메뉴 건너뛰기




Volumn 20, Issue 6, 2014, Pages 682-688

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

(36)  Van Allen, Eliezer M a,b   Wagle, Nikhil a,b   Stojanov, Petar a,b   Perrin, Danielle L b   Cibulskis, Kristian b   Marlow, Sara a,b   Jane Valbuena, Judit a,b   Friedrich, Dennis C b   Kryukov, Gregory b   Carter, Scott L b   McKenna, Aaron b,c   Sivachenko, Andrey b   Rosenberg, Mara b   Kiezun, Adam b   Voet, Douglas b   Lawrence, Michael b   Lichtenstein, Lee T b   Gentry, Jeff G b   Huang, Franklin W a,b   Fostel, Jennifer b   more..


Author keywords

[No Author keywords available]

Indexed keywords

BEVACIZUMAB; CARBOPLATIN; CYCLIN DEPENDENT KINASE INHIBITOR; DNA; JANUS KINASE 3 INHIBITOR; LY 2835219; NAVELBINE; PACLITAXEL; UNCLASSIFIED DRUG;

EID: 84902148239     PISSN: 10788956     EISSN: 1546170X     Source Type: Journal    
DOI: 10.1038/nm.3559     Document Type: Article
Times cited : (448)

References (48)
  • 1
    • 84875758730 scopus 로고    scopus 로고
    • Lessons from the cancer genome
    • Garraway, L.A. & Lander, E.S. Lessons from the cancer genome. Cell 153, 17-37 (2013).
    • (2013) Cell , vol.153 , pp. 17-37
    • Garraway, L.A.1    Lander, E.S.2
  • 2
    • 84880452562 scopus 로고    scopus 로고
    • Genomics-driven oncology: Framework for an emerging paradigm
    • Garraway, L.A. Genomics-driven oncology: framework for an emerging paradigm. J. Clin. Oncol. 31, 1806-1814 (2013).
    • (2013) J. Clin. Oncol , vol.31 , pp. 1806-1814
    • Garraway, L.A.1
  • 3
    • 84863652136 scopus 로고    scopus 로고
    • Circumventing cancer drug resistance in the era of personalized medicine
    • Garraway, L.A. & Janne, P.A. Circumventing cancer drug resistance in the era of personalized medicine. Cancer Discov. 2, 214-226 (2012).
    • (2012) Cancer Discov , vol.2 , pp. 214-226
    • Garraway, L.A.1    Janne, P.A.2
  • 5
    • 70849116358 scopus 로고    scopus 로고
    • Profiling critical cancer gene mutations in clinical tumor samples
    • MacConaill, L.E. et al. Profiling critical cancer gene mutations in clinical tumor samples. PLoS ONE 4, e7887 (2009).
    • (2009) PLoS ONE , vol.4
    • Macconaill, L.E.1
  • 6
    • 77954566882 scopus 로고    scopus 로고
    • Rapid targeted mutational analysis of human tumours: A clinical platform to guide personalized cancer medicine
    • Dias-Santagata, D. et al. Rapid targeted mutational analysis of human tumours: a clinical platform to guide personalized cancer medicine. EMBO Mol. Med. 2, 146-158 (2010).
    • (2010) EMBO Mol. Med , vol.2 , pp. 146-158
    • Dias-Santagata, D.1
  • 7
    • 84865833740 scopus 로고    scopus 로고
    • High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing
    • Wagle, N. et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov. 2, 82-93 (2012).
    • (2012) Cancer Discov , vol.2 , pp. 82-93
    • Wagle, N.1
  • 8
    • 84862776857 scopus 로고    scopus 로고
    • Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies
    • Lipson, D. et al. Identification of new ALK and RET gene fusions from colorectal and lung cancer biopsies. Nat. Med. 18, 382-384 (2012).
    • (2012) Nat. Med , vol.18 , pp. 382-384
    • Lipson, D.1
  • 9
    • 84876064523 scopus 로고    scopus 로고
    • Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity
    • Beltran, H. et al. Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity. Eur. Urol. 63, 920-926 (2013).
    • (2013) Eur. Urol , vol.63 , pp. 920-926
    • Beltran, H.1
  • 10
    • 82655184653 scopus 로고    scopus 로고
    • Personalized oncology through integrative high-throughput sequencing: A pilot study
    • Roychowdhury, S. et al. Personalized oncology through integrative high-throughput sequencing: a pilot study. Sci. Transl. Med. 3, 111ra121 (2011).
    • (2011) Sci. Transl. Med , vol.3
    • Roychowdhury, S.1
  • 11
    • 84872585155 scopus 로고    scopus 로고
    • Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities
