Genomic sequencing in cancer.

Genomic sequencing has provided critical insights into the etiology of both simple and complex diseases. The enormous reductions in cost for whole genome sequencing have allowed this technology to gain increasing use. Whole genome analysis has impacted research of complex diseases including cancer by allowing the systematic analysis of entire genomes in a single experiment, thereby facilitating the discovery of somatic and germline mutations, and identification of the insertions, deletions, and structural rearrangements, including translocations and inversions, in novel disease genes. Whole-genome sequencing can be used to provide the most comprehensive characterization of the cancer genome, the complexity of which we are only beginning to understand. Hence in this review, we focus on whole-genome sequencing in cancer.

[1]  S. Quake,et al.  Sequence information can be obtained from single DNA molecules , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[2]  R. Weinberg,et al.  Human EJ bladder carcinoma oncogene is homologue of Harvey sarcoma virus ras gene , 1982, Nature.

[3]  M. Barbacid,et al.  Malignant activation of a K-ras oncogene in lung carcinoma but not in normal tissue of the same patient. , 1984, Science.

[4]  J. Tchinda,et al.  Recurrent Fusion of TMPRSS2 and ETS Transcription Factor Genes in Prostate Cancer , 2005, Science.

[5]  Juliane C. Dohm,et al.  Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia , 2011, Nature.

[6]  F. Sanger,et al.  DNA sequencing with chain-terminating inhibitors. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[7]  Lee T. Sam,et al.  Personalized Oncology Through Integrative High-Throughput Sequencing: A Pilot Study , 2011, Science Translational Medicine.

[8]  L. Hood,et al.  Large-scale and automated DNA sequence determination. , 1991, Science.

[9]  M. Ronaghi,et al.  Real-time DNA sequencing using detection of pyrophosphate release. , 1996, Analytical biochemistry.

[10]  M. Tang,et al.  Cytosine methylation determines hot spots of DNA damage in the human P53 gene. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[11]  S. Gabriel,et al.  Advances in understanding cancer genomes through second-generation sequencing , 2010, Nature Reviews Genetics.

[12]  Angela N. Brooks,et al.  Mapping the Hallmarks of Lung Adenocarcinoma with Massively Parallel Sequencing , 2012, Cell.

[13]  J. Ptak,et al.  High Frequency of Mutations of the PIK3CA Gene in Human Cancers , 2004, Science.

[14]  Jinghui Zhang,et al.  Association of age at diagnosis and genetic mutations in patients with neuroblastoma. , 2012, JAMA.

[15]  C. Marshall,et al.  Amino-acid substitutions at codon 13 of the N-ras oncogene in human acute myeloid leukaemia , 1985, Nature.

[16]  Francesca Demichelis,et al.  Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma , 2010, Nature Medicine.

[17]  Trevor J Pugh,et al.  Initial genome sequencing and analysis of multiple myeloma , 2011, Nature.

[18]  C. Harris,et al.  Aflatoxin B1-induced DNA adduct formation and p53 mutations in CYP450-expressing human liver cell lines. , 1997, Carcinogenesis.

[19]  Joshua F. McMichael,et al.  Whole Genome Analysis Informs Breast Cancer Response to Aromatase Inhibition , 2012, Nature.

[20]  Antony V. Cox,et al.  Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing , 2008, Nature Genetics.

[21]  H. Aburatani,et al.  Identification of the transforming EML4–ALK fusion gene in non-small-cell lung cancer , 2007, Nature.

[22]  Steven J. M. Jones,et al.  Comprehensive molecular characterization of human colon and rectal cancer , 2012, Nature.

[23]  Judy H. Cho,et al.  Finding the missing heritability of complex diseases , 2009, Nature.

[24]  A. Børresen-Dale,et al.  The Life History of 21 Breast Cancers , 2012, Cell.

[25]  Matthew J. Betts,et al.  Dissecting the genomic complexity underlying medulloblastoma , 2012, Nature.

[26]  Patricia L. Harris,et al.  Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. , 2004, The New England journal of medicine.

