{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T17:32:08Z","timestamp":1775755928869,"version":"3.50.1"},"reference-count":57,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2022,11,9]],"date-time":"2022-11-09T00:00:00Z","timestamp":1667952000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["U01-HG009088"],"award-info":[{"award-number":["U01-HG009088"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["U01-HG012064"],"award-info":[{"award-number":["U01-HG012064"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["R35-CA197449"],"award-info":[{"award-number":["R35-CA197449"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","award":["U19-CA203654"],"award-info":[{"award-number":["U19-CA203654"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000050","name":"National Heart, Lung, and Blood Institute","doi-asserted-by":"publisher","award":["R01-HL163560"],"award-info":[{"award-number":["R01-HL163560"]}],"id":[{"id":"10.13039\/100000050","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Large biobank-scale whole genome sequencing (WGS) studies are rapidly identifying a multitude of coding and non-coding variants. They provide an unprecedented resource for illuminating the genetic basis of human diseases. Variant functional annotations play a critical role in WGS analysis, result interpretation, and prioritization of disease- or trait-associated causal variants. Existing functional annotation databases have limited scope to perform online queries and functionally annotate the genotype data of large biobank-scale WGS studies. We develop the Functional Annotation of Variants Online Resources (FAVOR) to meet these pressing needs. FAVOR provides a comprehensive multi-faceted variant functional annotation online portal that summarizes\u00a0and visualizes findings of all possible nine billion single nucleotide variants (SNVs) across the genome. It allows for rapid variant-, gene-\u00a0and region-level queries of variant functional annotations. FAVOR integrates variant functional information from multiple sources to describe the functional characteristics of variants and facilitates prioritizing plausible causal variants influencing human phenotypes. Furthermore, we provide a scalable annotation tool, FAVORannotator, to functionally annotate large-scale WGS studies and efficiently store the genotype and their variant functional annotation data in a single file using the annotated Genomic Data Structure (aGDS) format, making downstream analysis more convenient. FAVOR and FAVORannotator are available at https:\/\/favor.genohub.org.<\/jats:p>","DOI":"10.1093\/nar\/gkac966","type":"journal-article","created":{"date-parts":[[2022,10,14]],"date-time":"2022-10-14T17:16:39Z","timestamp":1665767799000},"page":"D1300-D1311","source":"Crossref","is-referenced-by-count":138,"title":["FAVOR: functional annotation of variants online resource and annotator for variation across the human genome"],"prefix":"10.1093","volume":"51","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9382-5674","authenticated-orcid":false,"given":"Hufeng","family":"Zhou","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health , Boston , MA , USA"}]},{"given":"Theodore","family":"Arapoglou","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health , Boston , MA , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8151-0106","authenticated-orcid":false,"given":"Xihao","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health , Boston , MA , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1521-8945","authenticated-orcid":false,"given":"Zilin","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health , Boston , MA , USA"},{"name":"Department of Biostatistics and Health Data Science, Indiana University School of Medicine , Indianapolis , IN, USA"}]},{"given":"Xiuwen","family":"Zheng","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, University of Washington , Seattle , WA \u00a098195, USA"}]},{"given":"Jill","family":"Moore","sequence":"additional","affiliation":[{"name":"Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School , Worcester , MA , USA"}]},{"given":"Abhijith","family":"Asok","sequence":"additional","affiliation":[{"name":"Microsoft Inc. Redmond , WA, USA"}]},{"given":"Sushant","family":"Kumar","sequence":"additional","affiliation":[{"name":"Department of Medical Biophysics, University of Toronto , Toronto , ON, Canada"},{"name":"Princess Margaret Cancer Centre , Toronto , ON, Canada"}]},{"given":"Elizabeth\u00a0E","family":"Blue","sequence":"additional","affiliation":[{"name":"Division of Medical Genetics, University