About FAVOR

Functional Annotation of Variants - Online Resource (FAVOR), is an open-access variant functional annotation portal for whole genome/exome sequencing (WGS/WES) data. FAVOR provides variant and indel functional annotation information obtained from a collection of databases. These annotations span a spectrum of variant attributes, for example, variant categories, allele frequencies, evidence of open chromatin, protein function, conservation, clinvar information, local nucleotide diversity. In its current release (V2.0), FAVOR includes functional annotation information for all possible SNVs (8,812,917,339 SNVs) across the human genome and observed INDELs (79,997,898 indels) from the Trans-Omics for Precision Medicine (TOPMed) BRAVO variant set (Build GRCh38) (NHLBI TOPMed Consortium, 2018; Taliun et al., 2021). All together FAVOR contains total 8,892,915,237 variants (all possible 8,812,917,339 SNVs and 79,997,898 Observed indels). More data will be provided in future releases.

This data is publicly available for the benefit of the bioscience community to all users who agree to the terms. FAVOR is being developed with the support from the NHGRI Genome Sequencing Program, in collaboration with TOPMed. There are no publication restrictions or embargos on these data.

See the Documentation for more info on using FAVOR. Post to the Discussion Forum for user support and feature requests. If you have any questions about this website or would like to report bugs, please email favor@genohub.org.

FAVOR Developers: Hufeng Zhou (Lead), Vineet Verma (Software Engineer Lead), Xihong Lin

FAVORannotator Developers: Hufeng Zhou (Lead), Xihao Li (Co Lead), Zilin Li (Co Lead), Xihong Lin

Other Contributors: NHGRI Genome Sequencing Program Functional Annotation Working Group: Xihong Lin (Chair), Theodore Arapoglou (Co-Lead), Xiuwen Zheng, Jill Moore, Abhijith Asok, Sushant Kumar, Elizabeth E. Blue, Steven Buyske, Nancy Cox, Adam Felsenfeld, Mark Gerstein, Eimear Kenny, Bingshan Li, Tara Matise, Anthony Philippakis, Heidi Rehm, Heidi J. Sofia, Grace Snyder, NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Zhiping Weng, Benjamin Neale, Shamil R. Sunyaev, Genevieve Wojcik.

Helpful Discussions: Sheila Gaynor, Ryan Sun, Genevieve Wojcik

Funding: This work was supported by grant nos. R35-CA197449, P01-CA134294, U19-CA203654 and R01-HL113338 (to X. Lin), U01-HG012064 (to Z. Weng and X. Lin), U01-HG009088 (to X. Lin, S.R.S. and B.M.N.).

Acknowledgement: NHGRI Genome Sequencing Program Analysis Centers, Centers of Mendelian Diseases, Centers for Common Diseases, and Coordinating Center; NHLBI TOPMed Steering Committee, Data Coordinating Center, Informatics Research Center, and TOPMed investigators.

Citation

1. FAVOR

Hufeng Zhou*, Theodore Arapoglou*, Xihao Li, Zilin Li, Xiuwen Zheng, Jill Moore, Abhijith Asok, Sushant Kumar, Elizabeth E. Blue, Steven Buyske, Nancy Cox, Adam Felsenfeld, Mark Gerstein, Eimear Kenny, Bingshan Li, Tara Matise, Anthony Philippakis, Heidi Rehm, Heidi J. Sofia, Grace Snyder, NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Zhiping Weng, Benjamin Neale, Shamil R. Sunyaev, Xihong Lin. FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome . Nucleic Acids Res 2022 Nov 9; gkac966. PMID: 36350676. DOI: 10.1093/nar/gkac966..

FAVOR Full Database, DOI: 10.7910/DVN/KFUBKG. FAVOR Esssential Database, DOI: 10.7910/DVN/1VGTJI.

2. STAAR

Li X, Li Z, Zhou H, Gaynor SM, Liu Y, Chen H, Sun R, Dey R, Arnett DK, Aslibekyan S, Ballantyne CM, Bielak LF, Blangero J, Boerwinkle E, Bowden DW, Broome JG, Conomos MP, Correa A, Cupples LA, Curran JE, Freedman BI, Guo X, Hindy G, Irvin MR, Kardia SLR, Kathiresan S, Khan AT, Kooperberg CL, Laurie CC, Liu XS, Mahaney MC, Manichaikul AW, Martin LW, Mathias RA, McGarvey ST, Mitchell BD, Montasser ME, Moore JE, Morrison AC, O’Connell JR, Palmer ND, Pampana A, Peralta JM, Peyser PA, Psaty BM, Redline S, Rice KM, Rich SS, Smith JA, Tiwari HK, Tsai MY, Vasan RS, Wang FF, Weeks DE, Weng Z, Wilson JG, Yanek LR, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Neale BM, Sunyaev SR, Abecasis GR, Rotter JI, Willer CJ, Peloso GM, Natarajan P, and Lin X. Dynamic incorporation of multiple in silico functional annotations empowers rare variant association analysis of large whole-genome sequencing studies at scale. Nature Genetics 2020; 52(9): 969-983. PMID: 32839606. DOI: 10.1038/s41588-020-0676-4.

3. STAARpipeline

Zilin Li*, Xihao Li*, Hufeng Zhou, Sheila M. Gaynor, Margaret S. Selvaraj, Theodore Arapoglou, Corbin Quick, Yaowu Liu, Han Chen, Ryan Sun, Rounak Dey, Donna K. Arnett, Lawrence F. Bielak, Joshua C. Bis, Thomas W. Blackwell, John Blangero, Eric Boerwinkle, Donald W. Bowden, Jennifer A. Brody, Brian E. Cade, Matthew P. Conomos, Adolfo Correa, L. Adrienne Cupples, Joanne E. Curran, Paul S. de Vries, Ravindranath Duggirala, Barry I. Freedman, Harald H. H. Göring, Xiuqing Guo, Rita R. Kalyani, Charles Kooperberg, Brian G. Kral, Leslie A. Lange, Ani Manichaikul, Lisa W. Martin, Braxton D. Mitchell, May E. Montasser, Alanna C. Morrison, Take Naseri, Jeffrey R. O’Connell, Nicholette D. Palmer, Patricia A. Peyser, Bruce M. Psaty, Laura M. Raffield, Susan Redline, Alexander P. Reiner, Muagututi‘a Sefuiva Reupena, Kenneth M. Rice, Stephen S. Rich, Jennifer A. Smith, Kent D. Taylor, Ramachandran S. Vasan, Daniel E. Weeks, James G. Wilson, Lisa R. Yanek, Wei Zhao, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium, TOPMed Lipids Working Group, Jerome I. Rotter, Cristen J. Willer, Pradeep Natarajan, Gina M. Peloso, Xihong Lin. A framework for detecting noncoding rare variant associations of large-scale whole-genome sequencing studies. Nature Methods 19, 1599–1611 (2022) DOI: s41592-022-01640-x.

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