{"entity": "journal", "iuid": "b2142ecf878b4708974cb8d76aa4155d", "timestamp": "2026-07-11T15:08:29.680Z", "links": {"self": {"href": "https://publications.scilifelab.se/journal/BMC%20Med%20Genomics.json"}, "display": {"href": "https://publications.scilifelab.se/journal/BMC%20Med%20Genomics"}}, "title": "BMC Med Genomics", "issn": "1755-8794", "issn-l": "1755-8794", "publications_count": 11, "publications": [{"entity": "publication", "iuid": "e4d664134fa14e3f9777bf6603b31f4a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/e4d664134fa14e3f9777bf6603b31f4a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/e4d664134fa14e3f9777bf6603b31f4a"}}, "title": "Visualization using NIPTviewer support the clinical interpretation of noninvasive prenatal testing results.", "authors": [{"family": "Smeds", "given": "Patrik", "initials": "P"}, {"family": "Baranowska K\u00f6rberg", "given": "Izabella", "initials": "I"}, {"family": "Melin", "given": "Malin", "initials": "M", "orcid": "0000-0002-6589-2375", "researcher": {"href": "https://publications.scilifelab.se/researcher/190c3991975c43ec952a81df72292c9a.json"}}, {"family": "Ladenvall", "given": "Claes", "initials": "C", "orcid": "0000-0002-7501-6598", "researcher": {"href": "https://publications.scilifelab.se/researcher/4c5c362dc308476195eb55d2e588ba60.json"}}], "type": "journal article", "published": "2025-01-20", "journal": {"title": "BMC Med Genomics", "issn": "1755-8794", "volume": "18", "issue": "1", "pages": "15", "issn-l": "1755-8794"}, "abstract": "Noninvasive prenatal testing (NIPT) is increasingly used to screen for fetal chromosomal aneuploidy by analyzing cell-free DNA (cfDNA) in peripheral maternal blood. The method provides an opportunity for early detection of large genetic abnormalities without an increased risk of miscarriage due to invasive procedures. Commercial applications for use at clinical laboratories often take advantage of DNA sequencing technologies and include the bioinformatic workup of the sequence data. The interpretation of the test results and the clinical report writing, however, remains the responsibility of the diagnostic laboratory. In order to facilitate this step, we developed NIPTviewer, a web-based application to visualize and guide the interpretation of NIPT data results.\n\nNIPTviewer has a database functionality to store the NIPT results and a web interface for user interaction and visualization. The application has been implemented as part of a novel analysis pipeline for NIPT in a diagnostic laboratory at Uppsala University Hospital. The validation data set included 84 previously analyzed plasma samples with known results regarding chromosomes 13, 18, 21, X and Y. They were sequenced in six different experiments, uploaded to NIPTviewer and assigned to a clinical laboratory geneticist for interpretation. The results of all previously analyzed samples were replicated.\n\nNIPTviewer facilitates NIPT results interpretation and has been implemented as part of a NIPT analysis routine that was accredited by the national accreditation body for Sweden (Swedac).", "doi": "10.1186/s12920-025-02086-8", "pmid": "39833870", "labels": {"Clinical Genomics Uppsala": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pmc", "key": "PMC11748546"}, {"db": "pii", "key": "10.1186/s12920-025-02086-8"}], "notes": [], "created": "2025-03-19T04:59:24.616Z", "modified": "2025-03-24T08:23:37.812Z"}, {"entity": "publication", "iuid": "d0290e65d9f045e798c9c885b9c72cbd", "links": {"self": {"href": "https://publications.scilifelab.se/publication/d0290e65d9f045e798c9c885b9c72cbd.json"}, "display": {"href": "https://publications.scilifelab.se/publication/d0290e65d9f045e798c9c885b9c72cbd"}}, "title": "Detection of leukemia gene fusions by targeted RNA-sequencing in routine diagnostics.", "authors": [{"family": "Engvall", "given": "Marie", "initials": "M", "orcid": "0000-0002-7394-9191", "researcher": {"href": "https://publications.scilifelab.se/researcher/0be7a9a5a518448ba7afb6f7a2cb3ca1.json"}}, {"family": "Cahill", "given": "Nicola", "initials": "N"}, {"family": "Jonsson", "given": "Britt-Inger", "initials": "BI"}, {"family": "H\u00f6glund", "given": "Martin", "initials": "M"}, {"family": "Hallb\u00f6\u00f6k", "given": "Helene", "initials": "H"}, {"family": "Cavelier", "given": "Lucia", "initials": "L", "orcid": "0009-0003-8195-370X", "researcher": {"href": "https://publications.scilifelab.se/researcher/f01226edb140436da0c9d166c1f5fe51.json"}}], "type": "journal article", "published": "2020-07-29", "journal": {"title": "BMC Med Genomics", "issn": "1755-8794", "volume": "13", "issue": "1", "pages": "106", "issn-l": "1755-8794"}, "abstract": "We have evaluated an NGS-based method to detect recurrent gene fusions of diagnostic and prognostic importance in hematological malignancies. Our goal was to achieve a highly specific assay with a simple workflow, short turnaround time and low cost.