Biology of Human Tumors Noninvasive Diagnosis of Actionable Mutations by Deep Sequencing of Circulating Free DNA in Lung Cancer from Never-Smokers : A Proof-of-Concept Study

Purpose:Tumor somaticmutation analysis is part of the standardmanagement ofmetastatic lung cancer. However, physicians often have to deal with small biopsies and consequently with challenging mutation testing. Circulating freeDNA (cfDNA) is a promising tool for accessing the tumor genome as a liquid biopsy. Here, we evaluated next-generation sequencing (NGS) on cfDNA samples obtained from a consecutive series of patients for the screening of a range of clinically relevant mutations. Experimental Design: A total of 107 plasma samples were collected from the BioCAST/IFCT-1002 lung cancer study (never-smokers cohort). Matched tumor DNA (tDNA) was obtained for 68 cases. Multiplex PCR-based assays were designed to target specific coding regions in EGFR,KRAS, BRAF, ERBB2, and PI3KCA genes, and amplicon sequencing was performed at deep coverage on the cfDNA/tDNA pairs using the NGS IonTorrent Personal Genome Machine Platform. Results: CfDNA concentration in plasma was significantly associated with both stage and number of metastatic sites. In tDNA, 50mutations (36 EGFR, 5 ERBB2, 4KRAS, 3BRAF, and 2 PIK3CA)were identified, of which 26 were detected in cfDNA. Sensitivity of the test was 58% (95% confidence interval, 43%–71%) and the estimated specificity was 87% (62%–96%). Conclusion: These data demonstrate the feasibility and potential utility of mutation screening in cfDNA using IonTorrent NGS for the detection of a range of tumor biomarkers in patients with metastatic lung cancer. Clin Cancer Res; 20(17); 4613–24. 2014 AACR. International Agency for Research on Cancer, Section of Mechanisms of Carcinogenesis, Molecular Mechanisms and Biomarkers Group, Lyon Cedex, France. Department of Pulmonology, Lyon Sud University Hospital, Hospices Civils de Lyon, Lyon, France. Lyon Sud Faculty of Medicine, Lyon 1 University, Pierre B enite Cedex, France. Laboratorio de Gen omica, Instituto Nacional de Cancerología, Tlalpan, M exico. Unidad de Biomedicina, FES-Iztacala, UNAM, M exico. International Agency for Research on Cancer, Genetic Cancer Susceptibility Group, Lyon Cedex, France. Centre for Clinical Epidemiology, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada. Department of Epidemiology and Biostatistics, McGill University, Montreal, Quebec, Canada. The Jean Dausset Foundation – CEPH, Paris, France. Department of Respiratory Medicine, Hôpital Louis Pradel, Hospices Civils de Lyon, Lyon, France. Claude Bernard University Lyon 1, Lyon (Bron), France. Department of Pulmonology, Paris – Saint Joseph Hospital, and Sorbonne Paris Cit e university, France. Pulmonology Unit, University Hospital of Tours, France and François Rabelais University, Respiratory Diseases Study Centre, Tours, France. Francois Baclesse Cancer Institute, Caen, France. Department of Chest, Strasbourg University Hospital, Strasbourg, France. Department of Pulmonology, Saint Joseph-Saint Luc Hospital, Lyon, France. Department of Respiratory Department, Percy Military Hospital, Clamart, France. Department of Pulmonology, Mâcon Hospital, Mâcon, France. Thoracic Oncology, Dijon University Hospital, Dijon, France. Department of Oncology, Mont elimar Hospital, Mont elimar, France. Intergroupe Francophone de Canc erologie Thoracique, Paris, France. Pulmonology and Thoracic Oncology Unit and UMR 1086 Inserm "Cancers and Pr eventions," Caen University Hospital, Caen, France. Note: Supplementary data for this article are available at Clinical Cancer Research Online (http://clincancerres.aacrjournals.org/). S. Couraud and F. Vaca-Paniagua contributed equally to this article. M. Olivier and P.-J. Souquet contributed equally to this article. Corresponding Author: S ebastien Couraud, CH Lyon Sud – Hospices Civils de Lyon, Service de Pneumologie, 165 chemin du Grand Revoyet, 69495 Pierre-B enite CEDEX. Phone: 33-4-78-86-44-05; Fax: 33-4-78-8644-19; E-mail: sebastien.couraud@chu-lyon.fr doi: 10.1158/1078-0432.CCR-13-3063 2014 American Association for Cancer Research. Clinical Cancer Research www.aacrjournals.org 4613 on May 29, 2017. © 2014 American Association for Cancer Research. clincancerres.aacrjournals.org Downloaded from Published OnlineFirst July 10, 2014; DOI: 10.1158/1078-0432.CCR-13-3063