DbNSFP v3.0: A One‐Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice‐Site SNVs. Issue 3 (5th January 2016)

• Record Type: Journal Article
• Authors: Liu, Xiaoming; Wu, Chunlei; Li, Chang; Boerwinkle, Eric
• Is Part Of: Human mutation. Volume 37:Issue 3(2016)
• Page Start: 235
• Page End: 241
• Publication Date: 2016-01-05
• Subjects: dbNSFP -- dbscSNV -- nonsynonymous mutation -- splice‐site mutation -- functional prediction -- database; Human chromosome abnormalities -- Periodicals; Mutation (Biology) -- Periodicals; 616.04205
• DOI: 10.1002/humu.22932
• Languages: English
• ISSNs: 1059-7794

Abstract

Abstract : The purpose of the dbNSFP is to provide a one‐stop resource for functional predictions and annotations for human non‐synonymous single‐nucleotide variants (nsSNVs) and splice site variants (ssSNVs), and to facilitate the steps of filtering and prioritizing SNVs from a large list of SNVs discovered in an exome‐sequencing study. Here we report a recent major update of the database to version 3.0 and some preliminary analyses comparing the 24 functional prediction scores and conservation scores in dbNSFP v3.0. ABSTRACT: The purpose of the dbNSFP is to provide a one‐stop resource for functional predictions and annotations for human nonsynonymous single‐nucleotide variants (nsSNVs) and splice‐site variants (ssSNVs), and to facilitate the steps of filtering and prioritizing SNVs from a large list of SNVs discovered in an exome‐sequencing study. A list of all potential nsSNVs and ssSNVs based on the human reference sequence were created and functional predictions and annotations were curated and compiled for each SNV. Here, we report a recent major update of the database to version 3.0. The SNV list has been rebuilt based on GENCODE 22 and currently the database includes 82, 832, 027 nsSNVs and ssSNVs. An attached database dbscSNV, which compiled all potential human SNVs within splicing consensus regions and their deleteriousness predictions, add another 15, 030, 459 potentially functional SNVs. Eleven prediction scores (MetaSVM, MetaLR, CADD, VEST3, PROVEAN, 4× fitCons, fathmm‐MKL, and DANN) and allele frequencies from the UK10K cohorts and the Exome Aggregation Consortium (ExAC), among others, have been added. The original seven prediction scores in v2.0 (SIFT, 2× Polyphen2, LRT, MutationTaster, MutationAssessor, and FATHMM) as well as many SNV and gene functional annotations have been updated. dbNSFP v3.0 is freely available athttp://sites.google.com/site/jpopgen/dbNSFP .