\n\nThe assay uses a commercially available anchored multiplex PCR panel for target enrichment and library preparation, followed by sequencing using a MiSeq instrument. The panel includes all recurrent gene fusions in AML and ALL and is designed to detect gene-specific fusions without prior knowledge of the partner sequence or specific break points. Diagnostic RNA samples from 27 cases with hematological malignancies encompassing 23 different transcript variants were analyzed. In addition, 12 cases from a validation cohort were assessed.\n\nAll known fusion transcripts were identified with a high degree of confidence, with a large number of reads covering the breakpoints. Importantly, we could identify gene fusions where conventional methods had failed due to cryptic rearrangements or rare fusion partners. The newly-identified fusion partners were verified by RT-PCR and transcript-specific qPCR was designed for patient-specific follow-up. In addition, 12 cases were correctly assessed in a blind test, without prior knowledge of molecular cytogenetics or diagnosis.\n\nIn summary, our results demonstrate that targeted RNA sequencing using anchored multiplex PCR can be implemented in a clinical laboratory for the detection of recurrent and rare gene fusions in hematological diagnostic samples.", "doi": "10.1186/s12920-020-00739-4", "pmid": "32727569", "labels": {"Clinical Genomics Uppsala": "Technology development", "Clinical Genomics": "Technology development"}, "xrefs": [{"db": "pii", "key": "10.1186/s12920-020-00739-4"}, {"db": "pmc", "key": "PMC7388219"}], "notes": [], "created": "2020-11-06T13:03:04.566Z", "modified": "2021-11-10T12:48:54.750Z"}, {"entity": "publication", "iuid": "3f9436baa42849ed95e219bbf949416e", "links": {"self": {"href": "https://publications.scilifelab.se/publication/3f9436baa42849ed95e219bbf949416e.json"}, "display": {"href": "https://publications.scilifelab.se/publication/3f9436baa42849ed95e219bbf949416e"}}, "title": "Whole genome sequencing of familial isolated oesophagus atresia uncover shared structural variants.", "authors": [{"family": "Klar", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4185-7409", "researcher": {"href": "https://publications.scilifelab.se/researcher/3310cb2ab70f43d78cc7cd7e36ac8f83.json"}}, {"family": "Engstrand-Lilja", "given": "Helene", "initials": "H"}, {"family": "Maqbool", "given": "Khurram", "initials": "K"}, {"family": "Mattisson", "given": "Jonas", "initials": "J"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}, {"family": "Dahl", "given": "Niklas", "initials": "N"}], "type": "journal article", "published": "2020-06-26", "journal": {"title": "BMC Med Genomics", "issn": "1755-8794", "volume": "13", "issue": "1", "pages": "85", "issn-l": "1755-8794"}, "abstract": "Oesophageal atresia (OA) is a life-threatening developmental defect characterized by a lost continuity between the upper and lower oesophagus. The most common form is a distal connection between the trachea and the oesophagus, i.e. a tracheoesophageal fistula (TEF). The condition may be part of a syndrome or occurs as an isolated feature. The recurrence risk in affected families is increased compared to the population-based incidence suggesting contributing genetic factors.\n\nTo gain insight into gene variants and genes associated with isolated OA we conducted whole genome sequencing on samples from three families with recurrent cases affected by congenital and isolated TEF.\n\nWe identified a combination of single nucleotide variants (SNVs), splice site variants (SSV) and structural variants (SV) annotated to altogether 100 coding genes in the six affected individuals.\n\nThis study highlights rare SVs among candidate gene variants in our individuals with OA and provides a gene framework for further investigations of genetic factors behind this malformation.", "doi": "10.1186/s12920-020-00737-6", "pmid": "32586322", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12920-020-00737-6"}, {"db": "pmc", "key": "PMC7318369"}], "notes": [], "created": "2020-07-03T05:25:29.915Z", "modified": "2024-01-16T13:48:42.333Z"}, {"entity": "publication", "iuid": "c0c6515cc557485e8d3397ecadcfd64b", "links": {"self": {"href": "https://publications.scilifelab.se/publication/c0c6515cc557485e8d3397ecadcfd64b.json"}, "display": {"href": "https://publications.scilifelab.se/publication/c0c6515cc557485e8d3397ecadcfd64b"}}, "title": "Linkage and exome analysis implicate multiple genes in non-syndromic intellectual disability in a large Swedish family.", "authors": [{"family": "Lindholm