dbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions.

TitledbNSFP: a lightweight database of human nonsynonymous SNPs and their functional predictions.
Publication TypeJournal Article
Year of Publication2011
AuthorsLiu, X, Jian, X, Boerwinkle, E
JournalHum Mutat
Volume32
Issue8
Pagination894-9
Date Published2011 Aug
ISSN1098-1004
KeywordsAlgorithms, Computational Biology, Databases, Nucleic Acid, Genetic Association Studies, Humans, Internet, Polymorphism, Single Nucleotide, Software
Abstract

With the advance of sequencing technologies, whole exome sequencing has increasingly been used to identify mutations that cause human diseases, especially rare Mendelian diseases. Among the analysis steps, functional prediction (of being deleterious) plays an important role in filtering or prioritizing nonsynonymous SNP (NS) for further analysis. Unfortunately, different prediction algorithms use different information and each has its own strength and weakness. It has been suggested that investigators should use predictions from multiple algorithms instead of relying on a single one. However, querying predictions from different databases/Web-servers for different algorithms is both tedious and time consuming, especially when dealing with a huge number of NSs identified by exome sequencing. To facilitate the process, we developed dbNSFP (database for nonsynonymous SNPs' functional predictions). It compiles prediction scores from four new and popular algorithms (SIFT, Polyphen2, LRT, and MutationTaster), along with a conservation score (PhyloP) and other related information, for every potential NS in the human genome (a total of 75,931,005). It is the first integrated database of functional predictions from multiple algorithms for the comprehensive collection of human NSs. dbNSFP is freely available for download at http://sites.google.com/site/jpopgen/dbNSFP.

DOI10.1002/humu.21517
Alternate JournalHum. Mutat.
PubMed ID21520341
PubMed Central IDPMC3145015
Grant ListRC2 HL102419 / HL / NHLBI NIH HHS / United States
RC2-HL02419-01 / HL / NHLBI NIH HHS / United States
1U01HG005728-01 / HG / NHGRI NIH HHS / United States
U01 HG005728 / HG / NHGRI NIH HHS / United States
U01 HG005728-01 / HG / NHGRI NIH HHS / United States
RC2 HL102419-01 / HL / NHLBI NIH HHS / United States
RC2 HL103010 / HL / NHLBI NIH HHS / United States
RC2 HL103010-01 / HL / NHLBI NIH HHS / United States