Annotation of Sequence Variants in Cancer Samples

The Journal of Molecular Diagnostics - Tập 17 - Trang 339-351 - 2015
Lobin A. Lee1, Kevin J. Arvai1, Dan Jones1
1Department of Pathology, Quest Diagnostics Nichols Institute, Chantilly, Virginia

Tài liệu tham khảo

King, 2003, Breast and ovarian cancer risks due to inherited mutations in BRCA1 and BRCA2, Science, 302, 643, 10.1126/science.1088759 Lynch, 1999, Genetic susceptibility to non-polyposis colorectal cancer, J Med Genet, 36, 801 2007, Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls, Nature, 447, 661, 10.1038/nature05911 Manolio, 2009, Finding the missing heritability of complex diseases, Nature, 461, 747, 10.1038/nature08494 Dong, 2008, Genetic susceptibility to cancer: the role of polymorphisms in candidate genes, JAMA, 299, 2423, 10.1001/jama.299.20.2423 McClellan, 2010, Genetic heterogeneity in human disease, Cell, 141, 210, 10.1016/j.cell.2010.03.032 Larson, 2012, SomaticSniper: identification of somatic point mutations in whole genome sequencing data, Bioinformatics, 28, 311, 10.1093/bioinformatics/btr665 Aziz, 2015, College of American Pathologists' laboratory standards for next-generation sequencing clinical tests, Arch Pathol Lab Med, 139, 481, 10.5858/arpa.2014-0250-CP 2003, The International HapMap Project, Nature, 426, 789, 10.1038/nature02168 Tennessen, 2012, Evolution and functional impact of rare coding variation from deep sequencing of human exomes, Science, 337, 64, 10.1126/science.1219240 Abecasis, 2012, An integrated map of genetic variation from 1,092 human genomes, Nature, 491, 56, 10.1038/nature11632 Yang, 2010, Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies, Bioinformatics, 26, 2474, 10.1093/bioinformatics/btq452 2014, Database resources of the National Center for Biotechnology Information, Nucleic Acids Res, 42, D7, 10.1093/nar/gkt1146 MacDonald, 2014, The Database of Genomic Variants: a curated collection of structural variation in the human genome, Nucleic Acids Res, 42, D986, 10.1093/nar/gkt958 Gorlov, 2008, Shifting paradigm of association studies: value of rare single-nucleotide polymorphisms, Am J Hum Genet, 82, 100, 10.1016/j.ajhg.2007.09.006 Abecasis, 2010, A map of human genome variation from population-scale sequencing, Nature, 467, 1061, 10.1038/nature09534 Landrum, 2014, ClinVar: public archive of relationships among sequence variation and human phenotype, Nucleic Acids Res, 42, D980, 10.1093/nar/gkt1113 Richards, 2008, ACMG recommendations for standards for interpretation and reporting of sequence variations: revisions 2007, Genet Med, 10, 294, 10.1097/GIM.0b013e31816b5cae Tavtigian, 2008, Assessing pathogenicity: overview of results from the IARC Unclassified Genetic Variants Working Group, Hum Mutat, 29, 1261, 10.1002/humu.20903 Goldgar, 2004, Integrated evaluation of DNA sequence variants of unknown clinical significance: application to BRCA1 and BRCA2, Am J Hum Genet, 75, 535, 10.1086/424388 Thompson, 2014, Application of a 5-tiered scheme for standardized classification of 2,360 unique mismatch repair gene variants in the InSiGHT locus-specific database, Nat Genet, 46, 107, 10.1038/ng.2854 Easton, 2007, A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes, Am J Hum Genet, 81, 873, 10.1086/521032 Greaves, 2012, Clonal evolution in cancer, Nature, 481, 306, 10.1038/nature10762 Gerlinger, 2012, Intratumor heterogeneity and branched evolution revealed by multiregion sequencing, N Engl J Med, 366, 883, 10.1056/NEJMoa1113205 Qi, 2014, Diversity and clonal selection in the human T-cell repertoire, Proc Natl Acad Sci U S A, 111, 13139, 10.1073/pnas.1409155111 Schumacher, 2014, A comparison of deep sequencing of TCRG rearrangements vs traditional capillary electrophoresis for assessment of clonality in T-cell lymphoproliferative disorders, Am J Clin Pathol, 141, 348, 10.1309/AJCP5TYGBVW4ZITR Lee, 2014, Assessment of mutation status in a large series of patients with suspected cytopenias with normal karyotypes and without increased blasts, Blood, 124, 4606, 10.1182/blood.V124.21.4606.4606 Lacey, 2008, Risk of subsequent endometrial carcinoma