Carlstr\u00f6m", "given": "Eva", "initials": "E", "orcid": "0000-0001-8055-7826", "researcher": {"href": "https://publications.scilifelab.se/researcher/c433744d926b450097e71784b8bcc27c.json"}}, {"family": "Halvardson", "given": "Jonatan", "initials": "J"}, {"family": "Etemadikhah", "given": "Mitra", "initials": "M"}, {"family": "Wetterberg", "given": "Lennart", "initials": "L"}, {"family": "Gustavson", "given": "Karl-Henrik", "initials": "KH"}, {"family": "Feuk", "given": "Lars", "initials": "L", "orcid": "0000-0003-2355-2919", "researcher": {"href": "https://publications.scilifelab.se/researcher/3eb2f826b3554d4b9971bf0766b275c4.json"}}], "type": "journal article", "published": "2019-11-06", "journal": {"volume": "12", "issn": "1755-8794", "issue": "1", "pages": "156", "title": "BMC Med Genomics", "issn-l": "1755-8794"}, "abstract": "Non-syndromic intellectual disability is genetically heterogeneous with dominant, recessive and complex forms of inheritance. We have performed detailed genetic studies in a large multi-generational Swedish family, including several members diagnosed with non-syndromic intellectual disability. Linkage analysis was performed on 22 family members, nine affected with mild to moderate intellectual disability and 13 unaffected family members.\n\nFamily members were analyzed with Affymetrix Genome-Wide Human SNP Array 6.0 and the genetic data was used to detect copy number variation and to perform genome wide linkage analysis with the SNP High Throughput Linkage analysis system and the Merlin software. For the exome sequencing, the samples were prepared using the Sure Select Human All Exon Kit (Agilent Technologies, Santa Clara, CA, USA) and sequenced using the Ion Proton\u2122 System. Validation of identified variants was performed with Sanger sequencing.\n\nThe linkage analysis results indicate that intellectual disability in this family is genetically heterogeneous, with suggestive linkage found on chromosomes 1q31-q41, 4q32-q35, 6p25 and 14q24-q31 (LOD scores of 2.4, simulated p-value of 0.000003 and a simulated genome-wide p-value of 0.06). Exome sequencing was then performed in 14 family members and 7 unrelated individuals from the same region. The analysis of coding variation revealed a pathogenic and candidate variants in different branches of the family. In three patients we find a known homozygous pathogenic mutation in the Homo sapiens solute carrier family 17 member 5 (SLC17A5), causing Salla disease. We also identify a deletion overlapping KDM3B and a duplication overlapping MAP3K4 and AGPAT4, both overlapping variants previously reported in developmental disorders.\n\nDNA samples from the large family analyzed in this study were initially collected based on a hypothesis that affected members shared a major genetic risk factor. Our results show that a complex phenotype such as mild intellectual disability in large families from genetically isolated populations may show considerable genetic heterogeneity.", "doi": "10.1186/s12920-019-0606-4", "pmid": "31694657", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (Uppsala Genome Center)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12920-019-0606-4"}, {"db": "pmc", "key": "PMC6833288"}], "notes": [], "created": "2019-11-25T14:38:27.833Z", "modified": "2024-01-16T13:48:43.569Z"}, {"entity": "publication", "iuid": "89ba79c4994045089043812f31525e65", "links": {"self": {"href": "https://publications.scilifelab.se/publication/89ba79c4994045089043812f31525e65.json"}, "display": {"href": "https://publications.scilifelab.se/publication/89ba79c4994045089043812f31525e65"}}, "title": "DNA methylation patterns associated with oxidative stress in an ageing population.", "authors": [{"family": "Hedman", "given": "\u00c5sa K", "initials": "\u00c5K"}, {"family": "Zilmer", "given": "Mihkel", "initials": "M"}, {"family": "Sundstr\u00f6m", "given": "Johan", "initials": "J"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}], "type": "journal article", "published": "2016-11-25", "journal": {"volume": "9", "issn": "1755-8794", "issue": "1", "pages": "72", "title": "BMC Med Genomics", "issn-l": "1755-8794"}, "abstract": "Oxidative stress has been related to type 2 diabetes (T2D) and cardiovascular disease (CVD), the leading global cause of death. Contributions of environmental factors such as oxidative stress on complex traits and disease may be partly mediated through changes in epigenetic marks (e.g. DNA methylation). Studies relating differential methylation with intermediate phenotypes and disease endpoints may be useful in identifying additional candidate genes and mechanisms involved in disease.\n\nTo investigate the role of epigenetic variation in oxidative stress marker levels and subsequent development of CVD and T2D, we performed analyses of genome-wide DNA methylation in blood, ten markers of oxidative stress (total glutathione [TGSH], reduced glutathione [GSH], oxidised glutathione [GSSG], GSSG to GSH ratio, homocysteine [HCY], oxidised low-density lipoprotein (oxLDL), antibodies against oxLDL [OLAB], conjugated dienes [CD], baseline conjugated dienes [BCD]-LDL and total antioxidant capacity [TAOC]) and incident disease in up to 966 age-matched individuals.