{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,3]],"date-time":"2026-04-03T03:56:02Z","timestamp":1775188562154,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"13","license":[{"start":{"date-parts":[[2020,10,16]],"date-time":"2020-10-16T00:00:00Z","timestamp":1602806400000},"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\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31871327"],"award-info":[{"award-number":["31871327"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32070675"],"award-info":[{"award-number":["32070675"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,7,27]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Sampling of control variants having matched properties with input variants is widely used in enrichment analysis of genome-wide association studies\/quantitative trait loci and negative data construction for pathogenic\/regulatory variant prediction methods. Spurious enrichment results because of confounding factors, such as minor allele frequency and linkage disequilibrium pattern, can be avoided by calibration of statistical significance based on matched controls. Here, we presented vSampler which can generate sets of randomly drawn variants with comprehensive choices of matching properties, such as tissue\/cell type-specific epigenomic features. Importantly, the development of a novel data structure and sampling algorithms for vSampler makes it significantly fast than existing tools.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>vSampler web server and local program are available at http:\/\/mulinlab.org\/vsampler.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa883","type":"journal-article","created":{"date-parts":[[2020,10,1]],"date-time":"2020-10-01T03:36:16Z","timestamp":1601523376000},"page":"1915-1917","source":"Crossref","is-referenced-by-count":20,"title":["vSampler: fast and annotation-based matched variant sampling tool"],"prefix":"10.1093","volume":"37","author":[{"given":"Dandan","family":"Huang","sequence":"first","affiliation":[{"name":"Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University , Tianjin 300070, China"},{"name":"Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University , Tianjin 300070, China"}]},{"given":"Zhao","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University , Tianjin 300070, China"}]},{"given":"Yao","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University , Tianjin 300070, China"}]},{"given":"Qian","family":"Liang","sequence":"additional","affiliation":[{"name":"Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University , Tianjin 300070, China"}]},{"given":"Pak Chung","family":"Sham","sequence":"additional","affiliation":[{"name":"Department of Psychiatry"}]},{"given":"Hongcheng","family":"Yao","sequence":"additional","affiliation":[{"name":"School of Biomedical Sciences, Li Ka Shing Faculty of Medicine , The University of Hong Kong, Hong Kong SAR 999077, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3598-3679","authenticated-orcid":false,"given":"Mulin Jun","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University , Tianjin 300070, China"},{"name":"Department of Pharmacology, Tianjin Key Laboratory of Inflammation Biology, School of Basic Medical Sciences, Tianjin Medical University , Tianjin 300070, China"}]}],"member":"286","published-online":{"date-parts":[[2020,10,16]]},"reference":[{"key":"2023051611452947500_btaa883-B1","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1038\/nature13835","article-title":"Genetic and epigenetic fine mapping of causal autoimmune disease variants","volume":"518","author":"Farh","year":"2015","journal-title":"Nature"},{"key":"2023051611452947500_btaa883-B2","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.schres.2010.07.001","article-title":"Common variants conferring risk of schizophrenia: a pathway analysis of GWAS data","volume":"122","author":"Jia","year":"2010","journal-title":"Schizophr Res"},{"key":"2023051611452947500_btaa883-B3","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1186\/s13059-017-1177-3","article-title":"cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes","volume":"18","author":"Li","year":"2017","journal-title":"Genome Biol"},{"key":"2023051611452947500_btaa883-B4","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1093\/bioinformatics\/btu655","article-title":"SNPsnap: a Web-based tool for identification and annotation of matched SNPs","volume":"31","author":"Pers","year":"2015","journal-title":"Bioinformatics"},{"key":"2023051611452947500_btaa883-B5","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1038\/nmeth.2832","article-title":"Functional annotation of noncoding sequence variants","volume":"11","author":"Ritchie","year":"2014","journal-title":"Nat. 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