    • Craig, D.W. et al. Genome and transcriptome sequencing in prospective metastatic triple-negative breast cancer uncovers therapeutic vulnerabilities. Mol. Cancer Ther. 12, 104-116 (2013).
    • (2013) Mol. Cancer Ther , vol.12 , pp. 104-116
    • Craig, D.W.1
  • 12
    • 80053173227 scopus 로고    scopus 로고
    • Targeted high throughput sequencing in clinical cancer settings: Formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity
    • Kerick, M. et al. Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity. BMC Med. Genomics 4, 68 (2011).
    • (2011) BMC Med. Genomics , vol.4 , pp. 68
    • Kerick, M.1
  • 13
    • 84871790986 scopus 로고    scopus 로고
    • Rebooting cancer tissue handling in the sequencing era: Toward routine use of frozen tumor tissue
    • Goetz, L., Bethel, K. & Topol, E.J. Rebooting cancer tissue handling in the sequencing era: toward routine use of frozen tumor tissue. J. Am. Med. Assoc. 309, 37-38 (2013).
    • (2013) J. Am. Med. Assoc , vol.309 , pp. 37-38
    • Goetz, L.1    Bethel, K.2    Topol, E.J.3
  • 14
    • 78650762588 scopus 로고    scopus 로고
    • A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries
    • Fisher, S. et al. A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol. 12, R1 (2011).
    • (2011) Genome Biol , vol.12
    • Fisher, S.1
  • 15
    • 84863393080 scopus 로고    scopus 로고
    • Intratumor heterogeneity and branched evolution revealed by multiregion sequencing
    • Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med. 366, 883-892 (2012).
    • (2012) N. Engl. J. Med , vol.366 , pp. 883-892
    • Gerlinger, M.1
  • 17
    • 0032755991 scopus 로고    scopus 로고
    • A high frequency of sequence alterations is due to formalin fixation of archival specimens
    • Williams, C. et al. A high frequency of sequence alterations is due to formalin fixation of archival specimens. Am. J. Pathol. 155, 1467-1471 (1999).
    • (1999) Am. J. Pathol , vol.155 , pp. 1467-1471
    • Williams, C.1
  • 18
    • 84882261506 scopus 로고    scopus 로고
    • Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens
    • Spencer, D.H. et al. Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens. J. Mol. Diagn. 15, 623-633 (2013).
    • (2013) J. Mol. Diagn , vol.15 , pp. 623-633
    • Spencer, D.H.1
  • 19
    • 84874025843 scopus 로고    scopus 로고
    • Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
    • Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31, 213-219 (2013).
    • (2013) Nat. Biotechnol , vol.31 , pp. 213-219
    • Cibulskis, K.1
  • 20
    • 84866410479 scopus 로고    scopus 로고
    • Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing
    • Imielinski, M. et al. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell 150, 1107-1120 (2012).
    • (2012) Cell , vol.150 , pp. 1107-1120
    • Imielinski, M.1
  • 21
    • 84862523863 scopus 로고    scopus 로고
    • Sequence analysis of mutations and translocations across breast cancer subtypes
    • Banerji, S. et al. Sequence analysis of mutations and translocations across breast cancer subtypes. Nature 486, 405-409 (2012).
    • (2012) Nature , vol.486 , pp. 405-409
    • Banerji, S.1
  • 22
    • 84864258996 scopus 로고    scopus 로고
    • A landscape of driver mutations in melanoma
    • Hodis, E. et al. A landscape of driver mutations in melanoma. Cell 150, 251-263 (2012).
    • (2012) Cell , vol.150 , pp. 251-263
    • Hodis, E.1
  • 23
    • 84861581164 scopus 로고    scopus 로고
    • Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer
    • Barbieri, C.E. et al. Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat. Genet. 44, 685-689 (2012).
    • (2012) Nat. Genet , vol.44 , pp. 685-689
    • Barbieri, C.E.1
  • 24
    • 80052158097 scopus 로고    scopus 로고
    • The mutational landscape of head and neck squamous cell carcinoma
    • Stransky, N. et al. The mutational landscape of head and neck squamous cell carcinoma. Science 333, 1157-1160 (2011).
    • (2011) Science , vol.333 , pp. 1157-1160