\n\nIn total, we found 66 cytosine-guanine (CpG) sites associated with one or more oxidative stress markers (false discovery rate [FDR] <0.05). These sites were enriched in regulatory regions of the genome. Genes annotated to CpG sites showed enrichment in annotation clusters relating to phospho-metabolism and proteins with pleckstrin domains. We investigated the contribution of oxidative stress-associated CpGs to development of cardiometabolic disease. Methylation variation at CpGs in the 3'-UTR of HIST1H4D (cg08170869; histone cluster 1, H4d) and in the body of DVL1 (cg03465880; dishevelled-1) were associated with incident T2D events during 10\u00a0years of follow-up (all permutation p-values <0.01), indicating a role of epigenetic regulation in oxidative stress processes leading to development or progression of diabetes. Methylation QTL (meQTL) analysis showed significant associations with genetic sequence variants in cis at 28 (42%) of oxidative stress phenotype-associated sites (FDR\u2009<\u20090.05). Integrating cis-meQTLs with genotype-phenotype associations indicated that genetic effects on oxidative stress phenotype at one locus (cg07547695; BCL2L11) may be mediated through DNA methylation.\n\nIn conclusion, we report novel associations of DNA methylation with oxidative stress, some of which also show evidence of a relation with T2D incidence.", "doi": "10.1186/s12920-016-0235-0", "pmid": "27884142", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service", "Bioinformatics Support for Computational Resources": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12920-016-0235-0"}, {"db": "pmc", "key": "PMC5123374"}], "notes": [], "created": "2017-05-03T13:00:22.231Z", "modified": "2024-01-16T13:48:48.928Z"}, {"entity": "publication", "iuid": "6ea2661e02474895adfcbed25184c524", "links": {"self": {"href": "https://publications.scilifelab.se/publication/6ea2661e02474895adfcbed25184c524.json"}, "display": {"href": "https://publications.scilifelab.se/publication/6ea2661e02474895adfcbed25184c524"}}, "title": "Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells.", "authors": [{"family": "Morin", "given": "Andr\u00e9anne", "initials": "A"}, {"family": "Kwan", "given": "Tony", "initials": "T"}, {"family": "Ge", "given": "Bing", "initials": "B"}, {"family": "Letourneau", "given": "Louis", "initials": "L"}, {"family": "Ban", "given": "Maria", "initials": "M"}, {"family": "Tandre", "given": "Karolina", "initials": "K"}, {"family": "Caron", "given": "Maxime", "initials": "M"}, {"family": "Sandling", "given": "Johanna K", "initials": "JK"}, {"family": "Carlsson", "given": "Jonas", "initials": "J"}, {"family": "Bourque", "given": "Guillaume", "initials": "G"}, {"family": "Laprise", "given": "Catherine", "initials": "C"}, {"family": "Montpetit", "given": "Alexandre", "initials": "A"}, {"family": "Syvanen", "given": "Ann-Christine", "initials": "AC", "orcid": "0000-0002-9681-9146", "researcher": {"href": "https://publications.scilifelab.se/researcher/f7012e35025543379380cb90efd71243.json"}}, {"family": "Ronnblom", "given": "Lars", "initials": "L"}, {"family": "Sawcer", "given": "Stephen J", "initials": "SJ"}, {"family": "Lathrop", "given": "Mark G", "initials": "MG"}, {"family": "Pastinen", "given": "Tomi", "initials": "T"}], "type": "journal article", "published": "2016-09-13", "journal": {"volume": "9", "issn": "1755-8794", "issue": "1", "pages": "59", "title": "BMC Med Genomics", "issn-l": "1755-8794"}, "abstract": "The observation that the genetic variants identified in genome-wide association studies (GWAS) frequently lie in non-coding regions of the genome that contain cis-regulatory elements suggests that altered gene expression underlies the development of many complex traits. In order to efficiently make a comprehensive assessment of the impact of non-coding genetic variation in immune related diseases we emulated the whole-exome sequencing paradigm and developed a custom capture panel for the known DNase I hypersensitive site (DHS) in immune cells - \"Immunoseq\".\n\nWe performed Immunoseq in 30 healthy individuals where we had existing transcriptome data from T cells. We identified a large number of novel non-coding variants in these samples. Relying on allele specific expression measurements, we also showed that our selected capture regions are enriched for functional variants that have an impact on differential allelic gene expression. The results from a replication set with 180 samples confirmed our observations.