Mutational signatures: the patterns of somatic mutations hidden in cancer genomes

Watson, 1953, Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid, Nature, 171, 37, 10.1038/171737a0 Rusch, 1939, Tumor production in mice with ultraviolet irradiation, Am J Cancer, 35, 55 Blum, 1950, On the mechanism of cancer induction by ultraviolet radiation, J Natl Cancer Inst, 11, 463 Witkin, 1969, Ultraviolet-induced mutation and DNA repair, Annu Rev Microbiol, 23, 487, 10.1146/annurev.mi.23.100169.002415 Howard, 1964, Identification of the altered bases in mutated single-stranded DNA. II. In vivo mutagenesis by 5-bromodeoxyuridine and 2-aminopurine, J Mol Biol, 9, 364, 10.1016/S0022-2836(64)80213-8 Setlow, 1966, Pyrimidine dimers in ultraviolet-irradiated DNA's, J Mol Biol, 17, 237, 10.1016/S0022-2836(66)80105-5 Sanger, 1977, DNA sequencing with chain-terminating inhibitors, Proc Natl Acad Sci USA, 74, 5463, 10.1073/pnas.74.12.5463 Brash, 1991, A role for sunlight in skin cancer: UV-induced p53 mutations in squamous cell carcinoma, Proc Natl Acad Sci USA, 88, 10124, 10.1073/pnas.88.22.10124 Ozturk, 1991, P53 mutation in hepatocellular carcinoma after aflatoxin exposure, Lancet, 338, 1356, 10.1016/0140-6736(91)92236-U Vogelstein, 1992, Carcinogens leave fingerprints, Nature, 355, 209, 10.1038/355209a0 Greenblatt, 1994, Mutations in the p53 tumor suppressor gene: clues to cancer etiology and molecular pathogenesis, Cancer Res, 54, 4855 Hollstein, 1991, P53 mutations in human cancers, Science, 253, 49, 10.1126/science.1905840 Hollstein, 1999, New approaches to understanding p53 gene tumor mutation spectra, Mutat Res, 431, 199, 10.1016/S0027-5107(99)00162-1 Capella, 1991, Frequency and spectrum of mutations at codons 12 and 13 of the c-k-ras gene in human tumors, Environ Health Perspect, 93, 125, 10.1289/ehp.9193125 Rodin, 2005, Origins and selection of p53 mutations in lung carcinogenesis, Semin Cancer Biol, 15, 103, 10.1016/j.semcancer.2004.08.005 Wogan, 1992, Aflatoxins as risk factors for hepatocellular carcinoma in humans, Cancer Res, 52, 2114s Hainaut, 2001, Tp53 mutation spectrum in lung cancers and mutagenic signature of components of tobacco smoke: lessons from the iarc tp53 mutation database, Mutagenesis, 16, 551, 10.1093/mutage/16.6.551 Cariello, 1994, Database and software for the analysis of mutations in the human p53 gene, Cancer Res, 54, 4454 Alexandrov, 2013, Signatures of mutational processes in human cancer, Nature, 500, 415, 10.1038/nature12477 Alexandrov, 2013, Deciphering signatures of mutational processes operative in human cancer, Cell Rep, 3, 246, 10.1016/j.celrep.2012.12.008 Stratton, 2011, Exploring the genomes of cancer cells: progress and promise, Science, 331, 1553, 10.1126/science.1204040 Stratton, 2009, The cancer genome, Nature, 458, 719, 10.1038/nature07943 Stephens, 2005, A screen of the complete protein kinase gene family identifies diverse patterns of somatic mutations in human breast cancer, Nat Genet, 37, 590, 10.1038/ng1571 Greenman, 2007, Patterns of somatic mutation in human cancer genomes, Nature, 446, 153, 10.1038/nature05610 Rubin, 2009, Mutation patterns in cancer genomes, Proc Natl Acad Sci USA, 106, 21766, 10.1073/pnas.0912499106 International Cancer Genome, 2010, International network of cancer genome projects, Nature, 464, 993, 10.1038/nature08987 Pleasance, 2010, A comprehensive catalogue of somatic mutations from a human cancer genome, Nature, 463, 191, 10.1038/nature08658 Pleasance, 2010, A small-cell lung cancer genome with complex signatures of tobacco exposure, Nature, 463, 184, 10.1038/nature08629 De Keersmaecker, 2013, Exome sequencing identifies mutation in cnot3 and ribosomal genes rpl5 and rpl10 in t-cell acute lymphoblastic leukemia, Nat Genet, 45, 186, 10.1038/ng.2508 Holmfeldt, 2013, The genomic landscape of hypodiploid acute lymphoblastic leukemia, Nat