dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations

By Xiaoming Liu, Xueqiu Jian, Eric Boerwinkle. Human Mutation, 2013

625 citations recorded by the source corpus.

dbNSFP is a database developed for functional prediction and annotation of all potential non‐synonymous single‐nucleotide variants (nsSNVs) in the human genome. This database significantly facilitates the process of querying predictions and annotations from different databases/web‐servers for large amounts of nsSNVs discovered in exome‐sequencing studies. Here we report a recent major update of the database to version 2.0. We have rebuilt the SNV collection based on GENCODE 9 and currently the database includes 87,347,043 nsSNVs and 2,270,742 essential splice site SNVs (an 18% increase compared to dbNSFP v1.0). For each nsSNV dbNSFP v2.0 has added two prediction scores (MutationAssessor and FATHMM) and two conservation scores (GERP++ and SiPhy). The original five prediction and conservation scores in v1.0 (SIFT, Polyphen2, LRT, MutationTaster and PhyloP) have been updated. Rich functional annotations for SNVs and genes have also been added into the new version, including allele frequencies observed in the 1000 Genomes Project phase 1 data and the NHLBI Exome Sequencing Project, various gene IDs from different databases, functional descriptions of genes, gene expression and gene interaction information, among others. dbNSFP v2.0 is freely available for download at http://sites.google.com/site/jpopgen/dbNSFP. ©2013 Wiley‐Liss, Inc.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/05c09c97121700a95801cb28e6c4854c2d25c55b

How researchers see this paper

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In Genetics

1. Eric Boerwinkle
2. Chunlei Wu
3. Chang Li
4. Xiaoming Liu
5. Xiaoming Liu
6. Yibo Dong
7. Yicheng Tu
8. Chang Li

In Molecular Biology

1. Eric Boerwinkle
2. Chunlei Wu
3. Chang Li
4. Xiaoming Liu
5. Xiaoming Liu
6. Yibo Dong
7. Yicheng Tu
8. Chang Li

Citations in the corpus

• dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Non-synonymous and Splice Site SNVs (2016, methodology): “As described previously [Liu et al., 2013], we artificially “mutated” each non-N reference allele to the three alternative alleles.”
• The ExAC browser: displaying reference data information from over 60 000 exomes (2016, methodology): “RSIDs were obtained from dbSNP version 142 and gene names and aliases were extracted from dbNSFP (13,14).”
• dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs (2020, methodology): “Previously, we developed dbNSFP version 1 [11], 2 [12], and 3 [13] to provide a”
• In silico prediction of splice-altering single nucleotide variants in the human genome (2014, background): “dbNSFP is a database for functional prediction and annotation of non-synonymous and splice-altering SNVs (49,50).”
• Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas (2017, methodology): “4 databases.(58) We also annotated the variants with an in-house database of common mutations in 219 normal WES cases (“Meganormal” database).”
• Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. (2015, methodology): “scores using LR and SVM algorithms and made the prediction scores for 87 347 044 possible variants in the whole-exome publicly available in ANNOVAR (35) software and dbNSFP database (36,37).”