\n\nWe show that Immunoseq is a powerful approach to detect novel rare variants in regulatory regions. We also demonstrate that these novel variants have a potential functional role in immune cells.", "doi": "10.1186/s12920-016-0220-7", "pmid": "27624058", "labels": {"National Genomics Infrastructure": "Collaborative", "NGI Uppsala (SNP&SEQ Technology Platform)": "Collaborative"}, "xrefs": [{"db": "pii", "key": "10.1186/s12920-016-0220-7"}, {"db": "pmc", "key": "PMC5022205"}], "notes": [], "created": "2017-05-03T13:01:56.634Z", "modified": "2021-07-07T15:11:02.504Z"}, {"entity": "publication", "iuid": "936727a5c88a4dd6a89143995a956c1a", "links": {"self": {"href": "https://publications.scilifelab.se/publication/936727a5c88a4dd6a89143995a956c1a.json"}, "display": {"href": "https://publications.scilifelab.se/publication/936727a5c88a4dd6a89143995a956c1a"}}, "title": "Longitudinal genome-wide methylation study of Roux-en-Y gastric bypass patients reveals novel CpG sites associated with essential hypertension.", "authors": [{"family": "Bostr\u00f6m", "given": "Adrian E", "initials": "AE"}, {"family": "Mwinyi", "given": "Jessica", "initials": "J"}, {"family": "Voisin", "given": "Sarah", "initials": "S"}, {"family": "Wu", "given": "Wenting", "initials": "W"}, {"family": "Schultes", "given": "Bernd", "initials": "B"}, {"family": "Zhang", "given": "Kang", "initials": "K"}, {"family": "Schi\u00f6th", "given": "Helgi B", "initials": "HB"}], "type": "journal article", "published": "2016-04-22", "journal": {"volume": "9", "issn": "1755-8794", "issue": null, "pages": "20", "title": "BMC Med Genomics", "issn-l": "1755-8794"}, "abstract": "Essential hypertension is a significant risk factor for cardiovascular diseases. Emerging research suggests a role of DNA methylation in blood pressure physiology. We aimed to investigate epigenetic associations of promoter related CpG sites to essential hypertension in a genome-wide methylation approach.\n\nThe genome-wide methylation pattern in whole blood was measured in 11 obese patients before and six months after Roux-en-Y gastric bypass surgery using the Illumina 450 k beadchip. CpG sites located within 1500 bp of the transcriptional start site of adjacent genes were included in our study, resulting in 124 199 probes investigated in the subsequent analysis. Percent changes in methylation states and SBP measured before and six months after surgery were calculated. These parameters were correlated to each other using the Spearman's rank correlation method (Edgeworth series approximation). To further investigate the detected relationship between candidate CpG sites and systolic blood pressure levels, binary logistic regression analyses were performed in a larger and independent cohort of 539 individuals aged 19-101 years to elucidate a relationship between EH and the methylation state in candidate CpG sites.\n\nWe identified 24 promoter associated CpG sites that correlated with change in SBP after RYGB surgery (p < 10(-16)). Two of these CpG loci (cg00875989, cg09134341) were significantly hypomethylated in dependency of EH (p < 10(-03)). These results were independent of age, BMI, ethnicity and sex.\n\nThe identification of these novel CpG sites may contribute to a further understanding of the epigenetic regulatory mechanisms underlying the development of essential hypertension.", "doi": "10.1186/s12920-016-0180-y", "pmid": "27105587", "labels": {"National Genomics Infrastructure": "Service", "NGI Uppsala (SNP&SEQ Technology Platform)": "Service"}, "xrefs": [{"db": "pii", "key": "10.1186/s12920-016-0180-y"}, {"db": "pmc", "key": "PMC4841955"}], "notes": [], "created": "2017-05-03T13:01:56.338Z", "modified": "2020-01-21T13:56:03.780Z"}, {"entity": "publication", "iuid": "5777fcc31a434305bb0a6ce50470d2fa", "links": {"self": {"href": "https://publications.scilifelab.se/publication/5777fcc31a434305bb0a6ce50470d2fa.json"}, "display": {"href": "https://publications.scilifelab.se/publication/5777fcc31a434305bb0a6ce50470d2fa"}}, "title": "Integrated molecular portrait of non-small cell lung cancers.", "authors": [{"family": "Lazar", "given": "Vladimir", "initials": "V"}, {"family": "Suo", "given": "Chen", "initials": "C"}, {"family": "Orear", "given": "Cedric", "initials": "C"}, {"family": "van den