of Washington , Seattle , WA , USA"},{"name":"Brotman Baty Institute for Precision Medicine , Seattle , WA , USA"}]},{"given":"Steven","family":"Buyske","sequence":"additional","affiliation":[{"name":"Department of Statistics, Rutgers, The State University of New Jersey , Piscataway, NJ, USA"}]},{"given":"Nancy","family":"Cox","sequence":"additional","affiliation":[{"name":"Department of Medicine, Vanderbilt University Medical Center , Nashville , TN, USA"}]},{"given":"Adam","family":"Felsenfeld","sequence":"additional","affiliation":[{"name":"National Human Genome Research Institute , Bethesda , DC, USA"}]},{"given":"Mark","family":"Gerstein","sequence":"additional","affiliation":[{"name":"Program in Computational Biology and Bioinformatics, Yale University , New Haven , CT, USA"},{"name":"Department of Molecular Biophysics and Biochemistry, Yale University , New Haven , CT, USA"}]},{"given":"Eimear","family":"Kenny","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai , New\u00a0York , NY , USA"},{"name":"Department of Medicine, Icahn School of Medicine at Mount Sinai , New\u00a0York , NY , USA"},{"name":"Institute for Genomic Health, Icahn School of Medicine at Mount Sinai , New\u00a0York , NY , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2129-168X","authenticated-orcid":false,"given":"Bingshan","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center , Nashville , TN, USA"}]},{"given":"Tara","family":"Matise","sequence":"additional","affiliation":[{"name":"Department of Genetics, Rutgers, The State University of New Jersey , Piscataway, NJ, USA"}]},{"given":"Anthony","family":"Philippakis","sequence":"additional","affiliation":[{"name":"Data Science Platform, Broad Institute of Harvard and MIT , Cambridge , MA , USA"}]},{"given":"Heidi L","family":"Rehm","sequence":"additional","affiliation":[{"name":"Program in Medical and Population Genetics, Broad Institute of Harvard and MIT , Cambridge , MA , USA"},{"name":"Center for Genomic Medicine, Massachusetts General Hospital , Boston , MA , USA"}]},{"given":"Heidi J","family":"Sofia","sequence":"additional","affiliation":[{"name":"National Human Genome Research Institute , Bethesda , DC, USA"}]},{"given":"Grace","family":"Snyder","sequence":"additional","affiliation":[{"name":"National Human Genome Research Institute , Bethesda , DC, USA"}]},{"name":"NHGRI\u00a0Genome\u00a0Sequencing\u00a0Program\u00a0Variant\u00a0Functional\u00a0Annotation\u00a0Working Group","sequence":"additional","affiliation":[]},{"given":"Zhiping","family":"Weng","sequence":"additional","affiliation":[{"name":"Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School , Worcester , MA , USA"}]},{"given":"Benjamin","family":"Neale","sequence":"additional","affiliation":[{"name":"Program in Medical and Population Genetics, Broad Institute of Harvard and MIT , Cambridge , MA , USA"},{"name":"Analytic and Translational Genetics Unit, Massachusetts General Hospital , Boston , MA , USA"}]},{"given":"Shamil\u00a0R","family":"Sunyaev","sequence":"additional","affiliation":[{"name":"Program in Medical and Population Genetics, Broad Institute of Harvard and MIT , Cambridge , MA , USA"},{"name":"Department of Biomedical Informatics, Harvard Medical School , Boston , MA , USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7067-7752","authenticated-orcid":false,"given":"Xihong","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Harvard T.H. Chan School of Public Health , Boston , MA , USA"},{"name":"Program in Medical and Population Genetics, Broad Institute of Harvard and MIT , Cambridge , MA , USA"},{"name":"Department of Statistics, Harvard University , Cambridge , MA , USA"}]}],"member":"286","published-online":{"date-parts":[[2022,11,9]]},"reference":[{"key":"2023010804345079700_B1","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/s41586-021-03205-y","article-title":"Sequencing of 53,831 diverse genomes from the NHLBI TOPMed program","volume":"590","author":"Taliun","year":"2021","journal-title":"Nature"},{"key":"2023010804345079700_B2","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1038\/s41586-022-04965-x","article-title":"The sequences of 150,119 genomes in the UK biobank","volume":"607","author":"Halldorsson","year":"2022","journal-title":"Nature"},{"key":"2023010804345079700_B3","doi-asserted-by":"crossref","first-page":"668","DOI":"10.1056\/NEJMsr1809937","article-title":"The \u201cAll of us\u201d research program","volume":"381","author":"All of Us Research Program Investigators","year":"2019","journal-title":"N. 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