dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations
TLDR
Rich functional annotations for SNVs and genes have 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.Abstract:
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.read more
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Mutational landscape determines sensitivity to PD-1 blockade in non–small cell lung cancer
Naiyer A. Rizvi,Naiyer A. Rizvi,Matthew D. Hellmann,Matthew D. Hellmann,Alexandra Snyder,Alexandra Snyder,Pia Kvistborg,Vladimir Makarov,Jonathan J. Havel,William Lee,Jianda Yuan,Phillip Wong,Teresa S. Ho,Martin L. Miller,Natasha Rekhtman,Andre L. Moreira,Fawzia Ibrahim,Cameron Bruggeman,Billel Gasmi,Roberta Zappasodi,Yuka Maeda,Chris Sander,Edward B. Garon,Taha Merghoub,Jedd D. Wolchok,Jedd D. Wolchok,Ton N. Schumacher,Timothy A. Chan,Timothy A. Chan +28 more
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The Ensembl Variant Effect Predictor.
William M. McLaren,Laurent Gil,Sarah E. Hunt,Harpreet Singh Riat,Graham R. S. Ritchie,Anja Thormann,Paul Flicek,Fiona Cunningham +7 more
TL;DR: The Ensembl Variant Effect Predictor can simplify and accelerate variant interpretation in a wide range of study designs.
Journal ArticleDOI
REVEL: An Ensemble Method for Predicting the Pathogenicity of Rare Missense Variants
Nilah M. Ioannidis,Joseph H. Rothstein,Joseph H. Rothstein,Vikas Pejaver,Sumit Middha,Shannon K. McDonnell,Saurabh Baheti,Anthony M. Musolf,Qing Li,Emily R. Holzinger,Danielle M. Karyadi,Lisa A. Cannon-Albright,Craig C. Teerlink,Janet L. Stanford,William B. Isaacs,Jianfeng Xu,Kathleen A. Cooney,Kathleen A. Cooney,Ethan M. Lange,Johanna Schleutker,John D. Carpten,Isaac J. Powell,Olivier Cussenot,Geraldine Cancel-Tassin,Graham G. Giles,Graham G. Giles,Robert J. MacInnis,Robert J. MacInnis,Christiane Maier,Chih-Lin Hsieh,Fredrik Wiklund,William J. Catalona,William D. Foulkes,Diptasri Mandal,Rosalind A. Eeles,Zsofia Kote-Jarai,Carlos Bustamante,Daniel J. Schaid,Trevor Hastie,Elaine A. Ostrander,Joan E. Bailey-Wilson,Predrag Radivojac,Stephen N. Thibodeau,Alice S. Whittemore,Weiva Sieh,Weiva Sieh +45 more
TL;DR: This work developed REVEL (rare exome variant ensemble learner), an ensemble method for predicting the pathogenicity of missense variants on the basis of individual tools: MutPred, FATHMM, VEST, PolyPhen, SIFT, PROVEAN, MutationAssessor, LRT, GERP, SiPhy, phyloP, and phastCons.
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The Human Gene Mutation Database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies
Peter D. Stenson,Matthew Mort,Edward V. Ball,Katy Evans,Matthew J. Hayden,Sally Heywood,Michelle Hussain,Andrew David Phillips,David Neil Cooper +8 more
TL;DR: The Human Gene Mutation Database constitutes de facto the central unified gene/disease-oriented repository of heritable mutations causing human genetic disease used worldwide by researchers, clinicians, diagnostic laboratories and genetic counsellors, and is an essential tool for the annotation of next-generation sequencing data.
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A High-Resolution Map of Human Evolutionary Constraint Using 29 Mammals
Stefan Washietl,Pouya Kheradpour,Jason Ernst,Lucas D. Ward,Irwin Jungreis,Matthew D. Rasmussen,Manolis Kellis +6 more
TL;DR: The comparison of related genomes has emerged as a powerful lens for genome interpretation as mentioned in this paper, which reveals a small number of new coding exons, candidate stop codon readthrough events and over 10,000 regions of overlapping synonymous constraint within protein-coding exons.
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