Bias-corrected targeted next-generation sequencing for rapid, multiplexed detection of actionable alterations in cell-free DNA from advanced lung cancer patients

Clinical Cancer Research

Volumn 22, Issue 4, 2016, Pages 915-922

  Paweletz, Cloud P ^a   Sacher, Adrian G ^a   Raymond, Chris K ^b   Alden, Ryan S ^a   O'Connell, Allison ^a   MacH, Stacy L ^a   Kuang, Yanan ^a   Gandhi, Leena ^a   Kirschmeier, Paul ^a   English, Jessie M ^a   Lim, Lee P ^b   Jänne, Pasi A ^a   Oxnard, Geoffrey R ^a  

^a DANA FARBER CANCER INSTITUTE   (United States)

^b Resolution Bioscience   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AFATINIB; COMPLEMENTARY DNA; CRIZOTINIB; EPIDERMAL GROWTH FACTOR RECEPTOR; ERLOTINIB; K RAS PROTEIN; OSIMERTINIB; DNA;

ADVANCED CANCER; ARTICLE; ARTIFACT; CANCER GROWTH; CANCER PATIENT; CELL FREE SYSTEM; CONTROLLED STUDY; EXON; GENE AMPLIFICATION; GENE DELETION; GENE FREQUENCY; GENE MUTATION; GENE TARGETING; GENOTYPE; HUMAN; HUMAN CELL; LUNG CANCER; NEXT GENERATION SEQUENCING; NON SMALL CELL LUNG CANCER; PATIENT CARE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; SENSITIVITY AND SPECIFICITY; TRANSLATIONAL RESEARCH; BLOOD; CANCER STAGING; DNA MUTATIONAL ANALYSIS; FEMALE; GENETICS; HIGH THROUGHPUT SEQUENCING; LUNG TUMOR; MALE; MIDDLE AGED; PATHOLOGY; SECONDARY; TUMOR CELL LINE;

CARCINOMA, NON-SMALL-CELL LUNG; CELL LINE, TUMOR; DNA MUTATIONAL ANALYSIS; DNA, NEOPLASM; FEMALE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; LUNG NEOPLASMS; MALE; MIDDLE AGED; NEOPLASM STAGING;

EID: 84964224932     PISSN: 10780432     EISSN: 15573265     Source Type: Journal    
DOI: 10.1158/1078-0432.CCR-15-1627-T     Document Type: Article

References (26)