Genet, 45, 242, 10.1038/ng.2532 Zhang, 2012, The genetic basis of early t-cell precursor acute lymphoblastic leukaemia, Nature, 481, 157, 10.1038/nature10725 Ding, 2012, Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing, Nature, 481, 506, 10.1038/nature10738 Nik-Zainal, 2012, Mutational processes molding the genomes of 21 breast cancers, Cell, 149, 979, 10.1016/j.cell.2012.04.024 Shah, 2012, The clonal and mutational evolution spectrum of primary triple-negative breast cancers, Nature, 486, 395, 10.1038/nature10933 Stephens, 2012, The landscape of cancer genes and mutational processes in breast cancer, Nature, 486, 400, 10.1038/nature11017 Puente, 2011, Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia, Nature, 475, 101, 10.1038/nature10113 Quesada, 2012, Exome sequencing identifies recurrent mutations of the splicing factor sf3b1 gene in chronic lymphocytic leukemia, Nat Genet, 44, 47, 10.1038/ng.1032 Cancer Genome Atlas, 2012, Comprehensive molecular characterization of human colon and rectal cancer, Nature, 487, 330, 10.1038/nature11252 Seshagiri, 2012, Recurrent r-spondin fusions in colon cancer, Nature, 488, 660, 10.1038/nature11282 Dulak, 2013, Exome and whole-genome sequencing of esophageal adenocarcinoma identifies recurrent driver events and mutational complexity, Nat Genet, 45, 478, 10.1038/ng.2591 Parsons, 2008, An integrated genomic analysis of human glioblastoma multiforme, Science, 321, 1807, 10.1126/science.1164382 Agrawal, 2011, Exome sequencing of head and neck squamous cell carcinoma reveals inactivating mutations in notch1, Science, 333, 1154, 10.1126/science.1206923 Stransky, 2011, The mutational landscape of head and neck squamous cell carcinoma, Science, 333, 1157, 10.1126/science.1208130 Cancer Genome Atlas Research Network, 2013, Comprehensive molecular characterization of clear cell renal cell carcinoma, Nature, 499, 43, 10.1038/nature12222 Guo, 2012, Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma, Nat Genet, 44, 17, 10.1038/ng.1014 Pena-Llopis, 2012, Bap1 loss defines a new class of renal cell carcinoma, Nat Genet, 44, 751, 10.1038/ng.2323 Kan, 2013, Whole-genome sequencing identifies recurrent mutations in hepatocellular carcinoma, Genome Res, 23, 1422, 10.1101/gr.154492.113 Fujimoto, 2012, Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators, Nat Genet, 44, 760, 10.1038/ng.2291 Seo, 2012, The transcriptional landscape and mutational profile of lung adenocarcinoma, Genome Res, 22, 2109, 10.1101/gr.145144.112 Imielinski, 2012, Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing, Cell, 150, 1107, 10.1016/j.cell.2012.08.029 Govindan, 2012, Genomic landscape of non-small cell lung cancer in smokers and never-smokers, Cell, 150, 1121, 10.1016/j.cell.2012.08.024 Ding, 2008, Somatic mutations affect key pathways in lung adenocarcinoma, Nature, 455, 1069, 10.1038/nature07423 Peifer, 2012, Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer, Nat Genet, 44, 1104, 10.1038/ng.2396 Rudin, 2012, Comprehensive genomic analysis identifies sox2 as a frequently amplified gene in small-cell lung cancer, Nat Genet, 44, 1111, 10.1038/ng.2405 Love, 2012, The genetic landscape of mutations in burkitt lymphoma, Nat Genet, 44, 1321, 10.1038/ng.2468 Morin, 2011, Frequent mutation of histone-modifying genes in non-hodgkin lymphoma, Nature, 476, 298, 10.1038/nature10351 Huang, 2013, Highly recurrent tert promoter mutations in human melanoma, Science, 339, 957, 10.1126/science.1229259 Stark, 2012, Frequent somatic mutations in map3k5 and map3k9 in metastatic melanoma identified by exome sequencing, Nat Genet, 44, 165, 10.1038/ng.1041 Berger, 2012, Melanoma genome sequencing reveals frequent prex2 mutations, Nature, 485, 502, 10.1038/nature11071 Hodis, 2012, A landscape of driver mutations in melanoma, Cell, 150, 251, 10.1016/j.cell.2012.06.024 Chapman, 2011, Initial genome sequencing