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"initials": "RA"}, {"family": "Grallert", "given": "Harald", "initials": "H"}, {"family": "Glaser", "given": "Benjamin", "initials": "B"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ"}, {"family": "Walker", "given": "Mark", "initials": "M"}, {"family": "Banks", "given": "Eric", "initials": "E"}, {"family": "Gieger", "given": "Christian", "initials": "C"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Im", "given": "Hae Kyung", "initials": "HK", "orcid": "0000-0003-0333-5685", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/3ed5a3f93f014438a1748b61168b0d06.json"}}, {"family": "Illig", "given": "Thomas", "initials": "T"}, {"family": "Franks", "given": "Paul W", "initials": "PW"}, {"family": "Buck", "given": "Gemma", "initials": "G"}, {"family": "Trakalo", "given": "Joseph", "initials": "J"}, {"family": "Buck", "given": "David", "initials": "D"}, {"family": "Prokopenko", "given": "Inga", "initials": "I", "orcid": "0000-0003-1624-7457", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aa86d82a5dc54f53b4ff6e622b7f07fb.json"}}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Lind", "given": "Lars", "initials": "L"}, {"family": "Farjoun", "given": "Yossi", "initials": "Y"}, {"family": "Owen", "given": "Katharine R", "initials": "KR"}, {"family": "Gloyn", "given": "Anna L", "initials": "AL", "orcid": "0000-0003-1205-1844", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/dfab778605a4478c973fbb49a8884ce3.json"}}, {"family": "Strauch", "given": "Konstantin", "initials": "K"}, {"family": "Tuomi", "given": "Tiinamaija", "initials": "T"}, {"family": "Kooner", "given": "Jaspal Singh", "initials": "JS"}, {"family": "Lee", "given": "Jong-Young", "initials": "JY", "orcid": "0000-0002-0092-9958", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7b57bb9c325747ea9ca3221c5fdad13f.json"}}, {"family": "Park", "given": "Taesung", "initials": "T"}, {"family": "Donnelly", "given": "Peter", "initials": "P"}, {"family": "Morris", "given": "Andrew D", "initials": "AD"}, {"family": "Hattersley", "given": "Andrew T", "initials": "AT"}, {"family": "Bowden", "given": "Donald W", "initials": "DW"}, {"family": "Collins", "given": "Francis S", "initials": "FS"}, {"family": "Atzmon", "given": "Gil", "initials": "G"}, {"family": "Chambers", "given": "John C", "initials": "JC"}, {"family": "Spector", "given": "Timothy D", "initials": "TD"}, {"family": "Laakso", "given": "Markku", "initials": "M"}, {"family": "Strom", "given": "Tim M", "initials": "TM"}, {"family": "Bell", "given": "Graeme I", "initials": "GI"}, {"family": "Blangero", "given": "John", "initials": "J"}, {"family": "Duggirala", "given": "Ravindranath", "initials": "R"}, {"family": "Tai", "given": "E Shyong", "initials": "ES"}, {"family": "McVean", "given": "Gilean", "initials": "G"}, {"family": "Hanis", "given": "Craig L", "initials": "CL"}, {"family": "Wilson", "given": "James G", "initials": "JG"}, {"family": "Seielstad", "given": "Mark", "initials": "M", "orcid": "0000-0001-5783-1401", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/1f7e91a1ee9e4ef78638e1d53d9efdba.json"}}, {"family": "Frayling", "given": "Timothy M", "initials": "TM"}, {"family": "Meigs", "given": "James B", "initials": "JB"}, {"family": "Cox", "given": "Nancy J", "initials": "NJ"}, {"family": "Sladek", "given": "Rob", "initials": "R"}, {"family": "Lander", "given": "Eric S", "initials": "ES"}, {"family": "Gabriel", "given": "Stacey", "initials": "S"}, {"family": "Mohlke", "given": "Karen