메뉴 건너뛰기




Volumn 13, Issue 1, 2016, Pages 3-11

Current practices and guidelines for clinical next-generation sequencing oncology testing

Author keywords

Cancer genomics; Molecular diagnostics; Next generation sequencing

Indexed keywords

DNA;

EID: 84969256082     PISSN: 20953941     EISSN: None     Source Type: Journal    
DOI: 10.28092/j.issn.2095-3941.2016.0004     Document Type: Review
Times cited : (119)

References (34)
  • 2
    • 84919363528 scopus 로고    scopus 로고
    • Ion torrent next-generation sequencing for routine identification of clinically relevant mutations in colorectal cancer patients
    • Malapelle U, Vigliar E, Sgariglia R, Bellevicine C, Colarossi L, Vitale D, et al. Ion torrent next-generation sequencing for routine identification of clinically relevant mutations in colorectal cancer patients. J Clin Pathol. 2015; 68: 64-8.
    • (2015) J Clin Pathol , vol.68 , pp. 64-68
    • Malapelle, U.1    Vigliar, E.2    Sgariglia, R.3    Bellevicine, C.4    Colarossi, L.5    Vitale, D.6
  • 3
    • 84907761755 scopus 로고    scopus 로고
    • Performance of amplicon-based next Generation DNA sequencing for diagnostic gene mutation profiling in oncopathology
    • Sie D, Snijders PJ, Meijer GA, Doeleman MW, Van Moorsel MI, Van Essen HF, et al. Performance of amplicon-based next Generation DNA sequencing for diagnostic gene mutation profiling in oncopathology. Cell Oncol (Dordr). 2014; 37: 353-61.
    • (2014) Cell Oncol (Dordr) , vol.37 , pp. 353-361
    • Sie, D.1    Snijders, P.J.2    Meijer, G.A.3    Doeleman, M.W.4    Van Moorsel, M.I.5    Van Essen, H.F.6
  • 4
    • 84882289495 scopus 로고    scopus 로고
    • Clinical validation of a next-generation sequencing screen for mutational hotspots in 46 cancer-related genes
    • Singh RR, Patel KP, Routbort MJ, Reddy NG, Barkoh BA, Handal B, et al. Clinical validation of a next-generation sequencing screen for mutational hotspots in 46 cancer-related genes. J Mol Diagn. 2013; 15: 607-22.
    • (2013) J Mol Diagn , vol.15 , pp. 607-622
    • Singh, R.R.1    Patel, K.P.2    Routbort, M.J.3    Reddy, N.G.4    Barkoh, B.A.5    Handal, B.6
  • 5
    • 84904611547 scopus 로고    scopus 로고
    • Multi-marker solid tumor panels using next-generation sequencing to direct molecularly targeted therapies
    • Marrone M, Filipski KK, Gillanders EM, Schully SD, Freedman AN. Multi-marker solid tumor panels using next-generation sequencing to direct molecularly targeted therapies. PLoS Curr. 2014; 6.
    • (2014) PLoS Curr , pp. 6
    • Marrone, M.1    Filipski, K.K.2    Gillanders, E.M.3    Schully, S.D.4    Freedman, A.N.5
  • 6
    • 84879301385 scopus 로고    scopus 로고
    • The development of next-generation sequencing assays for the mitochondrial genome and 108 nuclear genes associated with mitochondrial disorders
    • Dames S, Chou LS, Xiao Y, Wayman T, Stocks J, Singleton M, et al. The development of next-generation sequencing assays for the mitochondrial genome and 108 nuclear genes associated with mitochondrial disorders. J Mol Diagn. 2013; 15: 526-34.
    • (2013) J Mol Diagn , vol.15 , pp. 526-534
    • Dames, S.1    Chou, L.S.2    Xiao, Y.3    Wayman, T.4    Stocks, J.5    Singleton, M.6
  • 7
    • 84880799275 scopus 로고    scopus 로고
    • Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis
    • Mccourt CM, Mcart DG, Mills K, Catherwood MA, Maxwell P, Waugh DJ, et al. Validation of next generation sequencing technologies in comparison to current diagnostic gold standards for BRAF, EGFR and KRAS mutational analysis. PLoS One. 2013; 8: e69604.
