Prospective blinded study of somatic mutation detection in cell-free DNA utilizing a targeted 54-gene next generation sequencing panel in metastatic solid tumor patients

Oncotarget

Volumn 6, Issue 37, 2015, Pages 40360-40369

  Kim, Seung Tae ^a   Lee, Won Suk ^b   Lanman, Richard B ^c   Mortimer, Stefanie ^c   Zill, Oliver A ^c   Kim, Kyoung Mee ^a,d   Jang, Kee Taek ^a   Kim, Seok Hyung ^a   Park, Se Hoon ^a   Park, Joon Oh ^a,d   Park, Young Suk ^a   Lim, Ho Yeong ^a   Eltoukhy, Helmy ^c   Kang, Won Ki ^a   Lee, Woo Yong ^a   Kim, Hee Cheol ^a   Park, Keunchil ^a,d   Lee, Jeeyun ^a,d   Talasaz, AmirAli ^c  

^a Sungkyunkwan University School of Medicine   (South Korea)

^b Gachon University   (South Korea)

^c Guardant Health   (United States)

^d Samsung Medical Center   (South Korea)

Author keywords

Cell free DNA (cfDNA); Digital sequencing; Genomic test

Indexed keywords

B RAF KINASE; CETUXIMAB; DNA; FLUOROURACIL; FOLINIC ACID; IRINOTECAN; K RAS PROTEIN; ANTINEOPLASTIC AGENT; KRAS PROTEIN, HUMAN; PHOSPHATIDYLINOSITOL 3 KINASE; PIK3CA PROTEIN, HUMAN; PROTEIN P21;

ADULT; AGED; ARTICLE; BRAF GENE; CANCER PATIENT; CANCER RESISTANCE; CANCER STAGING; CHEMOTHERAPY; COLORECTAL CANCER; CONTROLLED STUDY; DIAGNOSTIC ACCURACY; DIAGNOSTIC TEST ACCURACY STUDY; DIGITAL SEQUENCING TECHNOLOGY; DNA DETERMINATION; DNA SEQUENCE; EXPLORATORY RESEARCH; FEMALE; GENE FREQUENCY; HOTSPOT ANALYSIS; HUMAN; HUMAN TISSUE; KIT GENE; MAJOR CLINICAL STUDY; MALE; MIDDLE AGED; MULTIPLE CYCLE TREATMENT; NEXT GENERATION SEQUENCING; ONCOGENE; ONCOGENE K RAS; POLYMERASE CHAIN REACTION; PROSPECTIVE STUDY; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SOLID TUMOR; SOMATIC MUTATION; BLOOD; CHEMISTRY; CLINICAL TRIAL; COLORECTAL NEOPLASMS; DNA MUTATIONAL ANALYSIS; GENETICS; HIGH THROUGHPUT SEQUENCING; METASTASIS; MUTATION; NEOPLASMS; PROCEDURES; REPRODUCIBILITY; VERY ELDERLY;

ADULT; AGED; AGED, 80 AND OVER; ANTINEOPLASTIC COMBINED CHEMOTHERAPY PROTOCOLS; CETUXIMAB; COLORECTAL NEOPLASMS; DNA MUTATIONAL ANALYSIS; DNA, NEOPLASM; FEMALE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MALE; MIDDLE AGED; MUTATION; NEOPLASM METASTASIS; NEOPLASM STAGING; NEOPLASMS; PHOSPHATIDYLINOSITOL 3-KINASES; PROSPECTIVE STUDIES; PROTO-ONCOGENE PROTEINS P21(RAS); REPRODUCIBILITY OF RESULTS;

EID: 84950131811     PISSN: None     EISSN: 19492553     Source Type: Journal    
DOI: 10.18632/oncotarget.5465     Document Type: Article

References (34)