L", "initials": "KL", "orcid": "0000-0001-6721-153X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/fac0e041c56347fe98cef9ae8f004b67.json"}}, {"family": "Meitinger", "given": "Thomas", "initials": "T"}, {"family": "Groop", "given": "Leif", "initials": "L", "orcid": "0000-0002-0187-3263", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/6b549c1ef49648bf81c481bc88857552.json"}}, {"family": "Abecasis", "given": "Goncalo", "initials": "G"}, {"family": "Scott", "given": "Laura J", "initials": "LJ"}, {"family": "Morris", "given": "Andrew P", "initials": "AP"}, {"family": "Kang", "given": "Hyun Min", "initials": "HM"}, {"family": "Altshuler", "given": "David", "initials": "D"}, {"family": "Burtt", "given": "No\u00ebl P", "initials": "NP"}, {"family": "Florez", "given": "Jose C", "initials": "JC"}, {"family": "Boehnke", "given": "Michael", "initials": "M"}, {"family": "McCarthy", "given": "Mark I", "initials": "MI"}], "type": "dataset", "published": "2017-12-19", "journal": {"title": "Sci Data", "issn": "2052-4463", "volume": "4", "issue": null, "pages": "170179", "issn-l": "2052-4463"}, "abstract": "To investigate the genetic basis of type 2 diabetes (T2D) to high resolution, the GoT2D and T2D-GENES consortia catalogued variation from whole-genome sequencing of 2,657 European individuals and exome sequencing of 12,940 individuals of multiple ancestries. Over 27M SNPs, indels, and structural variants were identified, including 99% of low-frequency (minor allele frequency [MAF] 0.1-5%) non-coding variants in the whole-genome sequenced individuals and 99.7% of low-frequency coding variants in the whole-exome sequenced individuals. Each variant was tested for association with T2D in the sequenced individuals, and, to increase power, most were tested in larger numbers of individuals (>80% of low-frequency coding variants in ~82 K Europeans via the exome chip, and ~90% of low-frequency non-coding variants in ~44 K Europeans via genotype imputation). The variants, genotypes, and association statistics from these analyses provide the largest reference to date of human genetic information relevant to T2D, for use in activities such as T2D-focused genotype imputation, functional characterization of variants or genes, and other novel analyses to detect associations between sequence variation and T2D.", "doi": "10.1038/sdata.2017.179", "pmid": "29257133", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC5735917"}, {"db": "pii", "key": "sdata2017179"}], "notes": [], "created": "2018-12-05T12:07:44.419Z", "modified": "2026-09-23T13:42:52.990Z"}, {"entity": "publication", "iuid": "c2a9df5941d3435a82dfa7ec3f89032d", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c2a9df5941d3435a82dfa7ec3f89032d.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c2a9df5941d3435a82dfa7ec3f89032d"}}, "title": "Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions.", "authors": [{"family": "Shungin", "given": "Dmitry", "initials": "D"}, {"family": "Deng", "given": "Wei Q", "initials": "WQ"}, {"family": "Varga", "given": "Tibor V", "initials": "TV", "orcid": "0000-0002-2383-699X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/23a2d18bbd794615a688cd67a13dccd6.json"}}, {"family": "Luan", "given": "Jian'an", "initials": "J"}, {"family": "Mihailov", "given": "Evelin", "initials": "E"}, {"family": "Metspalu", "given": "Andres", "initials": "A"}, {"family": "GIANT Consortium", "given": "", "initials": ""}, {"family": "Morris", "given": "Andrew P", "initials": "AP", "orcid": "0000-0002-6805-6014", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/aaff6a0afcdf464a8de49c2ece7399e2.json"}}, {"family": "Forouhi", "given": "Nita G", "initials": "NG"}, {"family": "Lindgren", "given": "Cecilia", "initials": "C", "orcid": "0000-0002-4903-9374", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b5c82df5e7bc43e4874726fb16924cf5.json"}}, {"family": "Magnusson", "given": "Patrik