, {"family": "Wichmann", "given": "H-Erich", "initials": "HE"}, {"family": "Whitfield", "given": "John B", "initials": "JB"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Waeber", "given": "G\u00e9rard", "initials": "G"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Uda", "given": "Manuela", "initials": "M"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Thompson", "given": "John R", "initials": "JR"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Surakka", "given": "Ida", "initials": "I"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Spector", "given": "Tim D", "initials": "TD"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Smit", "given": "Johannes H", "initials": "JH"}, {"family": "Sinisalo", "given": "Juha", "initials": "J"}, {"family": "Silander", "given": "Kaisa", "initials": "K"}, {"family": "Sijbrands", "given": "Eric J G", "initials": "EJ"}, {"family": "Scuteri", "given": "Angelo", "initials": "A"}, {"family": "Scott", "given": "James", "initials": "J"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Sanna", "given": "Serena", "initials": "S"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Saharinen", "given": "Juha", "initials": "J"}, {"family": "Sabatti", "given": "Chiara", "initials": "C"}, {"family": "Ruokonen", "given": "Aimo", "initials": "A"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Roberts", "given": "Robert", "initials": "R"}, {"family": "Rieder", "given": "Mark", "initials": "M"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Pramstaller", "given": "Peter P", "initials": "PP"}, {"family": "Pichler", "given": "Irene", "initials": "I"}, {"family": "Perola", "given": "Markus", "initials": "M"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BW"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Pattaro", "given": "Cristian", "initials": "C"}, {"family": "Parker", "given": "Alex N", "initials": "AN"}, {"family": "Pare", "given": "Guillaume", "initials": "G"}, {"family": "Oostra", "given": "Ben A", "initials": "BA"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}, {"family": "Nieminen", "given": "Markku S", "initials": "MS"}, {"family": "Nickerson", "given": "Deborah A", "initials": "DA"}, {"family": "Montgomery", "given": "Grant W", "initials": "GW"}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "McPherson", "given": "Ruth", "initials": "R"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "McArdle", "given": "Wendy", "initials": "W"}, {"family": "Masson", "given": "David", "initials": "D"}, {"family": "Martin", "given": "Nicholas G", "initials": "NG"}, {"family": "Marroni", "given": "Fabio", "initials": "F"}, {"family": "Mangino", "given": "Massimo", "initials": "M"}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PK"}, {"family": "Lucas", "given": "Gavin", "initials": "G"}, {"family": "Luben", "given": "Robert", "initials": "R"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Lokki", "given": "Marja-Liisa", "initials": "ML"}, {"family": "Lettre", "given": "Guillaume", "initials": "G"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Launer", "given": "Lenore J", "initials": "LJ"}, {"family": "Lakatta", "given": "Edward G", "initials": "EG"}, {"family": "Laaksonen", "given": "Reijo", "initials": "R"}, {"family": "Kyvik", "given": "Kirsten O", "initials": "KO"}, {"family": "Kronenberg", "given": "Florian", "initials": "F"}, {"family": "K\u00f6nig", "given": "Inke R", "initials": "IR"}, {"family": "Khaw", "given": "Kay-Tee", "initials": "KT"}, {"family": "Kaprio", "given": "Jaakko", "initials": "J"}, {"family": "Kaplan", "given": "Lee M", "initials": "LM"}, {"family": "Johansson", "given": "Asa", "initials": "A"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Janssens", "given": "A Cecile J W", "initials": "AC"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Igl", "given": "Wilmar", "initials": "W"}, {"family": "Kees Hovingh", "given": "G", "initials": "G"}, {"family": "Hottenga", "given": "Jouke-Jan", "initials": "JJ"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Hicks", "given": "Andrew A", "initials": "AA"}, {"family": "Hengstenberg", "given": "Christian", "initials": "C"}, {"family": "Heid", "given": "Iris M", "initials": "IM"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Havulinna", "given": "Aki S", "initials": "AS"}, {"family": "Hastie", "given": "Nicholas D", "initials": "ND"}, {"family": "Harris", "given": "Tamara B", "initials": "TB"}, {"family": "Haritunians", "given": "Talin", "initials": "T"}, {"family": "Hall", "given": "Alistair S", "initials": "AS"}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}, {"family": "Guiducci", "given": "Candace", "initials": "C"}, {"family": "Groop", "given": "Leif C", "initials": "LC"}, {"family": "Gonzalez", "given": "Elena", "initials": "E"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Freimer", "given": "Nelson B", "initials": "NB"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Erdmann", "given": "Jeanette", "initials": "J"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Ejebe", "given": "Kenechi G", "initials": "KG"}, {"family": "D\u00f6ring", "given": "Angela", "initials": "A"}, {"family": "Dominiczak", "given": "Anna F", "initials": "AF"}, {"family": "Demissie", "given": "Serkalem", "initials": "S"}, {"family": "Deloukas", "given": "Panagiotis", "initials": "P"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJ"}, {"family": "de Faire", "given": "Ulf", "initials": "U"}, {"family": "Crawford", "given": "Gabriel", "initials": "G"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Chen", "given": "Yii-der I", "initials": "YD"}, {"family": "Caulfield", "given": "Mark J", "initials": "MJ"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "Burtt", "given": "Noel P", "initials": "NP"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Boekholdt", "given": "S Matthijs", "initials": "SM"}, {"family": "Bergman", "given": "Richard N", "initials": "RN"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Bandinelli", "given": "Stefania", "initials": "S"}, {"family": "Ballantyne", "given": "Christie M", "initials": "CM"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Quertermous", "given": "Thomas", "initials": "T"}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "Seielstad", "given": "Mark", "initials": "M"}, {"family": "Wong", "given": "Tien Y", "initials": "TY"}, {"family": "Tai", "given": "E-Shyong", "initials": "ES"}, {"family": "Feranil", "given": "Alan B", "initials": "AB"}, {"family": "Kuzawa", "given": "Christopher W", "initials": "CW"}, {"family": "Adair", "given": "Linda S", "initials": "LS"}, {"family": "Taylor", "given": "Herman A", "initials": "HA"}, {"family": "Borecki", "given": "Ingrid B", "initials": "IB"}, {"family": "Gabriel", "given": "Stacey B", "initials": "SB"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Gudnason", "given": "Vilmundur", "initials": "V"}, {"family": "Krauss", "given": "Ronald M", "initials": "RM"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Ordovas", "given": "Jose M", "initials": "JM"}, {"family": "Munroe", "given": "Patricia B", "initials": "PB"}, {"family": "Kooner", "given": "Jaspal S", "initials": "JS"}, {"family": "Tall", "given": "Alan R", "initials": "AR"}, {"family": "Hegele", "given": "Robert A", "initials": "RA"}, {"family": "Kastelein", "given": "John J P", "initials": "JJ"}, {"family": "Schadt", "given": "Eric E", "initials": "EE"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Mooser", "given": "Vincent", "initials": "V"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Reilly", "given": "Muredach P", "initials": "MP"}, {"family": "Samani", "given": "Nilesh J", "initials": "NJ"}, {"family": "Schunkert", "given": "Heribert", "initials": "H"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Sandhu", "given": "Manjinder S", "initials": "MS"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Rader", "given": "Daniel J", "initials": "DJ"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Peltonen", "given": "Leena", "initials": "L"}, {"family": "Abecasis", "given": "Gon\u00e7alo R", "initials": "GR"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}], "type": "journal article", "published": "2010-08-05", "journal": {"volume": "466", "issn": "1476-4687", "issue": "7307", "pages": "707-713", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Plasma concentrations of total cholesterol, low-density lipoprotein cholesterol, high-density lipoprotein cholesterol and triglycerides are among the most important risk factors for coronary artery disease (CAD) and are targets for therapeutic intervention. We screened the genome for common variants associated with plasma lipids in >100,000 individuals of European ancestry. Here we report 95 significantly associated loci (P < 5 x 10(-8)), with 59 showing genome-wide significant association with lipid traits for the first time. The newly reported associations include single nucleotide polymorphisms (SNPs) near known lipid regulators (for example, CYP7A1, NPC1L1 and SCARB1) as well as in scores of loci not previously implicated in lipoprotein metabolism. The 95 loci contribute not only to normal variation in lipid traits but also to extreme lipid phenotypes and have an impact on lipid traits in three non-European populations (East Asians, South Asians and African Americans). Our results identify several novel loci associated with plasma lipids that are also associated with CAD. Finally, we validated three of the novel genes-GALNT2, PPP1R3B and TTC39B-with experiments in mouse models. Taken together, our findings provide the foundation to develop a broader biological understanding of lipoprotein metabolism and to identify new therapeutic opportunities for the prevention of CAD.", "doi": "10.1038/nature09270", "pmid": "20686565", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "nature09270"}, {"db": "pmc", "key": "PMC3039276"}, {"db": "mid", "key": "NIHMS213289"}], "notes": [], "created": "2017-10-30T13:58:08.229Z", "modified": "2020-01-21T13:56:08.485Z"}, {"entity": "publication", "iuid": "6c9b8f509dd04fe083834cb341627815", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6c9b8f509dd04fe083834cb341627815.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6c9b8f509dd04fe083834cb341627815"}}, "title": "Topoisomerase I amplification in melanoma is associated with more advanced tumours and poor prognosis.", "authors": [{"family": "Ryan", "given": "Denise", "initials": "D"}, {"family": "Rafferty", "given": "Mairin", "initials": "M"}, {"family": "Hegarty", "given": "Shauna", "initials": "S"}, {"family": "O'Leary", "given": "Patrick", "initials": "P"}, {"family": "Faller", "given": "William", "initials": "W"}, {"family": "Gremel", "given": "Gabriela", "initials": "G"}, {"family": "Bergqvist", "given": "Michael", "initials": "M"}, {"family": "Agnarsdottir", "given": "Margret", "initials": "M"}, {"family": "Str\u00f6mberg", "given": "Sara", "initials": "S"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Millikan", "given": "Robert C", "initials": "RC"}, {"family": "Dervan", "given": "Peter A", "initials": "PA"}, {"family": "Gallagher", "given": "William M", "initials": "WM"}], "type": "journal article", "published": "2010-08-00", "journal": {"volume": "23", "issn": "1755-148X", "issue": "4", "pages": "542-553", "title": "Pigment Cell Melanoma Res", "issn-l": "1755-1471"}, "abstract": "In this study, we used array-comparative genomic hybridization (aCGH) and fluorescent in situ hybridization (FISH) to examine genetic aberrations in melanoma cell lines and tissues. Array-comparative genomic hybridization revealed that the most frequent genetic changes found in melanoma cell lines were amplifications on chromosomes 7p and 20q, along with disruptions on Chr 9, 10, 11, 12, 22 and Y. Validation of the results using FISH on tissue microarrays (TMAs) identified TOP1 as being amplified in melanoma tissues. TOP1 amplification was detected in a high percentage (33%) of tumours and was associated with thicker, aggressive tumours. These results show that TOP1 amplification is associated with advanced tumours and poor prognosis in melanoma. These observations open the possibility that TOP1-targeted therapeutics may be of benefit in a particular subgroup of advanced stage melanoma patients.", "doi": "10.1111/j.1755-148X.2010.00720.x", "pmid": "20465595", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "PCR720"}], "notes": [], "created": "2017-05-04T14:55:45.011Z", "modified": "2017-05-30T12:54:47.926Z"}, {"entity": "publication", "iuid": "8a99d4f575d94e718e977888097b9404", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8a99d4f575d94e718e977888097b9404.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8a99d4f575d94e718e977888097b9404"}}, "title": "The role of IL-1beta in reduced IL-7 production by stromal and epithelial cells: a model for impaired T-cell numbers in the gut during HIV-1 infection.", "authors": [{"family": "Thang", "given": "P H", "initials": "PH"}, {"family": "Ruffin", "given": "N", "initials": "N"}, {"family": "Brodin", "given": "D", "initials": "D"}, {"family": "Rethi", "given": "B", "initials": "B"}, {"family": "Cam", "given": "P D", "initials": "PD"}, {"family": "Hien", "given": "N T", "initials": "NT"}, {"family": "Lopalco", "given": "L", "initials": "L"}, {"family": "Vivar", "given": "N", "initials": "N"}, {"family": "Chiodi", "given": "F", "initials": "F"}], "type": "journal article", "published": "2010-08-00", "journal": {"volume": "268", "issn": "1365-2796", "issue": "2", "pages": "181-193", "title": "J. Intern. Med.", "issn-l": "0954-6820"}, "abstract": "Interleukin (IL)-7 is a key cytokine in T-cell homeostasis. Stromal cells, intestinal epithelial cells and keratinocytes are known to produce this cytokine. The mechanisms and cellular factors regulating IL-7 production are still unclear. We assessed whether IL-1beta and interferon (IFN)-gamma, cytokines produced during inflammatory conditions, may impact on IL-7 production.\n\nWe used human intestinal epithelial cells (DLD-1 cell line) and bone marrow stromal cells (HS27 cell line), known to produce IL-7; IL-7 production was evaluated at the mRNA and protein levels. To assess whether treatment of HS27 cells with IL-1beta and/or IFN-gamma leads to changes in the gene expression of cytokines, Toll-like receptors (TLRs) and chemokines, we analysed gene expression profiles using the whole-genome microarray Human Gene 1.0 ST.\n\nWe found that IFN-gamma enhanced the expression of IL-7 mRNA (P < 0.001) in both cell lines. IL-1beta treatment led to a significant down-regulation (P < 0.001) of IL-7 mRNA expression in both cell lines. The IL-7 concentration in supernatants collected from treated DLD-1 and HS27 cell cultures reflected the trend of IL-7 mRNA levels. The gene profiles revealed dramatic changes in expression of cytokines and their receptors (IL-7/IL-7R alpha; IL-1alpha,IL-1beta/IL-1R1; IFN-gamma/IFN-gammaR1), of IFN regulatory factors (IRF-1 and 2), of TLRs and of important chemo-attractants for T cells. The microarray results were verified by additional methods.\n\nOur results are discussed in the setting of inflammation and T-cell survival in the gut compartment during HIV-1 infection where stromal and epithelial cells may produce factors that contribute to impaired IL-7 homeostasis and homing of T cells.", "doi": "10.1111/j.1365-2796.2010.02241.x", "pmid": "20497296", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "JIM2241"}], "notes": [], "created": "2017-05-04T15:03:06.625Z", "modified": "2017-05-30T12:39:19.247Z"}, {"entity": "publication", "iuid": "6f401df4058b43149303983209d73283", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6f401df4058b43149303983209d73283.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6f401df4058b43149303983209d73283"}}, "title": "Sex-linked barring in chickens is controlled by the CDKN2A /B tumour suppressor locus.", "authors": [{"family": "Hellstr\u00f6m", "given": "Anders R", "initials": "AR"}, {"family": "Sundstr\u00f6m", "given": "Elisabeth", "initials": "E"}, {"family": "Gunnarsson", "given": "Ulrika", "initials": "U"}, {"family": "Bed'Hom", "given": "Bertrand", "initials": "B"}, {"family": "Tixier-Boichard", "given": "Michele", "initials": "M"}, {"family": "Honaker", "given": "Christa F", "initials": "CF"}, {"family": "Sahlqvist", "given": "Anna-Stina", "initials": "AS"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "K\u00e4mpe", "given": "Olle", "initials": "O"}, {"family": "Siegel", "given": "Paul B", "initials": "PB"}, {"family": "Kerje", "given": "Susanne", "initials": "S", "orcid": "0000-0002-2944-9288", "researcher": {"href": "https://publications.scilifelab.se/researcher/078ca525f2cc4a68a430f2655e45efce.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal article", "published": "2010-08-00", "journal": {"volume": "23", "issn": "1755-148X", "issue": "4", "pages": "521-530", "title": "Pigment Cell Melanoma Res", "issn-l": "1755-1471"}, "abstract": "Sex-linked barring, a common plumage colour found in chickens, is characterized by black and white barred feathers. Previous studies have indicated that the white bands are caused by an absence of melanocytes in the feather follicle during the growth of this region. Here, we show that Sex-linked barring is controlled by the CDKN2A/B locus, which encodes the INK4b and ARF transcripts. We identified two non-coding mutations in CDKN2A that showed near complete association with the phenotype. In addition, two missense mutations were identified at highly conserved sites, V9D and R10C, and every bird tested with a confirmed Sex-linked barring phenotype carried one of these missense mutations. Further work is required to determine if one of these or a combined effect of two or more CDKN2A mutations is causing Sex-linked barring. This novel finding provides the first evidence that the tumour suppressor locus CDKN2A/B can affect pigmentation phenotypes and sheds new light on the functional significance of this gene.", "doi": "10.1111/j.1755-148X.2010.00700.x", "pmid": "20374521", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "PCR700"}], "notes": [], "created": "2017-05-04T15:00:37.681Z", "modified": "2021-07-07T15:26:06.504Z"}, {"entity": "publication", "iuid": "80415f482e8b4fcda52fb72fcc9d2211", "links": {"self": {"href": "https://publications.scilifelab.se/publication/80415f482e8b4fcda52fb72fcc9d2211.json"}, "display": {"href": "https://publications.scilifelab.se/publication/80415f482e8b4fcda52fb72fcc9d2211"}}, "title": "No evidence for Z-chromosome rearrangements between the pied flycatcher and the collared flycatcher as judged by gene-based comparative genetic maps.", "authors": [{"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}, {"family": "Palkopoulou", "given": "Eleftheria", "initials": "E"}, {"family": "Qvarnstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2010-08-00", "journal": {"volume": "19", "issn": "1365-294X", "issue": "16", "pages": "3394-3405", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Revealing the genetic basis of reproductive isolation is fundamental for understanding the speciation process. Chromosome speciation models propose a role for chromosomal rearrangements in promoting the build up of reproductive isolation between diverging populations and empirical data from several animal and plant taxa support these models. The pied flycatcher and the collared flycatcher are two closely related species that probably evolved reproductive isolation during geographical separation in Pleistocene glaciation refugia. Despite the short divergence time and current hybridization, these two species demonstrate a high degree of intrinsic post-zygotic isolation and previous studies have shown that traits involved in mate choice and hybrid viability map to the Z-chromosome. Could rearrangements of the Z-chromosome between the species explain their reproductive isolation? We developed high coverage Z-chromosome linkage maps for both species, using gene-based markers and large-scale SNP genotyping. Best order maps contained 57-62 gene markers with an estimated average density of one every 1-1.5 Mb. We estimated the recombination rates in flycatcher Z-chromosomes to 1.1-1.3 cM/Mb. A comparison of the maps of the two species revealed extensive co-linearity with no strong evidence for chromosomal rearrangements. This study does therefore not provide support the idea that sex chromosome rearrangements have caused the relatively strong post-zygotic reproductive isolation between these two Ficedula species.", "doi": "10.1111/j.1365-294X.2010.04742.x", "pmid": "20670368", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "MEC4742"}], "notes": [], "created": "2017-05-04T15:00:32.846Z", "modified": "2020-01-21T13:56:03.355Z"}, {"entity": "publication", "iuid": "0e378ea6650a4cc8aa89d142162dc16b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/0e378ea6650a4cc8aa89d142162dc16b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/0e378ea6650a4cc8aa89d142162dc16b"}}, "title": "Niemann-Pick C1 modulates hepatic triglyceride metabolism and its genetic variation contributes to serum triglyceride levels.", "authors": [{"family": "Uronen", "given": "Riikka-Liisa", "initials": "RL"}, {"family": "Lundmark", "given": "Per", "initials": "P"}, {"family": "Orho-Melander", "given": "Marju", "initials": "M"}, {"family": "Jauhiainen", "given": "Matti", "initials": "M"}, {"family": "Larsson", "given": "Kristina", "initials": "K"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Wallentin", "given": "Lars", "initials": "L"}, {"family": "Zethelius", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Melander", "given": "Olle", "initials": "O"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Ikonen", "given": "Elina", "initials": "E"}], "type": "journal article", "published": "2010-08-00", "journal": {"volume": "30", "issn": "1524-4636", "issue": "8", "pages": "1614-1620", "title": "Arterioscler. Thromb. Vasc. Biol.", "issn-l": "1079-5642"}, "abstract": "To study how Niemann-Pick disease type C1 (NPC1) influences hepatic triacylglycerol (TG) metabolism and to determine whether this is reflected in circulating lipid levels.\n\nIn Npc1(-/-) mice, the hepatic cholesterol content is increased but the TG content is decreased. We investigated lipid metabolism in Npc1(-/-) mouse hepatocytes and the association of NPC1 single-nucleotide polymorphisms with circulating TGs in humans. TGs were reduced in Npc1(-/-) mouse serum and hepatocytes. In Npc1(-/-) hepatocytes, the incorporation of [3H]oleic acid and [3H]acetate into TG was decreased, but shunting of oleic acid- or acetate-derived [3H]carbons into cholesterol was increased. Inhibition of cholesterol synthesis normalized TG synthesis, content, and secretion in Npc1(-/-) hepatocytes, suggesting increased hepatic cholesterol neogenesis as a cause for the reduced TG content and secretion. We found a significant association between serum TG levels and 5 common NPC1 single-nucleotide polymorphisms in a cohort of 1053 men, with the lowest P=8.7 x 10(-4) for the single-nucleotide polymorphism rs1429934. The association between the rs1429934 A allele and higher TG levels was replicated in 2 additional cohorts, which included 8041 individuals.\n\nThis study provides evidence of the following: (1) in mice, loss of NPC1 function reduces hepatocyte TG content and secretion by increasing the metabolic flux of carbons into cholesterol synthesis; and (2) common variation in NPC1 contributes to serum TG levels in humans.", "doi": "10.1161/ATVBAHA.110.207191", "pmid": "20489167", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ATVBAHA.110.207191"}], "notes": [], "created": "2017-05-04T15:00:27.054Z", "modified": "2021-07-07T15:11:02.283Z"}, {"entity": "publication", "iuid": "916e676485894409881279c4bf3e6348", "links": {"self": {"href": "https://publications.scilifelab.se/publication/916e676485894409881279c4bf3e6348.json"}, "display": {"href": "https://publications.scilifelab.se/publication/916e676485894409881279c4bf3e6348"}}, "title": "Genome-wide association study identifies a sequence variant within the DAB2IP gene conferring susceptibility to abdominal aortic aneurysm.", "authors": [{"family": "Gretarsdottir", "given": "Solveig", "initials": "S"}, {"family": "Baas", "given": "Annette F", "initials": "AF"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Holm", "given": "Hilma", "initials": "H"}, {"family": "den Heijer", "given": "Martin", "initials": "M"}, {"family": "de Vries", "given": "Jean-Paul P M", "initials": "JP"}, {"family": "Kranendonk", "given": "Steef E", "initials": "SE"}, {"family": "Zeebregts", "given": "Clark J A M", "initials": "CJ"}, {"family": "van Sterkenburg", "given": "Steven M", "initials": "SM"}, {"family": "Geelkerken", "given": "Robert H", "initials": "RH"}, {"family": "van Rij", "given": "Andre M", "initials": "AM"}, {"family": "Williams", "given": "Michael J A", "initials": "MJ"}, {"family": "Boll", "given": "Albert P M", "initials": "AP"}, {"family": "Kostic", "given": "Jelena P", "initials": "JP"}, {"family": "Jonasdottir", "given": "Adalbjorg", "initials": "A"}, {"family": "Jonasdottir", "given": "Aslaug", "initials": "A"}, {"family": "Walters", "given": "G Bragi", "initials": "GB"}, {"family": "Masson", "given": "Gisli", "initials": "G"}, {"family": "Sulem", "given": "Patrick", "initials": "P"}, {"family": "Saemundsdottir", "given": "Jona", "initials": "J"}, {"family": "Mouy", "given": "Magali", "initials": "M"}, {"family": "Magnusson", "given": "Kristinn P", "initials": "KP"}, {"family": "Tromp", "given": "Gerard", "initials": "G"}, {"family": "Elmore", "given": "James R", "initials": "JR"}, {"family": "Sakalihasan", "given": "Natzi", "initials": "N"}, {"family": "Limet", "given": "Raymond", "initials": "R"}, {"family": "Defraigne", "given": "Jean-Olivier", "initials": "JO"}, {"family": "Ferrell", "given": "Robert E", "initials": "RE"}, {"family": "Ronkainen", "given": "Antti", "initials": "A"}, {"family": "Ruigrok", "given": "Ynte M", "initials": "YM"}, {"family": "Wijmenga", "given": "Cisca", "initials": "C"}, {"family": "Grobbee", "given": "Diederick E", "initials": "DE"}, {"family": "Shah", "given": "Svati H", "initials": "SH"}, {"family": "Granger", "given": "Christopher B", "initials": "CB"}, {"family": "Quyyumi", "given": "Arshed A", "initials": "AA"}, {"family": "Vaccarino", "given": "Viola", "initials": "V"}, {"family": "Patel", "given": "Riyaz S", "initials": "RS"}, {"family": "Zafari", "given": "A Maziar", "initials": "AM"}, {"family": "Levey", "given": "Allan I", "initials": "AI"}, {"family": "Austin", "given": "Harland", "initials": "H"}, {"family": "Girelli", "given": "Domenico", "initials": "D"}, {"family": "Pignatti", "given": "Pier Franco", "initials": "PF"}, {"family": "Olivieri", "given": "Oliviero", "initials": "O"}, {"family": "Martinelli", "given": "Nicola", "initials": "N"}, {"family": "Malerba", "given": "Giovanni", "initials": "G"}, {"family": "Trabetti", "given": "Elisabetta", "initials": "E"}, {"family": "Becker", "given": "Lewis C", "initials": "LC"}, {"family": "Becker", "given": "Diane M", "initials": "DM"}, {"family": "Reilly", "given": "Muredach P", "initials": "MP"}, {"family": "Rader", "given": "Daniel J", "initials": "DJ"}, {"family": "Mueller", "given": "Thomas", "initials": "T"}, {"family": "Dieplinger", "given": "Benjamin", "initials": "B"}, {"family": "Haltmayer", "given": "Meinhard", "initials": "M"}, {"family": "Urbonavicius", "given": "Sigitas", "initials": "S"}, {"family": "Lindblad", "given": "Bengt", "initials": "B"}, {"family": "Gotts\u00e4ter", "given": "Anders", "initials": "A"}, {"family": "Gaetani", "given": "Eleonora", "initials": "E"}, {"family": "Pola", "given": "Roberto", "initials": "R"}, {"family": "Wells", "given": "Philip", "initials": "P"}, {"family": "Rodger", "given": "Marc", "initials": "M"}, {"family": "Forgie", "given": "Melissa", "initials": "M"}, {"family": "Langlois", "given": "Nicole", "initials": "N"}, {"family": "Corral", "given": "Javier", "initials": "J"}, {"family": "Vicente", "given": "Vicente", "initials": "V"}, {"family": "Fontcuberta", "given": "Jordi", "initials": "J"}, {"family": "Espa\u00f1a", "given": "Francisco", "initials": "F"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "J\u00f8rgensen", "given": "Torben", "initials": "T"}, {"family": "Witte", "given": "Daniel R", "initials": "DR"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Aben", "given": "Katja K", "initials": "KK"}, {"family": "de Graaf", "given": "Jacqueline", "initials": "J"}, {"family": "Holewijn", "given": "Suzanne", "initials": "S"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "Collier", "given": "David A", "initials": "DA"}, {"family": "Stefansson", "given": "Hreinn", "initials": "H"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Rafnar", "given": "Thorunn", "initials": "T"}, {"family": "Valdimarsson", "given": "Einar M", "initials": "EM"}, {"family": "Magnadottir", "given": "Hulda B", "initials": "HB"}, {"family": "Sveinbjornsdottir", "given": "Sigurlaug", "initials": "S"}, {"family": "Olafsson", "given": "Isleifur", "initials": "I"}, {"family": "Magnusson", "given": "Magnus Karl", "initials": "MK"}, {"family": "Palmason", "given": "Robert", "initials": "R"}, {"family": "Haraldsdottir", "given": "Vilhelmina", "initials": "V"}, {"family": "Andersen", "given": "Karl", "initials": "K"}, {"family": "Onundarson", "given": "Pall T", "initials": "PT"}, {"family": "Thorgeirsson", "given": "Gudmundur", "initials": "G"}, {"family": "Kiemeney", "given": "Lambertus A", "initials": "LA"}, {"family": "Powell", "given": "Janet T", "initials": "JT"}, {"family": "Carey", "given": "David J", "initials": "DJ"}, {"family": "Kuivaniemi", "given": "Helena", "initials": "H"}, {"family": "Lindholt", "given": "Jes S", "initials": "JS"}, {"family": "Jones", "given": "Gregory T", "initials": "GT"}, {"family": "Kong", "given": "Augustine", "initials": "A"}, {"family": "Blankensteijn", "given": "Jan D", "initials": "JD"}, {"family": "Matthiasson", "given": "Stefan E", "initials": "SE"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}], "type": "journal article", "published": "2010-08-00", "journal": {"volume": "42", "issn": "1546-1718", "issue": "8", "pages": "692-697", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "We performed a genome-wide association study on 1,292 individuals with abdominal aortic aneurysms (AAAs) and 30,503 controls from Iceland and The Netherlands, with a follow-up of top markers in up to 3,267 individuals with AAAs and 7,451 controls. The A allele of rs7025486 on 9q33 was found to associate with AAA, with an odds ratio (OR) of 1.21 and P = 4.6 x 10(-10). In tests for association with other vascular diseases, we found that rs7025486[A] is associated with early onset myocardial infarction (OR = 1.18, P = 3.1 x 10(-5)), peripheral arterial disease (OR = 1.14, P = 3.9 x 10(-5)) and pulmonary embolism (OR = 1.20, P = 0.00030), but not with intracranial aneurysm or ischemic stroke. No association was observed between rs7025486[A] and common risk factors for arterial and venous diseases-that is, smoking, lipid levels, obesity, type 2 diabetes and hypertension. Rs7025486 is located within DAB2IP, which encodes an inhibitor of cell growth and survival.", "doi": "10.1038/ng.622", "pmid": "20622881", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.622"}, {"db": "pmc", "key": "PMC4157066"}, {"db": "mid", "key": "NIHMS592048"}], "notes": [], "created": "2017-05-04T15:00:34.794Z", "modified": "2020-01-21T13:56:03.737Z"}, {"entity": "publication", "iuid": "b1721a830a36455094a71044b6ccc2be", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b1721a830a36455094a71044b6ccc2be.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b1721a830a36455094a71044b6ccc2be"}}, "title": "Association of genetic risk variants with expression of proximal genes identifies novel susceptibility genes for cardiovascular disease.", "authors": [{"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "van't Hooft", "given": "Ferdinand", "initials": "F"}, {"family": "Chernogubova", "given": "Ekaterina", "initials": "E"}, {"family": "Agardh", "given": "Hanna E", "initials": "HE"}, {"family": "Hansson", "given": "G\u00f6ran K", "initials": "GK"}, {"family": "Hedin", "given": "Ulf", "initials": "U"}, {"family": "Liska", "given": "Jan", "initials": "J"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Paulsson-Berne", "given": "Gabrielle", "initials": "G"}, {"family": "Paulssson-Berne", "given": "Gabrielle", "initials": "G"}, {"family": "Franco-Cereceda", "given": "Anders", "initials": "A"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Gabrielsen", "given": "Anders", "initials": "A"}, {"family": "Eriksson", "given": "Per", "initials": "P"}, {"family": "BiKE and ASAP study groups", "given": null, "initials": null}], "type": "journal article", "published": "2010-08-00", "journal": {"volume": "3", "issn": "1942-3268", "issue": "4", "pages": "365-373", "title": "Circ Cardiovasc Genet", "issn-l": null}, "abstract": "Population-based genome-wide association studies have identified several single nucleotide polymorphisms (SNPs) associated with cardiovascular disease or its risk factors. Genes in close proximity to these risk-SNPs are often thought to be pathogenetically important based on their location alone. However, the actual connections between SNPs and disease mechanisms remain largely unknown.\n\nTo identify novel susceptibility genes, we investigated how 166 SNPs previously found to be associated with increased cardiovascular risk and/or predisposing metabolic traits relate to the expression of nearby genes. Gene expression in 577 samples of aorta, liver, mammary artery, and carotid atherosclerotic plaque was measured using expression arrays. For 47 SNPs, the expression levels of proximal genes (located within 200 kb) were affected (P<0.005). More than 20 of these genes had not previously been identified as candidate genes for cardiovascular or related metabolic traits. SNP-associated gene effects were tissue-specific and the tissue specificity was phenotype-dependent.\n\nThis study demonstrates several instances of association between risk-SNPs and genes immediately adjacent to them. It also demonstrates instances in which the associated gene is not the immediately proximal and obvious candidate gene for disease. This shows the necessity of careful studies of genetic marker data as a first step toward application of genome-wide association studies findings in a clinical setting.", "doi": "10.1161/CIRCGENETICS.110.948935", "pmid": "20562444", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "CIRCGENETICS.110.948935"}], "notes": [], "created": "2017-05-04T15:00:28.565Z", "modified": "2021-07-07T15:11:02.671Z"}, {"entity": "publication", "iuid": "c3cf03b072144a19b7eca8c6cb472c37", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c3cf03b072144a19b7eca8c6cb472c37.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c3cf03b072144a19b7eca8c6cb472c37"}}, "title": "Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing.", "authors": [{"family": "Wetterbom", "given": "Anna", "initials": "A"}, {"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"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"}}], "type": "journal article", "published": "2010-07-23", "journal": {"volume": "11", "issn": "1474-760X", "issue": "7", "pages": "R78", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "We profile the chimpanzee transcriptome by using deep sequencing of cDNA from brain and liver, aiming to quantify expression of known genes and to identify novel transcribed regions.\n\nUsing stringent criteria for transcription, we identify 12,843 expressed genes, with a majority being found in both tissues. We further identify 9,826 novel transcribed regions that are not overlapping with annotated exons, mRNAs or ESTs. Over 80% of the novel transcribed regions map within or in the vicinity of known genes, and by combining sequencing data with de novo splice predictions we predict several of the novel transcribed regions to be new exons or 3' UTRs. For approximately 350 novel transcribed regions, the corresponding DNA sequence is absent in the human reference genome. The presence of novel transcribed regions in five genes and in one intergenic region is further validated with RT-PCR. Finally, we describe and experimentally validate a putative novel multi-exon gene that belongs to the ATP-cassette transporter gene family. This gene does not appear to be functional in human since one exon is absent from the human genome. In addition to novel exons and UTRs, novel transcribed regions may also stem from different types of noncoding transcripts. We note that expressed repeats and introns from unspliced mRNAs are especially common in our data.