1. Paez JG, Janne PA, Lee JC, Tracy S, Greulich H, Gabriel S, Herman P, Kaye FJ, Lindeman N, Boggon TJ, Naoki K, Sasaki H, Fujii Y, et al. EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy. Science. 2004; 304:1497-1500.
2. Flaherty KT, Puzanov I, Kim KB, Ribas A, McArthur GA, Sosman JA, O'Dwyer PJ, Lee RJ, Grippo JF, Nolop K, Chapman PB. Inhibition of mutated, activated BRAF in metastatic melanoma. N Engl J Med. 2010; 363:809-819.
3. Kwak EL, Bang YJ, Camidge DR, Shaw AT, Solomon B, Maki RG, Ou SH, Dezube BJ, Janne PA, Costa DB, Varella-Garcia M, Kim WH, Lynch TJ, et al. Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer. N Engl J Med. 2010; 363:1693-1703.
4. Karapetis CS, Khambata-Ford S, Jonker DJ, O'Callaghan CJ, Tu D, Tebbutt NC, Simes RJ, Chalchal H, Shapiro JD, Robitaille S, Price TJ, Shepherd L, Au HJ, et al. K-ras mutations and benefit from cetuximab in advanced colorectal cancer. N Engl J Med. 2008; 359:1757-1765.
5. Cardarella S, Ortiz TM, Joshi VA, Butaney M, Jackman DM, Kwiatkowski DJ, Yeap BY, Janne PA, Lindeman NI, Johnson BE. The introduction of systematic genomic testing for patients with non-small-cell lung cancer. J Thorac Oncol. 2012; 7:1767-1774.
6. Nowak F, Soria JC, Calvo F. Tumour molecular profiling for deciding therapy-the French initiative. Nat Rev Clin Oncol. 2012; 9:479-486.
7. Travis WD, Brambilla E, Noguchi M, Nicholson AG, Geisinger K, Yatabe Y, Ishikawa Y, Wistuba I, Flieder DB, Franklin W, Gazdar A, Hasleton PS, Henderson DW, et al. Diagnosis of lung adenocarcinoma in resected specimens: implications of the 2011 International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society classification. Arch Pathol Lab Med. 2013; 137:685-705.
8. Travis WD, Brambilla E, Noguchi M, Nicholson AG, Geisinger K, Yatabe Y, Ishikawa Y, Wistuba I, Flieder DB, Franklin W, Gazdar A, Hasleton PS, Henderson DW, et al. Diagnosis of lung cancer in small biopsies and cytology: implications of the 2011 International Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society classification. Arch Pathol Lab Med. 2013; 137:668-684.
9. Overman MJ, Modak J, Kopetz S, Murthy R, Yao JC, Hicks ME, Abbruzzese JL, Tam AL. Use of research biopsies in clinical trials: are risks and benefits adequately discussed?. J Clin Oncol. 2013; 31:17-22.
10. Alix-Panabieres C, Pantel K. Circulating tumor cells: liquid biopsy of cancer. Clin Chem. 2013; 59:110-118.
11. Yun J, Lee J, Jang J, Lee EJ, Jang KT, Kim JH, Kim KM. KIT amplification and gene mutations in acral/mucosal melanoma in Korea. APMIS. 2011; 119:330-335.
12. Perkins G, Yap TA, Pope L, Cassidy AM, Dukes JP, Riisnaes R, Massard C, Cassier PA, Miranda S, Clark J, Denholm KA, Thway K, Gonzalez De Castro D, et al. Multi-purpose utility of circulating plasma DNA testing in patients with advanced cancers. PLoS One. 2012; 7:e47020.
13. Dawson SJ, Tsui DW, Murtaza M, Biggs H, Rueda OM, Chin SF, Dunning MJ, Gale D, Forshew T, Mahler-Araujo B, Rajan S, Humphray S, Becq J, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med. 2013; 368:1199-1209.
14. Taniguchi K, Uchida J, Nishino K, Kumagai T, Okuyama T, Okami J, Higashiyama M, Kodama K, Imamura F, Kato K. Quantitative detection of EGFR mutations in circulating tumor DNA derived from lung adenocarcinomas. Clin Cancer Res. 2011; 17:7808-7815.
15. Bossuyt PM, Reitsma JB, Bruns DE, Gatsonis CA, Glasziou PP, Irwig LM, Lijmer JG, Moher D, Rennie D, de Vet HC. Toward complete and accurate reporting of studies of diagnostic accuracy. The STARD initiative. Am J Clin Pathol. 2003; 119:18-22.
16. Bossuyt PM, Reitsma JB, Bruns DE, Gatsonis CA, Glasziou PP, Irwig LM, Lijmer JG, Moher D, Rennie D, de Vet HC. Towards complete and accurate reporting of studies of diagnostic accuracy: The STARD Initiative. Radiology. 2003; 226:24-28.
17. Bando H, Yoshino T, Tsuchihara K, Ogasawara N, Fuse N, Kojima T, Tahara M, Kojima M, Kaneko K, Doi T, Ochiai A, Esumi H, Ohtsu A. KRAS mutations detected by the amplification refractory mutation system-Scorpion assays strongly correlate with therapeutic effect of cetuximab. Br J Cancer. 2011; 105:403-406.
18. Pritchard CC, Grady WM. Colorectal cancer molecular biology moves into clinical practice. Gut. 2011; 60:116-129.