    • (2013) PLoS One , vol.8
    • Mccourt, C.M.1    Mcart, D.G.2    Mills, K.3    Catherwood, M.A.4    Maxwell, P.5    Waugh, D.J.6
  • 8
    • 84869876659 scopus 로고    scopus 로고
    • The effect of strand bias in illumina short-read sequencing data
    • Guo Y, Li J, Li CI, Long J, Samuels DC, Shyr Y. The effect of strand bias in illumina short-read sequencing data. BMC Genomics. 2012; 13: 666.
    • (2012) BMC Genomics , vol.13 , pp. 666
    • Guo, Y.1    Li, J.2    Li, C.I.3    Long, J.4    Samuels, D.C.5    Shyr, Y.6
  • 9
    • 84940598295 scopus 로고    scopus 로고
    • Somatic mosaicism of a CDKL5 mutation identified by next-generation sequencing
    • Kato T, Morisada N, Nagase H, Nishiyama M, Toyoshima D, Nakagawa T, et al. Somatic mosaicism of a CDKL5 mutation identified by next-generation sequencing. Brain Dev. 2015; 37: 911-5.
    • (2015) Brain Dev , vol.37 , pp. 911-915
    • Kato, T.1    Morisada, N.2    Nagase, H.3    Nishiyama, M.4    Toyoshima, D.5    Nakagawa, T.6
  • 10
    • 84937412447 scopus 로고    scopus 로고
    • Not all next generation sequencing diagnostics are created equal: understanding the nuances of solid tumor assay design for somatic mutation detection
    • Gray PN, Dunlop CL, Elliott AM. Not all next generation sequencing diagnostics are created equal: understanding the nuances of solid tumor assay design for somatic mutation detection. Cancers (Basel). 2015; 7: 1313-32.
    • (2015) Cancers (Basel) , vol.7 , pp. 1313-1332
    • Gray, P.N.1    Dunlop, C.L.2    Elliott, A.M.3
  • 11
    • 84969200084 scopus 로고    scopus 로고
    • "Next Generation" Sequencing (NGS) guidelines for somatic genetic variant detection
    • [Last accessed on 2015 August 10].
    • "Next Generation" Sequencing (NGS) guidelines for somatic genetic variant detection. Available from http://www.wadsworth.org/labcert/TestApproval/forms/NextGenSe q_ONCO_Guidelines.pdf. [Last accessed on 2015 August 10].
  • 12
    • 84928209346 scopus 로고    scopus 로고
    • Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology
    • Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015; 17: 405-24.
    • (2015) Genet Med , vol.17 , pp. 405-424
    • Richards, S.1    Aziz, N.2    Bale, S.3    Bick, D.4    Das, S.5    Gastier-Foster, J.6
  • 15
  • 16
    • 84931397162 scopus 로고    scopus 로고
    • Annotation of sequence variants in cancer samples: processes and pitfalls for routine assays in the clinical laboratory
    • Lee LA, Arvai KJ, Jones D. Annotation of sequence variants in cancer samples: processes and pitfalls for routine assays in the clinical laboratory. J Mol Diagn. 2015; 17: 339-51.
    • (2015) J Mol Diagn , vol.17 , pp. 339-351
    • Lee, L.A.1    Arvai, K.J.2    Jones, D.3
  • 17
    • 84903284152 scopus 로고    scopus 로고
    • Assessing the necessity of confirmatory testing for exome- sequencing results in a clinical molecular diagnostic laboratory
    • Strom SP, Lee H, Das K, Vilain E, Nelson SF, Grody WW, Deignan JL, et al. Assessing the necessity of confirmatory testing for exome- sequencing results in a clinical molecular diagnostic laboratory. Genet Med. 2014;16:510-5.
    • (2014) Genet Med , vol.16 , pp. 510-515
    • Strom, S.P.1    Lee, H.2    Das, K.3    Vilain, E.4    Nelson, S.F.5    Grody, W.W.6    Deignan, J.L.7
  • 19
    • 84876809749 scopus 로고    scopus 로고
    • Practices and policies of clinical exome sequencing providers: analysis and implications
