|
[1] Chin C S, Sorenson J, Harris J B, et al. The origin of the Haitian cholera outbreak strain. The New England Journal of Medicine, 2011, 364: 33-42.
[2] Loomis E W, Eid J S, Peluso P, et al. Sequencing the unsequenceable: expanded CGG-repeat alleles of the fragile X gene. Genome Research, 2013, 23: 121-128.
[3] Rasko D A, Webster D R, Sahl J W, et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. The New England Journal of Medicine, 2011, 365: 709-717.
[4] Smith C C, Wang Q, Chin C S, et al. Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia. Nature, 2012, 485: 260-263.
[5] Ley T J, Mardis E R, Ding L, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature, 2008, 456: 66-72.
[6] International Human Genome Sequencing C. Finishing the euchromatic sequence of the human genome. Nature, 2004, 431: 931-945.
[7] McCabe M T, Ott H M, Ganji G, et al. EZH2 inhibition as a therapeutic strategy for lymphoma with EZH2-activating mutations. Nature, 2012, 492: 108-112.
[8] Nik-Zainal S, Alexandrov L B, Wedge D C, et al. Mutational processes molding the genomes of 21 breast cancers. Cell, 2012, 149: 979-993.
[9] Stephens P J, Greenman C D, Fu B, et al. Massive genomic rearrangement acquired in a single catastrophic event during cancer development. Cell, 2011, 144: 27-40.
[10] Misale S, Yaeger R, Hobor S, et al. Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer. Nature, 2012, 486: 532-536.
[11] Northcott P A, Jones D T, Kool M, et al. Medulloblastomics: the end of the beginning. Nature Rreviews Cancer, 2012, 12: 818-834.
[12] Castoe T A, de Koning A P, Pollock D D. Adaptive molecular convergence: molecular evolution versus molecular phylogenetics. Communicative & Integrative Biology, 2010, 3: 67-69.
[13] Fujimoto A, Totoki Y, Abe T, et al. Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nature Genetics, 2012, 44: 760-764.
[14] Berger M F, Hodis E, Heffernan T P, et al. Melanoma genome sequencing reveals frequent PREX2 mutations. Nature, 2012, 485: 502-506.
[15] Shah S P, Roth A, Goya R, et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature, 2012, 486: 395-399.
[16] Chapman M A, Lawrence M S, Keats J J, et al. Initial genome sequencing and analysis of multiple myeloma. Nature, 2011, 471: 467-472.
[17] Kimchi-Sarfaty C, Oh JM, Kim I W, et al. A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science, 2007, 315: 525-528.
[18] Pagani F, Raponi M, Baralle F E. Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution. Proceedings of the National Academy of Sciences of the United States of America, 2005, 102: 6368-6372.
[19] Morin R D, Mendez-Lago M, Mungall A J, et al. Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature, 2011, 476: 298-303.
[20] Molenaar J J, Koster J, Zwijnenburg D A, et al. Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes. Nature, 2012, 483: 589-593.
[21] Lee W, Jiang Z, Liu J, et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature, 2010, 465: 473-477.
[22] Jones S J, Laskin J, Li Y Y, et al. Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. Genome Biology, 2010, 11: R82.
[23] Jones D T, Jager N, Kool M, et al. Dissecting the genomic complexity underlying medulloblastoma. Nature, 2012, 488: 100-105.
[24] Cheung N K, Zhang J, Lu C, et al. Association of age at diagnosis and genetic mutations in patients with neuroblastoma. The Journal of the American Medical Association, 2012, 307: 1062-1071.
[25] Dees N D, Zhang Q, Kandoth C, et al. MuSiC: identifying mutational significance in cancer genomes. Genome Research, 2012, 22: 1589-1598.
[26] Ding L, Ley T J, Larson D E, et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature, 2012, 481: 506-510.
[27] Wu C, Wyatt A W, Lapuk A V, et al. Integrated genome and transcriptome sequencing identifies a novel form of hybrid and aggressive prostate cancer. The Journal of Pathology, 2012, 227: 53-61.
[28] Gerlinger M, Rowan A J, Horswell S, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. The New England Journal of Medicine, 2012, 366: 883-892.
[29] Walter M J, Shen D, Ding L, et al. Clonal architecture of secondary acute myeloid leukemia. The New England Journal of Medicine, 2012, 366: 1090-1098.
[30] Nik-Zainal S, Van Loo P, Wedge D C, et al. The life history of 21 breast cancers. Cell, 2012, 149: 994-1007.
[31] Ding L, Ellis M J, Li S, et al. Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature, 2010, 464: 999-1005.
[32] Tao Y, Ruan J, Yeh S H, et al. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data. Proceedings of the National Academy of Sciences of the United States of America, 2011, 108: 12042-12047.
[33] Weiss G J, Liang W S, Izatt T, et al. Paired tumor and normal whole genome sequencing of metastatic olfactory neuroblastoma. PloS One, 2012, 7: e37029.