Oord", "given": "Joost", "initials": "J"}, {"family": "Balogh", "given": "Zsofia", "initials": "Z"}, {"family": "Guegan", "given": "Justine", "initials": "J"}, {"family": "Job", "given": "Bastien", "initials": "B"}, {"family": "Meurice", "given": "Guillaume", "initials": "G"}, {"family": "Ripoche", "given": "Hugues", "initials": "H"}, {"family": "Calza", "given": "Stefano", "initials": "S"}, {"family": "Hasmats", "given": "Johanna", "initials": "J"}, {"family": "Lundeberg", "given": "Joakim", "initials": "J", "orcid": "0000-0003-4313-1601", "researcher": {"href": "https://publications.scilifelab.se/researcher/4a4e6ca0f29b4ead8569e2729481c3e0.json"}}, {"family": "Lacroix", "given": "Ludovic", "initials": "L"}, {"family": "Vielh", "given": "Philippe", "initials": "P"}, {"family": "Dufour", "given": "Fabienne", "initials": "F"}, {"family": "Lehti\u00f6", "given": "Janne", "initials": "J", "orcid": "0000-0002-8100-9562", "researcher": {"href": "https://publications.scilifelab.se/researcher/8406a97bac744a59b1bc951978994581.json"}}, {"family": "Napieralski", "given": "Rudolf", "initials": "R"}, {"family": "Eggermont", "given": "Alexander", "initials": "A"}, {"family": "Schmitt", "given": "Manfred", "initials": "M"}, {"family": "Cadranel", "given": "Jacques", "initials": "J"}, {"family": "Besse", "given": "Benjamin", "initials": "B"}, {"family": "Girard", "given": "Philippe", "initials": "P"}, {"family": "Blackhall", "given": "Fiona", "initials": "F"}, {"family": "Validire", "given": "Pierre", "initials": "P"}, {"family": "Soria", "given": "Jean-Charles", "initials": "JC"}, {"family": "Dessen", "given": "Philippe", "initials": "P"}, {"family": "Hansson", "given": "Johan", "initials": "J"}, {"family": "Pawitan", "given": "Yudi", "initials": "Y"}], "type": "journal article", "published": "2013-12-03", "journal": {"volume": "6", "issn": "1755-8794", "issue": null, "pages": "53", "title": "BMC Med Genomics", "issn-l": "1755-8794"}, "abstract": "Non-small cell lung cancer (NSCLC), a leading cause of cancer deaths, represents a heterogeneous group of neoplasms, mostly comprising squamous cell carcinoma (SCC), adenocarcinoma (AC) and large-cell carcinoma (LCC). The objectives of this study were to utilize integrated genomic data including copy-number alteration, mRNA, microRNA expression and candidate-gene full sequencing data to characterize the molecular distinctions between AC and SCC.\n\nComparative genomic hybridization followed by mutational analysis, gene expression and miRNA microarray profiling were performed on 123 paired tumor and non-tumor tissue samples from patients with NSCLC.\n\nAt DNA, mRNA and miRNA levels we could identify molecular markers that discriminated significantly between the various histopathological entities of NSCLC. We identified 34 genomic clusters using aCGH data; several genes exhibited a different profile of aberrations between AC and SCC, including PIK3CA, SOX2, THPO, TP63, PDGFB genes. Gene expression profiling analysis identified SPP1, CTHRC1 and GREM1 as potential biomarkers for early diagnosis of the cancer, and SPINK1 and BMP7 to distinguish between AC and SCC in small biopsies or in blood samples. Using integrated genomics approach we found in recurrently altered regions a list of three potential driver genes, MRPS22, NDRG1 and RNF7, which were consistently over-expressed in amplified regions, had wide-spread correlation with an average of ~800 genes throughout the genome and highly associated with histological types. Using a network enrichment analysis, the targets of these potential drivers were seen to be involved in DNA replication, cell cycle, mismatch repair, p53 signalling pathway and other lung cancer related signalling pathways, and many immunological pathways. Furthermore, we also identified one potential driver miRNA hsa-miR-944.\n\nIntegrated molecular characterization of AC and SCC helped identify clinically relevant markers and potential drivers, which are recurrent and stable changes at DNA level that have functional implications at RNA level and have strong association with histological subtypes.", "doi": "10.1186/1755-8794-6-53", "pmid": "24299561", "labels": {"National Genomics Infrastructure": null, "NGI Stockholm (Genomics Applications)": null, "NGI Stockholm (Genomics Production)": null}, "xrefs": [{"db": "pii", "key": "1755-8794-6-53"}, {"db": "pmc", "key": "PMC4222074"}], "notes": [], "created": "2017-05-04T14:57:50.305Z", "modified": "2021-07-08T13:26:08.184Z"}, {"entity": "publication", "iuid": "f61ae0b4ae3247e08413933bcabfd54c", "links": {"self": {"href": "https://publications.scilifelab.se/publication/f61ae0b4ae3247e08413933bcabfd54c.json"}, "display": {"href": "https://publications.scilifelab.se/publication/f61ae0b4ae3247e08413933bcabfd54c"}}, "title": "ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer.", "authors": [{"family": "Bysani", "given": "Madhusudhan", "initials": "M"}, {"family": "Wallerman", "given": "Ola", "initials": "O"}, {"family": "Bornel\u00f6v", "given": "Susanne", "initials": "S"}, {"family": "Zatloukal", "given": "Kurt", "initials": "K"}, {"family": "Komorowski", "given": "Jan", "initials": "J"}, {"family": "Wadelius", "given": "Claes", "initials": "C"}], "type": "journal article", "published": "2013-11-08", "journal": {"volume": "6", "issn": "1755-8794", "issue": null, "pages": "50", "title": "BMC Med Genomics", "issn-l": "1755-8794"}, "abstract": "Steatohepatitis occurs in alcoholic liver disease and may progress to liver cirrhosis and hepatocellular carcinoma. Its molecular pathogenesis is to a large degree unknown. Histone modifications play a key role in transcriptional regulations as marks for silencing and activation of gene expression and as marks for functional elements. Many transcription factors (TFs) are crucial for the control of the genes involved in metabolism, and abnormality in their function may lead to disease.