    • Jamal SM, Yu JH, Chong JX, Dent KM, Conta JH, Tabor HK, et al. Practices and policies of clinical exome sequencing providers: analysis and implications. Am J Med Genet A. 2013; 161A: 935-50.
    • (2013) Am J Med Genet A , vol.161A , pp. 935-950
    • Jamal, S.M.1    Yu, J.H.2    Chong, J.X.3    Dent, K.M.4    Conta, J.H.5    Tabor, H.K.6
  • 20
    • 84918840439 scopus 로고    scopus 로고
    • Clinical exome sequencing for genetic identification of rare Mendelian disorders
    • Lee H, Deignan JL, Dorrani N, Strom SP, Kantarci S, Quintero-Rivera F, et al. Clinical exome sequencing for genetic identification of rare Mendelian disorders. JAMA. 2014; 312: 1880-7.
    • (2014) JAMA , vol.312 , pp. 1880-1887
    • Lee, H.1    Deignan, J.L.2    Dorrani, N.3    Strom, S.P.4    Kantarci, S.5    Quintero-Rivera, F.6
  • 21
    • 2342471392 scopus 로고    scopus 로고
    • Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib
    • Lynch TJ, Bell DW, Sordella R, Gurubhagavatula S, Okimoto RA, Brannigan BW, et al. Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib. N Engl J Med. 2004; 350: 2129-39.
    • (2004) N Engl J Med , vol.350 , pp. 2129-2139
    • Lynch, T.J.1    Bell, D.W.2    Sordella, R.3    Gurubhagavatula, S.4    Okimoto, R.A.5    Brannigan, B.W.6
  • 22
    • 2342624080 scopus 로고    scopus 로고
    • EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy
    • Paez JG, Jänne PA, Lee JC, Tracy S, Greulich H, Gabriel S, et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science. 2004; 304: 1497-500.
    • (2004) Science , vol.304 , pp. 1497-1500
    • Paez, J.G.1    Jänne, P.A.2    Lee, J.C.3    Tracy, S.4    Greulich, H.5    Gabriel, S.6
  • 23
    • 4444344330 scopus 로고    scopus 로고
    • EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib
    • Pao W, Miller V, Zakowski M, Doherty J, Politi K, Sarkaria I, et al. EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc Natl Acad Sci U S A. 2004; 101: 13306-11.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 13306-13311
    • Pao, W.1    Miller, V.2    Zakowski, M.3    Doherty, J.4    Politi, K.5    Sarkaria, I.6
  • 24
    • 4143066760 scopus 로고    scopus 로고
    • Gefitinib-sensitizing EGFR mutations in lung cancer activate anti-apoptotic pathways
    • Sordella R, Bell DW, Haber DA, Settleman J. Gefitinib-sensitizing EGFR mutations in lung cancer activate anti-apoptotic pathways. Science. 2004; 305: 1163-7.
    • (2004) Science , vol.305 , pp. 1163-1167
    • Sordella, R.1    Bell, D.W.2    Haber, D.A.3    Settleman, J.4
  • 25
    • 84873415195 scopus 로고    scopus 로고
    • The dominant role of G12C over other KRAS mutation types in the negative prediction of efficacy of epidermal growth factor receptor tyrosine kinase inhibitors in non-small cell lung cancer
    • Fiala O, Pesek M, Finek J, Benesova L, Belsanova B, Minarik M. The dominant role of G12C over other KRAS mutation types in the negative prediction of efficacy of epidermal growth factor receptor tyrosine kinase inhibitors in non-small cell lung cancer. Cancer Genet. 2013; 206: 26-31.
    • (2013) Cancer Genet , vol.206 , pp. 26-31
    • Fiala, O.1    Pesek, M.2    Finek, J.3    Benesova, L.4    Belsanova, B.5    Minarik, M.6
  • 26
    • 53249145767 scopus 로고    scopus 로고
    • Frequency and distinctive spectrum of KRAS mutations in never smokers with lung adenocarcinoma
