FAVOR: functional annotation of variants online resource and annotator for variation across the human genome
Authors
Zhou, HufengArapoglou, Theodore
Li, Xihao
Li, Zilin
Zheng, Xiuwen
Moore, Jill
Asok, Abhijith
Kumar, Sushant
Blue, Elizabeth E
Buyske, Steven
Cox, Nancy
Felsenfeld, Adam
Gerstein, Mark
Kenny, Eimear
Li, Bingshan
Matise, Tara
Philippakis, Anthony
Rehm, Heidi L
Sofia, Heidi J
Snyder, Grace
Weng, Zhiping
Neale, Benjamin
Sunyaev, Shamil R
Lin, Xihong
UMass Chan Affiliations
Program in Bioinformatics and Integrative BiologyDocument Type
Journal ArticlePublication Date
2022-11-09
Metadata
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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 and visualizes findings of all possible nine billion single nucleotide variants (SNVs) across the genome. It allows for rapid variant-, gene- and 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.Source
Zhou H, Arapoglou T, Li X, Li Z, Zheng X, Moore J, Asok A, Kumar S, Blue EE, Buyske S, Cox N, Felsenfeld A, Gerstein M, Kenny E, Li B, Matise T, Philippakis A, Rehm HL, Sofia HJ, Snyder G; NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Weng Z, Neale B, Sunyaev SR, Lin X. FAVOR: functional annotation of variants online resource and annotator for variation across the human genome. Nucleic Acids Res. 2022 Nov 9:gkac966. doi: 10.1093/nar/gkac966. Epub ahead of print. PMID: 36350676.DOI
10.1093/nar/gkac966Permanent Link to this Item
http://hdl.handle.net/20.500.14038/51449PubMed ID
36350676Rights
© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.; Attribution 4.0 InternationalDistribution License
http://creativecommons.org/licenses/by/4.0/ae974a485f413a2113503eed53cd6c53
10.1093/nar/gkac966
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Except where otherwise noted, this item's license is described as © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which
permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.