    • Stransky, N.1
  • 25
    • 84857942952 scopus 로고    scopus 로고
    • Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing
    • Lohr, J.G. et al. Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc. Natl. Acad. Sci. USA 109, 3879-3884 (2012).
    • (2012) Proc. Natl. Acad. Sci. USA , vol.109 , pp. 3879-3884
    • Lohr, J.G.1
  • 26
    • 84864621910 scopus 로고    scopus 로고
    • Amplification of CRKL induces transformation and epidermal growth factor receptor inhibitor resistance in human non-small cell lung cancers
    • Cheung, H.W. et al. Amplification of CRKL induces transformation and epidermal growth factor receptor inhibitor resistance in human non-small cell lung cancers. Cancer Discov. 1, 608-625 (2011).
    • (2011) Cancer Discov , vol.1 , pp. 608-625
    • Cheung, H.W.1
  • 27
    • 84860995846 scopus 로고    scopus 로고
    • The CRKL gene encoding an adaptor protein is amplified, overexpressed, and a possible therapeutic target in gastric cancer
    • Natsume, H. et al. The CRKL gene encoding an adaptor protein is amplified, overexpressed, and a possible therapeutic target in gastric cancer. J. Transl. Med. 10, 97 (2012).
    • (2012) J. Transl. Med , vol.10 , pp. 97
    • Natsume, H.1
  • 28
    • 77955046517 scopus 로고    scopus 로고
    • Genomic and biological characterization of exon 4 KRAS mutations in human cancer
    • Janakiraman, M. et al. Genomic and biological characterization of exon 4 KRAS mutations in human cancer. Cancer Res. 70, 5901-5911 (2010).
    • (2010) Cancer Res , vol.70 , pp. 5901-5911
    • Janakiraman, M.1
  • 29
    • 77953238558 scopus 로고    scopus 로고
    • Integrative genomic and proteomic analyses identify targets for Lkb1-deficient metastatic lung tumors
    • Carretero, J. et al. Integrative genomic and proteomic analyses identify targets for Lkb1-deficient metastatic lung tumors. Cancer Cell 17, 547-559 (2010).
    • (2010) Cancer Cell , vol.17 , pp. 547-559
    • Carretero, J.1
  • 30
    • 78651330430 scopus 로고    scopus 로고
    • COSMIC: Mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer
    • Forbes, S.A. et al. COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer. Nucleic Acids Res. 39, D945-D950 (2011).
    • (2011) Nucleic Acids Res , vol.39
    • Forbes, S.A.1
  • 31
    • 54549094903 scopus 로고    scopus 로고
    • Somatic mutations affect key pathways in lung adenocarcinoma
    • Ding, L. et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455, 1069-1075 (2008).
    • (2008) Nature , vol.455 , pp. 1069-1075
    • Ding, L.1
  • 32
    • 84866434919 scopus 로고    scopus 로고
    • Genomic landscape of non-small cell lung cancer in smokers and never-smokers
    • Govindan, R. et al. Genomic landscape of non-small cell lung cancer in smokers and never-smokers. Cell 150, 1121-1134 (2012).
    • (2012) Cell , vol.150 , pp. 1121-1134
    • Govindan, R.1
  • 33
    • 77954279920 scopus 로고    scopus 로고
    • A synthetic lethal interaction between K-Ras oncogenes and Cdk4 unveils a therapeutic strategy for non-small cell lung carcinoma
    • Puyol, M. et al. A synthetic lethal interaction between K-Ras oncogenes and Cdk4 unveils a therapeutic strategy for non-small cell lung carcinoma. Cancer Cell 18, 63-73 (2010).
    • (2010) Cancer Cell , vol.18 , pp. 63-73
    • Puyol, M.1
  • 34
    • 84865202724 scopus 로고    scopus 로고
    • JAK-mutant myeloproliferative neoplasms
    • Levine, R.L. JAK-mutant myeloproliferative neoplasms. Curr. Top. Microbiol. Immunol. 355, 119-133 (2012).
    • (2012) Curr. Top. Microbiol. Immunol , vol.355 , pp. 119-133
    • Levine, R.L.1
  • 35
    • 23044495944 scopus 로고    scopus 로고
    • Crystal structure of the Jak3 kinase domain in complex with a staurosporine analog
    • DOI 10.1182/blood-2005-02-0707
    • Boggon, T.J., Li, Y., Manley, P.W. & Eck, M.J. Crystal structure of the Jak3 kinase domain in complex with a staurosporine analog. Blood 106, 996-1002 (2005). (Pubitemid 41076445)