[34] Ng C K, Cooke S L, Howe K, et al. The role of tandem duplicator phenotype in tumour evolution in high-grade serous ovarian cancer. The Journal of Pathology, 2012, 226: 703-712.
[35] Turajlic S, Furney S J, Lambros M B, et al. Whole genome sequencing of matched primary and metastatic acral melanomas. Genome Research, 2012, 22: 196-207.
[36] Link D C, Schuettpelz L G, Shen D, et al. Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. The Journal of the American Medical Association, 2011, 305: 1568-1576.
[37] Mardis E R, Ding L, Dooling D J, et al. Recurring mutations found by sequencing an acute myeloid leukemia genome. The New England Journal of Medicine, 2009, 361: 1058-1066.
[38] Pleasance E D, Stephens P J, O'Meara S, et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature, 2010, 463: 184-190.
[39] Ellis M J, Ding L, Shen D, et al. Whole-genome analysis informs breast cancer response to aromatase inhibition. Nature, 2012, 486: 353-360.
[40] Puente X S, Pinyol M, Quesada V, et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature, 2011, 475: 101-105.
[41] Campbell PJ, Yachida S, Mudie L J, et al. The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature, 2010, 467: 1109-1113.
[42] Pena-Llopis S, Vega S, Liao A, et al. BAP1 loss defines a new class of renal cell carcinoma. Nature Genetics, 2012, 44: 751-759.
[43] Stephens P J, McBride D J, Lin M L, et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature, 2009, 462: 1005-1010.
[44] Kloosterman W P, Hoogstraat M, Paling O, et al. Chromothripsis is a common mechanism driving genomic rearrangements in primary and metastatic colorectal cancer. Genome Biology, 2011, 12: R103.
[45] McBride D J, Etemadmoghadam D, Cooke SL, et al. Tandem duplication of chromosomal segments is common in ovarian and breast cancer genomes. The Journal of Pathology, 2012, 227: 446-455.
[46] Cancer Genome Atlas N. Comprehensive molecular characterization of human colon and rectal cancer. Nature, 2012, 487: 330-337.
[47] Korbel J O, Urban A E, Affourtit J P, et al. Paired-end mapping reveals extensive structural variation in the human genome. Science, 2007, 318: 420-426.
[48] Onishi-Seebacher M, Korbel J O. Challenges in studying genomic structural variant formation mechanisms: the short-read dilemma and beyond. BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology, 2011, 33: 840-850.
[49] Simpson J T, Wong K, Jackman S D, et al. ABySS: a parallel assembler for short read sequence data. Genome Research, 2009, 19: 1117-1123.
[50] Fullwood M J, Wei C L, Liu E T, et al. Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses. Genome Research, 2009, 19: 521-532.
[51] Druker B J, Guilhot F, O'Brien S G, et al. Five-year follow-up of patients receiving imatinib for chronic myeloid leukemia. The New England Journal of Medicine, 2006, 355: 2408-2417.
[52] Shah S P, Morin R D, Khattra J, et al. Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature, 2009, 461: 809-813.
[53] Bass A J, Lawrence M S, Brace L E, et al. Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion. Nature Genetics, 2011, 43: 964-968.
[54] Totoki Y, Tatsuno K, Yamamoto S, et al. High-resolution characterization of a hepatocellular carcinoma genome. Nature Genetics, 2011, 43: 464-469.
[55] Demeure M J, Craig D W, Sinari S, et al. Cancer of the ampulla of Vater: analysis of the whole genome sequence exposes a potential therapeutic vulnerability. Genome Medicine, 2012, 4: 56.
[56] Muller F L, Colla S, Aquilanti E, et al. Passenger deletions generate therapeutic vulnerabilities in cancer. Nature, 2012, 488: 337-342.
[57] Wu G, Broniscer A, McEachron T A, et al. Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas. Nature Genetics, 2012, 44: 251-253.
[58] Karakoc E, Alkan C, O'Roak B J, et al. Detection of structural variants and indels within exome data. Nature Methods, 2012, 9: 176-178.
[59] Banerji S, Cibulskis K, Rangel-Escareno C, et al. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature, 2012, 486: 405-409.
[60] Roberts K G, Morin R D, Zhang J, et al. Genetic alterations activating kinase and cytokine receptor signaling in high-risk acute lymphoblastic leukemia. Cancer Cell, 2012, 22: 153-166.
[61] Cancer Genome Atlas Research N. Comprehensive genomic characterization of squamous cell lung cancers. Nature, 2012, 489: 519-525.
[62] Vaske C J, Benz S C, Sanborn J Z, et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics, 2010, 26: i237-245.
[63] Hawkins R D, Hon G C, Ren B. Next-generation genomics: an integrative approach. Nature Reviews Genetics, 2010, 11: 476-486.
[64] Zhang J, Ding L, Holmfeldt L, et al. The genetic basis of early T-cell precursor acute lymphoblastic leukaemia. Nature, 2012, 481: 157-163.
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