\n\nWe performed ChIP-seq of the histone modifications H3K4me1, H3K4me3 and H3K27ac and a candidate transcription factor (USF1) in liver tissue from patients with steatohepatitis and normal livers and correlated results to mRNA-expression and genotypes.\n\nWe found several regions that are differentially enriched for histone modifications between disease and normal tissue, and qRT-PCR results indicated that the expression of the tested genes strongly correlated with differential enrichment of histone modifications but is independent of USF1 enrichment. By gene ontology analysis of differentially modified genes we found many disease associated genes, some of which had previously been implicated in the etiology of steatohepatitis. Importantly, the genes associated to the strongest histone peaks in the patient were over-represented in cancer specific pathways suggesting that the tissue was on a path to develop to cancer, a common complication to the disease. We also found several novel SNPs and GWAS catalogue SNPs that are candidates to be functional and therefore needs further study.\n\nIn summary we find that analysis of chromatin features in tissue samples provides insight into disease mechanisms.", "doi": "10.1186/1755-8794-6-50", "pmid": "24206787", "labels": {"National Genomics Infrastructure": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1755-8794-6-50"}, {"db": "pmc", "key": "PMC3831757"}, {"db": "SRA", "key": "SRA066400"}], "notes": [], "created": "2017-05-04T15:01:15.314Z", "modified": "2020-01-21T13:56:06.351Z"}, {"entity": "publication", "iuid": "21a96555ec1b4b9faeb9d22a4c6c6c25", "links": {"self": {"href": "https://publications.scilifelab.se/publication/21a96555ec1b4b9faeb9d22a4c6c6c25.json"}, "display": {"href": "https://publications.scilifelab.se/publication/21a96555ec1b4b9faeb9d22a4c6c6c25"}}, "title": "Transcriptome signatures in Helicobacter pylori-infected mucosa identifies acidic mammalian chitinase loss as a corpus atrophy marker.", "authors": [{"family": "Nookaew", "given": "Intawat", "initials": "I"}, {"family": "Thorell", "given": "Kaisa", "initials": "K"}, {"family": "Worah", "given": "Kuntal", "initials": "K"}, {"family": "Wang", "given": "Shugui", "initials": "S"}, {"family": "Hibberd", "given": "Martin Lloyd", "initials": "ML"}, {"family": "Sj\u00f6vall", "given": "Henrik", "initials": "H"}, {"family": "Pettersson", "given": "Sven", "initials": "S"}, {"family": "Nielsen", "given": "Jens", "initials": "J", "orcid": "0000-0002-9955-6003", "researcher": {"href": "https://publications.scilifelab.se/researcher/7a596e289be4438a8a2653b1f25fea8b.json"}}, {"family": "Lundin", "given": "Samuel B", "initials": "SB"}], "type": "journal article", "published": "2013-10-11", "journal": {"volume": "6", "issn": "1755-8794", "issue": null, "pages": "41", "title": "BMC Med Genomics", "issn-l": "1755-8794"}, "abstract": "The majority of gastric cancer cases are believed to be caused by chronic infection with the bacterium Helicobacter pylori, and atrophic corpus gastritis is a predisposing condition to gastric cancer development. We aimed to increase understanding of the molecular details of atrophy by performing a global transcriptome analysis of stomach tissue.\n\nBiopsies from patients with different stages of H. pylori infection were taken from both the antrum and corpus mucosa and analyzed on microarrays. The stages included patients without current H. pylori infection, H. pylori-infected without corpus atrophy and patients with current or past H. pylori-infection with corpus-predominant atrophic gastritis.\n\nUsing clustering and integrated analysis, we found firm evidence for antralization of the corpus mucosa of atrophy patients. This antralization harbored gain of gastrin expression, as well as loss of expression of corpus-related genes, such as genes associated with acid production, energy metabolism and blood clotting. The analyses provided detailed molecular evidence for simultaneous intestinal metaplasia (IM) and spasmolytic polypeptide expressing metaplasia (SPEM) in atrophic corpus tissue. Finally, acidic mammalian chitinase, a chitin-degrading enzyme produced by chief cells, was shown to be strongly down-regulated in corpus atrophy.