\n\nOur results extend the chimpanzee gene catalogue with a large number of novel exons and 3' UTRs and thus support the view that mammalian gene annotations are not yet complete.", "doi": "10.1186/gb-2010-11-7-r78", "pmid": "20653958", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "gb-2010-11-7-r78"}, {"db": "pmc", "key": "PMC2926789"}], "notes": [], "created": "2017-05-04T14:57:11.055Z", "modified": "2021-07-08T12:52:24.418Z"}, {"entity": "publication", "iuid": "183bf4607cd04640be865b214b2b8b98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/183bf4607cd04640be865b214b2b8b98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/183bf4607cd04640be865b214b2b8b98"}}, "title": "A functional polymorphism in the HMGCR promoter affects transcriptional activity but not the risk for Alzheimer disease in Swedish populations.", "authors": [{"family": "Keller", "given": "Lina", "initials": "L"}, {"family": "Murphy", "given": "Charlotte", "initials": "C"}, {"family": "Wang", "given": "Hui-Xin", "initials": "HX"}, {"family": "Fratiglioni", "given": "Laura", "initials": "L"}, {"family": "Olin", "given": "Maria", "initials": "M"}, {"family": "Gafvels", "given": "Mats", "initials": "M"}, {"family": "Bj\u00f6rkhem", "given": "Ingemar", "initials": "I"}, {"family": "Graff", "given": "Caroline", "initials": "C"}, {"family": "Meaney", "given": "Steve", "initials": "S"}], "type": "journal article", "published": "2010-07-16", "journal": {"volume": "1344", "issn": "1872-6240", "issue": null, "pages": "185-191", "title": "Brain Res.", "issn-l": "0006-8993"}, "abstract": "Variations in genes associated with cholesterol homeostasis have been reported to modify the risk of developing Alzheimer disease (AD). To date there have been few investigations into variations in genes directly involved in cholesterol biosynthesis and AD. We investigated the influence of the -911C>A polymorphism (rs3761740) in the hydroxy-methyl-glutaryl CoA reductase (HMGCR) gene promoter on basal and regulated transcription, plasma cholesterol levels and the association with AD. Under in vitro conditions the A allele was found to be significantly more responsive to SREBP-2 mediated regulation than the C allele. In an age and sex matched case-control study, the genotype distribution and allele frequency of this polymorphism were not associated with AD (OR=1.03; 95% CI=0.72-1.48). However, we did find evidence supporting an interaction between the HMGCR A allele, the APOE E4 allele and an altered risk of AD (OR=2.41; 95% CI=0.93-6.22).", "doi": "10.1016/j.brainres.2010.04.073", "pmid": "20450896", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "S0006-8993(10)01009-7"}], "notes": [], "created": "2017-05-04T15:03:27.982Z", "modified": "2017-05-30T12:43:41.736Z"}, {"entity": "publication", "iuid": "542df632abda49249bbf5f14dc948721", "links": {"self": {"href": "https://publications.scilifelab.se/publication/542df632abda49249bbf5f14dc948721.json"}, "display": {"href": "https://publications.scilifelab.se/publication/542df632abda49249bbf5f14dc948721"}}, "title": "Induction patterns of new CYP1 genes in environmentally exposed rainbow trout.", "authors": [{"family": "J\u00f6nsson", "given": "Maria E", "initials": "ME"}, {"family": "Gao", "given": "Kai", "initials": "K"}, {"family": "Olsson", "given": "Jan A", "initials": "JA"}, {"family": "Goldstone", "given": "Jared V", "initials": "JV"}, {"family": "Brandt", "given": "Ingvar", "initials": "I"}], "type": "journal article", "published": "2010-07-15", "journal": {"volume": "98", "issn": "1879-1514", "issue": "4", "pages": "311-321", "title": "Aquat. Toxicol.", "issn-l": "0166-445X"}, "abstract": "The cytochrome P4501 (CYP1) gene family comprises four subfamilies in fish: CYP1A, CYP1B, CYP1C, and CYP1D. Only two CYP1 genes, CYP1A1 and CYP1A3, are so far known in rainbow trout (Oncorhynchus mykiss). The present study aimed to identify other CYP1 subfamily genes in rainbow trout, to establish methods for quantitative mRNA expression analysis of these genes, and to determine their basal and induced mRNA expression in gills and liver. Another goal was to examine their mRNA expression in environmentally exposed fish. We cloned four new transcripts, denoted rbCYP1B1, rbCYP1C1, rbCYP1C2, and rbCYP1C3. Levels of these and the previously known rbCYP1A transcripts were determined by real-time PCR in unexposed fish, fish exposed to the potent aryl hydrocarbon receptor (AhR) agonist 3,3',4,4',5-pentachlorobiphenyl (PCB126), and fish caged in various waters in the Uppsala region (Sweden). The mRNA expression patterns observed in unexposed rainbow trout (basal levels) were markedly similar to those reported for orthologous genes in other species. All six transcripts were induced by PCB126 in gills and liver, suggesting all genes to be AhR regulated. The caged fish showed clear rbCYP1 induction in gills at all monitoring sites (up to 70-fold the basal level), whereas the liver responses were weak; induction (up to 5-fold) was recorded only at the Uppsala municipal sewage treatment plant outlet. Gill filament EROD activity was induced at all caging sites. Most interestingly, the rbCYP1 gene response patterns in gills differed among caging sites and among subfamilies. The EROD induction seemed to only reflect induction of rbCYP1A transcription. Response patterns of multiple CYP1 genes in gills and liver could provide an improved monitoring strategy. Such patterns could be used to characterize complex mixtures of AhR agonists and antagonists in aquatic environments.", "doi": "10.1016/j.aquatox.2010.03.003", "pmid": "20371123", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S0166-445X(10)00088-3"}, {"db": "pmc", "key": "PMC2892734"}, {"db": "mid", "key": "NIHMS194180"}], "notes": [], "created": "2017-05-04T15:01:48.887Z", "modified": "2020-01-21T13:56:02.354Z"}, {"entity": "publication", "iuid": "f12704da529244efaface4deeba2615e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f12704da529244efaface4deeba2615e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f12704da529244efaface4deeba2615e"}}, "title": "Different SNP combinations in the GCH1 gene and use of labor analgesia.", "authors": [{"family": "Dabo", "given": "Fatimah", "initials": "F"}, {"family": "Gr\u00f6nbladh", "given": "Alfhild", "initials": "A"}, {"family": "Nyberg", "given": "Fred", "initials": "F"}, {"family": "Sundstr\u00f6m-Poromaa", "given": "Inger", "initials": "I"}, {"family": "Akerud", "given": "Helena", "initials": "H"}], "type": "journal article", "published": "2010-07-15", "journal": {"volume": "6", "issn": "1744-8069", "issue": null, "pages": "41", "title": "Mol Pain", "issn-l": "1744-8069"}, "abstract": "The aim of this study was to investigate if there is an association between different SNP combinations in the guanosine triphosphate cyclohydrolase (GCH1) gene and a number of pain behavior related outcomes during labor. A population-based sample of pregnant women (n = 814) was recruited at gestational week 18. A plasma sample was collected from each subject. Genotyping was performed and three single nucleotide polymorphisms (SNP) previously defined as a pain-protective SNP combination of GCH1 were used.\n\nHomozygous carriers of the pain-protective SNP combination of GCH1 arrived to the delivery ward with a more advanced stage of cervical dilation compared to heterozygous carriers and non-carriers. However, homozygous carriers more often used second line labor analgesia compared to the others.\n\nThe pain-protective SNP combination of GCH1 may be of importance in the limited number of homozygous carriers during the initial dilation of cervix but upon arrival at the delivery unit these women are more inclined to use second line labor analgesia.", "doi": "10.1186/1744-8069-6-41", "pmid": "20633294", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1744-8069-6-41"}, {"db": "pmc", "key": "PMC2912270"}], "notes": [], "created": "2017-05-04T15:01:52.281Z", "modified": "2020-01-21T13:56:06.221Z"}, {"entity": "publication", "iuid": "3d5723b1ed7640219afa746149cf203a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3d5723b1ed7640219afa746149cf203a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3d5723b1ed7640219afa746149cf203a"}}, "title": "Topoisomerase I regulates open chromatin and controls gene expression in vivo.", "authors": [{"family": "Durand-Dubief", "given": "Micka\u00ebl", "initials": "M"}, {"family": "Persson", "given": "Jenna", "initials": "J"}, {"family": "Norman", "given": "Ulrika", "initials": "U"}, {"family": "Hartsuiker", "given": "Edgar", "initials": "E"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2010-07-07", "journal": {"volume": "29", "issn": "1460-2075", "issue": "13", "pages": "2126-2134", "title": "EMBO J.", "issn-l": "0261-4189"}, "abstract": "DNA topoisomerases regulate the topological state of the DNA double helix and are key enzymes in the processes of DNA replication, transcription and genome stability. Using the fission yeast model Schizosaccharomyces pombe, we investigate genome wide how DNA topoisomerases I and II affect chromatin dynamics and gene expression in vivo. We show that topoisomerase I activity is directly required for efficient nucleosome disassembly at gene promoter regions. Lack of topoisomerase activity results in increased nucleosome occupancy, perturbed histone modifications and reduced transcription from these promoters. Strong correlative evidence suggests that topoisomerase I cooperates with the ATP-dependent chromatin remodeller Hrp1 in nucleosome disassembly. Our study links topoisomerase activity to the maintenance of open chromatin and regulating transcription in vivo.", "doi": "10.1038/emboj.2010.109", "pmid": "20526281", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "emboj2010109"}, {"db": "pmc", "key": "PMC2905247"}], "notes": [], "created": "2017-05-04T15:03:04.526Z", "modified": "2017-05-30T12:38:46.532Z"}, {"entity": "publication", "iuid": "24677996eddc4304aa29e96d2a9e9948", "links": {"self": {"href": "https://publications.scilifelab.se/publication/24677996eddc4304aa29e96d2a9e9948.json"}, "display": {"href": "https://publications.scilifelab.se/publication/24677996eddc4304aa29e96d2a9e9948"}}, "title": "Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo.", "authors": [{"family": "Wei", "given": "Gong-Hong", "initials": "GH"}, {"family": "Badis", "given": "Gwenael", "initials": "G"}, {"family": "Berger", "given": "Michael F", "initials": "MF"}, {"family": "Kivioja", "given": "Teemu", "initials": "T"}, {"family": "Palin", "given": "Kimmo", "initials": "K"}, {"family": "Enge", "given": "Martin", "initials": "M"}, {"family": "Bonke", "given": "Martin", "initials": "M"}, {"family": "Jolma", "given": "Arttu", "initials": "A"}, {"family": "Varjosalo", "given": "Markku", "initials": "M"}, {"family": "Gehrke", "given": "Andrew R", "initials": "AR"}, {"family": "Yan", "given": "Jian", "initials": "J"}, {"family": "Talukder", "given": "Shaheynoor", "initials": "S"}, {"family": "Turunen", "given": "Mikko", "initials": "M"}, {"family": "Taipale", "given": "Mikko", "initials": "M"}, {"family": "Stunnenberg", "given": "Hendrik G", "initials": "HG"}, {"family": "Ukkonen", "given": "Esko", "initials": "E"}, {"family": "Hughes", "given": "Timothy R", "initials": "TR"}, {"family": "Bulyk", "given": "Martha L", "initials": "ML"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2010-07-07", "journal": {"volume": "29", "issn": "1460-2075", "issue": "13", "pages": "2147-2160", "title": "EMBO J.", "issn-l": "0261-4189"}, "abstract": "Members of the large ETS family of transcription factors (TFs) have highly similar DNA-binding domains (DBDs)-yet they have diverse functions and activities in physiology and oncogenesis. Some differences in DNA-binding preferences within this family have been described, but they have not been analysed systematically, and their contributions to targeting remain largely uncharacterized. We report here the DNA-binding profiles for all human and mouse ETS factors, which we generated using two different methods: a high-throughput microwell-based TF DNA-binding specificity assay, and protein-binding microarrays (PBMs). Both approaches reveal that the ETS-binding profiles cluster into four distinct classes, and that all ETS factors linked to cancer, ERG, ETV1, ETV4 and FLI1, fall into just one of these classes. We identify amino-acid residues that are critical for the differences in specificity between all the classes, and confirm the specificities in vivo using chromatin immunoprecipitation followed by sequencing (ChIP-seq) for a member of each class. The results indicate that even relatively small differences in in vitro binding specificity of a TF contribute to site selectivity in vivo.", "doi": "10.1038/emboj.2010.106", "pmid": "20517297", "labels": {"Karolinska High Throughput Center (KHTC)": null}, "xrefs": [{"db": "pii", "key": "emboj2010106"}, {"db": "pmc", "key": "PMC2905244"}], "notes": [], "created": "2017-05-04T14:57:02.756Z", "modified": "2017-05-30T11:43:48.260Z"}, {"entity": "publication", "iuid": "e40c4e4e3c504fe7987d32aa7e46b036", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e40c4e4e3c504fe7987d32aa7e46b036.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e40c4e4e3c504fe7987d32aa7e46b036"}}, "title": "Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.", "authors": [{"family": "Hedskog", "given": "Charlotte", "initials": "C"}, {"family": "Mild", "given": "Mattias", "initials": "M"}, {"family": "Jernberg", "given": "Johanna", "initials": "J"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Bratt", "given": "G\u00f6ran", "initials": "G"}, {"family": "Leitner", "given": "Thomas", "initials": "T"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Albert", "given": "Jan", "initials": "J"}], "type": "journal article", "published": "2010-07-07", "journal": {"volume": "5", "issn": "1932-6203", "issue": "7", "pages": "e11345", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Ultra-deep pyrosequencing (UDPS) allows identification of rare HIV-1 variants and minority drug resistance mutations, which are not detectable by standard sequencing.\n\nHere, UDPS was used to analyze the dynamics of HIV-1 genetic variation in reverse transcriptase (RT) (amino acids 180-220) in six individuals consecutively sampled before, during and after failing 3TC and AZT containing antiretroviral treatment. Optimized UDPS protocols and bioinformatic software were developed to generate, clean and analyze the data. The data cleaning strategy reduced the error rate of UDPS to an average of 0.05%, which is lower than previously reported. Consequently, the cut-off for detection of resistance mutations was very low. A median of 16,016 (range 2,406-35,401) sequence reads were obtained per sample, which allowed detection and quantification of minority resistance mutations at amino acid position 181, 184, 188, 190, 210, 215 and 219 in RT. In four of five pre-treatment samples low levels (0.07-0.09%) of the M184I mutation were observed. Other resistance mutations, except T215A and T215I were below the detection limit. During treatment failure, M184V replaced M184I and dominated the population in combination with T215Y, while wild-type variants were rarely detected. Resistant virus disappeared rapidly after treatment interruption and was undetectable as early as after 3 months. In most patients, drug resistant variants were replaced by wild-type variants identical to those present before treatment, suggesting rebound from latent reservoirs.\n\nWith this highly sensitive UDPS protocol preexisting drug resistance was infrequently observed; only M184I, T215A and T215I were detected at very low levels. Similarly, drug resistant variants in plasma quickly decreased to undetectable levels after treatment interruption. The study gives important insights into the dynamics of the HIV-1 quasispecies and is of relevance for future research and clinical use of the UDPS technology.", "doi": "10.1371/journal.pone.0011345", "pmid": "20628644", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC2898805"}], "notes": [], "created": "2017-05-04T14:57:14.378Z", "modified": "2021-07-08T13:26:08.381Z"}, {"entity": "publication", "iuid": "08724dafbd20444493259361ecf49fb8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/08724dafbd20444493259361ecf49fb8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/08724dafbd20444493259361ecf49fb8"}}, "title": "Classification of DNA sequences using Bloom filters.", "authors": [{"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "K\u00e4ller", "given": "Max", "initials": "M", "orcid": "0000-0001-6813-3051", "researcher": {"href": "https://publications.scilifelab.se/researcher/536ad902a272482aba853c078557e240.json"}}, {"family": "Allander", "given": "Tobias", "initials": "T"}, {"family": "Andersson", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Arvestad", "given": "Lars", "initials": "L"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2010-07-01", "journal": {"volume": "26", "issn": "1367-4811", "issue": "13", "pages": "1595-1600", "title": "Bioinformatics", "issn-l": "1367-4803"}, "abstract": "New generation sequencing technologies producing increasingly complex datasets demand new efficient and specialized sequence analysis algorithms. Often, it is only the 'novel' sequences in a complex dataset that are of interest and the superfluous sequences need to be removed.\n\nA novel algorithm, fast and accurate classification of sequences (FACSs), is introduced that can accurately and rapidly classify sequences as belonging or not belonging to a reference sequence. FACS was first optimized and validated using a synthetic metagenome dataset. An experimental metagenome dataset was then used to show that FACS achieves comparable accuracy as BLAT and SSAHA2 but is at least 21 times faster in classifying sequences.\n\nSource code for FACS, Bloom filters and MetaSim dataset used is available at http://facs.biotech.kth.se. The Bloom::Faster 1.6 Perl module can be downloaded from CPAN at http://search.cpan.org/ approximately palvaro/Bloom-Faster-1.6/\n\nhenrik.stranneheim@biotech.kth.se; joakiml@biotech.kth.se\n\nSupplementary data are available at Bioinformatics online.", "doi": "10.1093/bioinformatics/btq230", "pmid": "20472541", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "btq230"}, {"db": "pmc", "key": "PMC2887045"}], "notes": [], "created": "2017-05-04T14:57:09.345Z", "modified": "2021-07-08T13:26:08.074Z"}, {"entity": "publication", "iuid": "2b2f3a9dacdc41e9a187ace738d7a3fd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2b2f3a9dacdc41e9a187ace738d7a3fd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2b2f3a9dacdc41e9a187ace738d7a3fd"}}, "title": "Tissue factor pathway inhibitor-2 is induced by fluid shear stress in vascular smooth muscle cells and affects cell proliferation and survival.", "authors": [{"family": "Ekstrand", "given": "Johan", "initials": "J"}, {"family": "Razuvaev", "given": "Anton", "initials": "A"}, {"family": "Folkersen", "given": "Lasse", "initials": "L"}, {"family": "Roy", "given": "Joy", "initials": "J"}, {"family": "Hedin", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2010-07-00", "journal": {"volume": "52", "issn": "1097-6809", "issue": "1", "pages": "167-175", "title": "J. Vasc. Surg.", "issn-l": "0741-5214"}, "abstract": "Vascular smooth muscle cells (SMCs) are exposed to fluid shear stress (FSS) after interventional procedures such as balloon-angioplasty. Whereas the effects of hemodynamic forces on endothelial cells are explored in detail, the influence of FSS on smooth muscle cell function is poorly characterized. Here, we investigated the effect of FSS on SMC gene expression and function.\n\nLaminar FSS of arterial level (14 dynes/cm(2)) was applied to SMC cultures for 24 hours in a parallel-plate flow chamber. The effect of FSS on gene expression was first screened with microarray technology, and results further verified by real time polymerase chain reaction (RT-PCR) and immunoblotting. Tissue factor pathway inhibitor-2 (TFPI-2) and caspase-3 protein expression was studied in the rat carotid artery after balloon-injury, and the effect of TFPI-2 on SMC DNA synthesis and apoptosis was examined in vitro.\n\nMicroarrays identified TFPI-2 as one of the most differentially expressed gene by FSS in cultured SMCs (P < .001). Gene set enrichment analysis revealed significant regulation of genes linked to proliferation, apoptosis, and cell cycle regulation. TFPI-2 induction was confirmed by RT-PCR and immunoblotting demonstrating a more than 400-fold (P < .001) increase in TFPI-2 mRNA in SMCs exposed to FSS compared with static controls, and a consistent protein upregulation. Functionally, SMC proliferation was decreased by FSS (P < .001), and recombinant TFPI-2 was found to inhibit SMC proliferation (P < .001) and induce SMC apoptosis as indicated by activation of caspase-3 (P < .01). In vivo, TFPI-2 expression was found to be upregulated 5, 10, and 20 hours (P < .01) after rat carotid balloon injury, and immunohistochemistry demonstrated TFPI-2 protein in FSS-exposed luminal SMCs, co-localized with caspase-3 in the rat carotid neointima.\n\nFSS influenced gene expression associated with cell growth and apoptosis in cultured SMCs and strongly induced expression of TFPI-2 mRNA and protein. TFPI-2 was expressed in luminal, FSS-exposed SMCs together with caspase-3 in the rat carotid neointima after balloon injury. Functionally, TFPI-2 may play a role in vessel wall repair by regulating SMC proliferation and survival. Further studies are needed to elucidate the mechanisms by which TFPI-2 controls SMC function.", "doi": "10.1016/j.jvs.2010.02.282", "pmid": "20537494", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "S0741-5214(10)00667-1"}], "notes": [], "created": "2017-05-04T15:03:07.525Z", "modified": "2017-05-30T12:39:33.504Z"}, {"entity": "publication", "iuid": "23cecd9baed1410ea8fdb04121443a6b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/23cecd9baed1410ea8fdb04121443a6b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/23cecd9baed1410ea8fdb04121443a6b"}}, "title": "Subcellular distribution and expression of prenylated Rab acceptor 1 domain family, member 2 (PRAF2) in malignant glioma: Influence on cell survival and migration.", "authors": [{"family": "Borsics", "given": "Tam\u00e1s", "initials": "T"}, {"family": "Lundberg", "given": "Emma", "initials": "E", "orcid": "0000-0001-7034-0850", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ffe6259ceb540f385861b5ae52b3055.json"}}, {"family": "Geerts", "given": "Dirk", "initials": "D"}, {"family": "Koomoa", "given": "Dana-Lynn T", "initials": "DL"}, {"family": "Koster", "given": "Jan", "initials": "J"}, {"family": "Wester", "given": "Kenneth", "initials": "K"}, {"family": "Bachmann", "given": "Andr\u00e9 S", "initials": "AS"}], "type": "journal article", "published": "2010-07-00", "journal": {"volume": "101", "issn": "1349-7006", "issue": "7", "pages": "1624-1631", "title": "Cancer Sci.", "issn-l": "1347-9032"}, "abstract": "Our previous studies revealed that the expression of the 19-kDa protein prenylated Rab acceptor 1 domain family, member 2 (PRAF2) is elevated in cancer tissues of the breast, colon, lung, and ovary, when compared to noncancerous tissues of paired samples. PRAF2 mRNA expression also correlated with several genetic and clinical features and is a candidate prognostic marker in the pediatric cancer neuroblastoma. The PRAF2-related proteins, PRAF1 and PRAF3, play multiple roles in cellular processes, including endo/exocytic vesicle trafficking and glutamate uptake. PRAF2 shares a high sequence homology with these family members, but its function remains unknown. In this study, we examined PRAF2 mRNA and protein expression in 20 different human cancer types using Affymetrix microarray and human tissue microarray (TMA) analyses, respectively. In addition, we investigated the subcellular distribution of PRAF2 by immunofluorescence microscopy and cell fractionation studies. PRAF2 mRNA and protein expression was elevated in several cancer tissues with highest levels in malignant glioma. At the molecular level, we detected native PRAF2 in small, vesicle-like structures throughout the cytoplasm as well as in and around cell nuclei of U-87 malignant glioma cells. We further found that monomeric and dimeric forms of PRAF2 are associated with different cell compartments, suggesting possible functional differences. Importantly, PRAF2 down-regulation by RNA interference significantly reduced the cell viability, migration, and invasiveness of U-87 cells. This study shows that PRAF2 expression is elevated in various tumors with exceptionally high expression in malignant gliomas, and PRAF2 therefore presents a candidate molecular target for therapeutic intervention.", "doi": "10.1111/j.1349-7006.2010.01570.x", "pmid": "20412121", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "CAS1570"}], "notes": [], "created": "2017-05-04T14:55:06.853Z", "modified": "2021-07-05T16:33:38.588Z"}, {"entity": "publication", "iuid": "97352b4103e94523b7562e842be4a358", "links": {"self": {"href": "https://publications.scilifelab.se/publication/97352b4103e94523b7562e842be4a358.json"}, "display": {"href": "https://publications.scilifelab.se/publication/97352b4103e94523b7562e842be4a358"}}, "title": "Revolutionizing membrane protein overexpression in bacteria.", "authors": [{"family": "Schlegel", "given": "Susan", "initials": "S"}, {"family": "Klepsch", "given": "Mirjam", "initials": "M"}, {"family": "Gialama", "given": "Dimitra", "initials": "D"}, {"family": "Wickstr\u00f6m", "given": "David", "initials": "D"}, {"family": "Slotboom", "given": "Dirk Jan", "initials": "DJ"}, {"family": "de Gier", "given": "Jan-Willem", "initials": "JW"}], "type": "journal article", "published": "2010-07-00", "journal": {"volume": "3", "issn": "1751-7915", "issue": "4", "pages": "403-411", "title": "Microb Biotechnol", "issn-l": "1751-7915"}, "abstract": "The bacterium Escherichia coli is the most widely used expression host for overexpression trials of membrane proteins. Usually, different strains, culture conditions and expression regimes are screened for to identify the optimal overexpression strategy. However, yields are often not satisfactory, especially for eukaryotic membrane proteins. This has initiated a revolution of membrane protein overexpression in bacteria. Recent studies have shown that it is feasible to (i) engineer or select for E. coli strains with strongly improved membrane protein overexpression characteristics, (ii) use bacteria other than E. coli for the expression of membrane proteins, (iii) engineer or select for membrane protein variants that retain functionality but express better than the wild-type protein, and (iv) express membrane proteins using E. coli-based cell-free systems.", "doi": "10.1111/j.1751-7915.2009.00148.x", "pmid": "21255339", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC3815807"}], "notes": [], "created": "2017-05-04T14:57:12.269Z", "modified": "2020-01-21T13:56:03.893Z"}, {"entity": "publication", "iuid": "c6a2bbd1be584e2fb21c88a01174d803", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c6a2bbd1be584e2fb21c88a01174d803.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c6a2bbd1be584e2fb21c88a01174d803"}}, "title": "Ontogenetic complexity of sexual dimorphism and sex-specific selection.", "authors": [{"family": "Mank", "given": "Judith E", "initials": "JE"}, {"family": "Nam", "given": "Kiwoong", "initials": "K"}, {"family": "Brunstr\u00f6m", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "journal article", "published": "2010-07-00", "journal": {"volume": "27", "issn": "1537-1719", "issue": "7", "pages": "1570-1578", "title": "Mol. Biol. Evol.", "issn-l": "0737-4038"}, "abstract": "Sex-biased gene expression is becoming an increasingly important way to study sexual selection at the molecular genetic level. However, little is known about the timing, persistence, and continuity of gene expression required in the creation of distinct male and female phenotypes, and even less about how sex-specific selection pressures shift over the life cycle. Here, we present a time-series global transcription profile for autosomal genes in male and female chicken, beginning with embryonic development and spanning to reproductive maturity, for the gonad. Overall, the amount and magnitude of sex-biased expression increased as a function of age, though sex-biased gene expression was surprisingly ephemeral, with very few genes exhibiting continuous sex bias in both embryonic and adult tissues. Despite a large predicted role of the sex chromosomes in sexual dimorphism, our study indicates that the autosomes house the majority of genes with sex-biased expression. Most interestingly, sex-specific evolutionary pressures shifted over the course of the life cycle, acting equally strongly on female-biased genes and male-biased genes but at different ages. Female-biased genes exhibited high rates of divergence late in embryonic development, shortly before arrested meiosis halts oogenesis. The level of divergence on female-biased late embryonic genes is similar to that seen in male-biased genes expressed in adult gonads, which correlates with the onset of spermatogenesis. These analyses reveal that sex-specific selection pressure varies over the life cycle as a function of male and female biology.", "doi": "10.1093/molbev/msq042", "pmid": "20142440", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "msq042"}], "notes": [], "created": "2017-05-04T15:02:52.737Z", "modified": "2017-05-30T12:35:53.873Z"}, {"entity": "publication", "iuid": "77c0eaca5ad64428b33de4452864e526", "links": {"self": {"href": "https://publications.scilifelab.se/publication/77c0eaca5ad64428b33de4452864e526.json"}, "display": {"href": "https://publications.scilifelab.se/publication/77c0eaca5ad64428b33de4452864e526"}}, "title": "Gene expression analysis in hypoplastic lungs in the nitrofen model of congenital diaphragmatic hernia.", "authors": [{"family": "Burgos", "given": "Carmen Mesas", "initials": "CM"}, {"family": "Uggla", "given": "Andreas Ringman", "initials": "AR"}, {"family": "Fagerstr\u00f6m-Billai", "given": "Fredrik", "initials": "F"}, {"family": "Ekl\u00f6f", "given": "Ann-Christine", "initials": "AC"}, {"family": "Frenckner", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Nord", "given": "Magnus", "initials": "M"}], "type": "evaluation studies", "published": "2010-07-00", "journal": {"volume": "45", "issn": "1531-5037", "issue": "7", "pages": "1445-1454", "title": "J. Pediatr. Surg.", "issn-l": "0022-3468"}, "abstract": "Pulmonary hypoplasia and persistent pulmonary hypertension are the main causes of mortality and morbidity in newborns with congenital diaphragmatic hernia (CDH). Nitrofen is well known to induce CDH and lung hypoplasia in a rat model, but the mechanism remains unknown. To increase the understanding of the underlying pathogenesis of CDH, we performed a global gene expression analysis using microarray technology.\n\nPregnant rats were given 100 mg nitrofen on gestational day 9.5 to create CDH. On day 21, fetuses after nitrofen administration and control fetuses were removed; and lungs were harvested. Global gene expression analysis was performed using Affymetrix Platform and the RAE 230 set arrays. For validation of microarray data, we performed real-time polymerase chain reaction and Western blot analysis.\n\nSignificantly decreased genes after nitrofen administration included several growth factors and growth factors receptors involved in lung development, transcription factors, water and ion channels, and genes involved in angiogenesis and extracellular matrix. These results could be confirmed with real-time polymerase chain reaction and protein expression studies.\n\nThe pathogenesis of lung hypoplasia and CDH in the nitrofen model includes alteration at a molecular level of several pathways involved in lung development. The complexity of the nitrofen mechanism of action reminds of human CDH; and the picture is consistent with lung hypoplasia and vascular disease, both important contributors to the high mortality and morbidity in CDH. Increased understanding of the molecular mechanisms that control lung growth may be the key to develop novel therapeutic techniques to stimulate pre- and postnatal lung growth.", "doi": "10.1016/j.jpedsurg.2009.09.023", "pmid": "20638522", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "S0022-3468(09)00764-7"}], "notes": [], "created": "2017-05-04T15:03:07.225Z", "modified": "2017-05-31T08:17:14.359Z"}, {"entity": "publication", "iuid": "ba656281ab624babbca5bfd810453f8a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ba656281ab624babbca5bfd810453f8a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ba656281ab624babbca5bfd810453f8a"}}, "title": "Characterization of the RNA content of chromatin.", "authors": [{"family": "Mondal", "given": "Tanmoy", "initials": "T"}, {"family": "Rasmussen", "given": "Markus", "initials": "M"}, {"family": "Pandey", "given": "Gaurav Kumar", "initials": "GK"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Kanduri", "given": "Chandrasekhar", "initials": "C"}], "type": "journal article", "published": "2010-07-00", "journal": {"volume": "20", "issn": "1549-5469", "issue": "7", "pages": "899-907", "title": "Genome Res.", "issn-l": "1088-9051"}, "abstract": "Noncoding RNA (ncRNA) constitutes a significant portion of the mammalian transcriptome. Emerging evidence suggests that it regulates gene expression in cis or trans by modulating the chromatin structure. To uncover the functional role of ncRNA in chromatin organization, we deep sequenced chromatin-associated RNAs (CARs) from human fibroblast (HF) cells. This resulted in the identification of 141 intronic regions and 74 intergenic regions harboring CARs. The intronic and intergenic CARs show significant conservation across 44 species of placental mammals. Functional characterization of one of the intergenic CARs, Intergenic10, revealed that it regulates gene expression of neighboring genes through modulating the chromatin structure in cis. Our data suggest that ncRNA is an integral component of chromatin and that it may regulate various biological functions through fine-tuning of the chromatin architecture.", "doi": "10.1101/gr.103473.109", "pmid": "20404130", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "gr.103473.109"}, {"db": "pmc", "key": "PMC2892091"}, {"db": "GEO", "key": "GSE21227"}], "notes": [], "created": "2017-05-04T15:00:31.276Z", "modified": "2020-01-21T13:56:04.877Z"}, {"entity": "publication", "iuid": "5933b98ac67849ad9dd5aa7f9685761e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5933b98ac67849ad9dd5aa7f9685761e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5933b98ac67849ad9dd5aa7f9685761e"}}, "title": "Genetic evidence of multiple loci in dystocia--difficult labour.", "authors": [{"family": "Algovik", "given": "Michael", "initials": "M"}, {"family": "Kivinen", "given": "Katja", "initials": "K"}, {"family": "Peterson", "given": "Hanna", "initials": "H"}, {"family": "Westgren", "given": "Magnus", "initials": "M"}, {"family": "Kere", "given": "Juha", "initials": "J"}], "type": "journal article", "published": "2010-06-30", "journal": {"volume": "11", "issn": "1471-2350", "issue": null, "pages": "105", "title": "BMC Med. Genet.", "issn-l": "1471-2350"}, "abstract": "Dystocia, difficult labour, is a common but also complex problem during childbirth. It can be attributed to either weak contractions of the uterus, a large infant, reduced capacity of the pelvis or combinations of these. Previous studies have indicated that there is a genetic component in the susceptibility of experiencing dystocia. The purpose of this study was to identify susceptibility genes in dystocia.\n\nA total of 104 women in 47 families were included where at least two sisters had undergone caesarean section at a gestational length of 286 days or more at their first delivery. Study of medical records and a telephone interview was performed to identify subjects with dystocia. Whole-genome scanning using Affymetrix genotyping-arrays and non-parametric linkage (NPL) analysis was made in 39 women exhibiting the phenotype of dystocia from 19 families. In 68 women re-sequencing was performed of candidate genes showing suggestive linkage: oxytocin (OXT) on chromosome 20 and oxytocin-receptor (OXTR) on chromosome 3.\n\nWe found a trend towards linkage with suggestive NPL-score (3.15) on chromosome 12p12. Suggestive linkage peaks were observed on chromosomes 3, 4, 6, 10, 20. Re-sequencing of OXT and OXTR did not reveal any causal variants.\n\nDystocia is likely to have a genetic component with variations in multiple genes affecting the patient outcome. We found 6 loci that could be re-evaluated in larger patient cohorts.", "doi": "10.1186/1471-2350-11-105", "pmid": "20587075", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "1471-2350-11-105"}, {"db": "pmc", "key": "PMC2914646"}], "notes": [], "created": "2017-05-04T15:03:03.626Z", "modified": "2017-05-30T14:50:20.684Z"}, {"entity": "publication", "iuid": "dfd75a0f2f2041709f0800240240a411", "links": {"self": {"href": "https://publications.scilifelab.se/publication/dfd75a0f2f2041709f0800240240a411.json"}, "display": {"href": "https://publications.scilifelab.se/publication/dfd75a0f2f2041709f0800240240a411"}}, "title": "HIV-1 exposed uninfected men who have sex with men have increased levels of salivary CC-chemokines associated with sexual behavior.", "authors": [{"family": "Hasselrot", "given": "Klara", "initials": "K"}, {"family": "Bratt", "given": "G\u00f6ran", "initials": "G"}, {"family": "Duvefelt", "given": "Kristina", "initials": "K"}, {"family": "Hirbod", "given": "Taha", "initials": "T"}, {"family": "Sandstr\u00f6m", "given": "Eric", "initials": "E"}, {"family": "Broliden", "given": "Kristina", "initials": "K"}], "type": "journal article", "published": "2010-06-19", "journal": {"volume": "24", "issn": "1473-5571", "issue": "10", "pages": "1569-1575", "title": "AIDS", "issn-l": "0269-9370"}, "abstract": "To determine whether soluble molecules with known anti-HIV-1 activity are increased in saliva of HIV-1 exposed uninfected individuals of discordant couples of men who have sex with men (MSM), and whether the levels of these molecules are associated with genetic polymorphisms, sexual behavior and/or HIV-1 neutralizing capacity.