associated with endometrial intraepithelial neoplasia classification of endometrial biopsies, Cancer, 113, 2073, 10.1002/cncr.23808 2013, Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia, N Engl J Med, 368, 2059, 10.1056/NEJMoa1301689 Cervera, 2014, Gene mutations differently impact the prognosis of the myelodysplastic and myeloproliferative classes of chronic myelomonocytic leukemia, Am J Hematol, 89, 604, 10.1002/ajh.23702 Patnaik, 2013, Mayo prognostic model for WHO-defined chronic myelomonocytic leukemia: ASXL1 and spliceosome component mutations and outcomes, Leukemia, 27, 1504, 10.1038/leu.2013.88 Schnittger, 2012, Molecular analyses of 15,542 patients with suspected BCR-ABL1-negative myeloproliferative disorders allow to develop a stepwise diagnostic workflow, Haematologica, 97, 1582, 10.3324/haematol.2012.064683 Kandoth, 2013, Integrated genomic characterization of endometrial carcinoma, Nature, 497, 67, 10.1038/nature12113 Tothill, 2013, Massively-parallel sequencing assists the diagnosis and guided treatment of cancers of unknown primary, J Pathol, 231, 413, 10.1002/path.4251 Vardiman, 2009, The 2008 revision of the World Health Organization (WHO) classification of myeloid neoplasms and acute leukemia: rationale and important changes, Blood, 114, 937, 10.1182/blood-2009-03-209262 Fasan, 2013, Frequency and prognostic impact of CEBPA proximal, distal and core promoter methylation in normal karyotype AML: a study on 623 cases, PLoS One, 8, e54365, 10.1371/journal.pone.0054365 Jabbour, 2009, Long-term outcome of patients with chronic myeloid leukemia treated with second-generation tyrosine kinase inhibitors after imatinib failure is predicted by the in vitro sensitivity of BCR-ABL kinase domain mutations, Blood, 114, 2037, 10.1182/blood-2009-01-197715 Mok, 2013, Treating patients with EGFR-sensitizing mutations: first line or second line–is there a difference?, J Clin Oncol, 31, 1081, 10.1200/JCO.2012.43.0652 Chapman, 2011, Improved survival with vemurafenib in melanoma with BRAF V600E mutation, N Engl J Med, 364, 2507, 10.1056/NEJMoa1103782 Puig, 2014, Critical evaluation of ASO RQ-PCR for minimal residual disease evaluation in multiple myeloma: a comparative analysis with flow cytometry, Leukemia, 28, 391, 10.1038/leu.2013.217 Wu, 2012, High-throughput sequencing detects minimal residual disease in acute T lymphoblastic leukemia, Sci Transl Med, 4, 134ra63, 10.1126/scitranslmed.3003656 Stead, 2013, Accurately identifying low-allelic fraction variants in single samples with next-generation sequencing: applications in tumor subclone resolution, Hum Mutat, 34, 1432, 10.1002/humu.22365 Chen, 2015, Clinical actionability enhanced through deep targeted sequencing of solid tumors, Clin Chem, 61, 544, 10.1373/clinchem.2014.231100 Lin, 2014, IDH mutations are closely associated with mutations of DNMT3A, ASXL1 and SRSF2 in patients with myelodysplastic syndromes and are stable during disease evolution, Am J Hematol, 89, 137, 10.1002/ajh.23596 Daber, 2013, Understanding the limitations of next generation sequencing informatics, an approach to clinical pipeline validation using artificial data sets, Cancer Genet, 206, 441, 10.1016/j.cancergen.2013.11.005 Spencer, 2013, Detection of FLT3 internal tandem duplication in targeted, short-read-length, next-generation sequencing data, J Mol Diagn, 15, 81, 10.1016/j.jmoldx.2012.08.001 Forbes, 2011, COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer, Nucleic Acids Res, 39, D945, 10.1093/nar/gkq929 Bell, 2005, Inherited susceptibility to lung cancer may be associated with the T790M drug resistance mutation in EGFR, Nat Genet, 37, 1315, 10.1038/ng1671 Metzeler, 2011, TET2 mutations improve the new European LeukemiaNet risk classification of acute myeloid leukemia: a Cancer and Leukemia Group B study, J Clin Oncol, 29, 1373, 10.1200/JCO.2010.32.7742 Greenberg, 2012, Revised international prognostic scoring system for myelodysplastic syndromes, Blood, 120, 2454, 10.1182/blood-2012-03-420489 Malcovati, 2013, Diagnosis and treatment of primary myelodysplastic syndromes in adults: recommendations from the