Base-Position Error Rate Analysis of Next-Generation Sequencing Applied to Circulating Tumor DNA in Non-Small Cell Lung Cancer: A Prospective Study

1. Torre LA, Bray F, Siegel RL, Ferlay J, Lortet-Tieulent J, Jemal A. Global cancer statistics, 2012. CA Cancer J Clin. 2015;65: 87–108. doi: 10.3322/caac.21262 25651787

2. Howlader N, Noone AM, Krapcho M, Miller D, Bishop K, Altekruse SF, et al. SEER Cancer Statistics Review, 1975–2013, National Cancer Institute. Bethesda, MD, http://seer.cancer.gov/csr/1975_2013/, based on November 2015 SEER data submission, posted to the SEER web site, April 2016. from: http://seer.cancer.gov; 2013.

3. Swanton C, Govindan R. Clinical Implications of Genomic Discoveries in Lung Cancer. N Engl J Med. 2016;374: 1864–1873. doi: 10.1056/NEJMra1504688 27168435

4. Chen Z, Fillmore CM, Hammerman PS, Kim CF, Wong K-K. Non-small-cell lung cancers: a heterogeneous set of diseases. Nat Rev Cancer. 2014;14: 535–546. doi: 10.1038/nrc3775 25056707

5. Heitzer E, Ulz P, Geigl JB. Circulating tumor DNA as a liquid biopsy for cancer. Clin Chem. 2015;61: 112–123. doi: 10.1373/clinchem.2014.222679 25388429

6. De Mattos-Arruda L, Weigelt B, Cortes J, Won HH, Ng CKY, Nuciforo P, et al. Capturing intra-tumor genetic heterogeneity by de novo mutation profiling of circulating cell-free tumor DNA: a proof-of-principle. Ann Oncol. 2014;25: 1729–1735. doi: 10.1093/annonc/mdu239 25009010

7. Izumchenko E, Chang X, Brait M, Fertig E, Kagohara LT, Bedi A, et al. Targeted sequencing reveals clonal genetic changes in the progression of early lung neoplasms and paired circulating DNA. Nat Commun. 2015;6: 8258. doi: 10.1038/ncomms9258 26374070

8. Dawson S-J, Tsui DWY, Murtaza M, Biggs H, Rueda OM, Chin S-F, et al. Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer. N Engl J Med. 2013;368: 1199–1209. doi: 10.1056/NEJMoa1213261 23484797

9. Murtaza M, Dawson S-J, Pogrebniak K, Rueda OM, Provenzano E, Grant J, et al. Multifocal clonal evolution characterized using circulating tumour DNA in a case of metastatic breast cancer. Nat Commun. 2015;6: 8760. doi: 10.1038/ncomms9760 26530965

10. Lo YMD, Zhang J, Leung TN, Lau TK, Chang AMZ, Hjelm NM. Rapid Clearance of Fetal DNA from Maternal Plasma. Am J Hum Gen. 1999;64: 218–224.

11. Diehl F, Schmidt K, Choti MA, Romans K, Goodman S, Li M, et al. Circulating mutant DNA to assess tumor dynamics. Nat Med. 2008;14: 985–990. doi: 10.1038/nm.1789 18670422

12. Qiu M, Wang J, Xu Y, Ding X, Li M, Jiang F, et al. Circulating tumor DNA is effective for the detection of EGFR mutation in non-small cell lung cancer: a meta-analysis. Cancer Epidemiol Biomarkers Prev. 2015;24: 206–212. doi: 10.1158/1055-9965.EPI-14-0895 25339418

13. Douillard J-Y, Ostoros G, Cobo M, Ciuleanu T, Cole R, McWalter G, et al. Gefitinib treatment in EGFR mutated caucasian NSCLC: circulating-free tumor DNA as a surrogate for determination of EGFR status. J Thorac Oncol. 2014;9: 1345–1353. doi: 10.1097/JTO.0000000000000263 25122430

14. Karachaliou N, Mayo-de-las-Casas C, Queralt C, de Aguirre I, Melloni B, Cardenal F, et al. Association of EGFR L858R Mutation in Circulating Free DNA With Survival in the EURTAC Trial. JAMA Oncol. 2015;1: 149–157. doi: 10.1001/jamaoncol.2014.257 26181014

15. Uchida J, Kato K, Kukita Y, Kumagai T, Nishino K, Daga H, et al. Diagnostic Accuracy of Noninvasive Genotyping of EGFR in Lung Cancer Patients by Deep Sequencing of Plasma Cell-Free DNA. Clin Chem. 2015;61: 1191–1196. doi: 10.1373/clinchem.2015.241414 26206882

16. Sacher AG, Paweletz C, Dahlberg SE, Alden RS, O'Connell A, Feeney N, et al. Prospective Validation of Rapid Plasma Genotyping for the Detection of EGFR and KRAS Mutations in Advanced Lung Cancer. JAMA Oncol. 2016;: 1–14.