\n\nSaliva and PBMC were collected from exposed uninfected individuals (n=25), and low-risk controls (n=22). Levels of CCL2, CCL3, CCL4, CCL5 and CCL11 were detected by Luminex, and SLPI, LL-37, alpha-defensins and IgA2 were detected by ELISA. Single nucleotide polymorphisms (SNPs) were investigated using mass spectrometry or PCR-sequencing. HIV-1 neutralizing activity was assessed using PBMCbased neutralization assays. Self-reported questionnaires described sexual behavior.\n\nExposed uninfected individuals had significantly higher levels of salivary CCL2, CCL4, CCL5 and CCL11 as compared with controls although genetic polymorphisms within the corresponding regions were equally distributed. IgA2 was also increased in exposed uninfected individuals, whereas neither CCL3, SLPI, LL-37 nor alpha-defensins differed between exposed uninfected individuals and controls. The HIV-1 neutralizing capacity of saliva was associated with higher levels of CC-chemokines (but not SLPI, LL-37, alpha-defensins or IgA2) in both exposed uninfected individuals and controls. The increased levels of CC-chemokines were associated with a higher frequency of unprotected oral sex and/or additional casual sex partners.\n\nHIV-1 exposed uninfected MSM had higher levels of salivary CC-chemokines compared with controls, this finding associated with sexual behavior rather than with genetic polymorphisms. The increased levels of CC-chemokines associated with HIV-1 neutralizing capacity in saliva.", "doi": "10.1097/qad.0b013e32833ac646", "pmid": "20549845", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:27.682Z", "modified": "2021-06-22T12:32:00.256Z"}, {"entity": "publication", "iuid": "a06837e4b02a4214a16a4251b1951a98", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a06837e4b02a4214a16a4251b1951a98.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a06837e4b02a4214a16a4251b1951a98"}}, "title": "Genome-wide mapping of estrogen receptor-beta-binding regions reveals extensive cross-talk with transcription factor activator protein-1.", "authors": [{"family": "Zhao", "given": "Chunyan", "initials": "C"}, {"family": "Gao", "given": "Hui", "initials": "H"}, {"family": "Liu", "given": "Yawen", "initials": "Y"}, {"family": "Papoutsi", "given": "Zoi", "initials": "Z"}, {"family": "Jaffrey", "given": "Sadaf", "initials": "S"}, {"family": "Gustafsson", "given": "Jan-Ake", "initials": "JA"}, {"family": "Dahlman-Wright", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2010-06-15", "journal": {"volume": "70", "issn": "1538-7445", "issue": "12", "pages": "5174-5183", "title": "Cancer Res.", "issn-l": "0008-5472"}, "abstract": "Estrogen signaling can occur through a nonclassical pathway involving the interaction of estrogen receptors (ER) with other transcription factors such as activator protein-1 (AP-1) and SP-1. However, there is little mechanistic understanding about this pathway, with conflicting results from in vitro investigations. In this study, we applied the ChIP-on-chip approach to identify ERbeta-binding sites on a genome-wide scale, identifying 1,457 high-confidence binding sites in ERbeta-overexpressing MCF7 breast cancer cells. Genes containing ERbeta-binding sites can be regulated by E2. Notably, approximately 60% of the genomic regions bound by ERbeta contained AP-1-like binding regions and estrogen response element-like sites, suggesting a functional association between AP-1 and ERbeta signaling. Chromatin immunoprecipitation (ChIP) analysis confirmed the association of AP-1, which is composed of the oncogenic transcription factors c-Fos and c-Jun, to ERbeta-bound DNA regions. Using a re-ChIP assay, we showed co-occupancy of ERbeta and AP-1 on chromatin. Short interfering RNA-mediated knockdown of c-Fos or c-Jun expression decreased ERbeta recruitment to chromatin, consistent with the role of AP-1 in mediating estrogen signaling in breast cancer cells. Additionally, ERalpha and ERbeta recruitment to AP-1/ERbeta target regions exhibited gene-dependent differences in response to antiestrogens. Together, our results broaden insights into ERbeta DNA-binding at the genomic level by revealing crosstalk with the AP-1 transcription factor.", "doi": "10.1158/0008-5472.CAN-09-4407", "pmid": "20501845", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "0008-5472.CAN-09-4407"}], "notes": [], "created": "2017-05-04T15:03:04.225Z", "modified": "2017-05-30T12:38:41.916Z"}, {"entity": "publication", "iuid": "e9e2e9d5ed3149cab65af7954a5ba54a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e9e2e9d5ed3149cab65af7954a5ba54a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e9e2e9d5ed3149cab65af7954a5ba54a"}}, "title": "Interstitial Deletions at 6q14.1-q15 Associated with Obesity, Developmental Delay and a Distinct Clinical Phenotype.", "authors": [{"family": "Wentzel", "given": "C", "initials": "C"}, {"family": "Lynch", "given": "S A", "initials": "SA"}, {"family": "Stattin", "given": "E-L", "initials": "EL"}, {"family": "Sharkey", "given": "F H", "initials": "FH"}, {"family": "Anner\u00e9n", "given": "G", "initials": "G"}, {"family": "Thuresson", "given": "A-C", "initials": "AC"}], "type": "journal article", "published": "2010-06-09", "journal": {"volume": "1", "issn": "1661-8769", "issue": "2", "pages": "75-81", "title": "Mol Syndromol", "issn-l": null}, "abstract": "BACKGROUND: Interstitial deletions of the long arm of chromosome 6 have been described in several patients with obesity and a Prader-Willi-like phenotype. Haploinsufficiency of the SIM1 gene located at 6q16.3 is suggested as being responsible for the regulation of body weight. Here we report on 2 patients with interstitial deletions at 6q14.1-q15 presenting with obesity and symptoms strikingly similar to those reported for deletions involving the SIM1 gene despite not having a deletion of this gene. METHODS: Array comparative genomic hybridisation was used to diagnose 2 children with obesity and developmental delay, revealing 2 interstitial deletions at 6q14.1-q15 of 8.73 and 4.50 Mb, respectively, and a region of overlap of 4.2-Mb. RESULTS: The similar phenotype in the 2 patients was most likely due to a 4.2-Mb common microdeletion at 6q14.1-q15. Another patient has previously been described with an overlapping deletion. The 3 patients share several features, such as developmental delay, obesity, hernia, rounded face with full cheeks, epicanthal folds, short palpebral fissures, bulbous nose, large ears, and syndactyly between toes II and III. CONCLUSIONS: Together with a previously reported patient, our study suggests that the detected deletions may represent a novel clinically recognisable microdeletion syndrome caused by haploinsufficiency of dosage-sensitive genes in the 6q14.1-q15 region.", "doi": "10.1159/000314025", "pmid": "21045960", "labels": {"National Genomics Infrastructure": null, "Array and Analysis Facility": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pmc", "key": "PMC2941842"}, {"db": "pii", "key": "314025"}], "notes": [], "created": "2017-05-04T15:01:52.587Z", "modified": "2020-01-21T13:56:05.960Z"}, {"entity": "publication", "iuid": "338a92b4e43341e2aeeb0a1665c45e53", "links": {"self": {"href": "https://publications.scilifelab.se/publication/338a92b4e43341e2aeeb0a1665c45e53.json"}, "display": {"href": "https://publications.scilifelab.se/publication/338a92b4e43341e2aeeb0a1665c45e53"}}, "title": "Analysis of oestrogen regulation of alpha-, beta- and gamma-secretase gene and protein expression in cultured human neuronal and glial cells.", "authors": [{"family": "Nord", "given": "Linda Cs\u00f6regh", "initials": "LC"}, {"family": "Sundqvist", "given": "Johanna", "initials": "J"}, {"family": "Andersson", "given": "Eva", "initials": "E"}, {"family": "Fried", "given": "Gabriel", "initials": "G"}], "type": "journal article", "published": "2010-06-04", "journal": {"volume": "7", "issn": "1660-2862", "issue": "6", "pages": "349-364", "title": "Neurodegener Dis", "issn-l": "1660-2854"}, "abstract": "A key event in Alzheimer's disease pathology is the proteolytic processing of amyloid precursor protein (APP), whereby \u03b2-amyloid (A\u03b2) peptide is produced. Oestrogen is acknowledged to influence cognitive function and has been shown to regulate the secretory metabolism of APP and decrease the production of A\u03b2, thereby protecting the brain from neurodegeneration. The mechanism for this effect is unknown.\n\nTo investigate possible oestrogen regulation of the expression of the APP processing enzymes at the gene and/or protein level.\n\nThe effects of oestrogen on gene and protein expression of \u03b1- (TACE and ADAM10), \u03b2- (BACE) and \u03b3- (presenilin 1) secretases in cultured human fetal neurons and glial cells were studied. The RNase protection assay, gene expression microarray analysis and relative quantitative real-time PCR were used to analyse gene expression, while the protein expression and cellular localization of the secretases were studied by immunoblot and confocal microscopy.\n\nOestrogen is involved in the regulation of the gene expression of TACE and presenilin 1. Most importantly, BACE protein expression was downregulated by oestrogen treatment in mixed neuronal/glial cell cultures. Our results also show the cellular localization of the secretases in human neurons and glial cells, which has been thoroughly discussed in the light of the localization of APP processing.\n\nOur results indicate that oestrogen may affect APP processing directly by regulating the expression of the involved enzymes.", "doi": "10.1159/000282279", "pmid": "20523023", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "000282279"}], "notes": [], "created": "2017-05-04T15:03:08.430Z", "modified": "2017-05-30T14:50:34.506Z"}, {"entity": "publication", "iuid": "8fe8535859a245f6bba73d277e55cc42", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8fe8535859a245f6bba73d277e55cc42.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8fe8535859a245f6bba73d277e55cc42"}}, "title": "Genetic diversity and differentiation among Lagopus lagopus populations in Scandinavia and Scotland: evolutionary significant units confirmed by SNP markers.", "authors": [{"family": "Quintela", "given": "Mar\u00eda", "initials": "M"}, {"family": "Berlin", "given": "Sofia", "initials": "S"}, {"family": "Wang", "given": "Biao", "initials": "B"}, {"family": "H\u00f6glund", "given": "Jacob", "initials": "J"}], "type": "journal article", "published": "2010-06-01", "journal": {"volume": "19", "issn": "1365-294X", "issue": "12", "pages": "2380-2393", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Single Nucleotide Polymorphism in four Scandinavian populations of willow grouse (Lagopus lagopus) and two Scottish populations of red grouse (Lagopus lagopus scoticus) were assessed at 13 protein-coding loci. We found high levels of diversity, with one substitution every 55 bp as an average and a total of 76 unlinked parsimony informative SNPs. Different estimators of genetic diversity such as: number of synonymous and non-synonymous sites, average number of alleles, number and percentage of polymorphic loci, mean nucleotide diversity (pi(s), pi(a)) and gene diversity at synonymous and non-synonymous sites showed higher diversity in the northern populations compared to southern ones. Strong levels of purifying selection found in all the populations together with neutrality tests conforming to neutral expectations agree with large effective population sizes. Assignment tests reported a clear distinction between Scandinavian and Scottish grouse suggesting the existence of two different evolutionary significant units. The divergence time between willow and red grouse ranging between 12 500 and 125 000 years, in conjunction with the presence of 'specific' markers for each subspecies prompt a reassessment of the taxonomical status of the Scottish red grouse.", "doi": "10.1111/j.1365-294X.2010.04648.x", "pmid": "20636891", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "MEC4648"}], "notes": [], "created": "2017-05-04T15:00:33.145Z", "modified": "2020-01-21T13:56:03.704Z"}, {"entity": "publication", "iuid": "04f142bc4c6c4a33b0eed0b82cf20fcd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/04f142bc4c6c4a33b0eed0b82cf20fcd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/04f142bc4c6c4a33b0eed0b82cf20fcd"}}, "title": "Tissue tumor marker expression in smokers, including serum cotinine concentrations, in women with cervical intraepithelial neoplasia or normal squamous cervical epithelium.", "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": "2010-06-00", "journal": {"volume": "202", "issn": "1097-6868", "issue": "6", "pages": "579.e1-579.e7", "title": "Am. J. Obstet. Gynecol.", "issn-l": "0002-9378"}, "abstract": "The purpose of this study was to investigate correlations between smoking and serum cotinine, respectively, and tumor marker expression in cervical intraepithelial neoplasia (CIN) and normal epithelium.\n\nWomen (n = 228) with cervical biopsy specimens that ranged histologically from normal to carcinoma in situ (CIN III) were included. Expression of 11 tumor markers with possible relevance in cervical neoplasms was studied. Smoking habits were recorded, and serum was assessed for cotinine concentrations.\n\nNo differences were found in tumor marker expression in normal epithelium between smokers and nonsmokers. The tumor suppressors p53 and fragile histidine triad and the immunologic marker interleukin-10 were underexpressed, and the tumor markers cyclooxygenase-2 and Ki-67 were overexpressed in smoking, compared with nonsmoking, women with CIN and particularly in all fertile women.\n\nThe molecular pattern indicates that smoking exerts unfavorable effects in cervical neoplasia. This provides biologic evidence of smoking being a true cofactor in cervical neoplasia.", "doi": "10.1016/j.ajog.2009.11.034", "pmid": "20060094", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "S0002-9378(09)02208-X"}], "notes": [], "created": "2017-05-04T14:55:41.873Z", "modified": "2017-05-30T12:51:15.807Z"}, {"entity": "publication", "iuid": "19180cd5e1594314be45d213828fa5ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/19180cd5e1594314be45d213828fa5ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/19180cd5e1594314be45d213828fa5ac"}}, "title": "Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.", "authors": [{"family": "Jolma", "given": "Arttu", "initials": "A"}, {"family": "Kivioja", "given": "Teemu", "initials": "T"}, {"family": "Toivonen", "given": "Jarkko", "initials": "J"}, {"family": "Cheng", "given": "Lu", "initials": "L"}, {"family": "Wei", "given": "Gonghong", "initials": "G"}, {"family": "Enge", "given": "Martin", "initials": "M"}, {"family": "Taipale", "given": "Mikko", "initials": "M"}, {"family": "Vaquerizas", "given": "Juan M", "initials": "JM"}, {"family": "Yan", "given": "Jian", "initials": "J"}, {"family": "Sillanp\u00e4\u00e4", "given": "Mikko J", "initials": "MJ"}, {"family": "Bonke", "given": "Martin", "initials": "M"}, {"family": "Palin", "given": "Kimmo", "initials": "K"}, {"family": "Talukder", "given": "Shaheynoor", "initials": "S"}, {"family": "Hughes", "given": "Timothy R", "initials": "TR"}, {"family": "Luscombe", "given": "Nicholas M", "initials": "NM"}, {"family": "Ukkonen", "given": "Esko", "initials": "E"}, {"family": "Taipale", "given": "Jussi", "initials": "J"}], "type": "journal article", "published": "2010-06-00", "journal": {"volume": "20", "issn": "1549-5469", "issue": "6", "pages": "861-873", "title": "Genome Res.", "issn-l": "1088-9051"}, "abstract": "The genetic code-the binding specificity of all transfer-RNAs--defines how protein primary structure is determined by DNA sequence. DNA also dictates when and where proteins are expressed, and this information is encoded in a pattern of specific sequence motifs that are recognized by transcription factors. However, the DNA-binding specificity is only known for a small fraction of the approximately 1400 human transcription factors (TFs). We describe here a high-throughput method for analyzing transcription factor binding specificity that is based on systematic evolution of ligands by exponential enrichment (SELEX) and massively parallel sequencing. The method is optimized for analysis of large numbers of TFs in parallel through the use of affinity-tagged proteins, barcoded selection oligonucleotides, and multiplexed sequencing. Data are analyzed by a new bioinformatic platform that uses the hundreds of thousands of sequencing reads obtained to control the quality of the experiments and to generate binding motifs for the TFs. The described technology allows higher throughput and identification of much longer binding profiles than current microarray-based methods. In addition, as our method is based on proteins expressed in mammalian cells, it can also be used to characterize DNA-binding preferences of full-length proteins or proteins requiring post-translational modifications. We validate the method by determining binding specificities of 14 different classes of TFs and by confirming the specificities for NFATC1 and RFX3 using ChIP-seq. Our results reveal unexpected dimeric modes of binding for several factors that were thought to preferentially bind DNA as monomers.", "doi": "10.1101/gr.100552.109", "pmid": "20378718", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "Karolinska High Throughput Center (KHTC)": null}, "xrefs": [{"db": "pii", "key": "gr.100552.109"}, {"db": "pmc", "key": "PMC2877582"}], "notes": [], "created": "2017-05-04T14:57:03.059Z", "modified": "2020-01-21T13:56:00.915Z"}, {"entity": "publication", "iuid": "1b91c55735414fdc8cc0f72e9f37b548", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b91c55735414fdc8cc0f72e9f37b548.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b91c55735414fdc8cc0f72e9f37b548"}}, "title": "Improving Bayesian credibility intervals for classifier error rates using maximum entropy empirical priors.", "authors": [{"family": "Gustafsson", "given": "Mats G", "initials": "MG"}, {"family": "Wallman", "given": "Mikael", "initials": "M"}, {"family": "Wickenberg Bolin", "given": "Ulrika", "initials": "U"}, {"family": "G\u00f6ransson", "given": "Hanna", "initials": "H"}, {"family": "Frykn\u00e4s", "given": "M", "initials": "M"}, {"family": "Andersson", "given": "Claes R", "initials": "CR"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}], "type": "journal article", "published": "2010-06-00", "journal": {"volume": "49", "issn": "1873-2860", "issue": "2", "pages": "93-104", "title": "Artif Intell Med", "issn-l": "0933-3657"}, "abstract": "Successful use of classifiers that learn to make decisions from a set of patient examples require robust methods for performance estimation. Recently many promising approaches for determination of an upper bound for the error rate of a single classifier have been reported but the Bayesian credibility interval (CI) obtained from a conventional holdout test still delivers one of the tightest bounds. The conventional Bayesian CI becomes unacceptably large in real world applications where the test set sizes are less than a few hundred. The source of this problem is that fact that the CI is determined exclusively by the result on the test examples. In other words, there is no information at all provided by the uniform prior density distribution employed which reflects complete lack of prior knowledge about the unknown error rate. Therefore, the aim of the study reported here was to study a maximum entropy (ME) based approach to improved prior knowledge and Bayesian CIs, demonstrating its relevance for biomedical research and clinical practice.\n\nIt is demonstrated how a refined non-uniform prior density distribution can be obtained by means of the ME principle using empirical results from a few designs and tests using non-overlapping sets of examples.\n\nExperimental results show that ME based priors improve the CIs when employed to four quite different simulated and two real world data sets.\n\nAn empirically derived ME prior seems promising for improving the Bayesian CI for the unknown error rate of a designed classifier.", "doi": "10.1016/j.artmed.2010.02.004", "pmid": "20347582", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "S0933-3657(10)00025-4"}], "notes": [], "created": "2017-05-04T15:02:48.282Z", "modified": "2018-11-14T14:24:36.251Z"}, {"entity": "publication", "iuid": "ddc11c747e5a46b69b6a911e4a3d282e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ddc11c747e5a46b69b6a911e4a3d282e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ddc11c747e5a46b69b6a911e4a3d282e"}}, "title": "Genetics of HPA-axis, depression and suicidality.", "authors": [{"family": "Wasserman", "given": "D", "initials": "D"}, {"family": "Wasserman", "given": "J", "initials": "J"}, {"family": "Sokolowski", "given": "M", "initials": "M"}], "type": "journal article", "published": "2010-06-00", "journal": {"volume": "25", "issn": "1778-3585", "issue": "5", "pages": "278-280", "title": "Eur. Psychiatry", "issn-l": "0924-9338"}, "abstract": "The ultimate consequence of mental ill-health, suicidal behavior (SB), is a significant problem in most societies of the world. Suicide causes about one million deaths worldwide each year, and 10-20 times more people attempt suicide. The causes of why certain people engage in SB are complex, involving for e.g., both environmental and genetic factors, and interactions in-between. Well-established environmental risk factors are events causing significant psychological stress, which are particularly difficult to cope with, e.g. exposure to physical and sexual abuse. Excessive stress have the potential to induce unfavorable effects in a variety of higher brain-functions, incurred as side-effects to maladaptive responses in the genetically controlled stress-responsive neurosystems, e.g. the hypothalamic-pituitary-adrenal (HPA) axis; a major and systemic stress-modulator, which is mainly controlled by the regulatory corticotrophin releasing hormone receptor 1 (CRHR1) gene. Variation in-between individuals in such stress-regulatory genes such as CRHR1, may underlie the causes of the increased susceptibility of certain individuals towards SB. Here we review some of the current knowledge on what is known about the roles of the HPA axis in SB, with a focus on CRHR1.", "doi": "10.1016/j.eurpsy.2009.12.016", "pmid": "20444578", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0924-9338(10)00062-3"}], "notes": [], "created": "2017-05-04T15:00:29.857Z", "modified": "2020-01-21T13:56:05.677Z"}, {"entity": "publication", "iuid": "7f6a0088118c4698a5d791fd59549dcb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7f6a0088118c4698a5d791fd59549dcb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7f6a0088118c4698a5d791fd59549dcb"}}, "title": "Genetic analysis of metabolic traits in an intercross between body weight-selected chicken lines.", "authors": [{"family": "Ek", "given": "Weronica", "initials": "W"}, {"family": "Str\u00f6mstedt", "given": "Lina", "initials": "L"}, {"family": "Wahlberg", "given": "Per", "initials": "P"}, {"family": "Siegel", "given": "Paul", "initials": "P"}, {"family": "Andersson", "given": "Leif", "initials": "L"}, {"family": "Carlborg", "given": "Orjan", "initials": "O"}], "type": "journal article", "published": "2010-06-00", "journal": {"volume": "42", "issn": "1531-2267", "issue": "1", "pages": "20-22", "title": "Physiol. Genomics", "issn-l": "1094-8341"}, "abstract": "A network of four interacting loci has been reported previously to influence growth in two lines of chickens divergently selected for body weight at 56 days of age. Located on chromosomes 3 (Growth4), 4 (Growth6), 7 (Growth9), and 20 (Growth12), they explained nearly half of the difference in body weight at selection age between the two lines. The original study reported effects on body weight and fat deposition, but no attempts were made to explore the effects of the network on other phenotypes measured in the F(2) population. In this study we conducted further analyses to evaluate the specific effects of the four-locus network on other metabolic traits as well as refining results from the original study by including a larger number of genetic markers in the quantitative trait locus (QTL) regions. We confirm the previously described effect of the epistatic network on body weight and show that the network increases the total amount of muscle and fat as well as the weight of the internal organs. The network as a whole did not change the relative content of any studied organs or tissues in the body. There was, however, a significant interaction between the loci on chromosomes 3 and 7 that changed the relative proportion of abdominal fat and breast muscle in the chicken by increasing abdominal fat weight without a corresponding increase in muscle mass.", "doi": "10.1152/physiolgenomics.00149.2009", "pmid": "20332184", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "physiolgenomics.00149.2009"}], "notes": [], "created": "2017-05-04T15:00:37.377Z", "modified": "2020-01-21T13:56:03.315Z"}, {"entity": "publication", "iuid": "bca7359920d249f580926e20f55a251d", "links": {"self": {"href": "https://publications.scilifelab.se/publication/bca7359920d249f580926e20f55a251d.json"}, "display": {"href": "https://publications.scilifelab.se/publication/bca7359920d249f580926e20f55a251d"}}, "title": "Antibody-based proteomics for discovery and exploration of proteins expressed in pancreatic islets.", "authors": [{"family": "Lindskog", "given": "Cecilia", "initials": "C", "orcid": "0000-0001-5611-1015", "researcher": {"href": "https://publications.scilifelab.se/researcher/36b6a0f049274929b64dcb5061ca0588.json"}}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Engkvist", "given": "Margareta", "initials": "M"}, {"family": "Uhlen", "given": "Mathias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Korsgren", "given": "Olle", "initials": "O"}, {"family": "Ponten", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}], "type": "journal article", "published": "2010-06-00", "journal": {"volume": "9", "issn": "1944-7930", "issue": "49", "pages": "565-578", "title": "Discov Med", "issn-l": "1539-6509"}, "abstract": "Abnormal glucose tolerance and deviant blood glucose levels are late stage clinical parameters that signify diabetes mellitus. To be able to diagnose the disease at an earlier stage and develop new tools for beta cell imaging, new molecular markers are needed. In the present study, five proteins highly expressed in pancreatic islets with no expression in the surrounding exocrine glandular cells of pancreas, and one protein with the opposite expression pattern, were identified by searches in the Human Protein Atlas (www.proteinatlas.org). The proteins were analyzed immunohistochemically on a specially designed tissue microarray, containing isolated human islets and pancreatic tissues with different characteristics, and compared to the expression of previously known markers of endocrine and exocrine pancreatic cells. Of the five novel endocrine markers, tetraspanin-7 was identified as a membrane-bound protein with exclusive positivity in islet cells. Also beta-2-microglobulin and ubiquitin carboxyl-terminal hydrolase isozyme L1 were expressed in a majority of islet cells, whereas sad1/unc-84 domain-containing protein 1 and beta-1,3-glucuronyltransferase 1 were positive in a smaller subset of islet cells. The potential exocrine marker galectin-2 was expressed in both exocrine acinary cells and pancreatic ductal cells, with no or low positivity in islet cells. In conclusion, antibody-based proteomics and specially designed tissue microarrays enable identification and exploration of novel proteins with differential expression in pancreatic islets. Here we describe 5 candidate proteins for further investigation of their physiological role and potential involvement in the pathogenesis of diabetes. One of these proteins, tetraspanin-7, is expressed on the cell membrane and could thus be a potential candidate for future development of tracers for beta cell imaging.", "doi": null, "pmid": "20587347", "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:43.077Z", "modified": "2025-12-01T07:53:07.307Z"}, {"entity": "publication", "iuid": "1b906cd95a43425dae9ba7270d1e5338", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1b906cd95a43425dae9ba7270d1e5338.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1b906cd95a43425dae9ba7270d1e5338"}}, "title": "Alpha terpineol: a potential anticancer agent which acts through suppressing NF-kappaB signalling.", "authors": [{"family": "Hassan", "given": "Saadia Bashir", "initials": "SB"}, {"family": "Gali-Muhtasib", "given": "Hala", "initials": "H"}, {"family": "G\u00f6ransson", "given": "Hanna", "initials": "H"}, {"family": "Larsson", "given": "Rolf", "initials": "R", "orcid": "0000-0002-5261-7390", "researcher": {"href": "https://publications.scilifelab.se/researcher/b2fab759f00549cfaf3417d98e691323.json"}}], "type": "journal article", "published": "2010-06-00", "journal": {"volume": "30", "issn": "1791-7530", "issue": "6", "pages": "1911-1919", "title": "Anticancer Res.", "issn-l": "0250-7005"}, "abstract": "Alpha terpineol is a bioactive component of Salvia libanotica essential oil extract and has shown antitumour activity.\n\nThe cytotoxicity of alpha terpineol towards different tumour cell lines was evaluated in vitro. Mechanistic characterization was performed using analysis of drug activity in a cell line panel and drug-induced gene expression perturbation using the connectivity map approach.\n\nThe small cell lung carcinoma was the cell line most sensitive to alpha terpineol. The results proposed alpha terpineol as an NF-kappaB inhibitor, which was confirmed by the observed dose-dependent inhibition of NF-kappaB translocation and activity using two NF-kappaB assays, and by the down-regulation of the expression of several NF-kappaB-related genes such as IL-1 beta and IL1R1.\n\nThe results suggest that alpha terpineol inhibits the growth of tumour cells through a mechanism that involves inhibition of the NF-kappaB pathway.", "doi": null, "pmid": "20651334", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "30/6/1911"}], "notes": [], "created": "2017-05-04T15:02:47.977Z", "modified": "2025-11-17T10:02:57.365Z"}, {"entity": "publication", "iuid": "63cca50513ae41c2a6fa9fa0b38463f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/63cca50513ae41c2a6fa9fa0b38463f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/63cca50513ae41c2a6fa9fa0b38463f0"}}, "title": "A variant near the interleukin-6 gene is associated with fat mass in Caucasian men.", "authors": [{"family": "Andersson", "given": "N", "initials": "N"}, {"family": "Strandberg", "given": "L", "initials": "L"}, {"family": "Nilsson", "given": "S", "initials": "S"}, {"family": "Adamovic", "given": "S", "initials": "S"}, {"family": "Karlsson", "given": "M K", "initials": "MK"}, {"family": "Ljunggren", "given": "O", "initials": "O"}, {"family": "Mellstr\u00f6m", "given": "D", "initials": "D"}, {"family": "Lane", "given": "N E", "initials": "NE"}, {"family": "Zmuda", "given": "J M", "initials": "JM"}, {"family": "Nielsen", "given": "C", "initials": "C"}, {"family": "Orwoll", "given": "E", "initials": "E"}, {"family": "Lorentzon", "given": "M", "initials": "M"}, {"family": "Ohlsson", "given": "C", "initials": "C"}, {"family": "Jansson", "given": "J-O", "initials": "JO"}, {"family": "Osteoporotic Fractures in Men MrOS Research Group", "given": null, "initials": null}], "type": "journal article", "published": "2010-06-00", "journal": {"volume": "34", "issn": "1476-5497", "issue": "6", "pages": "1011-1019", "title": "Int J Obes (Lond)", "issn-l": "0307-0565"}, "abstract": "Regulation of fat mass appears to be associated with immune functions. Studies of knockout mice show that endogenous interleukin (IL)-6 can suppress mature-onset obesity.\n\nTo systematically investigate associations of single nucleotide polymorphisms (SNPs) near the IL-6 (IL6) and IL-6 receptor (IL6R) genes with body fat mass, in support for our hypothesis that variants of these genes can be associated with obesity.\n\nThe Gothenburg Osteoporosis and Obesity Determinants (GOOD) study is a population-based cross-sectional study of 18- to 20-year-old men (n=1049), from the Gothenburg area (Sweden). Major findings were confirmed in two additional cohorts consisting of elderly men from the Osteoporotic Fractures in Men (MrOS) Sweden (n=2851) and MrOS US (n=5611) multicenter population-based studies.\n\nThe genotype distributions and their association with fat mass in different compartments, measured with dual-energy X-ray absorptiometry.\n\nOut of 18 evaluated tag SNPs near the IL6 and IL6R genes, a recently identified SNP rs10242595 G/A (minor allele frequency=29%) 3' of the IL6 gene was negatively associated with the primary outcome total body fat mass (effect size -0.11 standard deviation (s.d.) units per A allele, P=0.02). This negative association with fat mass was also confirmed in the combined MrOS Sweden and MrOS US cohorts (effect size -0.05 s.d. units per A allele, P=0.002). When all three cohorts were combined (n=8927, Caucasian subjects), rs10242595(*)A showed a negative association with total body fat mass (effect size -0.05 s.d. units per A allele, P<0.0002). Furthermore, the rs10242595(*)A was associated with low body mass index (effect size -0.03, P<0.001) and smaller regional fat masses. None of the other SNPs investigated in the GOOD study were reproducibly associated with body fat.\n\nThe IL6 gene polymorphism rs10242595(*)A is associated with decreased fat mass in three combined cohorts of 8927 Caucasian men.", "doi": "10.1038/ijo.2010.27", "pmid": "20157327", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ijo201027"}, {"db": "pmc", "key": "PMC2885503"}, {"db": "mid", "key": "NIHMS169541"}], "notes": [], "created": "2017-05-04T15:00:32.234Z", "modified": "2020-01-21T13:56:02.715Z"}, {"entity": "publication", "iuid": "8347bc31d006484d9b51a42647ad9906", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8347bc31d006484d9b51a42647ad9906.