European LeukemiaNet, Blood, 122, 2943, 10.1182/blood-2013-03-492884 Solary, 2014, The Ten-Eleven Translocation-2 (TET2) gene in hematopoiesis and hematopoietic diseases, Leukemia, 28, 485, 10.1038/leu.2013.337 Ko, 2010, Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2, Nature, 468, 839, 10.1038/nature09586 Genovese, 2014, Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence, N Engl J Med, 371, 2477, 10.1056/NEJMoa1409405 Gaidzik, 2012, TET2 mutations in acute myeloid leukemia (AML): results from a comprehensive genetic and clinical analysis of the AML study group, J Clin Oncol, 30, 1350, 10.1200/JCO.2011.39.2886 Smith, 2010, Next-generation sequencing of the TET2 gene in 355 MDS and CMML patients reveals low-abundance mutant clones with early origins, but indicates no definite prognostic value, Blood, 116, 3923, 10.1182/blood-2010-03-274704 Hu, 2013, Crystal structure of TET2-DNA complex: insight into TET-mediated 5mC oxidation, Cell, 155, 1545, 10.1016/j.cell.2013.11.020 Lin, 2014, Clonal leukemic evolution in myelodysplastic syndromes with TET2 and IDH1/2 mutations, Haematologica, 99, 28, 10.3324/haematol.2013.091249 Nibourel, 2010, Incidence and prognostic value of TET2 alterations in de novo acute myeloid leukemia achieving complete remission, Blood, 116, 1132, 10.1182/blood-2009-07-234484 Tavtigian, 2008, In silico analysis of missense substitutions using sequence-alignment based methods, Hum Mutat, 29, 1327, 10.1002/humu.20892 Chan, 2007, Interpreting missense variants: comparing computational methods in human disease genes CDKN2A, MLH1, MSH2, MECP2, and tyrosinase (TYR), Hum Mutat, 28, 683, 10.1002/humu.20492 Gemovic, 2013, Feature-based classification of amino acid substitutions outside conserved functional protein domains, Scientific World Journal, 2013, 948617, 10.1155/2013/948617 Gonzalez-Perez, 2011, Improving the assessment of the outcome of nonsynonymous SNVs with a consensus deleteriousness score, Condel, Am J Hum Genet, 88, 440, 10.1016/j.ajhg.2011.03.004 Kroeze, 2014, Characterization of acute myeloid leukemia based on levels of global hydroxymethylation, Blood, 124, 1110, 10.1182/blood-2013-08-518514 Lawrence, 2013, Mutational heterogeneity in cancer and the search for new cancer-associated genes, Nature, 499, 214, 10.1038/nature12213 Weissmann, 2012, Landscape of TET2 mutations in acute myeloid leukemia, Leukemia, 26, 934, 10.1038/leu.2011.326 Kutny, 2010, TET2 SNP rs2454206 (I1762V) correlates with improved survival in pediatric acute myelogenous leukemia, a report from the Children's Oncology Group, Blood, 116, 418a Lindor, 2012, A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS), Hum Mutat, 33, 8, 10.1002/humu.21627 McArthur, 2014, Safety and efficacy of vemurafenib in BRAF(V600E) and BRAF(V600K) mutation-positive melanoma (BRIM-3): extended follow-up of a phase 3, randomised, open-label study, Lancet Oncol, 15, 323, 10.1016/S1470-2045(14)70012-9 Landsman-Blumberg, 2014, Metastatic colorectal cancer treatment patterns according to kirsten rat sarcoma viral oncogene homolog genotype in U.S. community-based oncology practices, Clin Colorectal Cancer, 13, 178, 10.1016/j.clcc.2014.05.001 Qu, 2013, Detection of BRAF V600 mutations in metastatic melanoma: comparison of the Cobas 4800 and Sanger sequencing assays, J Mol Diagn, 15, 790, 10.1016/j.jmoldx.2013.07.003 Ding, 2014, The predictive role of pretreatment epidermal growth factor receptor T790M mutation on the progression-free survival of tyrosine-kinase inhibitor-treated non-small cell lung cancer patients: a meta-analysis, Onco Targets Ther, 7, 387 Bradeen, 2006, Comparison of imatinib mesylate, dasatinib (BMS-354825), and nilotinib (AMN107) in an N-ethyl-N-nitrosourea (ENU)-based mutagenesis screen: high efficacy of drug combinations, Blood, 108, 2332, 10.1182/blood-2006-02-004580 Cottrell, 2014, Validation of a next-generation sequencing assay for clinical molecular oncology, J Mol Diagn, 16, 89, 10.1016/j.jmoldx.2013.10.002 Jung, 2013, Systematic investigation of cancer-associated somatic point mutations in SNP databases, Nat Biotechnol, 31, 787, 10.1038/nbt.2681