K E", "initials": "PKE"}, {"family": "Pedersen", "given": "Nancy L", "initials": "NL"}, {"family": "Hallmans", "given": "G\u00f6ran", "initials": "G"}, {"family": "Chu", "given": "Audrey Y", "initials": "AY"}, {"family": "Justice", "given": "Anne E", "initials": "AE"}, {"family": "Graff", "given": "Mariaelisa", "initials": "M"}, {"family": "Winkler", "given": "Thomas W", "initials": "TW", "orcid": "0000-0003-0292-5421", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/b1511736ab1f4f3cab1a2ccef342db34.json"}}, {"family": "Rose", "given": "Lynda M", "initials": "LM"}, {"family": "Langenberg", "given": "Claudia", "initials": "C"}, {"family": "Cupples", "given": "L Adrienne", "initials": "LA"}, {"family": "Ridker", "given": "Paul M", "initials": "PM"}, {"family": "Wareham", "given": "Nicholas J", "initials": "NJ", "orcid": "0000-0003-1422-2993", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/462fd4169f41418887a5a979e0808d87.json"}}, {"family": "Ong", "given": "Ken K", "initials": "KK"}, {"family": "Loos", "given": "Ruth J F", "initials": "RJF"}, {"family": "Chasman", "given": "Daniel I", "initials": "DI"}, {"family": "Ingelsson", "given": "Erik", "initials": "E"}, {"family": "Kilpel\u00e4inen", "given": "Tuomas O", "initials": "TO"}, {"family": "Scott", "given": "Robert A", "initials": "RA"}, {"family": "M\u00e4gi", "given": "Reedik", "initials": "R"}, {"family": "Par\u00e9", "given": "Guillaume", "initials": "G", "orcid": "0000-0002-6795-4760", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/ef5b393b30f54b5f9c4531ceddc51b90.json"}}, {"family": "Franks", "given": "Paul W", "initials": "PW"}], "type": "journal article", "published": "2017-06-00", "journal": {"title": "PLoS Genet", "issn": "1553-7404", "volume": "13", "issue": "6", "pages": "e1006812", "issn-l": "1553-7390"}, "abstract": "Phenotypic variance heterogeneity across genotypes at a single nucleotide polymorphism (SNP) may reflect underlying gene-environment (G\u00d7E) or gene-gene interactions. We modeled variance heterogeneity for blood lipids and BMI in up to 44,211 participants and investigated relationships between variance effects (Pv), G\u00d7E interaction effects (with smoking and physical activity), and marginal genetic effects (Pm). Correlations between Pv and Pm were stronger for SNPs with established marginal effects (Spearman's \u03c1 = 0.401 for triglycerides, and \u03c1 = 0.236 for BMI) compared to all SNPs. When Pv and Pm were compared for all pruned SNPs, only BMI was statistically significant (Spearman's \u03c1 = 0.010). Overall, SNPs with established marginal effects were overrepresented in the nominally significant part of the Pv distribution (Pbinomial <0.05). SNPs from the top 1% of the Pm distribution for BMI had more significant Pv values (PMann-Whitney = 1.46\u00d710-5), and the odds ratio of SNPs with nominally significant (<0.05) Pm and Pv was 1.33 (95% CI: 1.12, 1.57) for BMI. Moreover, BMI SNPs with nominally significant G\u00d7E interaction P-values (Pint<0.05) were enriched with nominally significant Pv values (Pbinomial = 8.63\u00d710-9 and 8.52\u00d710-7 for SNP \u00d7 smoking and SNP \u00d7 physical activity, respectively). We conclude that some loci with strong marginal effects may be good candidates for G\u00d7E, and variance-based prioritization can be used to identify them.", "doi": "10.1371/journal.pgen.1006812", "pmid": "28614350", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC5489225"}, {"db": "pii", "key": "PGENETICS-D-16-00716"}], "notes": [], "created": "2018-12-05T12:29:54.921Z", "modified": "2026-09-23T11:44:10.450Z"}]}