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8347bc31d006484d9b51a42647ad9906"}}, "title": "Molecular make-up of the glomerular filtration barrier.", "authors": [{"family": "Patrakka", "given": "Jaakko", "initials": "J"}, {"family": "Tryggvason", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2010-05-21", "journal": {"volume": "396", "issn": "1090-2104", "issue": "1", "pages": "164-169", "title": "Biochem. Biophys. Res. Commun.", "issn-l": "0006-291X"}, "abstract": "The glomerular filtration barrier is composed of glomerular endothelial cells, the glomerulus basement membrane and the podocyte cell layer. The filtration barrier is a target of injury in several systemic and renal diseases, and this often leads to progressive renal disease and kidney failure. Therefore, it is essential to understand the molecular biology of the glomerulus. During the last two decades, a lot of new information about molecular components of the glomerulus filtration barrier has been generated. Many of the key discoveries have been obtained through studies on the genetic background of inherited glomerular diseases. These studies have emphasized the role of podocytes in the filtration barrier function. During the last decade, the use of knockout mouse technology has become more available and given important new insights into the functional significance of glomerular components. Large-scale approaches, such as microarray profiling, have also given data about molecules involved in the biology and pathology of the glomerulus. In the coming decade, the use of global expression profiling platforms, transgenic mouse lines, and other in vivo gene delivery methods will rapidly expand our understanding of biology and pathology of the glomerular filtration barrier, and hopefully expose novel target molecules for therapy in progressive renal diseases.", "doi": "10.1016/j.bbrc.2010.04.069", "pmid": "20494132", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "S0006-291X(10)00738-2"}], "notes": [], "created": "2017-05-04T15:03:03.029Z", "modified": "2017-05-31T08:17:09.758Z"}, {"entity": "publication", "iuid": "ec78f43d06c64b1393b2f14542acec0b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ec78f43d06c64b1393b2f14542acec0b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ec78f43d06c64b1393b2f14542acec0b"}}, "title": "Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk.", "authors": [{"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Eriksson", "given": "Ulrika K", "initials": "UK"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Wiklund", "given": "Fredrik", "initials": "F"}, {"family": "Johansson", "given": "Boo", "initials": "B"}, {"family": "Malmberg", "given": "Bo", "initials": "B"}, {"family": "Berg", "given": "Stig", "initials": "S"}, {"family": "Alexeyenko", "given": "Andrey", "initials": "A"}, {"family": "Gr\u00f6nberg", "given": "Henrik", "initials": "H"}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Prince", "given": "Jonathan A", "initials": "JA"}], "type": "journal article", "published": "2010-05-15", "journal": {"volume": "19", "issn": "1460-2083", "issue": "10", "pages": "2068-2078", "title": "Hum. Mol. Genet.", "issn-l": "0964-6906"}, "abstract": "We conducted dense linkage disequilibrium (LD) mapping of a series of 25 genes putatively involved in lipid metabolism in 1567 dementia cases [including 1270 with Alzheimer disease (AD)] and 2203 Swedish controls. Across a total of 448 tested genetic markers, the strongest evidence of association was as anticipated for APOE (rs429358 at P approximately 10(-72)) followed by a previously reported association of ABCA1 (rs2230805 at P approximately 10(-8)). In the present study, we report two additional markers near the SREBF1 locus on chromosome 17p that were also significant after multiple testing correction (best P = 3.1 x 10(-6) for marker rs3183702). There was no convincing evidence of association for remaining genes, including candidates highlighted from recent genome-wide association studies of plasma lipids (CELSR2/PSRC1/SORT1, MLXIPL, PCSK9, GALNT2 and GCKR). The associated markers near SREBF1 reside in a large LD block, extending more than 400 kb across seven candidate genes. Secondary analyses of gene expression levels of candidates spanning the LD region together with an investigation of gene network context highlighted two possible susceptibility genes including ATPAF2 and TOM1L2. Several markers in strong LD (r(2) > 0.7) with rs3183702 were found to be significantly associated with AD risk in recent genome-wide association studies with similar effect sizes, providing independent support of the current findings.", "doi": "10.1093/hmg/ddq079", "pmid": "20167577", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ddq079"}, {"db": "pmc", "key": "PMC2860895"}], "notes": [], "created": "2017-05-04T15:00:31.583Z", "modified": "2020-01-21T13:56:06.020Z"}, {"entity": "publication", "iuid": "f6e5f676a068403583e89b8d29fd0d0a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f6e5f676a068403583e89b8d29fd0d0a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f6e5f676a068403583e89b8d29fd0d0a"}}, "title": "Adipose tissue pathways involved in weight loss of cancer cachexia.", "authors": [{"family": "Dahlman", "given": "I", "initials": "I"}, {"family": "Mejhert", "given": "N", "initials": "N"}, {"family": "Linder", "given": "K", "initials": "K"}, {"family": "Agustsson", "given": "T", "initials": "T"}, {"family": "Mutch", "given": "D M", "initials": "DM"}, {"family": "Kulyte", "given": "A", "initials": "A"}, {"family": "Isaksson", "given": "B", "initials": "B"}, {"family": "Permert", "given": "J", "initials": "J"}, {"family": "Petrovic", "given": "N", "initials": "N"}, {"family": "Nedergaard", "given": "J", "initials": "J"}, {"family": "Sj\u00f6lin", "given": "E", "initials": "E"}, {"family": "Brodin", "given": "D", "initials": "D"}, {"family": "Clement", "given": "K", "initials": "K"}, {"family": "Dahlman-Wright", "given": "K", "initials": "K"}, {"family": "Ryd\u00e9n", "given": "M", "initials": "M"}, {"family": "Arner", "given": "P", "initials": "P"}], "type": "journal article", "published": "2010-05-11", "journal": {"volume": "102", "issn": "1532-1827", "issue": "10", "pages": "1541-1548", "title": "Br. J. Cancer", "issn-l": "0007-0920"}, "abstract": "The regulatory gene pathways that accompany loss of adipose tissue in cancer cachexia are unknown and were explored using pangenomic transcriptome profiling.\n\nGlobal gene expression profiles of abdominal subcutaneous adipose tissue were studied in gastrointestinal cancer patients with (n=13) or without (n=14) cachexia.\n\nCachexia was accompanied by preferential loss of adipose tissue and decreased fat cell volume, but not number. Adipose tissue pathways regulating energy turnover were upregulated, whereas genes in pathways related to cell and tissue structure (cellular adhesion, extracellular matrix and actin cytoskeleton) were downregulated in cachectic patients. Transcriptional response elements for hepatic nuclear factor-4 (HNF4) were overrepresented in the promoters of extracellular matrix and adhesion molecule genes, and adipose HNF4 mRNA was downregulated in cachexia.\n\nCancer cachexia is characterised by preferential loss of adipose tissue; muscle mass is less affected. Loss of adipose tissue is secondary to a decrease in adipocyte lipid content and associates with changes in the expression of genes that regulate energy turnover, cytoskeleton and extracellular matrix, which suggest high tissue remodelling. Changes in gene expression in cachexia are reciprocal to those observed in obesity, suggesting that regulation of fat mass at least partly corresponds to two sides of the same coin.", "doi": "10.1038/sj.bjc.6605665", "pmid": "20407445", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "6605665"}, {"db": "pmc", "key": "PMC2869165"}], "notes": [], "created": "2017-05-04T15:03:03.926Z", "modified": "2017-05-30T12:38:37.153Z"}, {"entity": "publication", "iuid": "c66ffc1dfbfe4c829521cad5676192aa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c66ffc1dfbfe4c829521cad5676192aa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c66ffc1dfbfe4c829521cad5676192aa"}}, "title": "Genetic risk factors in lupus nephritis and IgA nephropathy--no support of an overlap.", "authors": [{"family": "Vuong", "given": "Mai Tuyet", "initials": "MT"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Lundberg", "given": "Sigrid", "initials": "S"}, {"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Wramner", "given": "Lars", "initials": "L"}, {"family": "Fernstr\u00f6m", "given": "Anders", "initials": "A"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Do", "given": "Lieu Thi", "initials": "LT"}, {"family": "Jacobson", "given": "Stefan H", "initials": "SH"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}], "type": "journal article", "published": "2010-05-10", "journal": {"volume": "5", "issn": "1932-6203", "issue": "5", "pages": "e10559", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "IgA nephropathy (IgAN) and nephritis in Systemic Lupus Erythematosus (SLE) are two common forms of glomerulonephritis in which genetic findings are of importance for disease development. We have recently reported an association of IgAN with variants of TGFB1. In several autoimmune diseases, particularly in SLE, IRF5, STAT4 genes and TRAF1-C5 locus have been shown to be important candidate genes. The aim of this study was to compare genetic variants from the TGFB1, IRF5, STAT4 genes and TRAF1-C5 locus with susceptibility to IgAN and lupus nephritis in two Swedish cohorts.\n\nWe genotyped 13 single nucleotide polymorphisms (SNPs) in four genetic loci in 1252 DNA samples from patients with biopsy proven IgAN or with SLE (with and without nephritis) and healthy age- and sex-matched controls from the same population in Sweden.\n\nGenotype and allelic frequencies for SNPs from selected genes did not differ significantly between lupus nephritis patients and SLE patients without nephritis. In addition, haplotype analysis for seven selected SNPs did not reveal a difference for the SLE patient groups with and without nephritis. Moreover, none of these SPNs showed a significant difference between IgAN patients and healthy controls. IRF5 and STAT4 variants remained significantly different between SLE cases and healthy controls. In addition, the data did not show an association of TRAF1-C5 polymorphism with susceptibility to SLE in this Swedish population.\n\nOur data do not support an overlap in genetic susceptibility between patients with IgAN or SLE and reveal no specific importance of SLE associated SNPs for the presence of lupus nephritis.", "doi": "10.1371/journal.pone.0010559", "pmid": "20479942", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pmc", "key": "PMC2866667"}], "notes": [], "created": "2017-05-04T15:00:38.319Z", "modified": "2021-07-07T15:11:02.733Z"}, {"entity": "publication", "iuid": "fb56aeb8a1f04bccbc29a1eec7c57464", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fb56aeb8a1f04bccbc29a1eec7c57464.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fb56aeb8a1f04bccbc29a1eec7c57464"}}, "title": "Chd1 remodelers maintain open chromatin and regulate the epigenetics of differentiation.", "authors": [{"family": "Persson", "given": "Jenna", "initials": "J"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2010-05-01", "journal": {"volume": "316", "issn": "1090-2422", "issue": "8", "pages": "1316-1323", "title": "Exp. Cell Res.", "issn-l": "0014-4827"}, "abstract": "Eukaryotic DNA is packaged around octamers of histone proteins into nucleosomes, the basic unit of chromatin. In addition to enabling meters of DNA to fit within the confines of a nucleus, the structure of chromatin has functional implications for cell identity. Covalent chemical modifications to the DNA and to histones, histone variants, ATP-dependent chromatin remodelers, small noncoding RNAs and the level of chromatin compaction all contribute to chromosomal structure and to the activity or silencing of genes. These chromatin-level alterations are defined as epigenetic when they are heritable from mother to daughter cell. The great diversity of epigenomes that can arise from a single genome permits a single, totipotent cell to generate the hundreds of distinct cell types found in humans. Two recent studies in mouse and in fly have highlighted the importance of Chd1 chromatin remodelers for maintaining an open, active chromatin state. Based on evidence from fission yeast as a model system, we speculate that Chd1 remodelers are involved in the disassembly of nucleosomes at promoter regions, thus promoting active transcription and open chromatin. It is likely that these nucleosomes are specifically marked for disassembly by the histone variant H2A.Z.", "doi": "10.1016/j.yexcr.2010.02.029", "pmid": "20211173", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "S0014-4827(10)00091-1"}], "notes": [], "created": "2017-05-04T15:03:04.825Z", "modified": "2017-05-30T12:38:51.227Z"}, {"entity": "publication", "iuid": "b2df56d90ea1429f87f61e9fef9a9962", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b2df56d90ea1429f87f61e9fef9a9962.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b2df56d90ea1429f87f61e9fef9a9962"}}, "title": "Variation in STAT4 is associated with systemic lupus erythematosus in a Finnish family cohort.", "authors": [{"family": "Hellquist", "given": "Anna", "initials": "A"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Zucchelli", "given": "Marco", "initials": "M"}, {"family": "Koskenmies", "given": "Sari", "initials": "S"}, {"family": "Julkunen", "given": "Heikki", "initials": "H"}, {"family": "D'Amato", "given": "Mauro", "initials": "M"}, {"family": "Garnier", "given": "Sophie", "initials": "S"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Kere", "given": "Juha", "initials": "J"}], "type": "journal article", "published": "2010-05-00", "journal": {"volume": "69", "issn": "1468-2060", "issue": "5", "pages": "883-886", "title": "Ann. Rheum. Dis.", "issn-l": "0003-4967"}, "abstract": "To investigate whether 10 single nucleotide polymorphisms (SNPs) and haplotypes in the STAT4 gene, previously associated with systemic lupus erythematosus (SLE) in a Swedish case-control cohort, are also associated with SLE risk in a Finnish SLE family cohort.\n\nGenotyping was performed in 192 Finnish families, with 237 affected subjects and their healthy relatives, using the SNPstream genotyping system.\n\nTransmission disequilibrium test analysis provided the strongest signal of association for two linked SNPs: rs7582694 (p=0.002, OR=2.57) and rs10181656 (p=0.001, OR=2.53). Haplotype association analysis using a sliding window approach was also performed and showed that the strongest association signal originates from SNPs in intron 3 of STAT4.\n\nThe main association signal for STAT4 with SLE previously reported in Caucasians is the same in the Finnish population. This is the first study that confirms the association of STAT4 with SLE in a family cohort.", "doi": "10.1136/ard.2009.112284", "pmid": "19717398", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ard.2009.112284"}], "notes": [], "created": "2017-05-04T15:00:26.429Z", "modified": "2021-07-07T15:11:02.692Z"}, {"entity": "publication", "iuid": "4c9618beb27b4bb089b1fd3545d1736b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4c9618beb27b4bb089b1fd3545d1736b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4c9618beb27b4bb089b1fd3545d1736b"}}, "title": "The impact of RNA standardization and heterogeneous gene expression on the results of cDNA array of human breast carcinoma.", "authors": [{"family": "Khoshnoud", "given": "Reza", "initials": "R"}, {"family": "He", "given": "Qimin", "initials": "Q"}, {"family": "Sylv\u00e1n", "given": "Maria", "initials": "M"}, {"family": "Khoshnoud", "given": "Aida", "initials": "A"}, {"family": "Ivarsson", "given": "Madleen", "initials": "M"}, {"family": "Fornander", "given": "Tommy", "initials": "T"}, {"family": "Bergh", "given": "Jonas", "initials": "J"}, {"family": "Frisell", "given": "Jan", "initials": "J"}, {"family": "Rutqvist", "given": "Lars-Erik", "initials": "L"}, {"family": "Skog", "given": "Sven", "initials": "S"}], "type": "journal article", "published": "2010-05-00", "journal": {"volume": "25", "issn": "1791-244X", "issue": "5", "pages": "735-741", "title": "Int. J. Mol. Med.", "issn-l": "1107-3756"}, "abstract": "cDNA microarray is an established technique. However, difficulties such as handling tissue samples under RNase-free conditions, the heterogeneous tumor composition, i.e. non-malignant versus malignant cells and different pathologic types of malignant cells, and lack of appropriate reference may limit the potentially benefit of this method in clinical use. In this study, we examined how standardization of gene expression to total mg RNA or mg tissue and tumor heterogeneity affect the final results. We found that the gene expression of human breast tumors was approximately 9 times higher in malignant tissue as compared to the non-malignant tissue when expressed per total mg RNA, but approximately 40 times higher when expressed per mg tissue. Genes that were expected to act as housekeeping genes (PUC18, RPL and beta-actin) varied between different parts of the tumor and also between non-malignant and malignant tissues, excluding them as reference genes. We also found that the gene expression differed in various parts of the breast tumor, probably due to a mixture of different types of cells, i.e. non-malignant and malignant cells. To find out if the variations in the gene expression were due to cell heterogeneity we used microdissection to collect malignant cells separately. We found that the gene expression was markedly different in the isolated malignant cells as compared to the gene expression of the bulk tumor tissue. Thus, to be able to evaluate results from cDNA array gene expression experiments it is, to our opinion, necessary to work with pure tumor cell populations, until solid information is available on the impact of stromal component. Housekeeping genes should be handling with care and mg tissue may be preferred instead of microg RNA for standardization.", "doi": "10.3892/ijmm_00000399", "pmid": "20372817", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:03:05.425Z", "modified": "2017-11-06T08:34:23.251Z"}, {"entity": "publication", "iuid": "502a7a8e7d64496aa6c1aac673caa148", "links": {"self": {"href": "https://publications.scilifelab.se/publication/502a7a8e7d64496aa6c1aac673caa148.json"}, "display": {"href": "https://publications.scilifelab.se/publication/502a7a8e7d64496aa6c1aac673caa148"}}, "title": "Mapping of the fibroblast growth factors in human white adipose tissue.", "authors": [{"family": "Mejhert", "given": "Niklas", "initials": "N"}, {"family": "Galitzky", "given": "Jean", "initials": "J"}, {"family": "Pettersson", "given": "Amanda T", "initials": "AT"}, {"family": "Bambace", "given": "Clara", "initials": "C"}, {"family": "Blomqvist", "given": "Lennart", "initials": "L"}, {"family": "Bouloumi\u00e9", "given": "Anne", "initials": "A"}, {"family": "Frayn", "given": "Keith N", "initials": "KN"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}, {"family": "Arner", "given": "Peter", "initials": "P"}, {"family": "Ryd\u00e9n", "given": "Mikael", "initials": "M"}], "type": "journal article", "published": "2010-05-00", "journal": {"volume": "95", "issn": "1945-7197", "issue": "5", "pages": "2451-2457", "title": "J. Clin. Endocrinol. Metab.", "issn-l": "0021-972X"}, "abstract": "Fibroblast growth factors (FGFs) regulate the development of white adipose tissue (WAT). However, the secretion and cellular origin of individual FGFs in WAT as well as the influence of obesity are unknown.\n\nOur objective was to map FGFs in human sc WAT, the cellular source, and association with obesity.\n\nSecretion, mRNA, and circulatory levels of FGFs in human abdominal sc WAT from nonobese and obese donors were examined by microarray, real-time quantitative PCR, and ELISA. The activity of FGFs in cultured human adipocytes was determined by phosphorylation assays.\n\nExpression of five FGFs (FGF1, FGF2, FGF7, FGF9, and FGF18) and FGF homologous factor (FHF2) was identified in WAT. Only FGF1 was released in a time-dependent manner from sc WAT, and fat cells were the major source of FGF1 secretion. FGF1 expression increased and FGF2 decreased during adipocyte differentiation. Furthermore, FGF1 was not secreted into the circulation. Although FGF1 levels were 2-fold increased in obesity, they were unaltered by weight reduction. Only FGF1 and FGF2 induced a marked concentration-dependent phosphorylation of p44/42 in cultured human adipocytes.\n\nOf the investigated FGFs, only FGF1 is secreted from sc WAT and predominantly so from the adipocyte fraction. The activity in adipocyte cultures and lack of secretion into the circulation suggest that FGF1 acts as an auto- or paracrine factor. FGF1 levels are increased in obesity but unaffected by weight reduction, suggesting a primary defect in obese individuals. In conclusion, FGF1 may play a superior role among the FGFs in sc WAT and obesity development.", "doi": "10.1210/jc.2009-2049", "pmid": "20228166", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "jc.2009-2049"}], "notes": [], "created": "2017-05-04T15:03:06.325Z", "modified": "2017-05-30T12:39:14.624Z"}, {"entity": "publication", "iuid": "143538165b3a488da6cf242482f928d7", "links": {"self": {"href": "https://publications.scilifelab.se/publication/143538165b3a488da6cf242482f928d7.json"}, "display": {"href": "https://publications.scilifelab.se/publication/143538165b3a488da6cf242482f928d7"}}, "title": "Gene-specific and global methylation patterns predict outcome in patients with acute myeloid leukemia.", "authors": [{"family": "Deneberg", "given": "S", "initials": "S"}, {"family": "Gr\u00f6vdal", "given": "M", "initials": "M"}, {"family": "Karimi", "given": "M", "initials": "M"}, {"family": "Jansson", "given": "M", "initials": "M"}, {"family": "Nahi", "given": "H", "initials": "H"}, {"family": "Corbacioglu", "given": "A", "initials": "A"}, {"family": "Gaidzik", "given": "V", "initials": "V"}, {"family": "D\u00f6hner", "given": "K", "initials": "K"}, {"family": "Paul", "given": "C", "initials": "C"}, {"family": "Ekstr\u00f6m", "given": "T J", "initials": "TJ"}, {"family": "Hellstr\u00f6m-Lindberg", "given": "E", "initials": "E"}, {"family": "Lehmann", "given": "S", "initials": "S"}], "type": "journal article", "published": "2010-05-00", "journal": {"volume": "24", "issn": "1476-5551", "issue": "5", "pages": "932-941", "title": "Leukemia", "issn-l": "0887-6924"}, "abstract": "This study was designed to analyze the effect of global and gene-specific DNA methylation patterns on the outcome of patients with acute myeloid leukemia (AML). Methylation of CDKN2B (p15), E-cadherin (CDH) and hypermethylated in cancer 1 (HIC1) promoters and global DNA methylation by luminometric methylation assay (LUMA) was analyzed in 107 AML patients and cytogenetic and molecular mutational analysis was performed. In addition, genome-wide promoter-associated methylation was assessed using the Illumina HumanMethylation27 array in a proportion of the patients. Promoter methylation was discovered in 66, 66 and 51% of the patients for p15, CDH and HIC1, respectively. In multivariate analysis, low global DNA methylation was associated with higher complete remission rate (hazard ratio (HR) 5.9, P=0.005) and p15 methylation was associated with better overall (HR 0.4, P=0.001) and disease-free survival (HR 0.4, P=0.016). CDH and HIC1 methylation were not associated with clinical outcome. Mutational status and karyotype were not significantly associated with gene-specific methylation or global methylation. Increased genome-wide promoter-associated methylation was associated with better overall and disease-free survival as well as with LUMA hypomethylation. We conclude that global and gene-specific methylation patterns are independently associated with the clinical outcome in AML patients.", "doi": "10.1038/leu.2010.41", "pmid": "20237504", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "leu201041"}], "notes": [], "created": "2017-05-04T15:03:07.831Z", "modified": "2017-05-30T12:39:39.233Z"}, {"entity": "publication", "iuid": "4896fad053ba487492e6c05d927705fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4896fad053ba487492e6c05d927705fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4896fad053ba487492e6c05d927705fa"}}, "title": "Detailed physiologic characterization reveals diverse mechanisms for novel genetic Loci regulating glucose and insulin metabolism in humans.", "authors": [{"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Hivert", "given": "Marie-France", "initials": "MF"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Sharp", "given": "Stephen", "initials": "S"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Assimes", "given": "Themistocles L", "initials": "TL"}, {"family": "Shrader", "given": "Peter", "initials": "P"}, {"family": "Knowles", "given": "Joshua W", "initials": "JW"}, {"family": "Zethelius", "given": "Bj\u00f6rn", "initials": "B"}, {"family": "Abbasi", "given": "Fahim A", "initials": "FA"}, {"family": "Bergman", "given": "Richard N", "initials": "RN"}, {"family": "Bergmann", "given": "Antje", "initials": "A"}, {"family": "Berne", "given": "Christian", "initials": "C"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Bornstein", "given": "Stefan R", "initials": "SR"}, {"family": "Buchanan", "given": "Thomas A", "initials": "TA"}, {"family": "Bumpstead", "given": "Suzannah J", "initials": "SJ"}, {"family": "B\u00f6ttcher", "given": "Yvonne", "initials": "Y"}, {"family": "Chines", "given": "Peter", "initials": "P"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Cooper", "given": "Cyrus C", "initials": "CC"}, {"family": "Dennison", "given": "Elaine M", "initials": "EM"}, {"family": "Erdos", "given": "Michael R", "initials": "MR"}, {"family": "Ferrannini", "given": "Ele", "initials": "E"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Graessler", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Hao", "given": "Ke", "initials": "K"}, {"family": "Isomaa", "given": "Bo", "initials": "B"}, {"family": "Jameson", "given": "Karen A", "initials": "KA"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Ladenvall", "given": "Claes", "initials": "C"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Morken", "given": "Mario A", "initials": "MA"}, {"family": "Narisu", "given": "Narisu", "initials": "N"}, {"family": "Nathan", "given": "David M", "initials": "DM"}, {"family": "Pascoe", "given": "Laura", "initials": "L"}, {"family": "Payne", "given": "Felicity", "initials": "F"}, {"family": "Petrie", "given": "John R", "initials": "JR"}, {"family": "Sayer", "given": "Avan A", "initials": "AA"}, {"family": "Schwarz", "given": "Peter E H", "initials": "PE"}, {"family": "Scott", "given": "Laura J", "initials": "LJ"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"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": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Valle", "given": "Timo T", "initials": "TT"}, {"family": "Williams", "given": "Gordon H", "initials": "GH"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Quertermous", "given": "Thomas", "initials": "T"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Watanabe", "given": "Richard M", "initials": "RM"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "MAGIC investigators", "given": null, "initials": null}], "type": "journal article", "published": "2010-05-00", "journal": {"volume": "59", "issn": "1939-327X", "issue": "5", "pages": "1266-1275", "title": "Diabetes", "issn-l": "0012-1797"}, "abstract": "OBJECTIVE Recent genome-wide association studies have revealed loci associated with glucose and insulin-related traits. We aimed to characterize 19 such loci using detailed measures of insulin processing, secretion, and sensitivity to help elucidate their role in regulation of glucose control, insulin secretion and/or action. RESEARCH DESIGN AND METHODS We investigated associations of loci identified by the Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC) with circulating proinsulin, measures of insulin secretion and sensitivity from oral glucose tolerance tests (OGTTs), euglycemic clamps, insulin suppression tests, or frequently sampled intravenous glucose tolerance tests in nondiabetic humans (n = 29,084). RESULTS The glucose-raising allele in MADD was associated with abnormal insulin processing (a dramatic effect on higher proinsulin levels, but no association with insulinogenic index) at extremely persuasive levels of statistical significance (P = 2.1 x 10(-71)). Defects in insulin processing and insulin secretion were seen in glucose-raising allele carriers at TCF7L2, SCL30A8, GIPR, and C2CD4B. Abnormalities in early insulin secretion were suggested in glucose-raising allele carriers at MTNR1B, GCK, FADS1, DGKB, and PROX1 (lower insulinogenic index; no association with proinsulin or insulin sensitivity). Two loci previously associated with fasting insulin (GCKR and IGF1) were associated with OGTT-derived insulin sensitivity indices in a consistent direction. CONCLUSIONS Genetic loci identified through their effect on hyperglycemia and/or hyperinsulinemia demonstrate considerable heterogeneity in associations with measures of insulin processing, secretion, and sensitivity. Our findings emphasize the importance of detailed physiological characterization of such loci for improved understanding of pathways associated with alterations in glucose homeostasis and eventually type 2 diabetes.", "doi": "10.2337/db09-1568", "pmid": "20185807", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "db09-1568"}, {"db": "pmc", "key": "PMC2857908"}], "notes": [], "created": "2017-05-04T15:00:29.201Z", "modified": "2021-07-07T15:11:02.433Z"}, {"entity": "publication", "iuid": "1fa9a8f1e3cc4b2593e33ace7d4c1104", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1fa9a8f1e3cc4b2593e33ace7d4c1104.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1fa9a8f1e3cc4b2593e33ace7d4c1104"}}, "title": "Abundance and expression of enantioselective rdpA and sdpA dioxygenase genes during degradation of the racemic herbicide (R,S)-2-(2,4-dichlorophenoxy)propionate in soil.", "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": "2010-05-00", "journal": {"volume": "76", "issn": "1098-5336", "issue": "9", "pages": "2873-2883", "title": "Appl. Environ. Microbiol.", "issn-l": "0099-2240"}, "abstract": "The rdpA and sdpA genes encode two enantioselective alpha-ketoglutarate-dependent dioxygenases catalyzing the initial step of microbial degradation of the chiral herbicide (R,S)-2-(2,4-dichlorophenoxy)propionate (R,S-dichlorprop). Primers were designed to assess abundance and transcription dynamics of rdpA and sdpA genes in a natural agricultural soil. No indigenous rdpA genes were detected, but sdpA genes were present at levels of approximately 10(3) copies g of soil(-1). Cloning and sequencing of partial sdpA genes revealed a high diversity within the natural sdpA gene pool that could be divided into four clusters by phylogenetic analysis. BLASTp analysis of deduced amino acids revealed that members of cluster I shared 68 to 69% identity, cluster II shared 78 to 85% identity, cluster III shared 58 to 64% identity, and cluster IV shared 55% identity to their closest SdpA relative in GenBank. Expression of rdpA and sdpA in Delftia acidovorans MC1 inoculated in soil was monitored by reverse transcription quantitative real-time PCR (qPCR) during in situ degradation of 2 and 50 mg kg(-1) of (R,S)-dichlorprop. (R,S)-Dichlorprop amendment created a clear upregulation of both rdpA and sdpA gene expression during the active phase of (14)C-labeled (R,S)-dichlorprop mineralization, particularly following the second dose of 50 mg kg(-1) herbicide. Expression of both genes was maintained at a low constitutive level in nonamended soil microcosms. This study is the first to report the presence of indigenous sdpA genes recovered directly from natural soil and also comprises the first investigation into the transcription dynamics of two enantioselective dioxygenase genes during the in situ degradation of the herbicide (R,S)-dichlorprop in soil.", "doi": "10.1128/AEM.02270-09", "pmid": "20305027", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "AEM.02270-09"}, {"db": "pmc", "key": "PMC2863469"}, {"db": "GENBANK", "key": "GQ922849"}, {"db": "GENBANK", "key": "GQ922850"}, {"db": "GENBANK", "key": "GQ922851"}, {"db": "GENBANK", "key": "GQ922852"}, {"db": "GENBANK", "key": "GQ922853"}, {"db": "GENBANK", "key": "GQ922854"}, {"db": "GENBANK", "key": "GQ922855"}, {"db": "GENBANK", "key": "GQ922856"}, {"db": "GENBANK", "key": "GQ922857"}, {"db": "GENBANK", "key": "GQ922858"}, {"db": "GENBANK", "key": "GQ922859"}, {"db": "GENBANK", "key": "GQ922860"}, {"db": "GENBANK", "key": "GQ922861"}, {"db": "GENBANK", "key": "GQ922862"}, {"db": "GENBANK", "key": "GQ922863"}, {"db": "GENBANK", "key": "GQ922864"}, {"db": "GENBANK", "key": "GQ922865"}, {"db": "GENBANK", "key": "GQ922866"}, {"db": "GENBANK", "key": "GQ922867"}, {"db": "GENBANK", "key": "GQ922868"}, {"db": "GENBANK", "key": "GQ922869"}, {"db": "GENBANK", "key": "GQ922870"}, {"db": "GENBANK", "key": "GQ922871"}, {"db": "GENBANK", "key": "GQ922872"}, {"db": "GENBANK", "key": "GQ922873"}, {"db": "GENBANK", "key": "GQ922874"}, {"db": "GENBANK", "key": "GQ922875"}, {"db": "GENBANK", "key": "GQ922876"}, {"db": "GENBANK", "key": "GQ922877"}, {"db": "GENBANK", "key": "GQ922878"}, {"db": "GENBANK", "key": "GQ922879"}, {"db": "GENBANK", "key": "GQ922880"}, {"db": "GENBANK", "key": "GQ922881"}, {"db": "GENBANK", "key": "GQ922882"}, {"db": "GENBANK", "key": "GQ922883"}], "notes": [], "created": "2017-05-04T15:01:48.578Z", "modified": "2020-01-21T13:56:01.021Z"}, {"entity": "publication", "iuid": "a81ebdee175445d3a29fdb452699f538", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a81ebdee175445d3a29fdb452699f538.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a81ebdee175445d3a29fdb452699f538"}}, "title": "A STAT4 risk allele is associated with ischaemic cerebrovascular events and anti-phospholipid antibodies in systemic lupus erythematosus.", "authors": [{"family": "Svenungsson", "given": "Elisabet", "initials": "E"}, {"family": "Gustafsson", "given": "Johanna", "initials": "J"}, {"family": "Leonard", "given": "Dag", "initials": "D"}, {"family": "Sandling", "given": "Johanna", "initials": "J"}, {"family": "Gunnarsson", "given": "Iva", "initials": "I"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "J\u00f6nsen", "given": "Andreas", "initials": "A"}, {"family": "Bengtsson", "given": "Anders A", "initials": "AA"}, {"family": "Sturfelt", "given": "Gunnar", "initials": "G"}, {"family": "Rantap\u00e4\u00e4-Dahlqvist", "given": "Solbritt", "initials": "S"}, {"family": "Elvin", "given": "Kerstin", "initials": "K"}, {"family": "Sundin", "given": "Ulf", "initials": "U"}, {"family": "Garnier", "given": "Sophie", "initials": "S"}, {"family": "Simard", "given": "Julia F", "initials": "JF"}, {"family": "Sigurdsson", "given": "Snaevar", "initials": "S"}, {"family": "Padyukov", "given": "Leonid", "initials": "L"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2010-05-00", "journal": {"volume": "69", "issn": "1468-2060", "issue": "5", "pages": "834-840", "title": "Ann. Rheum. Dis.", "issn-l": "0003-4967"}, "abstract": "To investigate whether the risk allele for systemic lupus erythematosus (SLE) in the signal transducer and activator of transcription factor 4 (STAT4) gene, defined by the single nucleotide polymorphism (SNP) rs10181656(G), is associated with vascular events and/or presence of prothrombotic anti-phospholipid antibodies (aPL) in patients with SLE.\n\nTwo independent groups of unrelated patients with SLE of Swedish ethnicity (n=424 and 154) were genotyped, and occurrence of previous manifestations of ischaemic heart disease (IHD), ischaemic cerebrovascular disease (ICVD) and venous thromboembolic events (VTE) was tabulated. aPL values were measured by ELISA. Matched controls (n=492 and 194) were genotyped.\n\nThe STAT4 risk allele was more frequent in patients with SLE with previous arterial events (combined OR (OR(c))=1.5, 95% CI 1.1 to 2.0) compared to patients without such events. The association was mainly attributable to an accumulation of the risk allele among patients with ICVD (OR(c)=2.3, CI 1.6 to 3.3). There was no association with IHD or VTE. The presence of two or more aPLs was associated with the risk allele (OR(c)=1.6, 95% CI 1.2 to 2.0). In multivariable-adjusted logistic regression analyses treatment for hypertension, at least one STAT4 risk allele, older age, IgG anti-cardiolipin antibodies and longer SLE duration remained independently associated with previous ICVD (p<or=0.02 for all).\n\nPatients with SLE with the STAT4 risk allele had a strikingly increased risk of ICVD, comparable in magnitude to that of hypertension. The results imply that a genetic predisposition is an important and previously unrecognised risk factor for ICVD in SLE, and that aPLs may be one underlying mechanism.", "doi": "10.1136/ard.2009.115535", "pmid": "19762360", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ard.2009.115535"}], "notes": [], "created": "2017-05-04T15:00:26.748Z", "modified": "2021-07-07T15:11:02.641Z"}, {"entity": "publication", "iuid": "90e28024d1b044f989e50b6052ceca1a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/90e28024d1b044f989e50b6052ceca1a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/90e28024d1b044f989e50b6052ceca1a"}}, "title": "A single fixation protocol for proteome-wide immunofluorescence localization studies.", "authors": [{"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": "Brismar", "given": "Hjalmar", "initials": "H", "orcid": "0000-0003-0578-4003", "researcher": {"href": "https://publications.scilifelab.se/researcher/1ec23336e2ef4e298f340876f1136dce.json"}}, {"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": "2010-04-18", "journal": {"volume": "73", "issn": "1876-7737", "issue": "6", "pages": "1067-1078", "title": "J Proteomics", "issn-l": "1874-3919"}, "abstract": "Immunofluorescence microscopy is a valuable tool for analyzing protein expression and localization at a subcellular level thus providing information regarding protein function, interaction partners and its role in cellular processes. When performing sample fixation, parameters such as difference in accessibility of proteins present in various cellular compartments as well as the chemical composition of the protein to be studied, needs to be taken into account. However, in systematic and proteome-wide efforts, a need exists for standard fixation protocol(s) that works well for the majority of all proteins independent of subcellular localization. Here, we report on a study with the goal to find a standardized protocol based on the analysis of 18 human proteins localized in 11 different organelles and subcellular structures. Six fixation protocols were tested based on either dehydration by alcohols (methanol, ethanol or iso-propanol) or cross-linking by paraformaldehyde followed by detergent permeabilization (Triton X-100 or saponin) in three human cell lines. Our results show that cross-linking is essential for proteome-wide localization studies and that cross-linking using paraformaldehyde followed by Triton X-100 permeabilization successfully can be used as a single fixation protocol for systematic studies.", "doi": "10.1016/j.jprot.2009.10.012", "pmid": "19896565", "labels": {"Spatial Proteomics": null}, "xrefs": [{"db": "pii", "key": "S1874-3919(09)00310-8"}], "notes": [], "created": "2017-05-04T14:55:07.153Z", "modified": "2021-07-08T13:44:33.428Z"}, {"entity": "publication", "iuid": "5fc6cb82fbc442d59885c1bf360c1fe5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5fc6cb82fbc442d59885c1bf360c1fe5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5fc6cb82fbc442d59885c1bf360c1fe5"}}, "title": "Increased throughput by parallelization of library preparation for massive sequencing.", "authors": [{"family": "Lundin", "given": "Sverker", "initials": "S"}, {"family": "Stranneheim", "given": "Henrik", "initials": "H"}, {"family": "Pettersson", "given": "Erik", "initials": "E"}, {"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2010-04-06", "journal": {"volume": "5", "issn": "1932-6203", "issue": "4", "pages": "e10029", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Massively parallel sequencing systems continue to improve on data output, while leaving labor-intensive library preparations a potential bottleneck. Efforts are currently under way to relieve the crucial and time-consuming work to prepare DNA for high-throughput sequencing.