1. Li T, Kung HJ, Mack PC, Gandara DR.Genotyping and genomic profiling of non-small-cell lung cancer: implications for current and future therapies. J Clin Oncol 2013;31:1039-49.
2. 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.
3. Kwak EL, Bang YJ, Camidge DR, Shaw AT, Solomon B, Maki RG, et al. Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer. N Engl J Med 2010;363:1693-703.
4. Hauschild A, Grob JJ, Demidov LV, Jouary T, Gutzmer R, Millward M, et al. Dabrafenib in BRAF-mutated metastatic melanoma: a multicentre, openlabel, phase 3 randomised controlled trial. Lancet 2012;380:358-65.
5. Cardarella S, Ortiz TM, Joshi VA, Butaney M, JackmanDM, Kwiatkowski DJ, et al. The introduction of systematic genomic testing for patients with nonsmall- cell lung cancer. J Thorac Oncol 2012;7:1767-74.
6. Planchard D, Kim T, Maziéres J, Quoix E, Riely G, Barlesi F, et al. Dabrafenib in patients with BRAF V600E-mutant advanced non-small cell lung cancer (NSCLC): a multicenter, open-label, phase II trial (BRF113928). Ann Oncol 2014;25 (Supplement 5): v1-v41.
7. Sholl LM, Aisner DL, Varella-Garcia M, Berry LD, Dias-Santagata D, Wistuba II, et al. Multi-institutional oncogenic driver mutation analysis in lung adenocarcinoma: the lung cancer mutation consortium experience. J Thorac Oncol 2015.
8. Wagle N, Berger MF, Davis MJ, Blumenstiel B, Defelice M, Pochanard P, et al. High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing. Cancer Discov 2012;2:82-93.
9. Hagemann IS, Devarakonda S, Lockwood CM, Spencer DH, Guebert K, Bredemeyer AJ, et al. Clinical next-generation sequencing in patients with non-small cell lung cancer. Cancer 2015;121:631-9.
10. Luke JJ, Oxnard GR, Paweletz CP, Camidge DR, Heymach JV, Solit DB, et al. Realizing the potential of plasma genotyping in an age of genotypedirected therapies. J Natl Cancer Inst 2014;106(8).
11. Couraud S, Vaca-Paniagua F, Villar S, Oliver J, Schuster T, Blanché H, et al. Noninvasive diagnosis of actionable mutations by deep sequencing of circulating free DNA in lung cancer from never-smokers: a proof-ofconcept study from BioCAST/IFCT-1002. Clin Cancer Res 2014;20: 4613-24.
12. Goto K, Ichinose Y, Ohe Y, Yamamoto N, Negoro S, Nishio K, et al. Epidermal growth factor receptor mutation status in circulating free DNA in serum: from IPASS, a phase III study of gefitinib or carboplatin/paclitaxel in non-small cell lung cancer. J Thorac Oncol 2012;7:115-21.
13. Lee YJ, Yoon KA, Han JY, Kim HT, Yun T, Lee GK, et al. Circulating cell-free DNA in plasma of never smokers with advanced lung adenocarcinoma receiving gefitinib or standard chemotherapy as first-line therapy. Clin Cancer Res 2011;17:5179-87.
14. Douillard JY, Ostoros G, Cobo M, Ciuleanu T, Cole R, McWalter G, et al. Gefitinib treatment in EGFR mutated caucasian NSCLC: circulating-free tumorDNAas a surrogate for determination of EGFR status. J Thorac Oncol 2014;9:1345-53.
15. Forshew T, Murtaza M, Parkinson C, Gale D, Tsui DW, Kaper F, et al. Noninvasive identification and monitoring of cancer mutations by targeted deep sequencing of plasma DNA. Sci Transl Med 2012;4:136ra68.
16. Oxnard GR, Paweletz CP, Kuang Y, Mach SL, O'Connell A, Messineo MM, et al. Noninvasive detection of response and resistance in EGFR-mutant lung cancer using quantitative next-generation genotyping of cell-free plasma DNA. Clin Cancer Res 2014;20:1698-705.
17. Sacher A, Oxnard G, Mach S, Messineo M, Jackman D, Jänne P, et al. Prediction of lung cancer genotype noninvasively using droplet digital PCR (ddPCR) analysis of cell-free plasma DNA (cfDNA). American Society of Clinical Oncology Annual Meeting; Chicago, United States 2014.
18. Newman AM, Bratman SV, To J, Wynne JF, Eclov NC, Modlin LA, et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med 2014;20:548-54.
19. Oxnard G, Lydon C, Lindeman N, Shivdasani P, Chin G, Kuo F, et al. Implementation of clinical next-generation sequencing (NGS) of nonsmall cell lung cancer (NSCLC) to identify EGFR amplification as a potentially targetable oncogenic alteration. American Society of Clinical Oncology Annual Meeting; Chicago, USA 2014.
20. Jänne PA, Yang JC, Kim DW, Planchard D, Ohe Y, Ramalingam SS, et al. AZD9291 in EGFR inhibitor-resistant non-small-cell lung cancer. N Engl J Med 2015;372:1689-99.
21. Thress KS, Paweletz CP, Felip E, Cho BC, Stetson D, Dougherty B, et al. Acquired EGFR C797S mutation mediates resistance to AZD9291 in nonsmall cell lung cancer harboring EGFR T790M. Nat Med 2015.
22. Niederst MJ, Hu H, Mulvey HE, Lockerman EL, Garcia AR, Piotrowska Z, et al. The allelic context of the C797S mutation acquired upon treatment with third-generation EGFR inhibitors impacts sensitivity to subsequent treatment strategies. Clin Cancer Res 2015;21:3924-33.
23. Yu HA, Tian SK, Drilon AE, Borsu L, Riely GJ, Arcila ME, et al. Acquired resistance of EGFR-mutant lung cancer to a T790M-Specific EGFR inhibitor: emergence of a third mutation (C797S) in the EGFR tyrosine kinase domain. JAMA Oncol 2015.
24. Luo J, Shen L, Zheng D. Diagnostic value of circulating free DNA for the detection of EGFR mutation status in NSCLC: a systematic review and meta-analysis. Sci Rep 2014;4:6269.
25. de Bruin EC, McGranahan N, Mitter R, Salm M, Wedge DC, Yates L, et al. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science 2014;346:251-6.
26. Zhang J, Fujimoto J, Wedge DC, Song X, Seth S, Chow CW, et al. Intratumor heterogeneity in localized lung adenocarcinomas delineated by multiregion sequencing. Science 2014;346:256-9.