\n\nTranscriptome analysis revealed several gene groups which are related to development of corpus atrophy, some of which were increased also in H. pylori-infected non-atrophic patients. Furthermore, loss of acidic chitinase expression is a promising marker for corpus atrophy.", "doi": "10.1186/1755-8794-6-41", "pmid": "24119614", "labels": {"Bioinformatics Support, Infrastructure and Training": null, "Bioinformatics Support and Infrastructure": null, "Bioinformatics (NBIS)": ""}, "xrefs": [{"db": "pii", "key": "1755-8794-6-41"}, {"db": "pmc", "key": "PMC4015281"}], "notes": [], "created": "2017-05-04T14:56:21.543Z", "modified": "2021-07-05T13:05:37.549Z"}, {"entity": "publication", "iuid": "9cb0ff13b56a40bb90599a1156b7c3c8", "links": {"self": {"href": "https://publications.scilifelab.se/publication/9cb0ff13b56a40bb90599a1156b7c3c8.json"}, "display": {"href": "https://publications.scilifelab.se/publication/9cb0ff13b56a40bb90599a1156b7c3c8"}}, "title": "Genome wide association study identifies KCNMA1 contributing to human obesity.", "authors": [{"family": "Jiao", "given": "Hong", "initials": "H"}, {"family": "Arner", "given": "Peter", "initials": "P"}, {"family": "Hoffstedt", "given": "Johan", "initials": "J"}, {"family": "Brodin", "given": "David", "initials": "D"}, {"family": "Dubern", "given": "Beatrice", "initials": "B"}, {"family": "Czernichow", "given": "S\u00e9bastien", "initials": "S"}, {"family": "van't Hooft", "given": "Ferdinand", "initials": "F"}, {"family": "Axelsson", "given": "Tomas", "initials": "T"}, {"family": "Pedersen", "given": "Oluf", "initials": "O"}, {"family": "Hansen", "given": "Torben", "initials": "T"}, {"family": "S\u00f8rensen", "given": "Thorkild I A", "initials": "TI"}, {"family": "Hebebrand", "given": "Johannes", "initials": "J"}, {"family": "Kere", "given": "Juha", "initials": "J"}, {"family": "Dahlman-Wright", "given": "Karin", "initials": "K"}, {"family": "Hamsten", "given": "Anders", "initials": "A"}, {"family": "Clement", "given": "Karine", "initials": "K"}, {"family": "Dahlman", "given": "Ingrid", "initials": "I"}], "type": "journal article", "published": "2011-06-28", "journal": {"volume": "4", "issn": "1755-8794", "issue": null, "pages": "51", "title": "BMC Med Genomics", "issn-l": "1755-8794"}, "abstract": "Recent genome-wide association (GWA) analyses have identified common single nucleotide polymorphisms (SNPs) that are associated with obesity. However, the reported genetic variation in obesity explains only a minor fraction of the total genetic variation expected to be present in the population. Thus many genetic variants controlling obesity remain to be identified. The aim of this study was to use GWA followed by multiple stepwise validations to identify additional genes associated with obesity.\n\nWe performed a GWA analysis in 164 morbidly obese subjects (BMI:body mass index>40 kg/m2) and 163 Swedish subjects (>45 years) who had always been lean. The 700 SNPs displaying the strongest association with obesity in the GWA were analyzed in a second cohort comprising 460 morbidly obese subjects and 247 consistently lean Swedish adults. 23 SNPs remained significantly associated with obesity (nominal P<0.05) and were in a step-wise manner followed up in five additional cohorts from Sweden, France, and Germany together comprising 4214 obese and 5417 lean or population-based control individuals. Three samples, n=4133, were used to investigate the population-based associations with BMI. Gene expression in abdominal subcutaneous adipose tissue in relation to obesity was investigated for14 adults.\n\nPotassium channel, calcium activated, large conductance, subfamily M, alpha member (KCNMA1) rs2116830*G and BDNF rs988712*G were associated with obesity in five of six investigated case-control cohorts. In meta-analysis of 4838 obese and 5827 control subjects we obtained genome-wide significant allelic association with obesity for KCNMA1 rs2116830*G with P=2.82\u00d710(-10) and an odds ratio (OR) based on cases vs controls of 1.26 [95% C.I. 1.12-1.41] and for BDNF rs988712*G with P=5.2\u00d710(-17) and an OR of 1.36 [95% C.I. 1.20-1.55]. KCNMA1 rs2116830*G was not associated with BMI in the population-based samples. Adipose tissue (P=0.0001) and fat cell (P=0.04) expression of KCNMA1 was increased in obesity.\n\nWe have identified KCNMA1 as a new susceptibility locus for obesity, and confirmed the association of the BDNF locus at the genome-wide significant level.", "doi": "10.1186/1755-8794-4-51", "pmid": "21708048", "labels": {"National Genomics Infrastructure": null, "Mutation Analysis Facility (MAF)": null, "Bioinformatics and Expression Analysis (BEA)": null, "NGI Uppsala (SNP&SEQ Technology Platform)": null}, "xrefs": [{"db": "pii", "key": "1755-8794-4-51"}, {"db": "pmc", "key": "PMC3148553"}], "notes": [], "created": "2017-05-04T15:00:41.084Z", "modified": "2020-01-21T13:56:04.059Z"}], "created": "2017-05-09T09:12:34.493Z", "modified": "2020-11-27T13:14:06.888Z"}