\n\nIn this study, we demonstrate an automated parallel library preparation protocol using generic carboxylic acid-coated superparamagnetic beads and polyethylene glycol precipitation as a reproducible and flexible method for DNA fragment length separation. With this approach the library preparation for DNA sequencing can easily be adjusted to a desired fragment length. The automated protocol, here demonstrated using the GS FLX Titanium instrument, was compared to the standard manual library preparation, showing higher yield, throughput and great reproducibility. In addition, 12 libraries were prepared and uniquely tagged in parallel, and the distribution of sequence reads between these indexed samples could be improved using quantitative PCR-assisted pooling.\n\nWe present a novel automated procedure that makes it possible to prepare 36 indexed libraries per person and day, which can be increased to up to 96 libraries processed simultaneously. The yield, speed and robust performance of the protocol constitute a substantial improvement to present manual methods, without the need of extensive equipment investments. The described procedure enables a considerable efficiency increase for small to midsize sequencing centers.", "doi": "10.1371/journal.pone.0010029", "pmid": "20386591", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC2850305"}], "notes": [], "created": "2017-05-04T14:57:15.277Z", "modified": "2021-07-08T13:26:08.195Z"}, {"entity": "publication", "iuid": "429804ab762c412ca8c87002ab2edf17", "links": {"self": {"href": "https://publications.scilifelab.se/publication/429804ab762c412ca8c87002ab2edf17.json"}, "display": {"href": "https://publications.scilifelab.se/publication/429804ab762c412ca8c87002ab2edf17"}}, "title": "Tumour-specific HMG-CoAR is an independent predictor of recurrence free survival in epithelial ovarian cancer.", "authors": [{"family": "Brennan", "given": "Donal J", "initials": "DJ"}, {"family": "Br\u00e4ndstedt", "given": "Jenny", "initials": "J"}, {"family": "Rexhepaj", "given": "Elton", "initials": "E"}, {"family": "Foley", "given": "Michael", "initials": "M"}, {"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": "Gallagher", "given": "William M", "initials": "WM"}, {"family": "O'Connor", "given": "Darran P", "initials": "DP"}, {"family": "O'Herlihy", "given": "Colm", "initials": "C"}, {"family": "Jirstrom", "given": "Karin", "initials": "K"}], "type": "journal article", "published": "2010-04-01", "journal": {"volume": "10", "issn": "1471-2407", "issue": null, "pages": "125", "title": "BMC Cancer", "issn-l": "1471-2407"}, "abstract": "Our group previously reported that tumour-specific expression of the rate-limiting enzyme in the mevalonate pathway, 3-hydroxy-3-methylglutharyl-coenzyme A reductase (HMG-CoAR) is associated with more favourable tumour parameters and a good prognosis in breast cancer. In the present study, the prognostic value of HMG-CoAR expression was examined in tumours from a cohort of patients with primary epithelial ovarian cancer.\n\nHMG-CoAR expression was assessed using immunohistochemistry (IHC) on tissue microarrays (TMA) consisting of 76 ovarian cancer cases, analysed using automated algorithms to develop a quantitative scoring model. Kaplan Meier analysis and Cox proportional hazards modelling were used to estimate the risk of recurrence free survival (RFS).\n\nSeventy-two tumours were suitable for analysis. Cytoplasmic HMG-CoAR expression was present in 65% (n = 46) of tumours. No relationship was seen between HMG-CoAR and age, histological subtype, grade, disease stage, estrogen receptor or Ki-67 status. Patients with tumours expressing HMG-CoAR had a significantly prolonged RFS (p = 0.012). Multivariate Cox regression analysis revealed that HMG-CoAR expression was an independent predictor of improved RFS (RR = 0.49, 95% CI (0.25-0.93); p = 0.03) when adjusted for established prognostic factors such as residual disease, tumour stage and grade.\n\nHMG-CoAR expression is an independent predictor of prolonged RFS in primary ovarian cancer. As HMG-CoAR inhibitors, also known as statins, have demonstrated anti-neoplastic effects in vitro, further studies are required to evaluate HMG-CoAR expression as a surrogate marker of response to statin treatment, especially in conjunction with current chemotherapeutic regimens.", "doi": "10.1186/1471-2407-10-125", "pmid": "20359358", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "1471-2407-10-125"}, {"db": "pmc", "key": "PMC3087316"}], "notes": [], "created": "2017-05-04T14:55:42.475Z", "modified": "2021-07-08T13:44:33.190Z"}, {"entity": "publication", "iuid": "5f2f9fd939be499bb22216fafb21e614", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5f2f9fd939be499bb22216fafb21e614.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5f2f9fd939be499bb22216fafb21e614"}}, "title": "The recombination landscape of the zebra finch Taeniopygia guttata genome.", "authors": [{"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}, {"family": "Forstmeier", "given": "Wolfgang", "initials": "W"}, {"family": "Schielzeth", "given": "Holger", "initials": "H"}, {"family": "Mellenius", "given": "Harriet", "initials": "H"}, {"family": "Nam", "given": "Kiwoong", "initials": "K"}, {"family": "Bolund", "given": "Elisabeth", "initials": "E"}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Ost", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "Schneider", "given": "Melanie", "initials": "M"}, {"family": "Kempenaers", "given": "Bart", "initials": "B"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}], "type": "comparative study", "published": "2010-04-00", "journal": {"volume": "20", "issn": "1549-5469", "issue": "4", "pages": "485-495", "title": "Genome Res.", "issn-l": "1088-9051"}, "abstract": "Understanding the causes and consequences of variation in the rate of recombination is essential since this parameter is considered to affect levels of genetic variability, the efficacy of selection, and the design of association and linkage mapping studies. However, there is limited knowledge about the factors governing recombination rate variation. We genotyped 1920 single nucleotide polymorphisms in a multigeneration pedigree of more than 1000 zebra finches (Taeniopygia guttata) to develop a genetic linkage map, and then we used these map data together with the recently available draft genome sequence of the zebra finch to estimate recombination rates in 1 Mb intervals across the genome. The average zebra finch recombination rate (1.5 cM/Mb) is higher than in humans, but significantly lower than in chicken. The local rates of recombination in chicken and zebra finch were only weakly correlated, demonstrating evolutionary turnover of the recombination landscape in birds. The distribution of recombination events was heavily biased toward ends of chromosomes, with a stronger telomere effect than so far seen in any organism. In fact, the recombination rate was as low as 0.1 cM/Mb in intervals up to 100 Mb long in the middle of the larger chromosomes. We found a positive correlation between recombination rate and GC content, as well as GC-rich sequence motifs. Levels of linkage disequilibrium (LD) were significantly higher in regions of low recombination, showing that heterogeneity in recombination rates have left a footprint on the genomic landscape of LD in zebra finch populations.", "doi": "10.1101/gr.101410.109", "pmid": "20357052", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "gr.101410.109"}, {"db": "pmc", "key": "PMC2847751"}], "notes": [], "created": "2017-05-04T15:00:30.455Z", "modified": "2020-01-21T13:56:02.573Z"}, {"entity": "publication", "iuid": "9ef62eced5e1409b90aec4ff52553390", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ef62eced5e1409b90aec4ff52553390.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ef62eced5e1409b90aec4ff52553390"}}, "title": "Reaction mechanism of 5,8-linoleate diol synthase, 10R-dioxygenase, and 8,11-hydroperoxide isomerase of Aspergillus clavatus.", "authors": [{"family": "Jerner\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Garscha", "given": "Ulrike", "initials": "U"}, {"family": "Hoffmann", "given": "Inga", "initials": "I"}, {"family": "Hamberg", "given": "Mats", "initials": "M"}, {"family": "Oliw", "given": "Ernst H", "initials": "EH"}], "type": "journal article", "published": "2010-04-00", "journal": {"volume": "1801", "issn": "0006-3002", "issue": "4", "pages": "503-507", "title": "Biochim. Biophys. Acta", "issn-l": null}, "abstract": "Aspergilli express fusion proteins of an animal haem peroxidase domain with fatty acid dioxygenase (DOX) activity ( approximately 600 amino acids) and a functional or non-functional hydroperoxide isomerase/cytochrome P450 domain ( approximately 500 amino acids with EXXR and GPHXCLG motifs). 5,8-Linoleate diol synthases (LDS; ppoA) and 10R-DOX (ppoC) of Aspergillusnidulans and A. fumigatus belong to this group. Our objective was to determine the oxylipins formed from linoleic acid by A. clavatus and their mechanism of biosynthesis. A. clavatus oxidized linoleic acid to (8R)-hydroperoxylinoleic acid (8R-HPODE), (10R)-hydroperoxy-8(E),12(Z)-octadecadienoic acid (10R-HPODE), and to (5S,8R)-dihydroxy- and (8R,11S)-dihydroxylinoleic acids (DiHODE) as major products. This occurred by abstraction of the pro-S hydrogen at C-8 and antarafacial dioxygenation at C-8 or at C-10 with double bond migration. 8R-HPODE was then isomerized to 5S,8R-DiHODE and to 8R,11S-DiHODE by abstraction of the pro-S hydrogens at C-5 and C-11 of 8R-HPODE, respectively, followed by suprafacial oxygenation. The genome of A. clavatus codes for two enzymes, which can be aligned with >65% amino acid identity to 10R-DOX and 5,8-LDS, respectively. The 5,8-LDS homologue likely forms and isomerizes 8R-HPODE to 5S,8R-DiHODE. A third gene (ppoB) codes for a protein which carries a serine residue at the cysteine position of the P450 motif. This Cys to Ser replacement is known to abolish P450 2B4 catalysis and the hydroperoxide isomerase activity of 5,8-LDS, suggesting that ppoB of A. clavatus may not be involved in the biosynthesis of 8R,11S-DiHODE.", "doi": "10.1016/j.bbalip.2009.12.012", "pmid": "20045744", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S1388-1981(09)00292-3"}], "notes": [], "created": "2017-05-04T15:01:49.189Z", "modified": "2020-01-21T13:56:04.101Z"}, {"entity": "publication", "iuid": "b415728393504e02b54392dedbf91a1e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b415728393504e02b54392dedbf91a1e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b415728393504e02b54392dedbf91a1e"}}, "title": "Increased serum progesterone and estradiol correlate to increased COX-2 tissue expression in cervical intraepithelial neoplasia.", "authors": [{"family": "Samir", "given": "Raghad", "initials": "R"}, {"family": "Tot", "given": "Tibor", "initials": "T"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Pekar", "given": "Gyula", "initials": "G"}, {"family": "Hellberg", "given": "Dan", "initials": "D"}], "type": "journal article", "published": "2010-04-00", "journal": {"volume": "30", "issn": "1791-7530", "issue": "4", "pages": "1217-1222", "title": "Anticancer Res.", "issn-l": "0250-7005"}, "abstract": "The aim of this study was to To investigate correlations between serum progesterone and serum estradiol levels and expression of tissue tumor markers in cervical intraepithelial neoplasia (CIN) and normal epithelium.\n\nEighty women of fertile ages with cervical biopsies ranging histologically from normal to CIN III were included. Expression of eleven tumor markers was studied. Serum levels of progesterone and estradiol were analyzed. Exclusion criterion was hormonal contraceptive use.\n\nIn normal epithelium, low progesterone levels correlated to expression of epidermal growth factor receptor (EGFR) and CD4+. In initial analyses of CIN, high progesterone levels correlated with expression of retinoblastoma protein, p16 and cyclooxygenase-2 (COX-2), but after adjustment for CIN grade, only correlation to COX-2 expression remained significant. Expression of COX-2 and CD4(+) correlated to serum estradiol levels in CIN.\n\nSerum levels of progesterone and estradiol appear to correlate with increased COX-2 expression in CIN. In addition, the study shows that evaluation of expression of tumor markers must take into account the grade of CIN.", "doi": null, "pmid": "20530431", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "30/4/1217"}], "notes": [], "created": "2017-05-04T14:55:42.173Z", "modified": "2025-12-01T07:52:54.584Z"}, {"entity": "publication", "iuid": "8099611119984c948ebfce6afb8896c2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8099611119984c948ebfce6afb8896c2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8099611119984c948ebfce6afb8896c2"}}, "title": "ELMOD2, a candidate gene for idiopathic pulmonary fibrosis, regulates antiviral responses.", "authors": [{"family": "Pulkkinen", "given": "Ville", "initials": "V"}, {"family": "Bruce", "given": "Sara", "initials": "S"}, {"family": "Rintahaka", "given": "Johanna", "initials": "J"}, {"family": "Hodgson", "given": "Ulla", "initials": "U"}, {"family": "Laitinen", "given": "Tarja", "initials": "T"}, {"family": "Alenius", "given": "Harri", "initials": "H"}, {"family": "Kinnula", "given": "Vuokko L", "initials": "VL"}, {"family": "Myll\u00e4rniemi", "given": "Marjukka", "initials": "M"}, {"family": "Matikainen", "given": "Sampsa", "initials": "S"}, {"family": "Kere", "given": "Juha", "initials": "J"}], "type": "journal article", "published": "2010-04-00", "journal": {"volume": "24", "issn": "1530-6860", "issue": "4", "pages": "1167-1177", "title": "FASEB J.", "issn-l": "0892-6638"}, "abstract": "Viral infections and abnormal host response are thought to cause epithelial injury in idiopathic pulmonary fibrosis (IPF). To understand IPF pathogenesis, we have used overexpression cell models and expression microarrays to discover genes networked with ELMO domain containing 2 (ELMOD2) gene genetically implicated in IPF. The identified pathways were confirmed in vitro, and ELMOD2 protein expression was characterized in tissue samples. Here 303 genes were significantly altered after ELMOD2 transfection of human alveolar epithelial A549 cell line. The enriched pathways were interferon induction, viral response, antigen processing and presentation, and I-/nuclear factor-kappaB signaling. ELMOD2 showed immunoreactivity in macrophages and type II alveolar epithelial cells in normal human lung. In A549 cells, forced expression of ELMOD2 increased type I and type III interferon mRNA expression, and ELMOD2-specific siRNA molecules inhibited expression of these antiviral cytokines in response to Toll-like receptor three (TLR3) activation. In human macrophages silencing of ELMOD2 inhibited TLR3-dependent expression of type I and type III interferon genes. Influenza A virus infection decreased ELMOD2 mRNA expression in A549 cells and macrophages suggesting negative regulation in viral infections. In summary, our results show that TLR3 pathway is dependent on ELMOD2.-Pulkkinen, V., Bruce, S., Rintahaka, J., Hodgson, U., Laitinen, T., Alenius, H., Kinnula, V. L., Myll\u00e4rniemi, M., Matikainen, S., Kere, J. ELMOD2, a candidate gene for idiopathic pulmonary fibrosis, regulates antiviral responses.", "doi": "10.1096/fj.09-138545", "pmid": "19966137", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "fj.09-138545"}], "notes": [], "created": "2017-05-04T15:03:05.121Z", "modified": "2017-05-30T12:38:55.838Z"}, {"entity": "publication", "iuid": "d77402aa0bfd4c2b9a5eff001d5d63bb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d77402aa0bfd4c2b9a5eff001d5d63bb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d77402aa0bfd4c2b9a5eff001d5d63bb"}}, "title": "Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution.", "authors": [{"family": "V\u00f6lker", "given": "Martin", "initials": "M"}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N"}, {"family": "Skinner", "given": "Benjamin M", "initials": "BM"}, {"family": "Langley", "given": "Elizabeth J", "initials": "EJ"}, {"family": "Bunzey", "given": "Sydney K", "initials": "SK"}, {"family": "Ellegren", "given": "Hans", "initials": "H"}, {"family": "Griffin", "given": "Darren K", "initials": "DK"}], "type": "comparative study", "published": "2010-04-00", "journal": {"volume": "20", "issn": "1549-5469", "issue": "4", "pages": "503-511", "title": "Genome Res.", "issn-l": "1088-9051"}, "abstract": "Chromosomal rearrangements and copy number variants (CNVs) play key roles in genome evolution and genetic disease; however, the molecular mechanisms underlying these types of structural genomic variation are not fully understood. The availability of complete genome sequences for two bird species, the chicken and the zebra finch, provides, for the first time, an ideal opportunity to analyze the relationship between structural genomic variation (chromosomal and CNV) and recombination on a genome-wide level. The aims of this study were therefore threefold: (1) to combine bioinformatics, physical mapping to produce comprehensive comparative maps of the genomes of chicken and zebra finch. In so doing, this allowed the identification of evolutionary chromosomal rearrangements distinguishing them. The previously reported interchromosomal conservation of synteny was confirmed, but a larger than expected number of intrachromosomal rearrangements were reported; (2) to hybridize zebra finch genomic DNA to a chicken tiling path microarray and identify CNVs in the zebra finch genome relative to chicken; 32 interspecific CNVs were identified; and (3) to test the hypothesis that there is an association between CNV, chromosomal rearrangements, and recombination by correlating data from (1) and (2) with recombination rate data from a high-resolution genetic linkage map of the zebra finch. We found a highly significant association of both chromosomal rearrangements and CNVs with elevated recombination rates. The results thus provide support for the notion of recombination-based processes playing a major role in avian genome evolution.", "doi": "10.1101/gr.103663.109", "pmid": "20357050", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "gr.103663.109"}, {"db": "pmc", "key": "PMC2847753"}], "notes": [], "created": "2017-05-04T15:00:30.971Z", "modified": "2020-01-21T13:56:05.521Z"}, {"entity": "publication", "iuid": "fcbf14320d5940089c81f815bf63a72e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/fcbf14320d5940089c81f815bf63a72e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/fcbf14320d5940089c81f815bf63a72e"}}, "title": "Novel associations of multiple genetic loci with plasma levels of factor VII, factor VIII, and von Willebrand factor: The CHARGE (Cohorts for Heart and Aging Research in Genome Epidemiology) Consortium.", "authors": [{"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Chen", "given": "Ming-Huei", "initials": "MH"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Strachan", "given": "David P", "initials": "DP"}, {"family": "Basu", "given": "Saonli", "initials": "S"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Hayward", "given": "Caroline", "initials": "C"}, {"family": "Rudan", "given": "Igor", "initials": "I"}, {"family": "Sabater-Lleal", "given": "Maria", "initials": "M"}, {"family": "Bis", "given": "Joshua C", "initials": "JC"}, {"family": "de Maat", "given": "Moniek P M", "initials": "MP"}, {"family": "Rumley", "given": "Ann", "initials": "A"}, {"family": "Kong", "given": "Xiaoxiao", "initials": "X"}, {"family": "Yang", "given": "Qiong", "initials": "Q"}, {"family": "Williams", "given": "Frances M K", "initials": "FM"}, {"family": "Vitart", "given": "Veronique", "initials": "V"}, {"family": "Campbell", "given": "Harry", "initials": "H"}, {"family": "M\u00e4larstig", "given": "Anders", "initials": "A"}, {"family": "Wiggins", "given": "Kerri L", "initials": "KL"}, {"family": "Van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "McArdle", "given": "Wendy L", "initials": "WL"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Johnson", "given": "Andrew D", "initials": "AD"}, {"family": "Silveira", "given": "Angela", "initials": "A"}, {"family": "McKnight", "given": "Barbara", "initials": "B"}, {"family": "Uitterlinden", "given": "Andre G", "initials": "AG"}, {"family": "Wellcome Trust Case Control Consortium;", "given": null, "initials": null}, {"family": "Aleksic", "given": "Nena", "initials": "N"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Peters", "given": "Annette", "initials": "A"}, {"family": "Koenig", "given": "Wolfgang", "initials": "W"}, {"family": "Cushman", "given": "Mary", "initials": "M"}, {"family": "Kathiresan", "given": "Sekar", "initials": "S"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Bovill", "given": "Edwin G", "initials": "EG"}, {"family": "Hofman", "given": "Albert", "initials": "A"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Tofler", "given": "Geoffrey H", "initials": "GH"}, {"family": "Peden", "given": "John F", "initials": "JF"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Leebeek", "given": "Frank", "initials": "F"}, {"family": "Folsom", "given": "Aaron R", "initials": "AR"}, {"family": "Larson", "given": "Martin G", "initials": "MG"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Wright", "given": "Alan F", "initials": "AF"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Lumley", "given": "Thomas", "initials": "T"}, {"family": "Witteman", "given": "Jacqueline C M", "initials": "JC"}, {"family": "Tang", "given": "Weihong", "initials": "W"}, {"family": "O'Donnell", "given": "Christopher J", "initials": "CJ"}], "type": "journal article", "published": "2010-03-30", "journal": {"volume": "121", "issn": "1524-4539", "issue": "12", "pages": "1382-1392", "title": "Circulation", "issn-l": "0009-7322"}, "abstract": "Plasma levels of coagulation factors VII (FVII), VIII (FVIII), and von Willebrand factor (vWF) influence risk of hemorrhage and thrombosis. We conducted genome-wide association studies to identify new loci associated with plasma levels.\n\nThe setting of the study included 5 community-based studies for discovery comprising 23 608 European-ancestry participants: Atherosclerosis Risk In Communities Study, Cardiovascular Health Study, British 1958 Birth Cohort, Framingham Heart Study, and Rotterdam Study. All subjects had genome-wide single-nucleotide polymorphism (SNP) scans and at least 1 phenotype measured: FVII activity/antigen, FVIII activity, and vWF antigen. Each study used its genotype data to impute to HapMap SNPs and independently conducted association analyses of hemostasis measures using an additive genetic model. Study findings were combined by meta-analysis. Replication was conducted in 7604 participants not in the discovery cohort. For FVII, 305 SNPs exceeded the genome-wide significance threshold of 5.0x10(-8) and comprised 5 loci on 5 chromosomes: 2p23 (smallest P value 6.2x10(-24)), 4q25 (3.6x10(-12)), 11q12 (2.0x10(-10)), 13q34 (9.0x10(-259)), and 20q11.2 (5.7x10(-37)). Loci were within or near genes, including 4 new candidate genes and F7 (13q34). For vWF, 400 SNPs exceeded the threshold and marked 8 loci on 6 chromosomes: 6q24 (1.2x10(-22)), 8p21 (1.3x10(-16)), 9q34 (<5.0x10(-324)), 12p13 (1.7x10(-32)), 12q23 (7.3x10(-10)), 12q24.3 (3.8x10(-11)), 14q32 (2.3x10(-10)), and 19p13.2 (1.3x10(-9)). All loci were within genes, including 6 new candidate genes, as well as ABO (9q34) and VWF (12p13). For FVIII, 5 loci were identified and overlapped vWF findings. Nine of the 10 new findings were replicated.\n\nNew genetic associations were discovered outside previously known biological pathways and may point to novel prevention and treatment targets of hemostasis disorders.", "doi": "10.1161/CIRCULATIONAHA.109.869156", "pmid": "20231535", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "CIRCULATIONAHA.109.869156"}, {"db": "pmc", "key": "PMC2861278"}, {"db": "mid", "key": "NIHMS189970"}], "notes": [], "created": "2017-05-04T15:00:28.878Z", "modified": "2020-01-21T13:56:06.495Z"}, {"entity": "publication", "iuid": "96615cb5b131417481f41f74a9157a2c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/96615cb5b131417481f41f74a9157a2c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/96615cb5b131417481f41f74a9157a2c"}}, "title": "Whole-genome resequencing reveals loci under selection during chicken domestication.", "authors": [{"family": "Rubin", "given": "Carl-Johan", "initials": "C"}, {"family": "Zody", "given": "Michael C", "initials": "MC"}, {"family": "Eriksson", "given": "Jonas", "initials": "J"}, {"family": "Meadows", "given": "Jennifer R S", "initials": "JRS"}, {"family": "Sherwood", "given": "Ellen", "initials": "E", "orcid": "0000-0003-3158-9957", "researcher": {"href": "https://publications.scilifelab.se/researcher/f17cb04d51c24494b9eab42010fd1a04.json"}}, {"family": "Webster", "given": "Matthew T", "initials": "MT"}, {"family": "Jiang", "given": "Lin", "initials": "L"}, {"family": "Ingman", "given": "Max", "initials": "M"}, {"family": "Sharpe", "given": "Ted", "initials": "T"}, {"family": "Ka", "given": "Sojeong", "initials": "S"}, {"family": "Hallb\u00f6\u00f6k", "given": "Finn", "initials": "F"}, {"family": "Besnier", "given": "Francois", "initials": "F"}, {"family": "Carlborg", "given": "Orjan", "initials": "O"}, {"family": "Bed'hom", "given": "Bertrand", "initials": "B"}, {"family": "Tixier-Boichard", "given": "Mich\u00e8le", "initials": "M"}, {"family": "Jensen", "given": "Per", "initials": "P"}, {"family": "Siegel", "given": "Paul", "initials": "P"}, {"family": "Lindblad-Toh", "given": "Kerstin", "initials": "K", "orcid": "0000-0001-8338-0253", "researcher": {"href": "https://publications.scilifelab.se/researcher/e0063145f7d6476f80ab42f94833f4cf.json"}}, {"family": "Andersson", "given": "Leif", "initials": "L"}], "type": "journal article", "published": "2010-03-25", "journal": {"volume": "464", "issn": "1476-4687", "issue": "7288", "pages": "587-591", "title": "Nature", "issn-l": "0028-0836"}, "abstract": "Domestic animals are excellent models for genetic studies of phenotypic evolution. They have evolved genetic adaptations to a new environment, the farm, and have been subjected to strong human-driven selection leading to remarkable phenotypic changes in morphology, physiology and behaviour. Identifying the genetic changes underlying these developments provides new insight into general mechanisms by which genetic variation shapes phenotypic diversity. Here we describe the use of massively parallel sequencing to identify selective sweeps of favourable alleles and candidate mutations that have had a prominent role in the domestication of chickens (Gallus gallus domesticus) and their subsequent specialization into broiler (meat-producing) and layer (egg-producing) chickens. We have generated 44.5-fold coverage of the chicken genome using pools of genomic DNA representing eight different populations of domestic chickens as well as red jungle fowl (Gallus gallus), the major wild ancestor. We report more than 7,000,000 single nucleotide polymorphisms, almost 1,300 deletions and a number of putative selective sweeps. One of the most striking selective sweeps found in all domestic chickens occurred at the locus for thyroid stimulating hormone receptor (TSHR), which has a pivotal role in metabolic regulation and photoperiod control of reproduction in vertebrates. Several of the selective sweeps detected in broilers overlapped genes associated with growth, appetite and metabolic regulation. We found little evidence that selection for loss-of-function mutations had a prominent role in chicken domestication, but we detected two deletions in coding sequences that we suggest are functionally important. This study has direct application to animal breeding and enhances the importance of the domestic chicken as a model organism for biomedical research.", "doi": "10.1038/nature08832", "pmid": "20220755", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "nature08832"}, {"db": "GENBANK", "key": "GU323512"}, {"db": "GENBANK", "key": "GU323513"}, {"db": "GENBANK", "key": "GU323514"}, {"db": "GENBANK", "key": "GU323515"}, {"db": "GENBANK", "key": "GU323516"}, {"db": "GENBANK", "key": "GU323517"}, {"db": "GENBANK", "key": "GU323518"}, {"db": "GENBANK", "key": "GU323519"}, {"db": "GENBANK", "key": "GU323520"}, {"db": "GENBANK", "key": "GU323521"}, {"db": "GENBANK", "key": "GU323522"}, {"db": "GENBANK", "key": "GU323523"}, {"db": "GENBANK", "key": "GU323524"}, {"db": "GENBANK", "key": "GU323525"}, {"db": "GENBANK", "key": "GU323526"}, {"db": "GENBANK", "key": "GU323527"}, {"db": "GENBANK", "key": "GU323528"}, {"db": "GENBANK", "key": "GU323529"}, {"db": "GENBANK", "key": "GU323530"}, {"db": "GENBANK", "key": "GU323531"}, {"db": "GENBANK", "key": "GU323532"}, {"db": "GENBANK", "key": "GU323533"}, {"db": "GENBANK", "key": "GU323534"}, {"db": "GENBANK", "key": "GU323535"}, {"db": "GENBANK", "key": "GU323536"}, {"db": "GENBANK", "key": "GU323537"}, {"db": "GENBANK", "key": "GU323538"}, {"db": "GENBANK", "key": "GU323539"}, {"db": "GENBANK", "key": "GU323540"}, {"db": "GENBANK", "key": "GU323541"}, {"db": "GENBANK", "key": "GU323542"}, {"db": "GENBANK", "key": "GU323543"}, {"db": "GENBANK", "key": "GU323544"}, {"db": "GENBANK", "key": "GU323545"}, {"db": "GENBANK", "key": "GU323546"}, {"db": "GENBANK", "key": "GU323547"}, {"db": "GENBANK", "key": "GU323548"}, {"db": "GENBANK", "key": "GU323549"}, {"db": "GENBANK", "key": "GU323550"}, {"db": "GENBANK", "key": "GU323551"}, {"db": "GENBANK", "key": "GU323552"}, {"db": "GENBANK", "key": "GU323553"}, {"db": "GENBANK", "key": "GU323554"}, {"db": "GENBANK", "key": "GU323555"}, {"db": "GENBANK", "key": "GU323556"}], "notes": [], "created": "2017-05-04T14:57:13.139Z", "modified": "2021-07-07T15:13:59.929Z"}, {"entity": "publication", "iuid": "a7c4ba8f72e04c9c8308399386e2a7b5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a7c4ba8f72e04c9c8308399386e2a7b5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a7c4ba8f72e04c9c8308399386e2a7b5"}}, "title": "In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines.", "authors": [{"family": "Klevebring", "given": "Daniel", "initials": "D"}, {"family": "Bjursell", "given": "Magnus", "initials": "M"}, {"family": "Emanuelsson", "given": "Olof", "initials": "O"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2010-03-25", "journal": {"volume": "5", "issn": "1932-6203", "issue": "3", "pages": "e9762", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Several recent studies have indicated that transcription is pervasive in regions outside of protein coding genes and that short antisense transcripts can originate from the promoter and terminator regions of genes. Here we investigate transcription of fragments longer than 200 nucleotides, focusing on antisense transcription for known protein coding genes and intergenic transcription. We find that roughly 12% to 16% of all reads that originate from promoter and terminator regions, respectively, map antisense to the gene in question. Furthermore, we detect a high number of novel transcriptionally active regions (TARs) that are generally expressed at a lower level than protein coding genes. We find that the correlation between RNA-seq data and microarray data is dependent on the gene length, with longer genes showing a better correlation. We detect high antisense transcriptional activity from promoter, terminator and intron regions of protein-coding genes and identify a vast number of previously unidentified TARs, including putative novel EGFR transcripts. This shows that in-depth analysis of the transcriptome using RNA-seq is a valuable tool for understanding complex transcriptional events. Furthermore, the development of new algorithms for estimation of gene expression from RNA-seq data is necessary to minimize length bias.", "doi": "10.1371/journal.pone.0009762", "pmid": "20360838", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pmc", "key": "PMC2845605"}], "notes": [], "created": "2017-05-04T14:57:14.979Z", "modified": "2021-07-08T13:26:08.280Z"}, {"entity": "publication", "iuid": "58f43beadb93437ea9cafbb654feb5e5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/58f43beadb93437ea9cafbb654feb5e5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/58f43beadb93437ea9cafbb654feb5e5"}}, "title": "Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles.", "authors": [{"family": "Xue-Franz\u00e9n", "given": "Yongtao", "initials": "Y"}, {"family": "Johnsson", "given": "Anna", "initials": "A"}, {"family": "Brodin", "given": "David", "initials": "D"}, {"family": "Henriksson", "given": "Johan", "initials": "J"}, {"family": "B\u00fcrglin", "given": "Thomas R", "initials": "TR"}, {"family": "Wright", "given": "Anthony P H", "initials": "AP"}], "type": "journal article", "published": "2010-03-25", "journal": {"volume": "11", "issn": "1471-2164", "issue": null, "pages": "200", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Gcn5 is a transcriptional coactivator with histone acetyltransferase activity that is conserved with regard to structure as well as its histone substrates throughout the eukaryotes. Gene regulatory networks within cells are thought to be evolutionarily diverged. The use of evolutionarily divergent yeast species, such as S. cerevisiae and S. pombe, which can be studied under similar environmental conditions, provides an opportunity to examine the interface between conserved regulatory components and their cellular applications in different organisms.\n\nWe show that Gcn5 is important for a common set of stress responses in evolutionarily diverged yeast species and that the activity of the conserved histone acetyltransferase domain is required. We define a group of KCl stress response genes in S. cerevisiae that are specifically dependent on Gcn5. Gcn5 is localised to many Gcn5-dependent genes including Gcn5 repressed targets such as FLO8. Gcn5 regulates divergent sets of KCl responsive genes in S. cerevisiae and S. pombe. Genome-wide localization studies showed a tendency for redistribution of Gcn5 during KCl stress adaptation in S. cerevisiae from short genes to the transcribed regions of long genes. An analogous redistribution was not observed in S. pombe.\n\nGcn5 is required for the regulation of divergent sets of KCl stress-response genes in S. cerevisiae and S. pombe even though it is required a common group of stress responses, including the response to KCl. Genes that are physically associated with Gcn5 require its activity for their repression or activation during stress adaptation, providing support for a role of Gcn5 as a corepressor as well as a coactivator. The tendency of Gcn5 to re-localise to the transcribed regions of long genes during KCl stress adaptation suggests that Gcn5 plays a specific role in the expression of long genes under adaptive conditions, perhaps by regulating transcriptional elongation as has been seen for Gcn5 in S. pombe. Interestingly an analogous redistribution of Gcn5 is not seen in S. pombe. The study thus provides important new insights in relation to why coregulators like Gcn5 are required for the correct expression of some genes but not others.", "doi": "10.1186/1471-2164-11-200", "pmid": "20338033", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-200"}, {"db": "pmc", "key": "PMC2861062"}], "notes": [], "created": "2017-05-04T15:03:03.327Z", "modified": "2017-05-30T14:50:16.038Z"}, {"entity": "publication", "iuid": "5fe24daff5ce4d53a26ce856d08b8163", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5fe24daff5ce4d53a26ce856d08b8163.