Whole exome sequencing for cancer – is there evidence of clinical utility?

License. The full terms of the License are available at http://creativecommons.org/licenses/by-nc/3.0/. Non-commercial uses of the work are permitted without any further permission from Dove Medical Press Limited, provided the work is properly attributed. Permissions beyond the scope of the License are administered by Dove Medical Press Limited. Information on how to request permission may be found at: http://www.dovepress.com/permissions.php Advances in Genomics and Genetics 2014:4 115–128 Advances in Genomics and Genetics

[1]  R. Gibbs,et al.  Exome Sequencing of Head and Neck Squamous Cell Carcinoma Reveals Inactivating Mutations in NOTCH1 , 2011, Science.

[2]  Sara B. Linker,et al.  Comparison of Three Targeted Enrichment Strategies on the SOLiD Sequencing Platform , 2011, PloS one.

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

[4]  Hugo Y. K. Lam,et al.  Performance comparison of exome DNA sequencing technologies , 2011, Nature Biotechnology.

[5]  A. Ferrando,et al.  Activating mutations in the NT5C2 nucleotidase gene drive chemotherapy resistance in relapsed ALL , 2013, Nature Medicine.

[6]  Johan Lindberg,et al.  The mitochondrial and autosomal mutation landscapes of prostate cancer. , 2013, European urology.

[7]  T. Boggon,et al.  Landscape of somatic single-nucleotide and copy-number mutations in uterine serous carcinoma , 2013, Proceedings of the National Academy of Sciences.

[8]  J. Shendure,et al.  Exome sequencing as a tool for Mendelian disease gene discovery , 2011, Nature Reviews Genetics.

[9]  A. Børresen-Dale,et al.  The landscape of cancer genes and mutational processes in breast cancer , 2012, Nature.

[10]  Qi Liu,et al.  Next generation sequencing in cancer research and clinical application , 2013, Biological Procedures Online.

[11]  J. Long,et al.  Exome sequencing generates high quality data in non-target regions , 2012, BMC Genomics.

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

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

[14]  Marc S. Williams,et al.  ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing , 2013, Genetics in Medicine.

[15]  G. Mills,et al.  Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer , 2012, Genome research.

[16]  X. Hua,et al.  Exome sequencing identifies MXRA5 as a novel cancer gene frequently mutated in non-small cell lung carcinoma from Chinese patients. , 2012, Carcinogenesis.

[17]  E. Giné,et al.  Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia , 2011, Nature Genetics.

[18]  R. Tothill,et al.  Exome Sequencing Identifies Rare Deleterious Mutations in DNA Repair Genes FANCC and BLM as Potential Breast Cancer Susceptibility Alleles , 2012, PLoS genetics.

[19]  David Dunson,et al.  Genetic heterogeneity of diffuse large B-cell lymphoma , 2013, Proceedings of the National Academy of Sciences.

[20]  A. Chakravarti.  Population genetics—making sense out of sequence , 1999, Nature Genetics.

[21]  S. Teutsch,et al.  The Evaluation of Genomic Applications in Practice and Prevention (EGAPP) initiative: methods of the EGAPP Working Group , 2009, Genetics in Medicine.

[22]  A. Sivachenko,et al.  Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer , 2012, Nature Genetics.

[23]  Richard Simon,et al.  Identifying cancer driver genes in tumor genome sequencing studies , 2011, Bioinform..

[24]  Marc S Williams,et al.  Rapid ACCE: Experience with a rapid and structured approach for evaluating gene-based testing , 2007, Genetics in Medicine.

[25]  Hui Jiang,et al.  Comprehensive comparison of three commercial human whole-exome capture platforms , 2011, Genome Biology.

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

[27]  Jing Pan,et al.  Identification of somatic mutations in non-small cell lung carcinomas using whole-exome sequencing. , 2012, Carcinogenesis.

[28]  I. Sohn,et al.  Somatic hypermutation and outcomes of platinum based chemotherapy in patients with high grade serous ovarian cancer. , 2012, Gynecologic oncology.

[29]  Jennifer S. Lin,et al.  Improving the efficiency and relevance of evidence-based recommendations in the era of whole-genome sequencing: an EGAPP methods update , 2012, Genetics in Medicine.

[30]  Yiping Shen,et al.  Exome and whole-genome sequencing as clinical tests: a transformative practice in molecular diagnostics. , 2012, Clinical chemistry.

[31]  K. Kinzler,et al.  Evaluation of DNA from the Papanicolaou Test to Detect Ovarian and Endometrial Cancers , 2013, Science Translational Medicine.

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

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

[34]  D. Bick,et al.  Whole Exome and Whole Genome Sequencing – Community Plan Medical Policy , 2018 .

[35]  A. McKenna,et al.  The Mutational Landscape of Head and Neck Squamous Cell Carcinoma , 2011, Science.

[36]  Eric S. Lander,et al.  Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing , 2012, Proceedings of the National Academy of Sciences.

[37]  J. Benítez,et al.  Whole Exome Sequencing Suggests Much of Non-BRCA1/BRCA2 Familial Breast Cancer Is Due to Moderate and Low Penetrance Susceptibility Alleles , 2013, PloS one.