    • (2005) Blood , vol.106 , Issue.3 , pp. 996-1002
    • Boggon, T.J.1    Li, Y.2    Manley, P.W.3    Eck, M.J.4
  • 36
    • 54049107944 scopus 로고    scopus 로고
    • Activating mutations in human acute megakaryoblastic leukemia
    • Malinge, S. et al. Activating mutations in human acute megakaryoblastic leukemia. Blood 112, 4220-4226 (2008).
    • (2008) Blood , vol.112 , pp. 4220-4226
    • Malinge, S.1
  • 37
    • 77954938591 scopus 로고    scopus 로고
    • Future of personalized medicine in oncology: A systems biology approach
    • Gonzalez-Angulo, A.M., Hennessy, B.T. & Mills, G.B. Future of personalized medicine in oncology: a systems biology approach. J. Clin. Oncol. 28, 2777-2783 (2010).
    • (2010) J. Clin. Oncol , vol.28 , pp. 2777-2783
    • Gonzalez-Angulo, A.M.1    Hennessy, B.T.2    Mills, G.B.3
  • 38
    • 84877097462 scopus 로고    scopus 로고
    • DNA-mutation Inventory to Refine and Enhance Cancer Treatment (DIRECT): A catalogue of clinically relevant cancer mutations to enable genome-directed cancer therapy
    • Yeh, P. et al. DNA-mutation Inventory to Refine and Enhance Cancer Treatment (DIRECT): a catalogue of clinically relevant cancer mutations to enable genome-directed cancer therapy. Clin. Cancer Res. 19, 1894-1901 (2013).
    • (2013) Clin. Cancer Res , vol.19 , pp. 1894-1901
    • Yeh, P.1
  • 39
    • 84866002291 scopus 로고    scopus 로고
    • The cBio cancer genomics portal: An open platform for exploring multidimensional cancer genomics data
    • Cerami, E. et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2, 401-404 (2012).
    • (2012) Cancer Discov , vol.2 , pp. 401-404
    • Cerami, E.1
  • 41
    • 80052707308 scopus 로고    scopus 로고
    • ContEst: Estimating cross-contamination of human samples in next-generation sequencing data
    • Cibulskis, K. et al. ContEst: estimating cross-contamination of human samples in next-generation sequencing data. Bioinformatics 27, 2601-2602 (2011).
    • (2011) Bioinformatics , vol.27 , pp. 2601-2602
    • Cibulskis, K.1
  • 42
    • 84873390533 scopus 로고    scopus 로고
    • Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability
    • Drier, Y. et al. Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. Genome Res. 23, 228-235 (2013).
    • (2013) Genome Res , vol.23 , pp. 228-235
    • Drier, Y.1
  • 43
    • 58149218240 scopus 로고    scopus 로고
    • High-resolution mapping of copy-number alterations with massively parallel sequencing
    • Chiang, D.Y. et al. High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat. Methods 6, 99-103 (2009).
    • (2009) Nat. Methods , vol.6 , pp. 99-103
    • Chiang, D.Y.1
  • 44
    • 3543105225 scopus 로고    scopus 로고
    • Circular binary segmentation for the analysis of array-based DNA copy number data
    • DOI 10.1093/biostatistics/kxh008
    • Olshen, A.B., Venkatraman, E.S., Lucito, R. & Wigler, M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics 5, 557-572 (2004). (Pubitemid 41180205)
    • (2004) Biostatistics , vol.5 , Issue.4 , pp. 557-572
    • Olshen, A.B.1    Venkatraman, E.S.2    Lucito, R.3    Wigler, M.4
  • 45
    • 58149178579 scopus 로고    scopus 로고
    • NCBI reference sequences: Current status, policy and new initiatives
    • Pruitt, K.D., Tatusova, T., Klimke, W. & Maglott, D.R. NCBI reference sequences: current status, policy and new initiatives. Nucleic Acids Res. 37, D32-D36 (2009).
    • (2009) Nucleic Acids Res , vol.37
    • Pruitt, K.D.1    Tatusova, T.2    Klimke, W.3    Maglott, D.R.4
  • 48
    • 84876244267 scopus 로고    scopus 로고
    • Nozzle: A report generation toolkit for data analysis pipelines
    • Gehlenborg, N., Noble, M.S., Getz, G., Chin, L. & Park, P.J. Nozzle: a report generation toolkit for data analysis pipelines. Bioinformatics 29, 1089-1091 (2013).
    • (2013) Bioinformatics , vol.29 , pp. 1089-1091
    • Gehlenborg, N.1    Noble, M.S.2    Getz, G.3    Chin, L.4    Park, P.J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.