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5fe24daff5ce4d53a26ce856d08b8163"}}, "title": "Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome.", "authors": [{"family": "Jakobsson", "given": "Hedvig E", "initials": "HE"}, {"family": "Jernberg", "given": "Cecilia", "initials": "C"}, {"family": "Andersson", "given": "Anders F", "initials": "AF"}, {"family": "Sj\u00f6lund-Karlsson", "given": "Maria", "initials": "M"}, {"family": "Jansson", "given": "Janet K", "initials": "JK"}, {"family": "Engstrand", "given": "Lars", "initials": "L"}], "type": "journal article", "published": "2010-03-24", "journal": {"volume": "5", "issn": "1932-6203", "issue": "3", "pages": "e9836", "title": "PLoS ONE", "issn-l": "1932-6203"}, "abstract": "Antibiotic administration is the standard treatment for the bacterium Helicobacter pylori, the main causative agent of peptic ulcer disease and gastric cancer. However, the long-term consequences of this treatment on the human indigenous microbiota are relatively unexplored. Here we studied short- and long-term effects of clarithromycin and metronidazole treatment, a commonly used therapy regimen against H. pylori, on the indigenous microbiota in the throat and in the lower intestine. The bacterial compositions in samples collected over a four-year period were monitored by analyzing the 16S rRNA gene using 454-based pyrosequencing and terminal-restriction fragment length polymorphism (T-RFLP). While the microbial communities of untreated control subjects were relatively stable over time, dramatic shifts were observed one week after antibiotic treatment with reduced bacterial diversity in all treated subjects in both locations. While the microbiota of the different subjects responded uniquely to the antibiotic treatment some general trends could be observed; such as a dramatic decline in Actinobacteria in both throat and feces immediately after treatment. Although the diversity of the microbiota subsequently recovered to resemble the pre treatment states, the microbiota remained perturbed in some cases for up to four years post treatment. In addition, four years after treatment high levels of the macrolide resistance gene erm(B) were found, indicating that antibiotic resistance, once selected for, can persist for longer periods of time than previously recognized. This highlights the importance of a restrictive antibiotic usage in order to prevent subsequent treatment failure and potential spread of antibiotic resistance.", "doi": "10.1371/journal.pone.0009836", "pmid": "20352091", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pmc", "key": "PMC2844414"}], "notes": [], "created": "2017-05-04T14:57:14.678Z", "modified": "2020-01-21T13:56:11.160Z"}, {"entity": "publication", "iuid": "5d2e408f2ad346f8b33e499d82501418", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5d2e408f2ad346f8b33e499d82501418.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5d2e408f2ad346f8b33e499d82501418"}}, "title": "Sustained inflammation due to nuclear factor-kappa B activation in irradiated human arteries.", "authors": [{"family": "Halle", "given": "Martin", "initials": "M"}, {"family": "Gabrielsen", "given": "Anders", "initials": "A"}, {"family": "Paulsson-Berne", "given": "Gabrielle", "initials": "G"}, {"family": "Gahm", "given": "Caroline", "initials": "C"}, {"family": "Agardh", "given": "Hanna E", "initials": "HE"}, {"family": "Farnebo", "given": "Filip", "initials": "F"}, {"family": "Tornvall", "given": "Per", "initials": "P"}], "type": "journal article", "published": "2010-03-23", "journal": {"volume": "55", "issn": "1558-3597", "issue": "12", "pages": "1227-1236", "title": "J. Am. Coll. Cardiol.", "issn-l": "0735-1097"}, "abstract": "The aim of this study was to investigate gene expression networks related to cardiovascular disease in radiated human arteries.\n\nRecent epidemiological studies have shown that radiotherapy is associated with cardiovascular disease years after treatment. However, the molecular mechanisms underlying late effects of radiation are poorly described.\n\nArterial biopsies from radiated and nonradiated human conduit arteries, from the same patient, were simultaneously harvested during microvascular free tissue transfer for cancer-reconstruction in 13 patients, 4 to 500 weeks from radiation treatment. Radiated and nonradiated arteries were compared, with Affymetrix (Santa Clara, California) microarrays on a subset of the material to generate candidate genes. A Taqman (Applied Biosystems, Foster City, California) low-density array of 45 selected genes was designed for analysis of the whole material.\n\nThirteen genes were synchronously expressed in all patients (p = 0.0015), including CCL8, CCL3, CXCL2, DUSP5, FGFR2, HMOX1, HOXA9, IL-6, MMP-1, PTX3, RDH10, SOD2, and TNFAIP3. A majority of differentially regulated genes related to the nuclear factor-kappa B (NF-kappaB) signaling pathway and were dysregulated even years after radiation. The NF-kappaB activation was confirmed by immunohistochemistry and immunofluorescence.\n\nIn the present study, we found sustained inflammation due to NF-kappaB activation in human radiated arteries. The results are supported by previous in vitro findings suggesting that deoxyribonucleic acid injury, after radiation, activates NF-kappaB. We also suggest that HOXA9 might be involved in the regulation of NF-kappaB activation. The observed sustained inflammatory response can explain cardiovascular disease years after radiation.", "doi": "10.1016/j.jacc.2009.10.047", "pmid": "20298930", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "S0735-1097(10)00142-7"}], "notes": [], "created": "2017-05-04T15:03:05.726Z", "modified": "2017-05-30T12:39:05.235Z"}, {"entity": "publication", "iuid": "1bd62d3b4fc04ffdb1f82baffda989e0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1bd62d3b4fc04ffdb1f82baffda989e0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1bd62d3b4fc04ffdb1f82baffda989e0"}}, "title": "Investigation of gene dosage imbalances in patients with Noonan syndrome using multiplex ligation-dependent probe amplification analysis.", "authors": [{"family": "Nystr\u00f6m", "given": "Anna-Maja", "initials": "AM"}, {"family": "Ekvall", "given": "Sara", "initials": "S"}, {"family": "Thuresson", "given": "Ann-Charlotte", "initials": "AC"}, {"family": "Denayer", "given": "Ellen", "initials": "E"}, {"family": "Legius", "given": "Eric", "initials": "E"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}, {"family": "Westermark", "given": "Bengt", "initials": "B"}, {"family": "Anner\u00e9n", "given": "G\u00f6ran", "initials": "G"}, {"family": "Bondeson", "given": "Marie-Louise", "initials": "ML"}], "type": "journal article", "published": "2010-03-17", "journal": {"volume": "53", "issn": "1878-0849", "issue": "3", "pages": "117-121", "title": "Eur J Med Genet", "issn-l": "1769-7212"}, "abstract": "The RAS-MAPK syndromes are a group of clinically and genetically related disorders caused by dysregulation of the RAS-MAPK pathway. A member of this group of disorders, Noonan syndrome (NS), is associated with several different genes within the RAS-MAPK pathway. To date, mutations in PTPN11, SOS1, KRAS, RAF1 and SHOC2 are known to cause NS and a small group of patients harbour mutations in BRAF, MEK1 or NRAS. The majority of the mutations are predicted to cause an up-regulation of the pathway; hence they are gain-of-function mutations. Despite recent advances in gene identification in NS, the genetic aetiology is still unknown in about 1/4 of patients. To investigate the contribution of gene dosage imbalances of RAS-MAPK-related genes to the pathogenesis of NS, a multiplex ligation-dependent probe amplification (MLPA) assay was developed. Two probe sets were designed for seven RAS-MAPK-syndrome-related candidate genes: PTPN11, SOS1, RAF1, KRAS, BRAF, MEK1 and MEK2. The probe sets were validated in 15 healthy control individuals and in glioma tumour cell lines. Subsequently, 44 NS patients negative for mutations in known NS-associated genes were screened using the two probe sets. The MLPA results for the patients revealed no gene dosage imbalances. In conclusion, the present results exclude copy number variation of PTPN11, SOS1, RAF1, KRAS, BRAF, MEK1 and MEK2 as a common pathogenic mechanism of NS. The validated and optimised RAS-MAPK probe sets presented here enable rapid high throughput screening of further patients with RAS-MAPK syndromes.", "doi": "10.1016/j.ejmg.2010.03.001", "pmid": "20302979", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "S1769-7212(10)00017-0"}], "notes": [], "created": "2017-05-04T15:01:51.981Z", "modified": "2021-07-08T10:16:52.805Z"}, {"entity": "publication", "iuid": "7607d00abcf8496ab4d3c0821314931f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7607d00abcf8496ab4d3c0821314931f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7607d00abcf8496ab4d3c0821314931f"}}, "title": "Global and unbiased detection of splice junctions from RNA-seq data.", "authors": [{"family": "Ameur", "given": "Adam", "initials": "A", "orcid": "0000-0001-6085-6749", "researcher": {"href": "https://publications.scilifelab.se/researcher/e960811513664a78b2804a00ee70f7c3.json"}}, {"family": "Wetterbom", "given": "Anna", "initials": "A"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Gyllensten", "given": "Ulf", "initials": "U"}], "type": "journal article", "published": "2010-03-17", "journal": {"volume": "11", "issn": "1474-760X", "issue": "3", "pages": "R34", "title": "Genome Biol.", "issn-l": "1474-7596"}, "abstract": "We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, >31,000 splice events were predicted, of which 88% bridged between two regions separated by <or=100 kb, and 74% connected two exons of the same RefSeq gene. Our method also reports genomic rearrangements such as insertions and deletions.", "doi": "10.1186/gb-2010-11-3-r34", "pmid": "20236510", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "gb-2010-11-3-r34"}, {"db": "pmc", "key": "PMC2864574"}], "notes": [], "created": "2017-05-04T14:57:10.753Z", "modified": "2021-07-07T14:37:06.514Z"}, {"entity": "publication", "iuid": "33d8bc4f851d44bab399bb25c345b0c5", "links": {"self": {"href": "https://publications.scilifelab.se/publication/33d8bc4f851d44bab399bb25c345b0c5.json"}, "display": {"href": "https://publications.scilifelab.se/publication/33d8bc4f851d44bab399bb25c345b0c5"}}, "title": "The sexually antagonistic genes of Drosophila melanogaster.", "authors": [{"family": "Innocenti", "given": "Paolo", "initials": "P"}, {"family": "Morrow", "given": "Edward H", "initials": "EH"}], "type": "journal article", "published": "2010-03-16", "journal": {"volume": "8", "issn": "1545-7885", "issue": "3", "pages": "e1000335", "title": "PLoS Biol.", "issn-l": "1544-9173"}, "abstract": "When selective pressures differ between males and females, the genes experiencing these conflicting evolutionary forces are said to be sexually antagonistic. Although the phenotypic effect of these genes has been documented in both wild and laboratory populations, their identity, number, and location remains unknown. Here, by combining data on sex-specific fitness and genome-wide transcript abundance in a quantitative genetic framework, we identified a group of candidate genes experiencing sexually antagonistic selection in the adult, which correspond to 8% of Drosophila melanogaster genes. As predicted, the X chromosome is enriched for these genes, but surprisingly they represent only a small proportion of the total number of sex-biased transcripts, indicating that the latter is a poor predictor of sexual antagonism. Furthermore, the majority of genes whose expression profiles showed a significant relationship with either male or female adult fitness are also sexually antagonistic. These results provide a first insight into the genetic basis of intralocus sexual conflict and indicate that genetic variation for fitness is dominated and maintained by sexual antagonism, potentially neutralizing any indirect genetic benefits of sexual selection.", "doi": "10.1371/journal.pbio.1000335", "pmid": "20305719", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pmc", "key": "PMC2838750"}], "notes": [], "created": "2017-05-04T15:02:50.889Z", "modified": "2018-11-14T14:25:11.656Z"}, {"entity": "publication", "iuid": "09a9a03772dd4a6c96457b18949cedff", "links": {"self": {"href": "https://publications.scilifelab.se/publication/09a9a03772dd4a6c96457b18949cedff.json"}, "display": {"href": "https://publications.scilifelab.se/publication/09a9a03772dd4a6c96457b18949cedff"}}, "title": "The tryptophan hydroxylase 1 (TPH1) gene, schizophrenia susceptibility, and suicidal behavior: a multi-centre case-control study and meta-analysis.", "authors": [{"family": "Saetre", "given": "Peter", "initials": "P"}, {"family": "Lundmark", "given": "Per", "initials": "P"}, {"family": "Wang", "given": "August", "initials": "A"}, {"family": "Hansen", "given": "Thomas", "initials": "T"}, {"family": "Rasmussen", "given": "Henrik B", "initials": "HB"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"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": "2010-03-05", "journal": {"volume": "153B", "issn": "1552-485X", "issue": "2", "pages": "387-396", "title": "Am. J. Med. Genet. B Neuropsychiatr. Genet.", "issn-l": "1552-4841"}, "abstract": "Serotonin (5-hydroxytryptamin; 5-HT) alternations has since long been suspected in the pathophysiology of schizophrenia. Tryptophan hydroxylase (tryptophan 5-monooxygenase; TPH) is the rate-limiting enzyme in the biosynthesis of 5-HT, and sequence variation in intron 6 of the TPH1 gene has been associated with schizophrenia. The minor allele (A) of this polymorphism (A218C) is also more frequent in patients who have attempted suicide and individuals who died by suicide, than in healthy control individuals. In an attempt to replicate previous findings, five single nucleotide polymorphisms (SNPs) were genotyped in 837 Scandinavian schizophrenia patients and 1,473 controls. Three SNPs spanning intron 6 and 7, including the A218C and A779C polymorphisms, were associated with schizophrenia susceptibility (P = 0.019). However there were no differences in allele frequencies of these loci between affected individuals having attempted suicide at least once and patients with no history of suicide attempts (P = 0.84). A systematic literature review and meta-analysis support the A218C polymorphism as a susceptibility locus for schizophrenia (odds ratio 1.17, 95% confidence interval 1.07-1.29). Association studies on suicide attempts are however conflicting (heterogeneity index I(2) = 0.54) and do not support the A218C/A779C polymorphisms being a susceptibility locus for suicidal behavior among individuals diagnosed with a psychiatric disorder (OR = 0.96 [0.80-1.16]). We conclude that the TPH1 A218/A779 locus increases the susceptibility of schizophrenia in Caucasian and Asian populations. In addition, the data at hand suggest that the locus contributes to the liability of psychiatric disorders characterized by elevated suicidal rates, rather than affecting suicidal behavior of individuals suffering from a psychiatric disorder.", "doi": "10.1002/ajmg.b.30991", "pmid": "19526457", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:25.510Z", "modified": "2020-01-21T13:56:00.628Z"}, {"entity": "publication", "iuid": "d603403f927947938d9152a4c4dc63d3", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d603403f927947938d9152a4c4dc63d3.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d603403f927947938d9152a4c4dc63d3"}}, "title": "Association between methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and age of onset in schizophrenia.", "authors": [{"family": "Vares", "given": "Maria", "initials": "M"}, {"family": "Saetre", "given": "Peter", "initials": "P"}, {"family": "Deng", "given": "Hong", "initials": "H"}, {"family": "Cai", "given": "Guiqing", "initials": "G"}, {"family": "Liu", "given": "Xiehe", "initials": "X"}, {"family": "Hansen", "given": "Thomas", "initials": "T"}, {"family": "Rasmussen", "given": "Henrik B", "initials": "HB"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"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": "2010-03-05", "journal": {"volume": "153B", "issn": "1552-485X", "issue": "2", "pages": "610-618", "title": "Am. J. Med. Genet. B Neuropsychiatr. Genet.", "issn-l": "1552-4841"}, "abstract": "Different lines of evidence indicate that methylenetetrahydrofolate reductase (MTHFR) functional gene polymorphisms, causative in aberrant folate-homocysteine metabolism, are associated with increased vulnerability to several heritable developmental disorders. Opposing views are expressed considering the possible association between MTHFR and susceptibility for schizophrenia. In order to evaluate if age of onset could explain some of this discrepancy we investigated the relationship between two functional MTHFR gene polymorphisms and age at onset in this disorder. Scandinavian patients (n = 820) diagnosed with schizophrenia, schizoaffective disorder, and schizophreniform disorder were investigated. Two functional MTHFR single nucleotide polymorphisms (SNPs; rs1801131 and rs1801133) were genotyped and the effect of MTHFR polymorphisms on the age of onset was examined with survival analysis. In an attempt to replicate the findings from the Scandinavian sample, the association between rs1801133 and age at onset was also analyzed in Chinese high-risk families, with two or more affected siblings (n = 243). Among the Scandinavian patients the functional MTHFR SNP rs1801133 (C677T) significantly affected age at onset of schizophrenia in a dose-dependent manner (P = 0.0015), with lower age of onset with increasing numbers of the mutant T-allele. There was no evidence of rs1801131 (A1298C) affecting age of onset in schizophrenia. Within the Chinese high-risk families carriers of the MTHFR 677T allele showed earlier age at onset than siblings being homozygous for the wild-type allele (P = 0.008). The MTHFR C677T polymorphism may play a role as a modifying factor for age of onset in schizophrenia.", "doi": "10.1002/ajmg.b.31030", "pmid": "19746410", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:26.122Z", "modified": "2020-01-21T13:56:05.460Z"}, {"entity": "publication", "iuid": "edae7ecf86524014a794009823055c99", "links": {"self": {"href": "https://publications.scilifelab.se/publication/edae7ecf86524014a794009823055c99.json"}, "display": {"href": "https://publications.scilifelab.se/publication/edae7ecf86524014a794009823055c99"}}, "title": "The impact of tissue fixatives on morphology and antibody-based protein profiling in tissues and cells.", "authors": [{"family": "Paavilainen", "given": "Linda", "initials": "L"}, {"family": "Edvinsson", "given": "Asa", "initials": "A"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Hober", "given": "Sophia", "initials": "S"}, {"family": "Kampf", "given": "Caroline", "initials": "C"}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F"}, {"family": "Wester", "given": "Kenneth", "initials": "K"}], "type": "comparative study", "published": "2010-03-00", "journal": {"volume": "58", "issn": "1551-5044", "issue": "3", "pages": "237-246", "title": "J. Histochem. Cytochem.", "issn-l": "0022-1554"}, "abstract": "Pathology archives harbor large amounts of formalin-fixed, paraffin-embedded tissue samples, used mainly in clinical diagnostics but also for research purposes. Introduction of heat-induced antigen retrieval has enabled the use of tissue samples for extensive immunohistochemical analysis, despite the fact that antigen retrieval may not recover all epitopes, owing to alterations of the native protein structure induced by formalin. The aim of this study was to investigate how different fixatives influence protein recognition by immunodetection methods in tissues, cell preparations, and protein lysates, as compared with formalin. Seventy-two affinity-purified polyclonal antibodies were used to evaluate seven different fixatives. The aldehyde-based fixative Glyo-fixx proved to be excellent for preservation of proteins in tissue detected by immunohistochemistry (IHC), similar to formalin. A non-aldehyde-based fixative, NEO-FIX was superior for fixation of cultured cells, in regard to morphology, and thereby also advantageous for IHC. Large variability in the amount of protein extracted from the differently fixed tissues was observed, and the HOPE fixative provided the overall highest yield of protein. In conclusion, morphological resolution and immunoreactivity were superior in tissues fixed with aldehyde-based fixatives, whereas the use of non-aldehyde-based fixatives can be advantageous in obtaining high protein yield for Western blot analysis. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.", "doi": "10.1369/jhc.2009.954321", "pmid": "19901271", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "jhc.2009.954321"}, {"db": "pmc", "key": "PMC2825489"}], "notes": [], "created": "2017-05-04T14:55:43.381Z", "modified": "2017-05-30T12:58:03.697Z"}, {"entity": "publication", "iuid": "164404029f4a4a9a9c060ce21f1eb099", "links": {"self": {"href": "https://publications.scilifelab.se/publication/164404029f4a4a9a9c060ce21f1eb099.json"}, "display": {"href": "https://publications.scilifelab.se/publication/164404029f4a4a9a9c060ce21f1eb099"}}, "title": "Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.", "authors": [{"family": "K\u00fcnstner", "given": "Axel", "initials": "A"}, {"family": "Wolf", "given": "Jochen B W", "initials": "JB", "orcid": "0000-0002-2958-5183", "researcher": {"href": "https://publications.scilifelab.se/researcher/6c4445d760a64905a9ea6d8664f6a32d.json"}}, {"family": "Backstr\u00f6m", "given": "Niclas", "initials": "N", "orcid": "0000-0002-0961-8427", "researcher": {"href": "https://publications.scilifelab.se/researcher/674a0756dcf44e79ac6a6a2499b01760.json"}}, {"family": "Whitney", "given": "Osceola", "initials": "O"}, {"family": "Balakrishnan", "given": "Christopher N", "initials": "CN", "orcid": "0000-0002-0788-0659", "researcher": {"href": "https://publications.scilifelab.se/researcher/363e6c4a51b647bba7e02e1c8e5464fd.json"}}, {"family": "Day", "given": "Lainy", "initials": "L", "orcid": "0000-0002-9122-3044", "researcher": {"href": "https://publications.scilifelab.se/researcher/0a99dd326b9640629732a9fdbded2662.json"}}, {"family": "Edwards", "given": "Scott V", "initials": "SV"}, {"family": "Janes", "given": "Daniel E", "initials": "DE"}, {"family": "Schlinger", "given": "Barney A", "initials": "BA"}, {"family": "Wilson", "given": "Richard K", "initials": "RK"}, {"family": "Jarvis", "given": "Erich D", "initials": "ED", "orcid": "0000-0001-8931-5049", "researcher": {"href": "https://publications.scilifelab.se/researcher/d565d5e1788e484d9d2da61af12f2120.json"}}, {"family": "Warren", "given": "Wesley C", "initials": "WC"}, {"family": "Ellegren", "given": "Hans", "initials": "H", "orcid": "0000-0002-5035-1736", "researcher": {"href": "https://publications.scilifelab.se/researcher/819e68cc7125446baec6165aabd2d19c.json"}}], "type": "journal article", "published": "2010-03-00", "journal": {"volume": "19 Suppl 1", "issn": "1365-294X", "issue": "Suppl 1", "pages": "266-276", "title": "Mol. Ecol.", "issn-l": "0962-1083"}, "abstract": "Next-generation sequencing technology provides an attractive means to obtain large-scale sequence data necessary for comparative genomic analysis. To analyse the patterns of mutation rate variation and selection intensity across the avian genome, we performed brain transcriptome sequencing using Roche 454 technology of 10 different non-model avian species. Contigs from de novo assemblies were aligned to the two available avian reference genomes, chicken and zebra finch. In total, we identified 6499 different genes across all 10 species, with approximately 1000 genes found in each full run per species. We found evidence for a higher mutation rate of the Z chromosome than of autosomes (male-biased mutation) and a negative correlation between the neutral substitution rate (d(S)) and chromosome size. Analyses of the mean d(N)/d(S) ratio (omega) of genes across chromosomes supported the Hill-Robertson effect (the effect of selection at linked loci) and point at stochastic problems with omega as an independent measure of selection. Overall, this study demonstrates the usefulness of next-generation sequencing for obtaining genomic resources for comparative genomic analysis of non-model organisms.", "doi": "10.1111/j.1365-294X.2009.04487.x", "pmid": "20331785", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "mid", "key": "NIHMS216459"}, {"db": "pmc", "key": "PMC2904817"}, {"db": "pii", "key": "MEC4487"}], "notes": [], "created": "2017-05-04T14:57:12.592Z", "modified": "2023-06-19T11:19:36.049Z"}, {"entity": "publication", "iuid": "761dcca202684ddd85283ce9be32b8c6", "links": {"self": {"href": "https://publications.scilifelab.se/publication/761dcca202684ddd85283ce9be32b8c6.json"}, "display": {"href": "https://publications.scilifelab.se/publication/761dcca202684ddd85283ce9be32b8c6"}}, "title": "Appearance of Cxcl10-expressing cell clusters is common for traumatic brain injury and neurodegenerative disorders.", "authors": [{"family": "Israelsson", "given": "Charlotte", "initials": "C"}, {"family": "Bengtsson", "given": "Henrik", "initials": "H"}, {"family": "Lobell", "given": "Anna", "initials": "A"}, {"family": "Nilsson", "given": "Lars N G", "initials": "LN"}, {"family": "Kylberg", "given": "Annika", "initials": "A"}, {"family": "Isaksson", "given": "Magnus", "initials": "M"}, {"family": "Wootz", "given": "Hanna", "initials": "H"}, {"family": "Lannfelt", "given": "Lars", "initials": "L"}, {"family": "Kullander", "given": "Klas", "initials": "K"}, {"family": "Hillered", "given": "Lars", "initials": "L"}, {"family": "Ebendal", "given": "Ted", "initials": "T"}], "type": "journal article", "published": "2010-03-00", "journal": {"volume": "31", "issn": "1460-9568", "issue": "5", "pages": "852-863", "title": "Eur. J. Neurosci.", "issn-l": "0953-816X"}, "abstract": "Traumatic brain injury (TBI) in the mouse results in the rapid appearance of scattered clusters of cells expressing the chemokine Cxcl10 in cortical and subcortical areas. To extend the observation of this unique pattern, we used neuropathological mouse models using quantitative reverse transcriptase-polymerase chain reaction, gene array analysis, in-situ hybridization and flow cytometry. As for TBI, cell clusters of 150-200 mum expressing Cxcl10 characterize the cerebral cortex of mice carrying a transgene encoding the Swedish mutation of amyloid precursor protein, a model of amyloid Alzheimer pathology. The same pattern was found in experimental autoimmune encephalomyelitis in mice modelling multiple sclerosis. In contrast, mice carrying a SOD1(G93A) mutant mimicking amyotrophic lateral sclerosis pathology lacked such cell clusters in the cerebral cortex, whereas clusters appeared in the brainstem and spinal cord. Mice homozygous for a null mutation of the Cxcl10 gene did not show detectable levels of Cxcl10 transcript after TBI, confirming the quantitative reverse transcriptase-polymerase chain reaction and in-situ hybridization signals. Moreover, unbiased microarray expression analysis showed that Cxcl10 was among 112 transcripts in the neocortex upregulated at least threefold in both TBI and ageing TgSwe mice, many of them involved in inflammation. The identity of the Cxcl10(+) cells remains unclear but flow cytometry showed increased numbers of activated microglia/macrophages as well as myeloid dendritic cells in the TBI and experimental autoimmune encephalomyelitis models. It is concluded that the Cxcl10(+) cells appear in the inflamed central nervous system and may represent a novel population of cells that it may be possible to target pharmacologically in a broad range of neurodegenerative conditions.", "doi": "10.1111/j.1460-9568.2010.07105.x", "pmid": "20374285", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "EJN7105"}], "notes": [], "created": "2017-05-04T15:02:48.802Z", "modified": "2018-11-14T14:29:39.539Z"}, {"entity": "publication", "iuid": "56cce9107c664ed28106aea7b9231404", "links": {"self": {"href": "https://publications.scilifelab.se/publication/56cce9107c664ed28106aea7b9231404.json"}, "display": {"href": "https://publications.scilifelab.se/publication/56cce9107c664ed28106aea7b9231404"}}, "title": "Molecular profiling using tissue microarrays as a tool to identify predictive biomarkers in laryngeal cancer treated with radiotherapy.", "authors": [{"family": "Holgersson", "given": "Georg", "initials": "G"}, {"family": "Ekman", "given": "Simon", "initials": "S", "orcid": "0000-0002-8343-6226", "researcher": {"href": "https://publications.scilifelab.se/researcher/0fcb2b2956a84f43a7b485573f445ff2.json"}}, {"family": "Reizenstein", "given": "Johan", "initials": "J"}, {"family": "Bergqvist", "given": "Michael", "initials": "M", "orcid": "0009-0003-5716-3716", "researcher": {"href": "https://publications.scilifelab.se/researcher/91d33e374d0642479a80683a989f095a.json"}}, {"family": "Pont\u00e9n", "given": "Fredrik", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Uhl\u00e9n", "given": "Mattias", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}, {"family": "Magnusson", "given": "Kristina", "initials": "K"}, {"family": "Jonnalagadda", "given": "Pallavi", "initials": "P"}, {"family": "Asplund", "given": "Anna", "initials": "A"}, {"family": "Str\u00f6mberg", "given": "Sara", "initials": "S"}, {"family": "Linder", "given": "Arne", "initials": "A"}, {"family": "Blomquist", "given": "Erik", "initials": "E"}, {"family": "Liljeholm", "given": "Martin", "initials": "M"}, {"family": "L\u00f6d\u00e9n", "given": "Britta", "initials": "B"}, {"family": "Hellstr\u00f6m", "given": "Karin", "initials": "K"}, {"family": "Bergstr\u00f6m", "given": "Stefan", "initials": "S"}], "type": "journal article", "published": "2010-02-26", "journal": {"volume": "7", "issn": "1790-6245", "issue": "1", "pages": "1-7", "title": "Cancer Genomics Proteomics", "issn-l": "1109-6535"}, "abstract": "To explore the usefulness of the expression of five potential cancer biomarkers in predicting outcome in patients with laryngeal cancer.\n\nIn the present study, the Swedish National Cancer Registry databases were used to identify patients with laryngeal cancer diagnosed during the years 1978-2004 in the Uppsala-Orebro region and treated with radiotherapy. The expression of Ki-67, MutS homolog 2, (MSH2), p53, B-cell CLL/lymphoma 2 (Bcl-2) and cyclin D1 in the cancer cells was assessed immunohistochemically using tissue microarrays (TMAs) and its predicitve value on survival and relapse was analyzed using Cox regression models.\n\nA total of 39 patients were included in the present study. Nuclear MSH2 staining was statistically significantly correlated to Ki-67 expression (p=0.022). However, univariate and multivariate Cox analyses showed no statistically significant association between the expression of the investigated biomarkers and overall survival or relapse.\n\nThe present exploratory study does not show any significant predictive value of the biomarkers examined with respect to survival or relapse. However, with larger patient cohorts, we believe that protein profiling using TMAs and immunohistochemistry is a feasible strategy for prognostic and predictive biomarker screening in laryngeal cancer.", "doi": null, "pmid": "20181625", "labels": {"Tissue Profiling": null}, "xrefs": [{"db": "pii", "key": "7/1/1"}], "notes": [], "created": "2017-05-04T14:55:42.778Z", "modified": "2025-11-17T09:52:58.446Z"}, {"entity": "publication", "iuid": "69b4e0a9132849dfa4d5a7cc15ddc6ac", "links": {"self": {"href": "https://publications.scilifelab.se/publication/69b4e0a9132849dfa4d5a7cc15ddc6ac.json"}, "display": {"href": "https://publications.scilifelab.se/publication/69b4e0a9132849dfa4d5a7cc15ddc6ac"}}, "title": "Gene-specific FACS sorting method for target selection in high-throughput amplicon sequencing.", "authors": [{"family": "Sandberg", "given": "Julia", "initials": "J"}, {"family": "Neiman", "given": "Marten", "initials": "M"}, {"family": "Ahmadian", "given": "Afshin", "initials": "A"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}], "type": "journal article", "published": "2010-02-26", "journal": {"volume": "11", "issn": "1471-2164", "issue": null, "pages": "140", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "In addition to shotgun sequencing, next generation sequencing has been shown to be suitable for deep sequencing of many specific PCR-amplified target genes in parallel. However, unspecific product formation is a common problem in amplicon sequencing since these fragments are difficult to fully remove by gel purification, and their presence inevitably reduces the number of mappable sequence reads that can be obtained in each sequencing run.\n\nWe have used a novel flow cytometric sorting approach to specifically enrich Roche/454 DNA Capture beads carrying target DNA sequences on their surface, and reject beads carrying unspecific sequences. This procedure gives a nearly three-fold increase in the fraction of informative sequences obtained. Presented results also show that there are no significant differences in the distribution or presence of different genotypes between a FACS-enriched sample and a standard-enriched control sample.\n\nTarget-specific FACS enrichment prior to Roche/454 sequencing provides a quick, inexpensive way of increasing the amount of high quality data obtained in a single sequencing run, without introducing any sequence bias.", "doi": "10.1186/1471-2164-11-140", "pmid": "20184782", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-140"}, {"db": "pmc", "key": "PMC2842249"}], "notes": [], "created": "2017-05-04T14:57:10.155Z", "modified": "2021-07-08T13:26:08.201Z"}, {"entity": "publication", "iuid": "10b55a25abea4522937f46c043a9c3f0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/10b55a25abea4522937f46c043a9c3f0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/10b55a25abea4522937f46c043a9c3f0"}}, "title": "High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus.", "authors": [{"family": "Berlin", "given": "Sofia", "initials": "S"}, {"family": "Lagercrantz", "given": "Ulf", "initials": "U"}, {"family": "von Arnold", "given": "Sara", "initials": "S"}, {"family": "Ost", "given": "Torbj\u00f6rn", "initials": "T"}, {"family": "R\u00f6nnberg-W\u00e4stljung", "given": "Ann Christin", "initials": "AC"}], "type": "journal article", "published": "2010-02-23", "journal": {"volume": "11", "issn": "1471-2164", "issue": null, "pages": "129", "title": "BMC Genomics", "issn-l": "1471-2164"}, "abstract": "Salix (willow) and Populus (poplar) are members of the Salicaceae family and they share many ecological as well as genetic and genomic characteristics. The interest of using willow for biomass production is growing, which has resulted in increased pressure on breeding of high yielding and resistant clones adapted to different environments. The main purpose of this work was to develop dense genetic linkage maps for mapping of traits related to yield and resistance in willow. We used the Populus trichocarpa genome to extract evenly spaced markers and mapped the orthologous loci in the willow genome. The marker positions in the two genomes were used to study genome evolution since the divergence of the two lineages some 45 mya.\n\nWe constructed two linkage maps covering the 19 linkage groups in willow. The most detailed consensus map, S1, contains 495 markers with a total genetic distance of 2477 cM and an average distance of 5.0 cM between the markers. The S3 consensus map contains 221 markers and has a total genetic distance of 1793 cM and an average distance of 8.1 cM between the markers. We found high degree of synteny and gene order conservation between willow and poplar. There is however evidence for two major interchromosomal rearrangements involving poplar LG I and XVI and willow LG Ib, suggesting a fission or a fusion in one of the lineages, as well as five intrachromosomal inversions. The number of silent substitutions were three times lower (median: 0.12) between orthologs than between paralogs (median: 0.37 - 0.41).\n\nThe relatively slow rates of genomic change between willow and poplar mean that the genomic resources in poplar will be most useful in genomic research in willow, such as identifying genes underlying QTLs of important traits. Our data suggest that the whole-genome duplication occurred long before the divergence of the two genera, events which have until now been regarded as contemporary. Estimated silent substitution rates were 1.28 x 10-9 and 1.68 x 10-9 per site and year, which are close to rates found in other perennials but much lower than rates in annuals.", "doi": "10.1186/1471-2164-11-129", "pmid": "20178595", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "NGI Uppsala (Uppsala Genome Center)": null}, "xrefs": [{"db": "pii", "key": "1471-2164-11-129"}, {"db": "pmc", "key": "PMC2834636"}], "notes": [], "created": "2017-05-04T15:00:28.266Z", "modified": "2020-01-21T13:56:00.745Z"}, {"entity": "publication", "iuid": "e1e9a5723dd34c29b362e21763b892c9", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e1e9a5723dd34c29b362e21763b892c9.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e1e9a5723dd34c29b362e21763b892c9"}}, "title": "Coffee consumption and CYP1A2 genotype in relation to bone mineral density of the proximal femur in elderly men and women: a cohort study.", "authors": [{"family": "Hallstr\u00f6m", "given": "Helena", "initials": "H"}, {"family": "Melhus", "given": "H\u00e5kan", "initials": "H"}, {"family": "Glynn", "given": "Anders", "initials": "A"}, {"family": "Lind", "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"}}, {"family": "Micha\u00eblsson", "given": "Karl", "initials": "K"}], "type": "journal article", "published": "2010-02-22", "journal": {"volume": "7", "issn": "1743-7075", "issue": null, "pages": "12", "title": "Nutr Metab (Lond)", "issn-l": "1743-7075"}, "abstract": "Drinking coffee has been linked to reduced calcium conservation, but it is less clear whether it leads to sustained bone mineral loss and if individual predisposition for caffeine metabolism might be important in this context. Therefore, the relation between consumption of coffee and bone mineral density (BMD) at the proximal femur in men and women was studied, taking into account, for the first time, genotypes for cytochrome P450 1A2 (CYP1A2) associated with metabolism of caffeine.