[27]  Andrew D. Yates,et al.  Somatic mutations of the protein kinase gene family in human lung cancer. , 2005, Cancer research.

[28]  Andrew Menzies,et al.  The patterns and dynamics of genomic instability in metastatic pancreatic cancer , 2010, Nature.

[29]  Winnie S. Liang,et al.  Paired Tumor and Normal Whole Genome Sequencing of Metastatic Olfactory Neuroblastoma , 2012, PloS one.

[30]  E. Birney,et al.  Patterns of somatic mutation in human cancer genomes , 2007, Nature.

[31]  A. Børresen-Dale,et al.  Mutational Processes Molding the Genomes of 21 Breast Cancers , 2012, Cell.

[32]  A. Sivachenko,et al.  SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. , 2011, The New England journal of medicine.

[33]  P. Hainaut,et al.  Patterns of p53 G-->T transversions in lung cancers reflect the primary mutagenic signature of DNA-damage by tobacco smoke. , 2001, Carcinogenesis.

[34]  Yuchen Jiao,et al.  ATM mutations in patients with hereditary pancreatic cancer. , 2012, Cancer discovery.

[35]  N. Tretyakova,et al.  Tobacco smoke carcinogens, DNA damage and p53 mutations in smoking-associated cancers , 2002, Oncogene.

[36]  Scott E. Kern,et al.  DPC4, A Candidate Tumor Suppressor Gene at Human Chromosome 18q21.1 , 1996, Science.

[37]  E. Birney,et al.  A small cell lung cancer genome reports complex tobacco exposure signatures , 2009, Nature.

[38]  S. Bohlander ETV6: a versatile player in leukemogenesis. , 2005, Seminars in cancer biology.

[39]  A. Kasarskis,et al.  A window into third-generation sequencing. , 2010, Human molecular genetics.

[40]  A. Jacquier The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs , 2009, Nature Reviews Genetics.

[41]  Stephen H. Friend,et al.  A human DNA segment with properties of the gene that predisposes to retinoblastoma and osteosarcoma , 1986, Nature.

[42]  Li Li,et al.  Exon Array Profiling Detects EML4-ALK Fusion in Breast, Colorectal, and Non–Small Cell Lung Cancers , 2009, Molecular Cancer Research.

[43]  Ken Chen,et al.  Clonal architecture of secondary acute myeloid leukemia. , 2012, The New England journal of medicine.

[44]  F. Sanger,et al.  A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. , 1975, Journal of molecular biology.

[45]  Tom Royce,et al.  A comprehensive catalogue of somatic mutations from a human cancer genome , 2010, Nature.

[46]  M. Wigler,et al.  Structure of the Ki-ras gene of the human lung carcinoma cell line Calu-1 , 1983, Nature.

[47]  G. Pfeifer,et al.  Sunlight induces pyrimidine dimers preferentially at 5-methylcytosine bases. , 1997, Cancer research.

[48]  Lovelace J. Luquette,et al.  Landscape of Somatic Retrotransposition in Human Cancers , 2012, Science.

[49]  M. Metzker Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[50]  Nicole Rusk Focus on next-generation sequencing data analysis , 2009, Nature Methods.

[51]  A. Sparks,et al.  The mutation spectrum revealed by paired genome sequences from a lung cancer patient , 2010, Nature.

[52]  R. McLendon,et al.  IDH1 and IDH2 mutations in gliomas. , 2009, The New England journal of medicine.

[53]  Kristian Cibulskis,et al.  Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion , 2011, Nature Genetics.

[54]  A. Tretyn,et al.  Sequencing technologies and genome sequencing , 2011, Journal of Applied Genetics.

[55]  Euan A Ashley,et al.  Performance comparison of whole-genome sequencing platforms , 2011, Nature Biotechnology.

[56]  Ryan D. Morin,et al.  Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution , 2009, Nature.

[57]  Joshua F. McMichael,et al.  Clonal evolution in relapsed acute myeloid leukemia revealed by whole genome sequencing , 2011, Nature.

[58]  S. Gabriel,et al.  EGFR Mutations in Lung Cancer: Correlation with Clinical Response to Gefitinib Therapy , 2004, Science.