    • Riely GJ, Kris MG, Rosenbaum D, Marks J, Li A, Chitale DA, et al. Frequency and distinctive spectrum of KRAS mutations in never smokers with lung adenocarcinoma. Clin Cancer Res. 2008; 14: 5731-4.
    • (2008) Clin Cancer Res , vol.14 , pp. 5731-5734
    • Riely, G.J.1    Kris, M.G.2    Rosenbaum, D.3    Marks, J.4    Li, A.5    Chitale, D.A.6
  • 27
    • 84981287976 scopus 로고    scopus 로고
    • Exploring the landscape of pathogenic genetic variation in the ExAC population database: insights of relevance to variant classification
    • Dec 17. [Epub ahead of print]
    • Song W, Gardner SA, Hovhannisyan H, Natalizio A, Weymouth KS, Chen W, et al. Exploring the landscape of pathogenic genetic variation in the ExAC population database: insights of relevance to variant classification. Genet Med. 2015 Dec 17. doi: 10.1038/gim.2015.180. [Epub ahead of print]
    • (2015) Genet Med
    • Song, W.1    Gardner, S.A.2    Hovhannisyan, H.3    Natalizio, A.4    Weymouth, K.S.5    Chen, W.6
  • 28
    • 84975795680 scopus 로고    scopus 로고
    • An integrated map of genetic variation from 1,092 human genomes
    • 1000 Genomes Project Consortium, Abecasis GR, Auton A, Brooks LD, Depristo MA, Durbin RM, et al. An integrated map of genetic variation from 1,092 human genomes. Nature. 2012; 491: 56-65.
    • (2012) Nature , vol.491 , pp. 56-65
    • Abecasis, G.R.1    Auton, A.2    Brooks, L.D.3    Depristo, M.A.4    Durbin, R.M.5
  • 29
    • 84926524933 scopus 로고    scopus 로고
    • Favorable prognosis of biallelic CEBPA gene mutations in acute myeloid leukemia patients: a meta-analysis
    • Li HY, Deng DH, Huang Y, Ye FH, Huang LL, Xiao Q, et al. Favorable prognosis of biallelic CEBPA gene mutations in acute myeloid leukemia patients: a meta-analysis. Eur J Haematol. 2015; 94: 439-48.
    • (2015) Eur J Haematol , vol.94 , pp. 439-448
    • Li, H.Y.1    Deng, D.H.2    Huang, Y.3    Ye, F.H.4    Huang, L.L.5    Xiao, Q.6
  • 30
    • 84908881428 scopus 로고    scopus 로고
    • Utilization of multigene panels in hereditary cancer predisposition testing: analysis of more than 2,000 patients
    • Laduca H, Stuenkel AJ, Dolinsky JS, Keiles S, Tandy S, Pesaran T, et al. Utilization of multigene panels in hereditary cancer predisposition testing: analysis of more than 2,000 patients. Genet Med. 2014; 16: 830-7.
    • (2014) Genet Med , vol.16 , pp. 830-837
    • Laduca, H.1    Stuenkel, A.J.2    Dolinsky, J.S.3    Keiles, S.4    Tandy, S.5    Pesaran, T.6
  • 31
    • 84880535720 scopus 로고    scopus 로고
    • ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing
    • Green RC, Berg JS, Grody WW, Kalia SS, Korf BR, Martin CL, et al. ACMG recommendations for reporting of incidental findings in clinical exome and genome sequencing. Genet Med. 2013; 15: 565-74.
    • (2013) Genet Med , vol.15 , pp. 565-574
    • Green, R.C.1    Berg, J.S.2    Grody, W.W.3    Kalia, S.S.4    Korf, B.R.5    Martin, C.L.6
  • 34
    • 85010703579 scopus 로고    scopus 로고
    • Diagnostic yield of clinical tumor and germline whole-exome sequencing for children with solid tumors
    • Jan 28. [Epub ahead of print]
    • Parsons DW, Roy A, Yang Y, Wang T, Scollon S, Bergstrom K, et al. Diagnostic yield of clinical tumor and germline whole-exome sequencing for children with solid tumors. JAMA Oncol. 2016 Jan 28. doi: 10.1001/jamaoncol.2015.5699. [Epub ahead of print]
    • (2016) JAMA Oncol
    • Parsons, D.W.1    Roy, A.2    Yang, Y.3    Wang, T.4    Scollon, S.5    Bergstrom, K.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.