{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,30]],"date-time":"2025-09-30T04:09:52Z","timestamp":1759205392232,"version":"3.37.3"},"reference-count":13,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2018,8,28]],"date-time":"2018-08-28T00:00:00Z","timestamp":1535414400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["1R01-HG008146"],"award-info":[{"award-number":["1R01-HG008146"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000867","name":"CSC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000867","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,3,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Expression quantitative loci (eQTL) are being used widely to annotate and interpret GWAS hits. Recent studies have demonstrated that individual gene expression is often regulated by multiple independent cis-acting eQTL. Diverse methods, frequentist and Bayesian, have already been developed to simultaneously detect and fine-map such multiple eQTL, but most of these ignore sample relatedness and potential population structure. This can result in false positives and disrupt the accuracy of fine-mapping. Here we introduce PolyQTL software for identifying and estimating eQTL effects. The package incorporates a genetic relatedness matrix to remove the influence of population structure and sample relatedness, while utilizing a Bayesian multiple eQTL detection pipeline to identify the most plausible candidate causal variants at one or more independent loci influencing abundance of a transcript.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Simulations demonstrate that our approach improves the rate of discovery of causal variants relative to methods that do not account for relatedness.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The software is written in C++, and freely available for download at https:\/\/github.com\/jxzb1988\/PolyQTL.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty728","type":"journal-article","created":{"date-parts":[[2018,8,23]],"date-time":"2018-08-23T19:31:23Z","timestamp":1535052683000},"page":"1061-1063","source":"Crossref","is-referenced-by-count":6,"title":["PolyQTL: Bayesian multiple eQTL detection with control for population structure and sample relatedness"],"prefix":"10.1093","volume":"35","author":[{"given":"Biao","family":"Zeng","sequence":"first","affiliation":[{"name":"School of Biological Sciences and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5352-5877","authenticated-orcid":false,"given":"Greg","family":"Gibson","sequence":"additional","affiliation":[{"name":"School of Biological Sciences and Center for Integrative Genomics, Georgia Institute of Technology, Atlanta, GA 30332, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2018,8,28]]},"reference":[{"key":"2023013107261239400_bty728-B1","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1086\/339705","article-title":"Quantitative-trait homozygosity and association mapping and empirical genome-wide significance in large, complex pedigrees: fasting serum-insulin level in the Hutterites","volume":"70","author":"Abney","year":"2002","journal-title":"Am. J. Hum. Genet"},{"key":"2023013107261239400_bty728-B2","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/nrg3891","article-title":"The role of regulatory variation in complex traits and disease","volume":"16","author":"Albert","year":"2015","journal-title":"Nat. Rev. Genet"},{"key":"2023013107261239400_bty728-B3","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","author":"Auton","year":"2015","journal-title":"Nature"},{"key":"2023013107261239400_bty728-B4","doi-asserted-by":"crossref","first-page":"1493","DOI":"10.1093\/bioinformatics\/btw018","article-title":"FINEMAP: efficient variable selection using summary data from genome-wide association studies","volume":"32","author":"Benner","year":"2016","journal-title":"Bioinformatics"},{"key":"2023013107261239400_bty728-B5","doi-asserted-by":"crossref","first-page":"719","DOI":"10.1534\/genetics.115.176107","article-title":"Fine mapping causal variants with an approximate Bayesian method using marginal test statistics","volume":"200","author":"Chen","year":"2015","journal-title":"Genetics"},{"key":"2023013107261239400_bty728-B6","doi-asserted-by":"crossref","first-page":"1365","DOI":"10.1038\/nature04244","article-title":"Mapping determinants of human gene expression by regional and genome-wide association","volume":"437","author":"Cheung","year":"2005","journal-title":"Nature"},{"key":"2023013107261239400_bty728-B7","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1038\/nature24277","article-title":"Genetic effects on gene expression across human tissues","volume":"550","year":"2017","journal-title":"Nature"},{"key":"2023013107261239400_bty728-B8","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1534\/genetics.114.167908","article-title":"Identifying causal variants at loci with multiple signals of association","volume":"198","author":"Hormozdiari","year":"2014","journal-title":"Genetics"},{"key":"2023013107261239400_bty728-B10","doi-asserted-by":"crossref","first-page":"1114","DOI":"10.1016\/j.ajhg.2016.03.029","article-title":"Efficient integrative multi-SNP association analysis via deterministic approximation of posteriors","volume":"98","author":"Wen","year":"2016","journal-title":"Am. J. Hum. Genet"},{"key":"2023013107261239400_bty728-B11","doi-asserted-by":"crossref","first-page":"e1005176","DOI":"10.1371\/journal.pgen.1005176","article-title":"Cross-population joint analysis of eQTLs: fine mapping and functional annotation","volume":"11","author":"Wen","year":"2015","journal-title":"PLoS Genet"},{"key":"2023013107261239400_bty728-B12","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1038\/ng.2213","article-title":"Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits","volume":"44","author":"Yang","year":"2012","journal-title":"Nat. Genet"},{"key":"2023013107261239400_bty728-B13","doi-asserted-by":"crossref","first-page":"100","DOI":"10.1038\/ng.2876","article-title":"Advantages and pitfalls in the application of mixed-model association methods","volume":"46","author":"Yang","year":"2014","journal-title":"Nat. Genet"},{"key":"2023013107261239400_bty728-B14","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1038\/ng.2310","article-title":"Genome-wide efficient mixed-model analysis for association studies","volume":"44","author":"Zhou","year":"2012","journal-title":"Nat. Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/6\/1061\/48966427\/bioinformatics_35_6_1061.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/35\/6\/1061\/48966427\/bioinformatics_35_6_1061.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T10:22:37Z","timestamp":1675160557000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/35\/6\/1061\/5085375"}},"subtitle":[],"editor":[{"given":"Oliver","family":"Stegle","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2018,8,28]]},"references-count":13,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2019,3,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bty728","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"type":"print","value":"1367-4803"},{"type":"electronic","value":"1367-4811"}],"subject":[],"published-other":{"date-parts":[[2019,3,15]]},"published":{"date-parts":[[2018,8,28]]}}}