Oncotator: Cancer Variant Annotation Tool
Tóm tắt
Từ khóa
Tài liệu tham khảo
1000 Genomes Project Consortium, 2010, A map of human genome variation from population-scale sequencing, Nature, 467, 1061, 10.1038/nature09534
Adzhubei, 2010, A method and server for predicting damaging missense mutations, Nat Methods, 7, 248, 10.1038/nmeth0410-248
Alexandrov, 2013, Signatures of mutational processes in human cancer, Nature, 500, 415, 10.1038/nature12477
Banerji, 2012, Sequence analysis of mutations and translocations across breast cancer subtypes, Nature, 486, 405, 10.1038/nature11154
Barbieri, 2012, Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer, Nat Genet, 44, 685, 10.1038/ng.2279
Barretina, 2012, The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity, Nature, 483, 603, 10.1038/nature11003
Bass, 2011, Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion, Nat Genet, 43, 964, 10.1038/ng.936
Berger, 2012, Melanoma genome sequencing reveals frequent PREX2 mutations, Nature, 485, 502, 10.1038/nature11071
Berger, 2011, The genomic complexity of primary human prostate cancer, Nature, 470, 214, 10.1038/nature09744
Biesecker, 2014, Diagnostic Clinical Genome and Exome Sequencing, N Engl J Med, 370, 2418, 10.1056/NEJMra1312543
Cancer Genome Atlas Research Network, 2011, Integrated genomic analyses of ovarian carcinoma, Nature, 474, 609, 10.1038/nature10166
Cancer Genome Atlas Network, 2013, Comprehensive molecular characterization of human colon and rectal cancer, Nature, 487, 330, 10.1038/nature11252
Cancer Genome Atlas Network, 2014, Comprehensive molecular characterization of urothelial bladder carcinoma, Nature, 507, 315, 10.1038/nature12965
Chapman, 2011, Initial genome sequencing and analysis of multiple myeloma, Nature, 471, 467, 10.1038/nature09837
Hodis, 2012, A Landscape of Driver Mutations in Melanoma, Cell, 150, 251, 10.1016/j.cell.2012.06.024
Chun, 2009, Identification of deleterious mutations within three human genomes, Genome Res, 19, 1553, 10.1101/gr.092619.109
Cibulskis, 2013, Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples, Nat Biotechnol, 31, 213, 10.1038/nbt.2514
Cingolani, 2012, A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3, Fly (Austin), 6, 80, 10.4161/fly.19695
Ciriello, 2013, Emerging landscape of oncogenic signatures across human cancers, Nat Genet, 45, 1127, 10.1038/ng.2762
Costello, 2013, Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation, Nucleic Acids Res, 41, e67, 10.1093/nar/gks1443
Danecek, 2011, The variant call format and VCFtools, Bioinformatics, 27, 2156, 10.1093/bioinformatics/btr330
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
den Dunnen, 2000, Mutation nomenclature extensions and suggestions to describe complex mutations: a discussion, Hum Mutat, 15, 7, 10.1002/(SICI)1098-1004(200001)15:1<7::AID-HUMU4>3.0.CO;2-N
Forbes, 2010, COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer, Nucleic Acids Res, 39, D945, 10.1093/nar/gkq929
Francis, 2013, Somatic mutation of CDKN1B in small intestine neuroendocrine tumors, Nat Genet, 45, 1483, 10.1038/ng.2821
Garber, 2009, Identifying novel constrained elements by exploiting biased substitution patterns, Bioinformatics, 25, i54, 10.1093/bioinformatics/btp190
Hammerman, 2011, Mutations in the DDR2 Kinase Gene Identify a Novel Therapeutic Target in Squamous Cell Lung Cancer, Cancer Discov, 1, 78, 10.1158/2159-8274.CD-11-0005
Harrow, 2012, GENCODE: the reference human genome annotation for The ENCODE Project, Genome Res, 22, 1760, 10.1101/gr.135350.111
Imielinski, 2012, Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing, Cell, 150, 1107, 10.1016/j.cell.2012.08.029
Imielinski, 2014, Oncogenic and sorafenib-sensitive ARAF mutations in lung adenocarcinoma, J Clin Invest, 124, 1582, 10.1172/JCI72763
Knox, 2011, DrugBank 3.0: a comprehensive resource for ‘omics’ research on drugs, Nucleic Acids Res, 39, D1035, 10.1093/nar/gkq1126
Kumar, 2009, Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm, Nat Protoc, 4, 1073, 10.1038/nprot.2009.86
Lawrence, 2013, Mutational heterogeneity in cancer and the search for new cancer-associated genes, Nature, 499, 214, 10.1038/nature12213
Landrum, 2014, ClinVar: public archive of relationships among sequence variation and human phenotype, Nucleic Acids Res, 42, D980, 10.1093/nar/gkt1113
Pera, 2010, PICMI: mapping point mutations on genomes, Bioinformatics, 26, 2904, 10.1093/bioinformatics/btq547
Lee, 2012, A remarkably simple genome underlies highly malignant pediatric rhabdoid cancers, J Clin Invest, 122, 2983, 10.1172/JCI64400
Liu, 2013, dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations, Hum Mutat, 34, E2393, 10.1002/humu.22376
Lohr, 2012, Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing, Proc Natl Acad Sci U S A, 109, 3879, 10.1073/pnas.1121343109
McLaren, 2010, Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor, Bioinformatics, 26, 2069, 10.1093/bioinformatics/btq330
NHLBI GO Exome Sequencing Project 2014 http://evs.gs.washington.edu/EVS/
Ojesina, 2013, Landscape of genomic alterations in cervical carcinomas, Nature, 506, 371, 10.1038/nature12881
Pugh, 2012, Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations, Nature, 488, 106, 10.1038/nature11329
Pugh, 2014, Exome sequencing of pleuropulmonary blastoma reveals frequent biallelic loss of TP53 and two hits in DICER1 resulting in retention of 5p-derived miRNA hairpin loop sequences, Oncogene, 33, 5295, 10.1038/onc.2014.150
Reva, 2011, Predicting the functional impact of protein mutations: application to cancer genomics, Nucleic Acids Res, 39, e118, 10.1093/nar/gkr407
Sana, 2011, GAMES identifies and annotates mutations in next-generation sequencing projects, Bioinformatics, 27, 9, 10.1093/bioinformatics/btq603
Schwarz, 2010, MutationTaster evaluates disease-causing potential of sequence alterations, Nat Methods, 7, 575, 10.1038/nmeth0810-575
Sherry, 2001, dbSNP: the NCBI database of genetic variation, Nucleic Acids Res, 29, 308, 10.1093/nar/29.1.308
Shihab, 2013, Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models, Human Mutat, 34, 57, 10.1002/humu.22225
Stransky, 2011, The mutational landscape of head and neck squamous cell carcinoma, Science, 333, 1157, 10.1126/science.1208130
UniProt Consortium, 2011, Ongoing and future developments at the Universal Protein Resource, Nucleic Acids Res, 39, D214, 10.1093/nar/gkq1020
Allen, 2013, Clinical Analysis and Interpretation of Cancer Genome Data, J Clin Oncol, 31, 1825, 10.1200/JCO.2013.48.7215
Wang, 2010, ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data, Nucleic Acids Res, 38, e164, 10.1093/nar/gkq603
Wang, 2011, SF3B1 and other novel cancer genes in chronic lymphocytic leukemia, N Engl J Med, 365, 2497, 10.1056/NEJMoa1109016