and analysis of multiple myeloma, Nature, 471, 467, 10.1038/nature09837 Jones, 2010, Frequent mutations of chromatin remodeling gene arid1a in ovarian clear cell carcinoma, Science, 330, 228, 10.1126/science.1196333 Jiao, 2011, Daxx/atrx, men1, and mtor pathway genes are frequently altered in pancreatic neuroendocrine tumors, Science, 331, 1199, 10.1126/science.1200609 Wu, 2011, Whole-exome sequencing of neoplastic cysts of the pancreas reveals recurrent mutations in components of ubiquitin-dependent pathways, Proc Natl Acad Sci USA, 108, 21188, 10.1073/pnas.1118046108 Baca, 2013, Punctuated evolution of prostate cancer genomes, Cell, 153, 666, 10.1016/j.cell.2013.03.021 Grasso, 2012, The mutational landscape of lethal castration-resistant prostate cancer, Nature, 487, 239, 10.1038/nature11125 Barbieri, 2012, Exome sequencing identifies recurrent spop, foxa1 and med12 mutations in prostate cancer, Nat Genet, 44, 685, 10.1038/ng.2279 Berger, 2011, The genomic complexity of primary human prostate cancer, Nature, 470, 214, 10.1038/nature09744 Zang, 2012, Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes, Nat Genet, 44, 570, 10.1038/ng.2246 Wang, 2011, Exome sequencing identifies frequent mutation of arid1a in molecular subtypes of gastric cancer, Nat Genet, 43, 1219, 10.1038/ng.982 Nagarajan, 2012, Whole-genome reconstruction and mutational signatures in gastric cancer, Genome Biol, 13, R115, 10.1186/gb-2012-13-12-r115 Cancer Genome Atlas Research Network, 2013, Integrated genomic characterization of endometrial carcinoma, Nature, 497, 67, 10.1038/nature12113 Robinson, 2012, Novel mutations target distinct subgroups of medulloblastoma, Nature, 488, 43, 10.1038/nature11213 Rausch, 2012, Genome sequencing of pediatric medulloblastoma links catastrophic DNA rearrangements with tp53 mutations, Cell, 148, 59, 10.1016/j.cell.2011.12.013 Pugh, 2012, Medulloblastoma exome sequencing uncovers subtype-specific somatic mutations, Nature, 488, 106, 10.1038/nature11329 Jones, 2012, Dissecting the genomic complexity underlying medulloblastoma, Nature, 488, 100, 10.1038/nature11284 Pugh, 2013, The genetic landscape of high-risk neuroblastoma, Nat Genet, 45, 279, 10.1038/ng.2529 Sausen, 2013, Integrated genomic analyses identify arid1a and arid1b alterations in the childhood cancer neuroblastoma, Nat Genet, 45, 12, 10.1038/ng.2493 Zhang, 2013, Whole-genome sequencing identifies genetic alterations in pediatric low-grade gliomas, Nat Genet, 45, 602, 10.1038/ng.2611 Spencer, 2005, Hypermutation at a–t base pairs: the a nucleotide replacement spectrum is affected by adjacent nucleotides and there is no reverse complementarity of sequences flanking mutated a and t nucleotides, J Immunol, 175, 5170, 10.4049/jimmunol.175.8.5170 Hoang, 2013, Mutational signature of aristolochic acid exposure as revealed by whole-exome sequencing, Sci Transl Med, 5, 197ra102, 10.1126/scitranslmed.3006200 Comon, 2010 Lee, 1999, Learning the parts of objects by non-negative matrix factorization, Nature, 401, 788, 10.1038/44565 Taylor, 2013, DNA deaminases induce break-associated mutation showers with implication of apobec3b and 3a in breast cancer kataegis, eLife, 2, e00534, 10.7554/eLife.00534 Harris, 2002, Rna editing enzyme apobec1 and some of its homologs can act as DNA mutators, Mol Cell, 10, 1247, 10.1016/S1097-2765(02)00742-6 Nik-Zainal, 2012, The life history of 21 breast cancers, Cell, 149, 994, 10.1016/j.cell.2012.04.023 van Zeeland, 2005, Transcription-coupled repair: impact on uv-induced mutagenesis in cultured rodent cells and mouse skin tumors, Mutat Res, 577, 170, 10.1016/j.mrfmmm.2005.03.018 Roberts, 2013, An apobec cytidine deaminase mutagenesis pattern is widespread in human cancers, Nat Genet, 45, 970, 10.1038/ng.2702 Burns, 2013, Evidence for apobec3b mutagenesis in multiple human cancers, Nat Genet, 45, 977, 10.1038/ng.2701