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

Human Mutation - Tập 34 Số 9 - Trang E2393-E2402 - 2013
Xiaoming Liu1, Xueqiu Jian2, Eric Boerwinkle2
1Human Genetics Center, School of Public Health, University of Texas Health Science, Center at Houston, Houston, Texas 77030, USA.
2Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA

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Tài liệu tham khảo

Abecasis, 2012, An integrated map of genetic variation from 1,092 human genomes, Nature, 491, 56, 10.1038/nature11632

Adzhubei, 2010, A method and server for predicting damaging missense mutations, Nature Methods, 7, 248, 10.1038/nmeth0410-248

Amberger, 2011, A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®), Human Mutation, 32, 564, 10.1002/humu.21466

Chang, 2012, wANNOVAR: annotating genetic variants for personal genomes via the web, Journal of Medical Genetics, 49, 433, 10.1136/jmedgenet-2012-100918

Chatr-aryamontri, 2012, The BioGRID interaction database: 2013 update, Nucleic Acids Research, 41, D816, 10.1093/nar/gks1158

Chun, 2009, Identification of deleterious mutations within three human genomes, Genome Research, 19, 1553, 10.1101/gr.092619.109

Cooper, 2010, Single-nucleotide evolutionary constraint scores highlight disease-causing mutations, Nature Methods, 7, 250, 10.1038/nmeth0410-250

Davydov, 2010, Identifying a high fraction of the human genome to be under selective constraint using GERP++, PLoS Comput Biol, 6, e1001025, 10.1371/journal.pcbi.1001025

Fu, 2013, Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants, Nature, 493, 216, 10.1038/nature11690

Garber, 2009, Identifying novel constrained elements by exploiting biased substitution patterns, Bioinformatics, 25, i54, 10.1093/bioinformatics/btp190

Gray, 2013, Genenames.org: the HGNC resources in 2013, Nucleic Acids Research, 41, D545, 10.1093/nar/gks1066

Guberman, 2011, BioMart Central Portal: an open database network for the biological community, Database: The Journal of Biological Databases and Curation, 2011, bar041, 10.1093/database/bar041

Harrow, 2012, GENCODE: the reference human genome annotation for The ENCODE Project, Genome Research, 22, 1760, 10.1101/gr.135350.111

Hindorff, 2009, Potential etiologic and functional implications of genome-wide association loci for human diseases and traits, Proceedings of the National Academy of Sciences of the United States of America, 106, 9362, 10.1073/pnas.0903103106

Huang, 2010, Characterising and predicting haploinsufficiency in the human genome, PLoS Genetics, 6, e1001154, 10.1371/journal.pgen.1001154

Hunter, 2012, InterPro in 2011: new developments in the family and domain prediction database, Nucleic Acids Research, 40, D306, 10.1093/nar/gkr948

Kelso, 2003, eVOC: a controlled vocabulary for unifying gene expression data, Genome Research, 13, 1222, 10.1101/gr.985203

Kerrien, 2011, The IntAct molecular interaction database in 2012, Nucleic Acids Research, 40, D841, 10.1093/nar/gkr1088

Kumar, 2009, Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm, Nature Protocols, 4, 1073, 10.1038/nprot.2009.86

Li, 2011, GWASdb: a database for human genetic variants identified by genome-wide association studies, Nucleic Acids Research, 40, D1047, 10.1093/nar/gkr1182

Li, 2012, A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases, Nucleic Acids Research, 40, e53, 10.1093/nar/gkr1257

Li, 2013, Predicting Mendelian Disease-Causing Non-Synonymous Single Nucleotide Variants in Exome Sequencing Studies, PLoS Genetics, 9, e1003143, 10.1371/journal.pgen.1003143

Lindblad-Toh, 2011, A high-resolution map of human evolutionary constraint using 29 mammals, Nature, 478, 476, 10.1038/nature10530

Lindenbaum, 2011, Knime4Bio: a set of custom nodes for the interpretation of next-generation sequencing data with KNIME, Bioinformatics, 27, 3200, 10.1093/bioinformatics/btr554

Liu, 2011, dbNSFP: A lightweight database of human nonsynonymous SNPs and their functional predictions, Human Mutation, 32, 894, 10.1002/humu.21517

MacArthur, 2012, A systematic survey of loss-of-function variants in human protein-coding genes, Science, 335, 823, 10.1126/science.1215040

Maglott, 2011, Entrez Gene: gene-centered information at NCBI, Nucleic Acids Research, 39, D52, 10.1093/nar/gkq1237

Massingham, 2005, Detecting amino acid sites under positive selection and purifying selection, Genetics, 169, 1753, 10.1534/genetics.104.032144

Meyer, 2012, The UCSC Genome Browser database: Extensions and updates 2013, Nucleic Acids Research, 41, D64, 10.1093/nar/gks1048

Pruitt, 2009, The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes, Genome Research, 19, 1316, 10.1101/gr.080531.108

Pruitt, 2012, NCBI Reference Sequences (RefSeq): Current status, new features and genome annotation policy, Nucleic Acids Research, 40, D130, 10.1093/nar/gkr1079

Reva, 2011, Predicting the functional impact of protein mutations: Application to cancer genomics, Nucleic Acids Research, 39, e118, 10.1093/nar/gkr407

Lucas, 2012, Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools, Bioinformatics, 28, 421, 10.1093/bioinformatics/btr667

Schwarz, 2010, MutationTaster evaluates disease-causing potential of sequence alterations, Nature Methods, 7, 575, 10.1038/nmeth0810-575

Shihab, 2013, Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models, Human Mutation, 34, 57, 10.1002/humu.22225

Sifrim, 2012, Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease, Genome Medicine, 4, 73, 10.1186/gm374

Siepel A Pollard KS Haussler D 2006 New methods for detecting lineage-specific selection 190 205

Su, 2002, Large-scale analysis of the human and mouse transcriptomes, Proceedings of the National Academy of Sciences of the United States of America, 99, 4465, 10.1073/pnas.012025199

The UniProt Consortium, 2011, Reorganizing the protein space at the Universal Protein Resource (UniProt), Nucleic Acids Research, 40, D71, 10.1093/nar/gkr981

Wang, 2010, ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data, Nucleic Acids Research, 38, e164, 10.1093/nar/gkq603

Zhang, 2013, PriVar: a toolkit for prioritizing SNVs and indels from next-generation sequencing data, Bioinformatics, 29, 124, 10.1093/bioinformatics/bts627