\n\nDietary intakes of 359 men and 358 women (aged 72 years), participants of the Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS), were assessed by a 7-day food diary. Two years later, BMD for total proximal femur, femoral neck and trochanteric regions of the proximal femur were measured by Dual-energy X-ray absorptiometry (DXA). Genotypes of CYP1A2 were determined. Adjusted means of BMD for each category of coffee consumption were calculated.\n\nMen consuming 4 cups of coffee or more per day had 4% lower BMD at the proximal femur (p = 0.04) compared with low or non-consumers of coffee. This difference was not observed in women. In high consumers of coffee, those with rapid metabolism of caffeine (C/C genotype) had lower BMD at the femoral neck (p = 0.01) and at the trochanter (p = 0.03) than slow metabolizers (T/T and C/T genotypes). Calcium intake did not modify the relation between coffee and BMD.\n\nHigh consumption of coffee seems to contribute to a reduction in BMD of the proximal femur in elderly men, but not in women. BMD was lower in high consumers of coffee with rapid metabolism of caffeine, suggesting that rapid metabolizers of caffeine may constitute a risk group for bone loss induced by coffee.", "doi": "10.1186/1743-7075-7-12", "pmid": "20175915", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1743-7075-7-12"}, {"db": "pmc", "key": "PMC2842270"}], "notes": [], "created": "2017-05-04T15:00:36.479Z", "modified": "2021-07-07T15:11:02.765Z"}, {"entity": "publication", "iuid": "db252fe3a6d444f78780657e81e994ed", "links": {"self": {"href": "https://publications.scilifelab.se/publication/db252fe3a6d444f78780657e81e994ed.json"}, "display": {"href": "https://publications.scilifelab.se/publication/db252fe3a6d444f78780657e81e994ed"}}, "title": "DNA methylation for subtype classification and prediction of treatment outcome in patients with childhood acute lymphoblastic leukemia.", "authors": [{"family": "Milani", "given": "Lili", "initials": "L"}, {"family": "Lundmark", "given": "Anders", "initials": "A"}, {"family": "Kiialainen", "given": "Anna", "initials": "A"}, {"family": "Nordlund", "given": "Jessica", "initials": "J", "orcid": "0000-0001-8699-9959", "researcher": {"href": "https://publications.scilifelab.se/researcher/ddf48c9262134821bcc6ce1180049753.json"}}, {"family": "Flaegstad", "given": "Trond", "initials": "T"}, {"family": "Forestier", "given": "Erik", "initials": "E"}, {"family": "Heyman", "given": "Mats", "initials": "M"}, {"family": "Jonmundsson", "given": "Gudmundur", "initials": "G"}, {"family": "Kanerva", "given": "Jukka", "initials": "J"}, {"family": "Schmiegelow", "given": "Kjeld", "initials": "K"}, {"family": "S\u00f6derh\u00e4ll", "given": "Stefan", "initials": "S"}, {"family": "Gustafsson", "given": "Mats G", "initials": "MG"}, {"family": "L\u00f6nnerholm", "given": "Gudmar", "initials": "G"}, {"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": "2010-02-11", "journal": {"volume": "115", "issn": "1528-0020", "issue": "6", "pages": "1214-1225", "title": "Blood", "issn-l": "0006-4971"}, "abstract": "Despite improvements in the prognosis of childhood acute lymphoblastic leukemia (ALL), subgroups of patients would benefit from alternative treatment approaches. Our aim was to identify genes with DNA methylation profiles that could identify such groups. We determined the methylation levels of 1320 CpG sites in regulatory regions of 416 genes in cells from 401 children diagnosed with ALL. Hierarchical clustering of 300 CpG sites distinguished between T-lineage ALL and B-cell precursor (BCP) ALL and between the main cytogenetic subtypes of BCP ALL. It also stratified patients with high hyperdiploidy and t(12;21) ALL into 2 subgroups with different probability of relapse. By using supervised learning, we constructed multivariate classifiers by external cross-validation procedures. We identified 40 genes that consistently contributed to accurate discrimination between the main subtypes of BCP ALL and gene sets that discriminated between subtypes of ALL and between ALL and controls in pairwise classification analyses. We also identified 20 individual genes with DNA methylation levels that predicted relapse of leukemia. Thus, methylation analysis should be explored as a method to improve stratification of ALL patients. The genes highlighted in our study are not enriched to specific pathways, but the gene expression levels are inversely correlated to the methylation levels.", "doi": "10.1182/blood-2009-04-214668", "pmid": "19965625", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "S0006-4971(20)49253-5"}], "notes": [], "created": "2017-05-04T15:00:27.962Z", "modified": "2021-07-07T15:11:02.760Z"}, {"entity": "publication", "iuid": "a8606ec944474ea6978ada299d0a0417", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a8606ec944474ea6978ada299d0a0417.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a8606ec944474ea6978ada299d0a0417"}}, "title": "SUMOylation mediates the nuclear translocation and signaling of the IGF-1 receptor.", "authors": [{"family": "Sehat", "given": "Bita", "initials": "B"}, {"family": "Tofigh", "given": "Ali", "initials": "A"}, {"family": "Lin", "given": "Yingbo", "initials": "Y"}, {"family": "Trocm\u00e9", "given": "Eric", "initials": "E"}, {"family": "Liljedahl", "given": "Ulrika", "initials": "U", "orcid": "0000-0002-1250-392X", "researcher": {"href": "https://publications.scilifelab.se/researcher/241618974ae142b38e5fe84236819f2b.json"}}, {"family": "Lagergren", "given": "Jens", "initials": "J"}, {"family": "Larsson", "given": "Olle", "initials": "O"}], "type": "journal article", "published": "2010-02-09", "journal": {"title": "Sci Signal", "issn": "1937-9145", "issn-l": "1945-0877", "volume": "3", "issue": "108", "pages": "ra10"}, "abstract": "The insulin-like growth factor 1 receptor (IGF-1R) plays crucial roles in developmental and cancer biology. Most of its biological effects have been ascribed to its tyrosine kinase activity, which propagates signaling through the phosphatidylinositol 3-kinase and mitogen-activated protein kinase pathways. Here, we report that IGF-1 promotes the modification of IGF-1R by small ubiquitin-like modifier protein-1 (SUMO-1) and its translocation to the nucleus. Nuclear IGF-1R associated with enhancer-like elements and increased transcription in reporter assays. The SUMOylation sites of IGF-1R were identified as three evolutionarily conserved lysine residues-Lys(1025), Lys(1100), and Lys(1120)-in the beta subunit of the receptor. Mutation of these SUMO-1 sites abolished the ability of IGF-1R to translocate to the nucleus and activate transcription but did not alter its kinase-dependent signaling. Thus, we demonstrate a SUMOylation-mediated mechanism of IGF-1R signaling that has potential implications for gene regulation.", "doi": "10.1126/scisignal.2000628", "pmid": "20145208", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "3/108/ra10"}], "notes": [], "created": "2017-05-04T15:00:39.225Z", "modified": "2022-03-31T15:22:33.212Z"}, {"entity": "publication", "iuid": "9ff3b98dad3642b68fabcabed6994ec4", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9ff3b98dad3642b68fabcabed6994ec4.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9ff3b98dad3642b68fabcabed6994ec4"}}, "title": "Sequence variation in SORL1 and dementia risk in Swedes.", "authors": [{"family": "Reynolds", "given": "Chandra A", "initials": "CA"}, {"family": "Hong", "given": "Mun-Gwan", "initials": "MG"}, {"family": "Eriksson", "given": "Ulrika K", "initials": "UK"}, {"family": "Blennow", "given": "Kaj", "initials": "K"}, {"family": "Johansson", "given": "Boo", "initials": "B"}, {"family": "Malmberg", "given": "Bo", "initials": "B"}, {"family": "Berg", "given": "Stig", "initials": "S"}, {"family": "Gatz", "given": "Margaret", "initials": "M"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Bennet", "given": "Anna M", "initials": "AM"}, {"family": "Prince", "given": "Jonathan A", "initials": "JA"}], "type": "journal article", "published": "2010-02-00", "journal": {"volume": "11", "issn": "1364-6753", "issue": "1", "pages": "139-142", "title": "Neurogenetics", "issn-l": "1364-6745"}, "abstract": "The gene encoding the neuronal sortilin-related receptor SORL1 has been claimed to be associated with Alzheimer's disease (AD) by independent groups and across various human populations. We evaluated six genetic markers in SORL1 in a sample of 1,558 Swedish dementia cases (including 1,270 AD cases) and 2,179 controls. For both single-marker-based and haplotype-based analyses, we found no strong support for SORL1 as a dementia or AD risk-modifying gene in our sample in isolation nor did we observe association with AD/dementia-related traits, including cerebrospinal fluid beta-amyloid(1-42), tau levels, or age at onset. However, meta-analyses of markers in this study together with previously published studies on SORL1 encompassing in excess of 13,000 individuals does suggest significant association with AD (best odds ratio = 1.097; 95% confidence interval = 1.038-1.158, p = 0.001). All six markers were significant in meta-analyses and it is notable that they occur in two distinct linkage disequilibrium blocks. These data are consistent with either allelic heterogeneity or the existence of as yet untested functional variants and these will be important considerations in further attempts to evaluate the importance of sequence variation in SORL1 with AD risk.", "doi": "10.1007/s10048-009-0210-4", "pmid": "19653016", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pmc", "key": "PMC2867467"}, {"db": "mid", "key": "NIHMS196956"}], "notes": [], "created": "2017-05-04T15:00:36.174Z", "modified": "2020-01-21T13:56:04.120Z"}, {"entity": "publication", "iuid": "2ce366571c2d45828cf045d514322f38", "links": {"self": {"href": "https://publications.scilifelab.se/publication/2ce366571c2d45828cf045d514322f38.json"}, "display": {"href": "https://publications.scilifelab.se/publication/2ce366571c2d45828cf045d514322f38"}}, "title": "Sensitive plasma protein analysis by microparticle-based proximity ligation assays.", "authors": [{"family": "Darmanis", "given": "Spyros", "initials": "S"}, {"family": "Nong", "given": "Rachel Yuan", "initials": "RY"}, {"family": "Hammond", "given": "Maria", "initials": "M", "orcid": "0000-0002-8375-6676", "researcher": {"href": "https://publications.scilifelab.se/researcher/78703c93891e4827aabb35c2011be9f2.json"}}, {"family": "Gu", "given": "Jijuan", "initials": "J"}, {"family": "Alderborn", "given": "Anders", "initials": "A"}, {"family": "V\u00e4nelid", "given": "Johan", "initials": "J"}, {"family": "Siegbahn", "given": "Agneta", "initials": "A"}, {"family": "Gustafsdottir", "given": "Sigrun", "initials": "S"}, {"family": "Ericsson", "given": "Olle", "initials": "O"}, {"family": "Landegren", "given": "Ulf", "initials": "U"}, {"family": "Kamali-Moghaddam", "given": "Masood", "initials": "M", "orcid": "0000-0002-1303-2218", "researcher": {"href": "https://publications.scilifelab.se/researcher/290dd535fb414c68bc49a8a2b7995770.json"}}], "type": "journal article", "published": "2010-02-00", "journal": {"volume": "9", "issn": "1535-9484", "issue": "2", "pages": "327-335", "title": "Mol. Cell Proteomics", "issn-l": "1535-9476"}, "abstract": "Detection of proteins released in the bloodstream from tissues damaged by disease can promote early detection of pathological conditions, differential diagnostics, and follow-up of therapy. Despite these prospects and a plethora of candidate biomarkers, efforts in recent years to establish new protein diagnostic assays have met with limited success. One important limiting factor has been the challenge of detecting proteins present at trace levels in complex bodily fluids. To achieve robust, sensitive, and specific detection, we have developed a microparticle-based solid-phase proximity ligation assay, dependent on simultaneous recognition of target proteins by three antibody molecules for added specificity. After capture on a microparticle, solid-phase pairs of proximity probes are added followed by washes, enabling detection and identification of rare protein molecules in blood while consuming small amounts of sample. We demonstrate that single polyclonal antibody preparations raised against target proteins of interest can be readily used to establish assays where detection depends on target recognition by three individual antibody molecules, recognizing separate epitopes. The assay was compared with state-of-the-art sandwich ELISAs for detection of vascular endothelial growth factor, interleukin-8 and interleukin-6, and it was found to be superior both with regard to dynamic range and minimal numbers of molecules detected. Furthermore, the assays exhibited excellent performance in undiluted plasma and serum as well as in whole blood, producing comparable results for nine different antigens. We thus show that solid-phase proximity ligation assay is suitable for validation of a variety of protein biomarkers over broad dynamic ranges in clinical samples.", "doi": "10.1074/mcp.M900248-MCP200", "pmid": "19955079", "labels": {"PLA and Single Cell Proteomics": "", "Affinity Proteomics Uppsala": "Technology development"}, "xrefs": [{"db": "pii", "key": "M900248-MCP200"}, {"db": "pmc", "key": "PMC2830843"}], "notes": [], "created": "2017-05-04T14:55:21.065Z", "modified": "2023-04-14T13:56:32.269Z"}, {"entity": "publication", "iuid": "44a038e26eb24be997b53892bb9dd3ba", "links": {"self": {"href": "https://publications.scilifelab.se/publication/44a038e26eb24be997b53892bb9dd3ba.json"}, "display": {"href": "https://publications.scilifelab.se/publication/44a038e26eb24be997b53892bb9dd3ba"}}, "title": "Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae.", "authors": [{"family": "Lantermann", "given": "Alexandra B", "initials": "AB"}, {"family": "Straub", "given": "Tobias", "initials": "T"}, {"family": "Str\u00e5lfors", "given": "Annelie", "initials": "A"}, {"family": "Yuan", "given": "Guo-Cheng", "initials": "GC"}, {"family": "Ekwall", "given": "Karl", "initials": "K"}, {"family": "Korber", "given": "Philipp", "initials": "P"}], "type": "comparative study", "published": "2010-02-00", "journal": {"volume": "17", "issn": "1545-9985", "issue": "2", "pages": "251-257", "title": "Nat. Struct. Mol. Biol.", "issn-l": "1545-9985"}, "abstract": "Positioned nucleosomes limit the access of proteins to DNA and implement regulatory features encoded in eukaryotic genomes. Here we have generated the first genome-wide nucleosome positioning map for Schizosaccharomyces pombe and annotated transcription start and termination sites genome wide. Using this resource, we found surprising differences from the previously published nucleosome organization of the distantly related yeast Saccharomyces cerevisiae. DNA sequence guides nucleosome positioning differently: for example, poly(dA-dT) elements are not enriched in S. pombe nucleosome-depleted regions. Regular nucleosomal arrays emanate more asymmetrically-mainly codirectionally with transcription-from promoter nucleosome-depleted regions, but promoters harboring the histone variant H2A.Z also show regular arrays upstream of these regions. Regular nucleosome phasing in S. pombe has a very short repeat length of 154 base pairs and requires a remodeler, Mit1, that is conserved in humans but is not found in S. cerevisiae. Nucleosome positioning mechanisms are evidently not universal but evolutionarily plastic.", "doi": "10.1038/nsmb.1741", "pmid": "20118936", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "nsmb.1741"}, {"db": "GEO", "key": "GSE16040"}], "notes": [], "created": "2017-05-04T15:03:08.130Z", "modified": "2017-05-30T14:50:29.888Z"}, {"entity": "publication", "iuid": "b7d36330de3a46088fdbdb9fc386bc1f", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b7d36330de3a46088fdbdb9fc386bc1f.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b7d36330de3a46088fdbdb9fc386bc1f"}}, "title": "New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.", "authors": [{"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Saxena", "given": "Richa", "initials": "R"}, {"family": "Soranzo", "given": "Nicole", "initials": "N"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Wheeler", "given": "Eleanor", "initials": "E"}, {"family": "Glazer", "given": "Nicole L", "initials": "NL"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N"}, {"family": "Gloyn", "given": "Anna L", "initials": "AL"}, {"family": "Lindgren", "given": "Cecilia M", "initials": "CM"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Randall", "given": "Joshua", "initials": "J"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Elliott", "given": "Paul", "initials": "P"}, {"family": "Rybin", "given": "Denis", "initials": "D"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Henneman", "given": "Peter", "initials": "P"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Dehghan", "given": "Abbas", "initials": "A"}, {"family": "Hottenga", "given": "Jouke Jan", "initials": "JJ"}, {"family": "Franklin", "given": "Christopher S", "initials": "CS"}, {"family": "Navarro", "given": "Pau", "initials": "P"}, {"family": "Song", "given": "Kijoung", "initials": "K"}, {"family": "Goel", "given": "Anuj", "initials": "A"}, {"family": "Perry", "given": "John R B", "initials": "JR"}, {"family": "Egan", "given": "Josephine M", "initials": "JM"}, {"family": "Lajunen", "given": "Taina", "initials": "T"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Spars\u00f8", "given": "Thomas", "initials": "T"}, {"family": "Doney", "given": "Alex", "initials": "A"}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Kanoni", "given": "Stavroula", "initials": "S"}, {"family": "Shrader", "given": "Peter", "initials": "P"}, {"family": "Cavalcanti-Proen\u00e7a", "given": "Christine", "initials": "C"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "Timpson", "given": "Nicholas J", "initials": "NJ"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Zabena", "given": "Carina", "initials": "C"}, {"family": "Rocheleau", "given": "Ghislain", "initials": "G"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "An", "given": "Ping", "initials": "P"}, {"family": "O'Connell", "given": "Jeffrey", "initials": "J"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Elliott", "given": "Amanda", "initials": "A"}, {"family": "McCarroll", "given": "Steven A", "initials": "SA"}, {"family": "Payne", "given": "Felicity", "initials": "F"}, {"family": "Roccasecca", "given": "Rosa Maria", "initials": "RM"}, {"family": "Pattou", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Sethupathy", "given": "Praveen", "initials": "P"}, {"family": "Ardlie", "given": "Kristin", "initials": "K"}, {"family": "Ariyurek", "given": "Yavuz", "initials": "Y"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Barter", "given": "Philip", "initials": "P"}, {"family": "Beilby", "given": "John P", "initials": "JP"}, {"family": "Ben-Shlomo", "given": "Yoav", "initials": "Y"}, {"family": "Benediktsson", "given": "Rafn", "initials": "R"}, {"family": "Bennett", "given": "Amanda J", "initials": "AJ"}, {"family": "Bergmann", "given": "Sven", "initials": "S"}, {"family": "Bochud", "given": "Murielle", "initials": "M"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Bonnefond", "given": "Am\u00e9lie", "initials": "A"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Borch-Johnsen", "given": "Knut", "initials": "K"}, {"family": "B\u00f6ttcher", "given": "Yvonne", "initials": "Y"}, {"family": "Brunner", "given": "Eric", "initials": "E"}, {"family": "Bumpstead", "given": "Suzannah J", "initials": "SJ"}, {"family": "Charpentier", "given": "Guillaume", "initials": "G"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YD"}, {"family": "Chines", "given": "Peter", "initials": "P"}, {"family": "Clarke", "given": "Robert", "initials": "R"}, {"family": "Coin", "given": "Lachlan J M", "initials": "LJ"}, {"family": "Cooper", "given": "Matthew N", "initials": "MN"}, {"family": "Cornelis", "given": "Marilyn", "initials": "M"}, {"family": "Crawford", "given": "Gabe", "initials": "G"}, {"family": "Crisponi", "given": "Laura", "initials": "L"}, {"family": "Day", "given": "Ian N M", "initials": "IN"}, {"family": "de Geus", "given": "Eco J C", "initials": "EJ"}, {"family": "Delplanque", "given": "Jerome", "initials": "J"}, {"family": "Dina", "given": "Christian", "initials": "C"}, {"family": "Erdos", "given": "Michael R", "initials": 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"Hattersley", "given": "Andrew T", "initials": "AT"}, {"family": "Silander", "given": "Kaisa", "initials": "K"}, {"family": "Salomaa", "given": "Veikko", "initials": "V"}, {"family": "Smith", "given": "George Davey", "initials": "GD"}, {"family": "Bornstein", "given": "Stefan R", "initials": "SR"}, {"family": "Schwarz", "given": "Peter", "initials": "P"}, {"family": "Spranger", "given": "Joachim", "initials": "J"}, {"family": "Karpe", "given": "Fredrik", "initials": "F"}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Cooper", "given": "Cyrus", "initials": "C"}, {"family": "Dedoussis", "given": "George V", "initials": "GV"}, {"family": "Serrano-R\u00edos", "given": "Manuel", "initials": "M"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Palmer", "given": "Lyle J", "initials": "LJ"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Franks", "given": "Paul W", 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"given": "James F", "initials": "JF"}, {"family": "Anders Hamsten on behalf of Procardis Consortium", "given": null, "initials": null}, {"family": "MAGIC investigators", "given": null, "initials": null}, {"family": "Bergman", "given": "Richard N", "initials": "RN"}, {"family": "Buchanan", "given": "Thomas A", "initials": "TA"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Valle", "given": "Timo T", "initials": "TT"}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Penninx", "given": "Brenda W J H", "initials": "BW"}, {"family": "Boomsma", "given": "Dorret I", "initials": "DI"}, {"family": "Deloukas", "given": "Panos", "initials": "P"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Kong", "given": "Augustine", "initials": "A"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "van Duijn", "given": "Cornelia M", "initials": "CM"}, {"family": "Aulchenko", "given": "Yurii S", "initials": "YS"}, {"family": "Cao", "given": "Antonio", "initials": "A"}, {"family": "Scuteri", "given": "Angelo", "initials": "A"}, {"family": "Schlessinger", "given": "David", "initials": "D"}, {"family": "Uda", "given": "Manuela", "initials": "M"}, {"family": "Ruokonen", "given": "Aimo", "initials": "A"}, {"family": "Jarvelin", "given": "Marjo-Riitta", "initials": "MR"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Peltonen", "given": "Leena", "initials": "L"}, {"family": "Mooser", "given": "Vincent", "initials": "V"}, {"family": "Abecasis", "given": "Goncalo R", "initials": "GR"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Sladek", "given": "Robert", "initials": "R"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Watanabe", "given": "Richard M", "initials": "RM"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}], "type": "journal article", "published": "2010-02-00", "journal": {"volume": "42", "issn": "1546-1718", "issue": "2", "pages": "105-116", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Levels of circulating glucose are tightly regulated. To identify new loci influencing glycemic traits, we performed meta-analyses of 21 genome-wide association studies informative for fasting glucose, fasting insulin and indices of beta-cell function (HOMA-B) and insulin resistance (HOMA-IR) in up to 46,186 nondiabetic participants. Follow-up of 25 loci in up to 76,558 additional subjects identified 16 loci associated with fasting glucose and HOMA-B and two loci associated with fasting insulin and HOMA-IR. These include nine loci newly associated with fasting glucose (in or near ADCY5, MADD, ADRA2A, CRY2, FADS1, GLIS3, SLC2A2, PROX1 and C2CD4B) and one influencing fasting insulin and HOMA-IR (near IGF1). We also demonstrated association of ADCY5, PROX1, GCK, GCKR and DGKB-TMEM195 with type 2 diabetes. Within these loci, likely biological candidate genes influence signal transduction, cell proliferation, development, glucose-sensing and circadian regulation. Our results demonstrate that genetic studies of glycemic traits can identify type 2 diabetes risk loci, as well as loci containing gene variants that are associated with a modest elevation in glucose levels but are not associated with overt diabetes.", "doi": "10.1038/ng.520", "pmid": "20081858", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.520"}, {"db": "pmc", "key": "PMC3018764"}, {"db": "mid", "key": "NIHMS259059"}], "notes": [], "created": "2017-05-04T15:00:34.398Z", "modified": "2021-07-07T15:11:02.708Z"}, {"entity": "publication", "iuid": "ebcd0009f3a841cf85ed682bb9d32f78", "links": {"self": {"href": "https://publications.scilifelab.se/publication/ebcd0009f3a841cf85ed682bb9d32f78.json"}, "display": {"href": "https://publications.scilifelab.se/publication/ebcd0009f3a841cf85ed682bb9d32f78"}}, "title": "Infection of mast cells with live streptococci causes a toll-like receptor 2- and cell-cell contact-dependent cytokine and chemokine response.", "authors": [{"family": "R\u00f6nnberg", "given": "Elin", "initials": "E"}, {"family": "Guss", "given": "Bengt", "initials": "B"}, {"family": "Pejler", "given": "Gunnar", "initials": "G"}], "type": "journal article", "published": "2010-02-00", "journal": {"volume": "78", "issn": "1098-5522", "issue": "2", "pages": "854-864", "title": "Infect. Immun.", "issn-l": "0019-9567"}, "abstract": "Mast cells (MCs) are strongly implicated in immunity toward bacterial infection, but the molecular mechanisms by which MCs contribute to the host response are only partially understood. We addressed this issue by examining the direct effects of a Gram-positive pathogen, Streptococcus equi, on bone marrow-derived MCs (BMMCs). Ultrastructural analysis revealed extensive formation of dilated rough endoplasmic reticulum in response to bacterial infection, indicating strong induction of protein synthesis. However, the BMMCs did not show signs of extensive degranulation, and this was supported by only slow release of histamine in response to infection. Coculture of live bacteria with BMMCs caused a profound secretion of CCL2/MCP-1, CCL7/MCP-3, CXCL2/MIP-2, CCL5/RANTES, interleukin-4 (IL-4), IL-6, IL-12, IL-13, and tumor necrosis factor alpha, as shown by antibody-based cytokine/chemokine arrays and/or enzyme-linked immunosorbent assay. In contrast, heat-inactivated bacteria caused only minimal cytokine/chemokine release. The cytokine/chemokine responses were substantially attenuated in Toll-like receptor 2-deficient BMMCs and were strongly dependent on cell-cell contacts between bacteria and BMMCs. Gene chip microarray analysis confirmed a massively upregulated expression of the genes coding for the secreted cytokines and chemokines and also identified a pronounced upregulation of numerous additional genes, including transcription factors, signaling molecules, and proteases. Together, the present study outlines MC-dependent molecular events associated with Gram-positive infection and thus provides an advancement in our understanding of how MCs may contribute to host defense toward bacterial insults.", "doi": "10.1128/IAI.01004-09", "pmid": "19933827", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "IAI.01004-09"}, {"db": "pmc", "key": "PMC2812202"}], "notes": [], "created": "2017-05-04T15:02:50.056Z", "modified": "2018-11-14T14:07:27.086Z"}, {"entity": "publication", "iuid": "3f8aa16f05694fb8acaff1255796495c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f8aa16f05694fb8acaff1255796495c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f8aa16f05694fb8acaff1255796495c"}}, "title": "Global gene expression analysis of rodent motor neurons following spinal cord injury associates molecular mechanisms with development of postinjury spasticity.", "authors": [{"family": "Wienecke", "given": "J", "initials": "J"}, {"family": "Westerdahl", "given": "A-C", "initials": "AC"}, {"family": "Hultborn", "given": "H", "initials": "H"}, {"family": "Kiehn", "given": "O", "initials": "O"}, {"family": "Ryge", "given": "J", "initials": "J"}], "type": "journal article", "published": "2010-02-00", "journal": {"volume": "103", "issn": "1522-1598", "issue": "2", "pages": "761-778", "title": "J. Neurophysiol.", "issn-l": "0022-3077"}, "abstract": "Spinal cord injury leads to severe problems involving impaired motor, sensory, and autonomic functions. After spinal injury there is an initial phase of hyporeflexia followed by hyperreflexia, often referred to as spasticity. Previous studies have suggested a relationship between the reappearance of endogenous plateau potentials in motor neurons and the development of spasticity after spinalization. To unravel the molecular mechanisms underlying the increased excitability of motor neurons and the return of plateau potentials below a spinal cord injury we investigated changes in gene expression in this cell population. We adopted a rat tail-spasticity model with a caudal spinal transection that causes a progressive development of spasticity from its onset after 2 to 3 wk until 2 mo postinjury. Gene expression changes of fluorescently identified tail motor neurons were studied 21 and 60 days postinjury. The motor neurons undergo substantial transcriptional regulation in response to injury. The patterns of differential expression show similarities at both time points, although there are 20% more differentially expressed genes 60 days compared with 21 days postinjury. The study identifies targets of regulation relating to both ion channels and receptors implicated in the endogenous expression of plateaux. The regulation of excitatory and inhibitory signal transduction indicates a shift in the balance toward increased excitability, where the glutamatergic N-methyl-d-aspartate receptor complex together with cholinergic system is up-regulated and the gamma-aminobutyric acid type A receptor system is down-regulated. The genes of the pore-forming proteins Cav1.3 and Nav1.6 were not up-regulated, whereas genes of proteins such as nonpore-forming subunits and intracellular pathways known to modulate receptor and channel trafficking, kinetics, and conductivity showed marked regulation. On the basis of the identified changes in global gene expression in motor neurons, the present investigation opens up for new potential targets for treatment of motor dysfunction following spinal cord injury.", "doi": "10.1152/jn.00609.2009", "pmid": "19939961", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "00609.2009"}], "notes": [], "created": "2017-05-04T15:03:06.925Z", "modified": "2017-05-30T12:39:23.946Z"}, {"entity": "publication", "iuid": "8ac1c52c4ef64f118486c582f1ba47ee", "links": {"self": {"href": "https://publications.scilifelab.se/publication/8ac1c52c4ef64f118486c582f1ba47ee.json"}, "display": {"href": "https://publications.scilifelab.se/publication/8ac1c52c4ef64f118486c582f1ba47ee"}}, "title": "Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge.", "authors": [{"family": "Saxena", "given": "Richa", "initials": "R"}, {"family": "Hivert", "given": "Marie-France", "initials": "MF"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Tanaka", "given": "Toshiko", "initials": "T"}, {"family": "Pankow", "given": "James S", "initials": "JS"}, {"family": "Vollenweider", "given": "Peter", "initials": "P"}, {"family": "Lyssenko", "given": "Valeriya", "initials": "V"}, {"family": "Bouatia-Naji", "given": "Nabila", "initials": "N"}, {"family": "Dupuis", "given": "Jos\u00e9e", "initials": "J"}, {"family": "Jackson", "given": "Anne U", "initials": "AU"}, {"family": "Kao", "given": "W H Linda", "initials": "WH"}, {"family": "Li", "given": "Man", "initials": "M"}, {"family": "Glazer", "given": "Nicole L", "initials": "NL"}, {"family": "Manning", "given": "Alisa K", "initials": "AK"}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Stringham", "given": "Heather M", "initials": "HM"}, {"family": "Prokopenko", "given": "Inga", "initials": "I"}, {"family": "Johnson", "given": "Toby", "initials": "T"}, {"family": "Grarup", "given": "Niels", "initials": "N"}, {"family": "Boesgaard", "given": "Trine W", "initials": "TW"}, {"family": "Lecoeur", "given": "C\u00e9cile", "initials": "C"}, {"family": "Shrader", "given": "Peter", "initials": "P"}, {"family": "O'Connell", "given": "Jeffrey", "initials": "J"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Couper", "given": "David J", "initials": "DJ"}, {"family": "Rice", "given": "Kenneth", "initials": "K"}, {"family": "Song", "given": "Kijoung", "initials": "K"}, {"family": "Andreasen", "given": "Camilla H", "initials": "CH"}, {"family": "Dina", "given": "Christian", "initials": "C"}, {"family": "K\u00f6ttgen", "given": "Anna", "initials": "A"}, {"family": "Le Bacquer", "given": "Olivier", "initials": "O"}, {"family": "Pattou", "given": "Fran\u00e7ois", "initials": "F"}, {"family": "Taneera", "given": "Jalal", "initials": "J"}, {"family": "Steinthorsdottir", "given": "Valgerdur", "initials": "V"}, {"family": "Rybin", "given": "Denis", "initials": "D"}, {"family": "Ardlie", "given": "Kristin", "initials": "K"}, {"family": "Sampson", "given": "Michael", "initials": "M"}, {"family": "Qi", "given": "Lu", "initials": "L"}, {"family": "van Hoek", "given": "Mandy", "initials": "M"}, {"family": "Weedon", "given": "Michael N", "initials": "MN"}, {"family": "Aulchenko", "given": "Yurii S", "initials": "YS"}, {"family": "Voight", "given": "Benjamin F", "initials": "BF"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Balkau", "given": "Beverley", "initials": "B"}, {"family": "Bergman", "given": "Richard N", "initials": "RN"}, {"family": "Bielinski", "given": "Suzette J", "initials": "SJ"}, {"family": "Bonnefond", "given": "Amelie", "initials": "A"}, {"family": "Bonnycastle", "given": "Lori L", "initials": "LL"}, {"family": "Borch-Johnsen", "given": "Knut", "initials": "K"}, {"family": "B\u00f6ttcher", "given": "Yvonne", "initials": "Y"}, {"family": "Brunner", "given": "Eric", "initials": "E"}, {"family": "Buchanan", "given": "Thomas A", "initials": "TA"}, {"family": "Bumpstead", "given": "Suzannah J", "initials": "SJ"}, {"family": "Cavalcanti-Proen\u00e7a", "given": "Christine", "initials": "C"}, {"family": "Charpentier", "given": "Guillaume", "initials": "G"}, {"family": "Chen", "given": "Yii-Der Ida", "initials": "YD"}, {"family": "Chines", "given": "Peter S", "initials": "PS"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Cornelis", "given": "Marilyn", "initials": "M"}, {"family": "J Crawford", "given": "Gabriel", "initials": "G"}, {"family": "Delplanque", "given": "Jerome", "initials": "J"}, {"family": "Doney", "given": "Alex", "initials": "A"}, {"family": "Egan", "given": "Josephine M", "initials": "JM"}, {"family": "Erdos", "given": "Michael R", "initials": "MR"}, {"family": "Firmann", "given": "Mathieu", "initials": "M"}, {"family": "Forouhi", "given": "Nita G", "initials": "NG"}, {"family": "Fox", "given": "Caroline S", "initials": "CS"}, {"family": "Goodarzi", "given": "Mark O", "initials": "MO"}, {"family": "Graessler", "given": "J\u00fcrgen", "initials": "J"}, {"family": "Hingorani", "given": "Aroon", "initials": "A"}, {"family": "Isomaa", "given": "Bo", "initials": "B"}, {"family": "J\u00f8rgensen", "given": "Torben", "initials": "T"}, {"family": "Kivimaki", "given": "Mika", "initials": "M"}, {"family": "Kovacs", "given": "Peter", "initials": "P"}, {"family": "Krohn", "given": "Knut", "initials": "K"}, {"family": "Kumari", "given": "Meena", "initials": "M"}, {"family": "Lauritzen", "given": "Torsten", "initials": "T"}, {"family": "L\u00e9vy-Marchal", "given": "Claire", "initials": "C"}, {"family": "Mayor", "given": "Vladimir", "initials": "V"}, {"family": "McAteer", "given": "Jarred B", "initials": "JB"}, {"family": "Meyre", "given": "David", "initials": "D"}, {"family": "Mitchell", "given": "Braxton D", "initials": "BD"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL"}, {"family": "Morken", "given": "Mario A", "initials": "MA"}, {"family": "Narisu", "given": "Narisu", "initials": "N"}, {"family": "Palmer", "given": "Colin N A", "initials": "CN"}, {"family": "Pakyz", "given": "Ruth", "initials": "R"}, {"family": "Pascoe", "given": "Laura", "initials": "L"}, {"family": "Payne", "given": "Felicity", "initials": "F"}, {"family": "Pearson", "given": "Daniel", "initials": "D"}, {"family": "Rathmann", "given": "Wolfgang", "initials": "W"}, {"family": "Sandbaek", "given": "Annelli", "initials": "A"}, {"family": "Sayer", "given": "Avan Aihie", "initials": "AA"}, {"family": "Scott", "given": "Laura J", "initials": "LJ"}, {"family": "Sharp", "given": "Stephen J", "initials": "SJ"}, {"family": "Sijbrands", "given": "Eric", "initials": "E"}, {"family": "Singleton", "given": "Andrew", "initials": "A"}, {"family": "Siscovick", "given": "David