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FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome

View ORCID ProfileHufeng Zhou, Theodore Arapoglou, View ORCID ProfileXihao Li, View ORCID ProfileZilin Li, View ORCID ProfileXiuwen Zheng, Jill Moore, Abhijith Asok, Sushant Kumar, View ORCID ProfileElizabeth E. Blue, Steven Buyske, Nancy Cox, Adam Felsenfeld, Mark Gerstein, Eimear Kenny, Bingshan Li, Tara Matise, Anthony Philippakis, View ORCID ProfileHeidi Rehm, Heidi J. Sofia, Grace Snyder, NHGRI Genome Sequencing Program Variant Functional Annotation Working Group, Zhiping Weng, View ORCID ProfileBenjamin Neale, Shamil R. Sunyaev, Xihong Lin
doi: https://doi.org/10.1101/2022.08.28.505582
Hufeng Zhou
1Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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  • For correspondence: hzhou@hsph.harvard.edu xlin@hsph.harvard.edu
Theodore Arapoglou
1Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Xihao Li
1Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Zilin Li
1Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Xiuwen Zheng
2Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
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Jill Moore
3Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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Abhijith Asok
4Microsoft Inc. Redmond, WA
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Sushant Kumar
5Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
6Princess Margaret Cancer Centre, University of Toronto, Toronto, ON, Canada
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Elizabeth E. Blue
7Division of Medical Genetics, University of Washington, Seattle, Washington, USA
8Brotman Baty Institute for Precision Medicine, Seattle, Washington, USA
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Steven Buyske
9Department of Statistics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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Nancy Cox
10Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
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Adam Felsenfeld
11National Human Genome Research Institute, Bethesda, DC, USA
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Mark Gerstein
12Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA
13Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
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Eimear Kenny
14Department of Genetics and Genomic Science, Icahn School of Medicine at Mount Sinai, New York, NY, USA
15Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
16Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Bingshan Li
17Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
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Tara Matise
18Department of Genetics, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
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Anthony Philippakis
19Data Science Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA
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Heidi Rehm
20Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
21Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
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Heidi J. Sofia
11National Human Genome Research Institute, Bethesda, DC, USA
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Grace Snyder
11National Human Genome Research Institute, Bethesda, DC, USA
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Zhiping Weng
3Program in Bioinformatics and Integrative Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
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Benjamin Neale
20Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
22Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
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Shamil R. Sunyaev
20Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
23Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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Xihong Lin
1Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
20Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
24Department of Statistics, Harvard University, Cambridge, MA, USA
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  • For correspondence: hzhou@hsph.harvard.edu xlin@hsph.harvard.edu
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ABSTRACT

Large-scale whole genome sequencing (WGS) studies and biobanks are rapidly generating 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 or are unable to functionally annotate the genotype data of large WGS studies and biobanks for downstream analysis. We develop the Functional Annotation of Variants Online Resources (FAVOR) to meet these pressing needs. FAVOR provides a comprehensive online multi-faceted portal with summarization and visualization of all possible 9 billion single nucleotide variants (SNVs) across the genome, and allows for rapid variant-, gene-, and region-level online queries. It integrates variant functional information from multiple sources to describe the functional characteristics of variants and facilitates prioritizing plausible causal variants influencing human phenotypes. Furthermore, a scalable annotation tool, FAVORannotator, is provided for functionally annotating and efficiently storing the genotype and variant functional annotation data of a large-scale sequencing study in an annotated GDS file format to facilitate downstream analysis. FAVOR and FAVORannotator are available at https://favor.genohub.org.

Competing Interest Statement

B.M.N. is on the Scientific Advisory Board of Deep Genomics, a consultant for Camp4 Therapeu-tics, Takeda Pharmaceutical and Biogen. S.R.S. is consultant to NGM Biopharmaceuticals and Inari agriculture. He is also on Scientific Advisory Board of Veritas Genetics. G.R.A. is an employee of Regeneron Pharmaceuticals and owns stock and stock options for Regeneron Pharmaceuticals. X. L. is a consultant of AbbVie Pharmaceuticals. Z. W. co-founded and serves as a scientific advisor for Rgenta Inc. A.P. is a Venture Partner at GV, a subsidiary of Alphabet corporation. He has received funding from Verily, MSFT, Intel, IBM, Bayer, Novartis, Pfizer, Biogen, Abbvie.

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  • https://favor.genohub.org

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome
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
bioRxiv 2022.08.28.505582; doi: https://doi.org/10.1101/2022.08.28.505582
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FAVOR: Functional Annotation of Variants Online Resource and Annotator for Variation across the Human Genome
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
bioRxiv 2022.08.28.505582; doi: https://doi.org/10.1101/2022.08.28.505582

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