[59]  Kiran C. Bobba,et al.  The genetic basis of early T-cell precursor acute lymphoblastic leukaemia , 2012, Nature.

[60]  K. Cibulskis,et al.  Integrative genome analyses identify key somatic driver mutations of small-cell lung cancer , 2012, Nature Genetics.

[61]  G. Pfeifer,et al.  Mutational spectra of human cancer , 2009, Human Genetics.

[62]  Elaine R. Mardis,et al.  Novel mutations target distinct subgroups of medulloblastoma , 2012, Nature.

[63]  A. Sivachenko,et al.  Sequence analysis of mutations and translocations across breast cancer subtypes , 2012, Nature.

[64]  W. Gilbert,et al.  A new method for sequencing DNA. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[65]  M. Caligiuri,et al.  IDH1 and IDH2 gene mutations identify novel molecular subsets within de novo cytogenetically normal acute myeloid leukemia: a Cancer and Leukemia Group B study. , 2010, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[66]  M. Hollstein,et al.  TP53 mutation signature supports involvement of aristolochic acid in the aetiology of endemic nephropathy‐associated tumours , 2009, International journal of cancer.

[67]  Hagan Bayley,et al.  Toward single molecule DNA sequencing: direct identification of ribonucleoside and deoxyribonucleoside 5'-monophosphates by using an engineered protein nanopore equipped with a molecular adapter. , 2006 .

[68]  A. Børresen-Dale,et al.  COMPLEX LANDSCAPES OF SOMATIC REARRANGEMENT IN HUMAN BREAST CANCER GENOMES , 2009, Nature.

[69]  Eric S. Lander,et al.  The genomic complexity of primary human prostate cancer , 2010, Nature.

[70]  Keith A. Boroevich,et al.  Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators , 2012, Nature Genetics.

[71]  Amy E. Hawkins,et al.  DNA sequencing of a cytogenetically normal acute myeloid leukemia genome , 2008, Nature.

[72]  J. V. Moran,et al.  Initial sequencing and analysis of the human genome. , 2001, Nature.

[73]  Hidenori Ojima,et al.  High-resolution characterization of a hepatocellular carcinoma genome , 2011, Nature Genetics.

[74]  Li Ding,et al.  Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers , 2012, Cell.

[75]  Joshua F. McMichael,et al.  DNMT3A mutations in acute myeloid leukemia. , 2010, The New England journal of medicine.

[76]  S. Dhanasekaran,et al.  Distinct classes of chromosomal rearrangements create oncogenic ETS gene fusions in prostate cancer , 2007, Nature.

[77]  Joshua F. McMichael,et al.  Genome Remodeling in a Basal-like Breast Cancer Metastasis and Xenograft , 2010, Nature.

[78]  J. Rowley,et al.  Chromosome translocations: dangerous liaisons revisited , 2001, Nature Reviews Cancer.

[79]  Fatih Ozsolak,et al.  Single‐molecule direct RNA sequencing without cDNA synthesis , 2011, Wiley interdisciplinary reviews. RNA.

[80]  G. Pfeifer,et al.  Mutations induced by ultraviolet light. , 2005, Mutation research.

[81]  Ken Chen,et al.  Use of whole-genome sequencing to diagnose a cryptic fusion oncogene. , 2011, JAMA.

[82]  Ken Chen,et al.  Recurring mutations found by sequencing an acute myeloid leukemia genome. , 2009, The New England journal of medicine.

[83]  Melanie A. Huntley,et al.  Recurrent R-spondin fusions in colon cancer , 2012, Nature.

[84]  Li Ding,et al.  Identification of a novel TP53 cancer susceptibility mutation through whole-genome sequencing of a patient with therapy-related AML. , 2011, JAMA.

[85]  Irmtraud M. Meyer,et al.  The clonal and mutational evolution spectrum of primary triple-negative breast cancers , 2012, Nature.

[86]  T. Fennell,et al.  Melanoma genome sequencing reveals frequent PREX2 mutations , 2012, Nature.