S", "initials": "DS"}, {"family": "Smith", "given": "Nicholas L", "initials": "NL"}, {"family": "Spars\u00f8", "given": "Thomas", "initials": "T"}, {"family": "Swift", "given": "Amy J", "initials": "AJ"}, {"family": "Syddall", "given": "Holly", "initials": "H"}, {"family": "Thorleifsson", "given": "Gudmar", "initials": "G"}, {"family": "T\u00f6njes", "given": "Anke", "initials": "A"}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T"}, {"family": "Tuomilehto", "given": "Jaakko", "initials": "J"}, {"family": "Valle", "given": "Timo T", "initials": "TT"}, {"family": "Waeber", "given": "G\u00e9rard", "initials": "G"}, {"family": "Walley", "given": "Andrew", "initials": "A"}, {"family": "Waterworth", "given": "Dawn M", "initials": "DM"}, {"family": "Zeggini", "given": "Eleftheria", "initials": "E"}, {"family": "Zhao", "given": "Jing Hua", "initials": "JH"}, {"family": "GIANT consortium", "given": null, "initials": null}, {"family": "MAGIC investigators", "given": null, "initials": null}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Wichmann", "given": "H Erich", "initials": "HE"}, {"family": "Wilson", "given": "James F", "initials": "JF"}, {"family": "van Duijn", "given": "Cornelia", "initials": "C"}, {"family": "Hu", "given": "Frank B", "initials": "FB"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Hattersley", "given": "Andrew T", "initials": "AT"}, {"family": "Thorsteinsdottir", "given": "Unnur", "initials": "U"}, {"family": "Stefansson", "given": "Kari", "initials": "K"}, {"family": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-5652-8459", "researcher": {"href": "https://publications.scilifelab.se/researcher/f23c2a10ac2a4d73a8f62b94855635f1.json"}}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Shuldiner", "given": "Alan R", "initials": "AR"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Bornstein", "given": "Stefan R", "initials": "SR"}, {"family": "Schwarz", "given": "Peter", "initials": "P"}, {"family": "Williams", "given": "Gordon H", "initials": "GH"}, {"family": "Nathan", "given": "David M", "initials": "DM"}, {"family": "Kuusisto", "given": "Johanna", "initials": "J"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Cooper", "given": "Cyrus", "initials": "C"}, {"family": "Marmot", "given": "Michael", "initials": "M"}, {"family": "Ferrucci", "given": "Luigi", "initials": "L"}, {"family": "Mooser", "given": "Vincent", "initials": "V"}, {"family": "Stumvoll", "given": "Michael", "initials": "M"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJ"}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "Psaty", "given": "Bruce M", "initials": "BM"}, {"family": "Rotter", "given": "Jerome I", "initials": "JI"}, {"family": "Boerwinkle", "given": "Eric", "initials": "E"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "Barroso", "given": "In\u00eas", "initials": "I"}, {"family": "Sladek", "given": "Robert", "initials": "R"}, {"family": "Froguel", "given": "Philippe", "initials": "P"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Groop", "given": "Leif", "initials": "L"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Watanabe", "given": "Richard M", "initials": "RM"}], "type": "journal article", "published": "2010-02-00", "journal": {"volume": "42", "issn": "1546-1718", "issue": "2", "pages": "142-148", "title": "Nat. Genet.", "issn-l": "1061-4036"}, "abstract": "Glucose levels 2 h after an oral glucose challenge are a clinical measure of glucose tolerance used in the diagnosis of type 2 diabetes. We report a meta-analysis of nine genome-wide association studies (n = 15,234 nondiabetic individuals) and a follow-up of 29 independent loci (n = 6,958-30,620). We identify variants at the GIPR locus associated with 2-h glucose level (rs10423928, beta (s.e.m.) = 0.09 (0.01) mmol/l per A allele, P = 2.0 x 10(-15)). The GIPR A-allele carriers also showed decreased insulin secretion (n = 22,492; insulinogenic index, P = 1.0 x 10(-17); ratio of insulin to glucose area under the curve, P = 1.3 x 10(-16)) and diminished incretin effect (n = 804; P = 4.3 x 10(-4)). We also identified variants at ADCY5 (rs2877716, P = 4.2 x 10(-16)), VPS13C (rs17271305, P = 4.1 x 10(-8)), GCKR (rs1260326, P = 7.1 x 10(-11)) and TCF7L2 (rs7903146, P = 4.2 x 10(-10)) associated with 2-h glucose. Of the three newly implicated loci (GIPR, ADCY5 and VPS13C), only ADCY5 was found to be associated with type 2 diabetes in collaborating studies (n = 35,869 cases, 89,798 controls, OR = 1.12, 95% CI 1.09-1.15, P = 4.8 x 10(-18)).", "doi": "10.1038/ng.521", "pmid": "20081857", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "ng.521"}, {"db": "pmc", "key": "PMC2922003"}, {"db": "mid", "key": "NIHMS226512"}], "notes": [], "created": "2017-05-04T15:00:35.510Z", "modified": "2021-07-07T15:57:26.524Z"}, {"entity": "publication", "iuid": "360d1f119ecc432284c62bf9a350c785", "links": {"self": {"href": "https://publications.scilifelab.se/publication/360d1f119ecc432284c62bf9a350c785.json"}, "display": {"href": "https://publications.scilifelab.se/publication/360d1f119ecc432284c62bf9a350c785"}}, "title": "Genetic variants and disease-associated factors contribute to enhanced interferon regulatory factor 5 expression in blood cells of patients with systemic lupus erythematosus.", "authors": [{"family": "Feng", "given": "Di", "initials": "D"}, {"family": "Stone", "given": "Rivka C", "initials": "RC"}, {"family": "Eloranta", "given": "Maija-Leena", "initials": "ML"}, {"family": "Sangster-Guity", "given": "Niquiche", "initials": "N"}, {"family": "Nordmark", "given": "Gunnel", "initials": "G"}, {"family": "Sigurdsson", "given": "Snaevar", "initials": "S"}, {"family": "Wang", "given": "Chuan", "initials": "C"}, {"family": "Alm", "given": "Gunnar", "initials": "G"}, {"family": "Syv\u00e4nen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "R\u00f6nnblom", "given": "Lars", "initials": "L"}, {"family": "Barnes", "given": "Betsy J", "initials": "BJ"}], "type": "journal article", "published": "2010-02-00", "journal": {"volume": "62", "issn": "0004-3591", "issue": "2", "pages": "562-573", "title": "Arthritis Rheum.", "issn-l": null}, "abstract": "Genetic variants of the interferon (IFN) regulatory factor 5 gene (IRF5) are associated with susceptibility to systemic lupus erythematosus (SLE). The contribution of these variants to IRF-5 expression in primary blood cells of SLE patients has not been addressed, nor has the role of type I IFNs. The aim of this study was to determine the association between increased IRF-5 expression and the IRF5 risk haplotype in SLE patients.\n\nIRF-5 transcript and protein levels in 44 Swedish patients with SLE and 16 healthy controls were measured by quantitative real-time polymerase chain reaction, minigene assay, and flow cytometry. Single-nucleotide polymorphisms rs2004640, rs10954213, and rs10488631 and the CGGGG insertion/deletion were genotyped in these patients. Genotypes of these polymorphisms defined both a common risk haplotype and a common protective haplotype.\n\nIRF-5 expression and alternative splicing were significantly up-regulated in SLE patients compared with healthy donors. Enhanced transcript and protein levels were associated with the risk haplotype of IRF5; rs10488631 displayed the only significant independent association that correlated with increased transcription from the noncoding first exon 1C. Minigene experiments demonstrated an important role for rs2004640 and the CGGGG insertion/deletion, along with type I IFNs, in regulating IRF5 expression.\n\nThis study provides the first formal proof that IRF-5 expression and alternative splicing are significantly up-regulated in primary blood cells of patients with SLE. Furthermore, the risk haplotype is associated with enhanced IRF-5 transcript and protein expression in patients with SLE.", "doi": "10.1002/art.27223", "pmid": "20112383", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pmc", "key": "PMC3213692"}, {"db": "mid", "key": "NIHMS190566"}], "notes": [], "created": "2017-05-04T15:00:27.359Z", "modified": "2021-07-07T15:11:02.390Z"}, {"entity": "publication", "iuid": "7e7f39ef3a3f4f6ab83a443c923bf98c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/7e7f39ef3a3f4f6ab83a443c923bf98c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/7e7f39ef3a3f4f6ab83a443c923bf98c"}}, "title": "Connective tissue growth factor is expressed in malignant cells of Hodgkin lymphoma but not in other mature B-cell lymphomas.", "authors": [{"family": "Birgersdotter", "given": "Anna", "initials": "A"}, {"family": "Baumforth", "given": "Karl R N", "initials": "KR"}, {"family": "Wei", "given": "Wenbin", "initials": "W"}, {"family": "Murray", "given": "Paul G", "initials": "PG"}, {"family": "Sj\u00f6berg", "given": "Jan", "initials": "J"}, {"family": "Bj\u00f6rkholm", "given": "Magnus", "initials": "M"}, {"family": "Porwit", "given": "Anna", "initials": "A"}, {"family": "Ernberg", "given": "Ingemar", "initials": "I"}], "type": "comparative study", "published": "2010-02-00", "journal": {"volume": "133", "issn": "1943-7722", "issue": "2", "pages": "271-280", "title": "Am. J. Clin. Pathol.", "issn-l": "0002-9173"}, "abstract": "Connective tissue growth factor (CTGF) has a major role in development of fibrosis and in the wound-healing process. Microarray analysis of 44 classical Hodgkin lymphoma (cHL) samples showed higher CTGF messenger RNA expression in the nodular sclerosis (NS) than in the mixed cellularity (MC) subtype. When analyzed by immunohistochemical analysis, Hodgkin-Reed-Sternberg (H-RS) cells and macrophages in 23 cHLs and \"popcorn\" cells in 2 nodular lymphocyte predominant Hodgkin lymphomas showed expression of CTGF protein correlating with the extent of fibrosis. In NS, CTGF was also expressed in fibroblasts and occasional lymphocytes. Malignant cells in 32 samples of various non-Hodgkin lymphomas were negative for CTGF. A staining pattern of stromal cells similar to that of NS cHL was seen in anaplastic large cell lymphoma. Macrophages stained positively in Burkitt lymphomas and in some mantle cell lymphomas. The high occurrence of fibrosis in cHL may be related to CTGF expression by malignant H-RS cells.", "doi": "10.1309/AJCPG7H0SSRYKNKH", "pmid": "20093237", "labels": {"Bioinformatics and Expression Analysis (BEA)": null}, "xrefs": [{"db": "pii", "key": "133/2/271"}], "notes": [], "created": "2017-05-04T15:03:02.731Z", "modified": "2017-05-30T12:38:18.651Z"}, {"entity": "publication", "iuid": "948787308e4448c8b8ce4ef0438881e2", "links": {"self": {"href": "https://publications.scilifelab.se/publication/948787308e4448c8b8ce4ef0438881e2.json"}, "display": {"href": "https://publications.scilifelab.se/publication/948787308e4448c8b8ce4ef0438881e2"}}, "title": "Comparative protein profiling of serum and plasma using an antibody suspension bead array approach.", "authors": [{"family": "Schwenk", "given": "Jochen M", "initials": "JM", "orcid": "0000-0001-8141-8449", "researcher": {"href": "https://publications.scilifelab.se/researcher/aba5822711b246b397fffacb7ae403b3.json"}}, {"family": "Igel", "given": "Ulrika", "initials": "U"}, {"family": "Kato", "given": "Bernet S", "initials": "BS"}, {"family": "Nicholson", "given": "George", "initials": "G"}, {"family": "Karpe", "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": "Nilsson", "given": "Peter", "initials": "P", "orcid": "0000-0002-4657-8532", "researcher": {"href": "https://publications.scilifelab.se/researcher/799bcf1cf8cf451296f4535dd4ca9dc0.json"}}], "type": "comparative study", "published": "2010-02-00", "journal": {"volume": "10", "issn": "1615-9861", "issue": "3", "pages": "532-540", "title": "Proteomics", "issn-l": "1615-9853"}, "abstract": "In the pursuit towards a systematic analysis of human diseases, array-based approaches within antibody proteomics offer high-throughput strategies to discover protein biomarkers in serum and plasma. To investigate the influence of sample preparation on such discovery attempts, we report on a systematic effort to compare serum and plasma protein profiles determined with an antibody suspension bead array. The intensity levels were used to define protein profiles and no significant differences between serum and plasma were observed for 79% of the 174 antibodies (targeting 156 proteins). By excluding 36 antibodies giving rise to differential intensity levels, cluster analysis revealed donor-specific rather than preparation-dependent grouping. With a cohort from a clinically relevant medical condition, the metabolic syndrome, the influence of the sample type on a multiplexed biomarker discovery approach was further investigated. Independent comparisons of protein profiles in serum and plasma revealed an antibody targeting ADAMTSL-4, a protein that would qualify to be studied further in association with the condition. In general, the preparation type had an impact on the results of the applied antibody suspension bead array, and while the technical variability was equal, plasma offered a greater biological variability and allowed to give rise to more discoveries than serum.", "doi": "10.1002/pmic.200900657", "pmid": "19953555", "labels": {"Affinity Proteomics Stockholm": "Technology development"}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:29.681Z", "modified": "2021-07-08T13:44:33.443Z"}, {"entity": "publication", "iuid": "15ef40b017654d21a684bf04354b27db", "links": {"self": {"href": "https://publications.scilifelab.se/publication/15ef40b017654d21a684bf04354b27db.json"}, "display": {"href": "https://publications.scilifelab.se/publication/15ef40b017654d21a684bf04354b27db"}}, "title": "Coexisting NRAS and BRAF mutations in primary familial melanomas with specific CDKN2A germline alterations.", "authors": [{"family": "Jovanovic", "given": "Braslav", "initials": "B"}, {"family": "Egyhazi", "given": "Suzanne", "initials": "S"}, {"family": "Eskandarpour", "given": "Malihe", "initials": "M"}, {"family": "Ghiorzo", "given": "Paola", "initials": "P"}, {"family": "Palmer", "given": "Jane M", "initials": "JM"}, {"family": "Bianchi Scarr\u00e0", "given": "Giovanna", "initials": "G"}, {"family": "Hayward", "given": "Nicholas K", "initials": "NK"}, {"family": "Hansson", "given": "Johan", "initials": "J"}], "type": "letter", "published": "2010-02-00", "journal": {"title": "J. Invest. Dermatol.", "issn": "1523-1747", "issn-l": "0022-202X", "volume": "130", "issue": "2", "pages": "618-620"}, "abstract": null, "doi": "10.1038/jid.2009.287", "pmid": "19759551", "labels": {"National Genomics Infrastructure": "Service", "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null, "NGI Short read": "Service"}, "xrefs": [{"db": "pii", "key": "S0022-202X(15)34686-8"}, {"db": "pmc", "key": "PMC3665509"}, {"db": "mid", "key": "NIHMS468846"}], "notes": [], "created": "2017-05-04T14:57:11.959Z", "modified": "2022-08-19T09:04:31.750Z"}, {"entity": "publication", "iuid": "403d09b60abf4bac9d77c30dde70eae0", "links": {"self": {"href": "https://publications.scilifelab.se/publication/403d09b60abf4bac9d77c30dde70eae0.json"}, "display": {"href": "https://publications.scilifelab.se/publication/403d09b60abf4bac9d77c30dde70eae0"}}, "title": "Genetic and biochemical studies of SNPs of the mitochondrial A beta-degrading protease, hPreP.", "authors": [{"family": "Pinho", "given": "Catarina Moreira", "initials": "CM"}, {"family": "Bj\u00f6rk", "given": "Behnosh F", "initials": "BF"}, {"family": "Alikhani", "given": "Nyosha", "initials": "N"}, {"family": "B\u00e4ckman", "given": "Hans G", "initials": "HG"}, {"family": "Eneqvist", "given": "Therese", "initials": "T"}, {"family": "Fratiglioni", "given": "Laura", "initials": "L"}, {"family": "Glaser", "given": "Elzbieta", "initials": "E"}, {"family": "Graff", "given": "Caroline", "initials": "C"}], "type": "journal article", "published": "2010-01-22", "journal": {"volume": "469", "issn": "1872-7972", "issue": "2", "pages": "204-208", "title": "Neurosci. Lett.", "issn-l": "0304-3940"}, "abstract": "Several studies suggest mitochondrial dysfunction as a possible mechanism underlying the development of Alzheimer disease (AD). There is data showing that amyloid-beta (A beta) peptide is present in AD brain mitochondria. The human presequence protease (hPreP) was recently shown to be the major mitochondrial A beta-degrading enzyme. We investigated if there is an increased susceptibility to AD, which can be attributed to genetic variation in the hPreP gene PITRM1 and if the proteolytic efficiency of recombinant hPreP variants is affected. When a total of 673 AD cases and 649 controls were genotyped for 18 single nucleotide polymorphisms (SNPs), no genetic association between any of the SNPs and the risk for AD was found. In contrast, functional analysis of four non-synonymous SNPs in hPreP revealed a decreased activity compared to wild type hPreP. Using A beta, the presequence of ATP synthase F(1)beta subunit and a fluorescent peptide as substrates, the lowest activity was observed for the hPreP(A525D) variant, corresponding to rs1224893, which displayed only 20-30% of wild type activity. Furthermore, the activity of all variants was restored by the addition of Mg(2+), suggesting an important role for this metal during proteolysis. In conclusion, our data suggest that genetic variation in the hPreP gene PITRM1 may potentially contribute to mitochondrial dysfunctions.", "doi": "10.1016/j.neulet.2009.11.075", "pmid": "19962426", "labels": {"Mutation Analysis Facility (MAF)": null}, "xrefs": [{"db": "pii", "key": "S0304-3940(09)01566-3"}], "notes": [], "created": "2017-05-04T15:03:28.937Z", "modified": "2017-05-30T12:43:55.686Z"}, {"entity": "publication", "iuid": "a5dfb0f136e4469e92b29eeff0b619cb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a5dfb0f136e4469e92b29eeff0b619cb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a5dfb0f136e4469e92b29eeff0b619cb"}}, "title": "Differential genome-wide array-based methylation profiles in prognostic subsets of chronic lymphocytic leukemia.", "authors": [{"family": "Kanduri", "given": "Meena", "initials": "M"}, {"family": "Cahill", "given": "Nicola", "initials": "N"}, {"family": "G\u00f6ransson", "given": "Hanna", "initials": "H"}, {"family": "Enstr\u00f6m", "given": "Camilla", "initials": "C"}, {"family": "Ryan", "given": "Fergus", "initials": "F"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Rosenquist", "given": "Richard", "initials": "R"}], "type": "journal article", "published": "2010-01-14", "journal": {"volume": "115", "issn": "1528-0020", "issue": "2", "pages": "296-305", "title": "Blood", "issn-l": "0006-4971"}, "abstract": "Global hypomethylation and regional hypermethylation are well-known epigenetic features of cancer; however, in chronic lymphocytic leukemia (CLL), studies on genome-wide epigenetic modifications are limited. Here, we analyzed the global methylation profiles in CLL, by applying high-resolution methylation microarrays (27,578 CpG sites) to 23 CLL samples, belonging to the immunoglobulin heavy-chain variable (IGHV) mutated (favorable) and IGHV unmutated/IGHV3-21 (poor-prognostic) subsets. Overall, results demonstrated significant differences in methylation patterns between these subgroups. Specifically, in IGHV unmutated CLL, we identified methylation of 7 known or candidate tumor suppressor genes (eg, VHL, ABI3, and IGSF4) as well as 8 unmethylated genes involved in cell proliferation and tumor progression (eg, ADORA3 and PRF1 enhancing the nuclear factor-kappaB and mitogen-activated protein kinase pathways, respectively). In contrast, these latter genes were silenced by methylation in IGHV mutated patients. The array data were validated for selected genes using methylation-specific polymerase chain reaction, quantitative reverse transcriptase-polymerase chain reaction, and bisulfite sequencing. Finally, the significance of DNA methylation in regulating gene promoters was shown by reinducing 4 methylated tumor suppressor genes (eg, VHL and ABI3) in IGHV unmutated samples using the methyl-inhibitor 5-aza-2'-deoxycytidine. Taken together, our data for the first time reveal differences in global methylation profiles between prognostic subsets of CLL, which may unfold epigenetic silencing mechanisms involved in CLL pathogenesis.", "doi": "10.1182/blood-2009-07-232868", "pmid": "19897574", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null, "Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "blood-2009-07-232868"}], "notes": [], "created": "2017-05-04T15:00:27.663Z", "modified": "2020-01-21T13:56:11.374Z"}, {"entity": "publication", "iuid": "4777d0495b8640e0aa5243cc1d702afb", "links": {"self": {"href": "https://publications.scilifelab.se/publication/4777d0495b8640e0aa5243cc1d702afb.json"}, "display": {"href": "https://publications.scilifelab.se/publication/4777d0495b8640e0aa5243cc1d702afb"}}, "title": "Association study of PDE4B gene variants in Scandinavian schizophrenia and bipolar disorder multicenter case-control samples.", "authors": [{"family": "K\u00e4hler", "given": "Anna K", "initials": "AK"}, {"family": "Otnaess", "given": "Mona K", "initials": "MK"}, {"family": "Wirgenes", "given": "Katrine V", "initials": "KV"}, {"family": "Hansen", "given": "Thomas", "initials": "T"}, {"family": "J\u00f6nsson", "given": "Erik G", "initials": "EG"}, {"family": "Agartz", "given": "Ingrid", "initials": "I"}, {"family": "Hall", "given": "H\u00e5kan", "initials": "H"}, {"family": "Werge", "given": "Thomas", "initials": "T"}, {"family": "Morken", "given": "Gunnar", "initials": "G"}, {"family": "Mors", "given": "Ole", "initials": "O"}, {"family": "Mellerup", "given": "Erling", "initials": "E"}, {"family": "Dam", "given": "Henrik", "initials": "H"}, {"family": "Koefod", "given": "Pernille", "initials": "P"}, {"family": "Melle", "given": "Ingrid", "initials": "I"}, {"family": "Steen", "given": "Vidar M", "initials": "VM"}, {"family": "Andreassen", "given": "Ole A", "initials": "OA"}, {"family": "Djurovic", "given": "Srdjan", "initials": "S"}], "type": "journal article", "published": "2010-01-05", "journal": {"volume": "153B", "issn": "1552-485X", "issue": "1", "pages": "86-96", "title": "Am. J. Med. Genet. B Neuropsychiatr. Genet.", "issn-l": "1552-4841"}, "abstract": "The phosphodiesterase 4B (PDE4B), which is involved in cognitive function in animal models, is a candidate susceptibility gene for schizophrenia (SZ) and bipolar disorder (BP). Variations in PDE4B have previously been associated with SZ, with a suggested gender-specific effect. We have genotyped and analyzed 40 and 72 tagging single nucleotide polymorphisms (tagSNPs) in SZ and BP multicenter samples, respectively, from the Scandinavian Collaboration on Psychiatric Etiology (SCOPE), involving 837 SZ cases and 1,473 controls plus 594 BP cases and 1,421 partly overlapping controls. Six and 16 tagSNPs were nominally associated (0.0005 < or = P < or = 0.05) with SZ and BP, respectively, in the combined samples or in gender-specific subgroups. None of these findings remained significant after correction for multiple testing. However, a number of tagSNPs found to be nominally associated with SZ and BP were located in a high LD region spanning the splice site of PDE4B3, an isoform with altered brain expression in BP patients. Four tagSNPs were associated with SZ in women, but none in men, in agreement with the previously reported gender-specific effect. Proxies of two nominally associated SNPs in the SZ sample were also associated with BP, but the genotypic effect (i.e., homozygosity for the minor allele), pointed in opposite directions. Finally, four SNPs were found to be associated with Positive And Negative Syndrome Scale (PANSS) positive symptom scores in a subgroup of SZ patients (n = 153) or SZ female patients (n = 70). Further studies are needed to evaluate the implicated PDE4B region of interest, for potential involvement in SZ and BP susceptibility.", "doi": "10.1002/ajmg.b.30958", "pmid": "19350560", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:00:25.206Z", "modified": "2020-01-21T13:56:02.064Z"}, {"entity": "publication", "iuid": "b8147baeed3043a69713f4f1ac2f613a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/b8147baeed3043a69713f4f1ac2f613a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/b8147baeed3043a69713f4f1ac2f613a"}}, "title": "A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins.", "authors": [{"family": "Enster\u00f6", "given": "Mats", "initials": "M"}, {"family": "Akerborg", "given": "Orjan", "initials": "O"}, {"family": "Lundin", "given": "Daniel", "initials": "D"}, {"family": "Wang", "given": "Bei", "initials": "B"}, {"family": "Furey", "given": "Terrence S", "initials": "TS"}, {"family": "Ohman", "given": "Marie", "initials": "M"}, {"family": "Lagergren", "given": "Jens", "initials": "J"}], "type": "journal article", "published": "2010-01-04", "journal": {"volume": "11", "issn": "1471-2105", "issue": null, "pages": "6", "title": "BMC Bioinformatics", "issn-l": "1471-2105"}, "abstract": "Several bioinformatic approaches have previously been used to find novel sites of ADAR mediated A-to-I RNA editing in human. These studies have discovered thousands of genes that are hyper-edited in their non-coding intronic regions, especially in alu retrotransposable elements, but very few substrates that are site-selectively edited in coding regions. Known RNA edited substrates suggest, however, that site selective A-to-I editing is particularly important for normal brain development in mammals.\n\nWe have compiled a screen that enables the identification of new sites of site-selective editing, primarily in coding sequences. To avoid hyper-edited repeat regions, we applied our screen to the alu-free mouse genome. Focusing on the mouse also facilitated better experimental verification. To identify candidate sites of RNA editing, we first performed an explorative screen based on RNA structure and genomic sequence conservation. We further evaluated the results of the explorative screen by determining which transcripts were enriched for A-G mismatches between the genomic template and the expressed sequence since the editing product, inosine (I), is read as guanosine (G) by the translational machinery. For expressed sequences, we only considered coding regions to focus entirely on re-coding events. Lastly, we refined the results from the explorative screen using a novel scoring scheme based on characteristics for known A-to-I edited sites. The extent of editing in the final candidate genes was verified using total RNA from mouse brain and 454 sequencing.\n\nUsing this method, we identified and confirmed efficient editing at one site in the Gabra3 gene. Editing was also verified at several other novel sites within candidates predicted to be edited. Five of these sites are situated in genes coding for the neuron-specific RNA binding proteins HuB and HuD.", "doi": "10.1186/1471-2105-11-6", "pmid": "20047656", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1471-2105-11-6"}, {"db": "pmc", "key": "PMC2831006"}], "notes": [], "created": "2017-05-04T14:57:09.643Z", "modified": "2020-01-21T13:56:04.822Z"}, {"entity": "publication", "iuid": "c97dc7656927434aa4bdef678dad5e34", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c97dc7656927434aa4bdef678dad5e34.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c97dc7656927434aa4bdef678dad5e34"}}, "title": "The 2009 Nobel conference on the role of genetics in promoting suicide prevention and the mental health of the population.", "authors": [{"family": "Wasserman", "given": "D", "initials": "D"}, {"family": "Terenius", "given": "L", "initials": "L"}, {"family": "Wasserman", "given": "J", "initials": "J"}, {"family": "Sokolowski", "given": "M", "initials": "M"}], "type": "journal article", "published": "2010-01-00", "journal": {"volume": "15", "issn": "1476-5578", "issue": "1", "pages": "12-17", "title": "Mol. Psychiatry", "issn-l": "1359-4184"}, "abstract": "A 3-day Nobel Conference entitled 'The role of genetics in promoting suicide prevention and the mental health of the population' was held at the Nobel Forum, Karolinska Institute (KI) in Stockholm, Sweden, during 8-10 June 2009. The conference was sponsored by the Nobel Assembly for Physiology or Medicine and organized by the National Prevention for Suicide and Mental Ill-Health and the Center for Molecular Medicine at KI. The program consisted of 19 invited presentations, covering the genetic basis of mood/psychotic disorders and substance abuse in relation to suicide, with topics ranging from cellular-molecular mechanisms to (endo)phenotypes of mental disorders at the level of the individual and populations. Here, we provide an overview based on the highlights of what was presented.", "doi": "10.1038/mp.2009.113", "pmid": "20029410", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "mp2009113"}], "notes": [], "created": "2017-05-04T15:00:34.065Z", "modified": "2020-01-21T13:56:05.164Z"}, {"entity": "publication", "iuid": "1da7009322084dd19cdb9230f1f7bace", "links": {"self": {"href": "https://publications.scilifelab.se/publication/1da7009322084dd19cdb9230f1f7bace.json"}, "display": {"href": "https://publications.scilifelab.se/publication/1da7009322084dd19cdb9230f1f7bace"}}, "title": "Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: a high-resolution genomic screening of newly diagnosed patients.", "authors": [{"family": "Gunnarsson", "given": "R", "initials": "R"}, {"family": "Isaksson", "given": "A", "initials": "A"}, {"family": "Mansouri", "given": "M", "initials": "M"}, {"family": "G\u00f6ransson", "given": "H", "initials": "H"}, {"family": "Jansson", "given": "M", "initials": "M"}, {"family": "Cahill", "given": "N", "initials": "N"}, {"family": "Rasmussen", "given": "M", "initials": "M"}, {"family": "Staaf", "given": "J", "initials": "J"}, {"family": "Lundin", "given": "J", "initials": "J"}, {"family": "Norin", "given": "S", "initials": "S"}, {"family": "Buhl", "given": "A M", "initials": "AM"}, {"family": "Smedby", "given": "K E", "initials": "KE"}, {"family": "Hjalgrim", "given": "H", "initials": "H"}, {"family": "Karlsson", "given": "K", "initials": "K"}, {"family": "Jurlander", "given": "J", "initials": "J"}, {"family": "Juliusson", "given": "G", "initials": "G"}, {"family": "Rosenquist", "given": "R", "initials": "R"}], "type": "letter", "published": "2010-01-00", "journal": {"volume": "24", "issn": "1476-5551", "issue": "1", "pages": "211-215", "title": "Leukemia", "issn-l": "0887-6924"}, "abstract": null, "doi": "10.1038/leu.2009.187", "pmid": "19741724", "labels": {"Array and Analysis Facility": null}, "xrefs": [{"db": "pii", "key": "leu2009187"}, {"db": "GEO", "description": "Genome variation profiling by SNP array", "key": "GSE16406"}], "notes": [], "created": "2017-05-04T15:02:50.357Z", "modified": "2018-11-14T14:16:15.622Z"}, {"entity": "publication", "iuid": "6390ec72923c41d59b4190f3dbf9493e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6390ec72923c41d59b4190f3dbf9493e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6390ec72923c41d59b4190f3dbf9493e"}}, "title": "Characterization of the cytotoxic properties of the benzimidazole fungicides, benomyl and carbendazim, in human tumour cell lines and primary cultures of patient tumour cells.", "authors": [{"family": "Laryea", "given": "Daniel", "initials": "D"}, {"family": "Gullbo", "given": "Joachim", "initials": "J"}, {"family": "Isaksson", "given": "Anders", "initials": "A"}, {"family": "Larsson", "given": "Rolf", "initials": "R"}, {"family": "Nygren", "given": "Peter", "initials": "P"}], "type": "journal article", "published": "2010-01-00", "journal": {"volume": "21", "issn": "1473-5741", "issue": "1", "pages": "33-42", "title": "Anticancer Drugs", "issn-l": "0959-4973"}, "abstract": "The benzimidazoles, benomyl and carbendazim, are fungicides suggested to target microtubules. Benomyl is metabolized to carbendazim, which has already been explored as an anticancer drug in phase 1 clinical trials. We further characterized the cytotoxic properties of benomyl and carbendazim in 12 human cell lines and in primary cultures of patient tumour cells with the overall aims of elucidating mechanisms of action and anticancer activity spectrum. Cytotoxicity was assessed in the short-term fluorometric microculture cytotoxicity assay and was correlated with the activity of other anticancer drugs and gene expression assessed by cDNA microarray analysis. Benomyl was generally more potent than its metabolite, carbendazim. Both showed high drug activity correlations with several established and experimental anticancer drugs, but modest association with established mechanisms of drug resistance. Furthermore, these benzimidazoles showed high correlations with genes considered relevant for the activity of several mechanistically different standard and experimental anticancer drugs, indicating multiple and broad mechanisms of action. In patient tumour samples, benomyl tended to be more active in haematological compared with solid tumour malignancies, whereas the opposite was observed for carbendazim. In conclusion, benomyl and carbendazim show interesting and diverse cytotoxic mechanisms of action and seem suitable as lead compounds for the development of new anticancer drugs.", "doi": "10.1097/CAD.0b013e328330e74e", "pmid": "19786863", "labels": {"Array and Analysis Facility": null}, "xrefs": [], "notes": [], "created": "2017-05-04T15:02:47.652Z", "modified": "2018-11-14T14:21:05.005Z"}, {"entity": "publication", "iuid": "a4e6280a8bc749d2a9cd215b6c63bc61", "links": {"self": {"href": "https://publications.scilifelab.se/publication/a4e6280a8bc749d2a9cd215b6c63bc61.json"}, "display": {"href": "https://publications.scilifelab.se/publication/a4e6280a8bc749d2a9cd215b6c63bc61"}}, "title": "Association of polymorphisms in the SLIT2 axonal guidance gene with anger in suicide attempters.", "authors": [{"family": "Sokolowski", "given": "M", "initials": "M"}, {"family": "Wasserman", "given": "J", "initials": "J"}, {"family": "Wasserman", "given": "D", "initials": "D"}], "type": "letter", "published": "2010-01-00", "journal": {"volume": "15", "issn": "1476-5578", "issue": "1", "pages": "10-11", "title": "Mol. Psychiatry", "issn-l": "1359-4184"}, "abstract": null, "doi": "10.1038/mp.2009.70", "pmid": "20029409", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "mp200970"}], "notes": [], "created": "2017-05-04T15:00:33.760Z", "modified": "2020-01-21T13:56:04.244Z"}, {"entity": "publication", "iuid": "9e8e6184e92141b8947d4bd5b6f3c8df", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9e8e6184e92141b8947d4bd5b6f3c8df.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9e8e6184e92141b8947d4bd5b6f3c8df"}}, "title": "Tissue-Specific Protein Expression in Human Cells, Tissues and Organs", "authors": [{"family": "Marcus", "given": "Gry", "initials": "G"}, {"family": "Oksvold", "given": "Per", "initials": "P"}, {"family": "Pont\u00e9n", "given": "F", "initials": "F", "orcid": "0000-0003-0703-3940", "researcher": {"href": "https://publications.scilifelab.se/researcher/a8b56979a6c74891aa277fb28848b6ce.json"}}, {"family": "Uhl\u00e9n", "given": "M", "initials": "M", "orcid": "0000-0002-4858-8056", "researcher": {"href": "https://publications.scilifelab.se/researcher/ff81da3cb0cf4262873b993a1b06798c.json"}}], "type": "journal-article", "published": "2010-00-00", "journal": {"title": "JPB", "issn": "0974-276X", "issn-l": "0974-276X", "volume": "03", "issue": "10", "pages": null}, "abstract": "An important part of understanding human biology is the study of tissue-speci fi c expression both at the gene and protein level. In this study, the analysis of tissue speci fi c protein expression was performed based on tissue micro array data available on the public Human Protein Atlas database (www.proteinatlas.org). An analysis of human proteins, corresponding to approximately one third of the protein-encoding genes, was carried out in 65 human tissues and cell types. The spatial distribution and relative abundance of 6,678 human proteins, were analyzed in different cell populations from various organs and tissues in the human body using unsupervised methods, such as hierarchical clustering and principal component analysis, as well as with supervised methods (Breiman, 2001). Well-known markers, such as neuromodulin for the central nervous system, keratin 20 for gastrointestinal tract and CD45 for hematopoietic cells, were identi fi ed as tissue-speci fi c. Proteins expressed in a tissue-speci fi c manner were identi fi ed for cells in all of the investigated tissues, including the central nervous system, hematopoietic system, squamous epithelium, mesenchymal cells and cells from the gastrointestinal tract. Several proteins not yet associated with tissue-speci fi city were identi fi ed, providing starting points for further studies to explore tissue-speci fi c functions. This includes proteins with no known function, such as ZNF509 expressed in CNS and C1orf201 expressed in the gastro-intestinal tract. In general, the majority of the gene products are expressed in a ubiquitous manner and few proteins are detected exclusively in cells from a particular tissue class, as exempli fi ed by less than 1% of the analyzed proteins found only in the brain.", "doi": "10.4172/jpb.1000153", "pmid": null, "labels": {"Tissue Profiling": null}, "xrefs": [], "notes": [], "created": "2017-05-04T14:55:44.151Z", "modified": "2021-06-22T12:11:12.782Z"}]}