Abstract
Whole exome sequencing has been increasingly used in human disease studies. Prioritization based on appropriate functional annotations has been used as an indispensable step to select candidate variants. Here we present the latest updates to dbNSFP (version 4.1), a database designed to facilitate this step by providing deleteriousness prediction and functional annotation for all potential nonsynonymous and splice-site SNVs (a total of 84,013,093) in the human genome. The current version compiled 36 deleteriousness prediction scores, including 12 transcript-specific scores, and other variant and gene-level functional annotations. The database is available at http://database.liulab.science/dbNSFP with a downloadable version and a web-service.
Highlights
Whole-exome sequencing (WES) and whole-genome sequencing (WGS) have been increasingly used in human disease studies in the research and clinical setting [1,2,3]
Identifying variants that cause diseases or are associated with disease risks from a large number of DNA variants identified in sequencing requires an excessive amount of time and effort. To accomplish this daunting task, investigators have relied on functional annotations to filter or prioritize variants based on our current knowledge or prediction models
We developed Database for nonsynonymous SNPs’ functional predictions (dbNSFP) version 1 [11], 2 [12], and 3 [13] to provide a “one-stop-shop” for functional annotations for nonsynonymous Single nucleotide variant (SNV) and splice site SNVs, top candidate variant types for Mendelian diseases. It collected all possible Nonsynonymous SNV (nsSNV) and Splice site SNV (ssSNV) based on human reference sequences and multiple deleteriousness predictions and annotations for each SNV
Summary
Whole-exome sequencing (WES) and whole-genome sequencing (WGS) have been increasingly used in human disease studies in the research and clinical setting [1,2,3]. Liu et al Genome Medicine (2020) 12:103 geneticists and genetic epidemiologists, including functional prediction of variants, conservation information, predicted promoters, enhancers, and epigenomic markers, among others Another challenge faced by the investigators is that different gene-model-based annotation tools all have their advantages and disadvantages, and the results sometimes do not agree with each other [10]. We developed dbNSFP version 1 [11], 2 [12], and 3 [13] to provide a “one-stop-shop” for functional annotations for nonsynonymous SNVs (nsSNVs) and splice site SNVs (ssSNVs), top candidate variant types for Mendelian diseases It collected all possible nsSNVs and ssSNVs based on human reference sequences and multiple deleteriousness predictions and annotations for each SNV. The output will be displayed on the web page and available as a downloadable TAB-delimited text file for further filtering
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