19. Van Cutsem E, Kohne CH, Lang I, Folprecht G, Nowacki MP, Cascinu S, Shchepotin I, Maurel J, Cunningham D, Tejpar S, Schlichting M, Zubel A, Celik I, et al. Cetuximab plus irinotecan, fluorouracil, and leucovorin as first-line treatment for metastatic colorectal cancer: updated analysis of overall survival according to tumor KRAS and BRAF mutation status. J Clin Oncol. 2011; 29:2011-2019.
20. Laurent-Puig P, Cayre A, Manceau G, Buc E, Bachet JB, Lecomte T, Rougier P, Lievre A, Landi B, Boige V, Ducreux M, Ychou M, Bibeau F, et al. Analysis of PTEN, BRAF, and EGFR status in determining benefit from cetuximab therapy in wild-type KRAS metastatic colon cancer. J Clin Oncol. 2009; 27:5924-5930.
21. Bibeau F, Lopez-Crapez E, Di Fiore F, Thezenas S, Ychou M, Blanchard F, Lamy A, Penault-Llorca F, Frebourg T, Michel P, Sabourin JC, Boissiere-Michot F. Impact of Fc[gamma]RIIa-Fc[gamma]RIIIa polymorphisms and KRAS mutations on the clinical outcome of patients with metastatic colorectal cancer treated with cetuximab plus irinotecan. J Clin Oncol. 2009; 27:1122-1129.
22. Pinto P, Rocha P, Veiga I, Guedes J, Pinheiro M, Peixoto A, Pinto C, Fragoso M, Sanches E, Araujo A, Alves F, Coutinho C, Lopes P, et al. Comparison of methodologies for KRAS mutation detection in metastatic colorectal cancer. Cancer Genet. 2011; 204:439-446.
23. Heinemann V, von Weikersthal LF, Decker T, Kiani A, Vehling-Kaiser U, Al-Batran SE, Heintges T, Lerchenmuller C, Kahl C, Seipelt G, Kullmann F, Stauch M, Scheithauer W, et al. FOLFIRI plus cetuximab versus FOLFIRI plus bevacizumab as first-line treatment for patients with metastatic colorectal cancer (FIRE-3): a randomised, open-label, phase 3 trial. Lancet Oncol. 2014; 15:1065-1075.
24. Diaz LA Jr., Williams RT, Wu J, Kinde I, Hecht JR, Berlin J, Allen B, Bozic I, Reiter JG, Nowak MA, Kinzler KW, Oliner KS, Vogelstein B. The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature. 2012; 486:537-540.
25. Misale S, Yaeger R, Hobor S, Scala E, Janakiraman M, Liska D, Valtorta E, Schiavo R, Buscarino M, Siravegna G, Bencardino K, Cercek A, Chen CT, et al. Emergence of KRAS mutations and acquired resistance to anti-EGFR therapy in colorectal cancer. Nature. 2012; 486:532-536.
26. Chan KC, Jiang P, Zheng YW, Liao GJ, Sun H, Wong J, Siu SS, Chan WC, Chan SL, Chan AT, Lai PB, Chiu RW, Lo YM. Cancer genome scanning in plasma: detection of tumor-associated copy number aberrations, single-nucleotide variants, and tumoral heterogeneity by massively parallel sequencing. Clin Chem. 2013; 59:211-224.
27. Tran B, Brown AM, Bedard PL, Winquist E, Goss GD, Hotte SJ, Welch SA, Hirte HW, Zhang T, Stein LD, Ferretti V, Watt S, Jiao W, et al. Feasibility of real time next generation sequencing of cancer genes linked to drug response: results from a clinical trial. Int J Cancer. 2013; 132:1547-1555.
28. Murtaza M, Dawson SJ, Tsui DW, Gale D, Forshew T, Piskorz AM, Parkinson C, Chin SF, Kingsbury Z, Wong AS, Marass F, Humphray S, Hadfield J, et al. Noninvasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature. 2013; 497:108-112.
29. Leary RJ, Sausen M, Kinde I, Papadopoulos N, Carpten JD, Craig D, O'Shaughnessy J, Kinzler KW, Parmigiani G, Vogelstein B, Diaz LA Jr., Velculescu VE. Detection of chromosomal alterations in the circulation of cancer patients with whole-genome sequencing. Sci Transl Med. 2012; 4: 162ra154.
30. Narayan A, Carriero NJ, Gettinger SN, Kluytenaar J, Kozak KR, Yock TI, Muscato NE, Ugarelli P, Decker RH, Patel AA. Ultrasensitive measurement of hotspot mutations in tumor DNA in blood using error-suppressed multiplexed deep sequencing. Cancer Res. 2012; 72:3492-3498.
31. Kim ST, Lim do H, Jang KT, Lim T, Lee J, Choi YL, Jang HL, Yi JH, Baek KK, Park SH, Park YS, Lim HY, Kang WK1, et al. Impact of KRAS mutations on clinical outcomes in pancreatic cancer patients treated with first-line gemcitabine-based chemotherapy. Mol Cancer Ther. 2011; 10:1993-1999.
32. Cho JH, Kim KM, Kwon M, Kim JH, Lee J. Nilotinib in patients with metastatic melanoma harboring KIT gene aberration. Invest New Drugs. 2012; 30:2008-2014.
33. Beadling C, Jacobson-Dunlop E, Hodi FS, Le C, Warrick A, Patterson J, Town A, Harlow A, Cruz F 3rd, Azar S, Rubin BP, Muller S, West R, et al. KIT gene mutations and copy number in melanoma subtypes. Clin Cancer Res. 2008; 14:6821-6828.
34. Altman DG, Bland JM. Diagnostic tests 1: Sensitivity and specificity. BMJ. 1994; 308:1552.