17. 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: 1698–1705. doi: 10.1158/1078-0432.CCR-13-2482 24429876

18. Thress KS, Paweletz CP, Felip E, Cho BC, Stetson D, Dougherty B, et al. Acquired EGFR C797S mutation mediates resistance to AZD9291 in non–small cell lung cancer harboring EGFR T790M. Nat Med. 2015;21: 560–562. doi: 10.1038/nm.3854 25939061

19. Thress KS, Brant R, Carr TH, Dearden S, Jenkins S, Brown H, et al. EGFR mutation detection in ctDNA from NSCLC patient plasma: A cross-platform comparison of leading technologies to support the clinical development of AZD9291. Lung Cancer. 2015;90: 509–515. doi: 10.1016/j.lungcan.2015.10.004 26494259

20. Zheng D, Ye X, Zhang MZ, Sun Y, Wang JY, Ni J, et al. Plasma EGFR T790M ctDNA status is associated with clinical outcome in advanced NSCLC patients with acquired EGFR-TKI resistance. Sci Rep. 2016;6: 20913. doi: 10.1038/srep20913 26867973

21. Thierry AR, Mouliere F, Messaoudi El S, Mollevi C, Lopez-Crapez E, Rolet F, et al. Clinical validation of the detection of KRAS and BRAF mutations from circulating tumor DNA. Nat Med. 2014;20: 430–435. doi: 10.1038/nm.3511 24658074

22. Taly V, Pekin D, Benhaim L, Kotsopoulos SK, Le Corre D, Li X, et al. Multiplex picodroplet digital PCR to detect KRAS mutations in circulating DNA from the plasma of colorectal cancer patients. Clin Chem. 2013;59: 1722–1731. doi: 10.1373/clinchem.2013.206359 23938455

23. Diehl F, Li M, Dressman D, He Y, Shen D, Szabo S, et al. Detection and quantification of mutations in the plasma of patients with colorectal tumors. Proc Natl Acad Sci U S A. 2005;102: 16368–16373. doi: 10.1073/pnas.0507904102 16258065

24. Forshew T, Murtaza M, Parkinson C, Gale D, Tsui DWY, Kaper F, et al. Noninvasive Identification and Monitoring of Cancer Mutations by Targeted Deep Sequencing of Plasma DNA. Sci Transl Med. 2012;4: 136ra68–136ra68. doi: 10.1126/scitranslmed.3003726 22649089

25. Kinde I, Wu J, Papadopoulos N, Kinzler KW, Vogelstein B. Detection and quantification of rare mutations with massively parallel sequencing. Proc Natl Acad Sci U S A; 2011;108: 9530–9535. doi: 10.1073/pnas.1105422108 21586637

26. Tie J, Kinde I, Wang Y, Wong HL, Roebert J, Christie M, et al. Circulating tumor DNA as an early marker of therapeutic response in patients with metastatic colorectal cancer. Ann Oncol. 2015;26: 1715–1722. doi: 10.1093/annonc/mdv177 25851626

27. Pécuchet N, Rozenholc Y, Zonta E, Pietraz D, Didelot A, Combe P, et al. Analysis of Base-Position Error Rate of Next-Generation Sequencing to Detect Tumor Mutations in Circulating DNA. Clin Chem. 2016;62: 1492–1503. doi: 10.1373/clinchem.2016.258236 27624137

28. Gerber DE, Dahlberg SE, Sandler AB, Ahn DH, Schiller JH, Brahmer JR, et al. Baseline tumour measurements predict survival in advanced non-small cell lung cancer. Br J Cancer. 2013;109: 1476–1481. doi: 10.1038/bjc.2013.472 23942074

29. Milbury CA, Zhong Q, Lin J, Williams M, Olson J, Link DR, et al. Determining lower limits of detection of digital PCR assays for cancer-related gene mutations. Biomol Detect Quantif. 2014;1: 8–22.

30. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20: 1297–1303. doi: 10.1101/gr.107524.110 20644199

31. Barlési F, Mazieres J, Merlio J-P, Debieuvre D, Mosser J, Lena H, et al. Routine molecular profiling of patients with advanced non-small-cell lung cancer: results of a 1-year nationwide programme of the French Cooperative Thoracic Intergroup (IFCT). Lancet. 2016;387: 1415–1426. doi: 10.1016/S0140-6736(16)00004-0 26777916

32. Whittaker SR, Theurillat J-P, Van Allen E, Wagle N, Hsiao J, Cowley GS, et al. A genome-scale RNA interference screen implicates NF1 loss in resistance to RAF inhibition. Cancer Discov. 2013;3: 350–362. doi: 10.1158/2159-8290.CD-12-0470 23288408

33. Tong Y-H, Zhang B, Fan Y, Lin N-M. Keap1-Nrf2 pathway: A promising target towards lung cancer prevention and therapeutics. Chronic Dis Transl Med. 2015;1: 175–186.

34. Newman AM, Bratman SV, To J, Wynne JF, Eclov NCW, Modlin LA, et al. An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage. Nat Med. 2014;20: 548–554. doi: 10.1038/nm.3519 24705333

35. Saukkonen K, Lakkisto P, Pettila V, Varpula M, Karlsson S, Ruokonen E, et al. Cell-Free Plasma DNA as a Predictor of Outcome in Severe Sepsis and Septic Shock. Clin Chem. 2008;54: 1000–1007. doi: 10.1373/clinchem.2007.101030 18420731

36. Mok T, Wu Y-L, Lee JS, Yu C-J, Sriuranpong V, Sandoval-Tan J, et al. Detection and Dynamic Changes of EGFR Mutations from Circulating Tumor DNA as a Predictor of Survival Outcomes in NSCLC Patients Treated with First-line Intercalated Erlotinib and Chemotherapy. Clin Cancer Res. 2015;21: 3196–3203. doi: 10.1158/1078-0432.CCR-14-2594 25829397

37. Lee JY, Qing X, Xiumin W, Yali B, Chi S, Bak SH, et al. Longitudinal monitoring of EGFR mutations in plasma predicts outcomes of NSCLC patients treated with EGFR TKIs: Korean Lung Cancer Consortium (KLCC-12-02). Oncotarget. 2016;7: 6984–6993. doi: 10.18632/oncotarget.6874 26755650