title: Noninvasive diagnosis of actionable mutations by deep sequencing of circulating free DNA in lung cancer from never-smokers: a proof-of-concept study from BioCAST/IFCT-1002.
abstract: OBJECTIVE
  Tumor somatic mutation analysis is part of the standard management of metastatic lung cancer. However, physicians often have to deal with small biopsies and consequently with challenging mutation testing. Circulating free DNA (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.
  
  
  METHODS
  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, 50 mutations (36 EGFR, 5 ERBB2, 4 KRAS, 3 BRAF, 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%).
  
  
  CONCLUSIONS
  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.
authors.affiliation: 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 Bénite Cedex, France. sebastien.couraud@chu-lyon.fr.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Couraud
authors.affiliation: International Agency for Research on Cancer, Section of Mechanisms of Carcinogenesis, Molecular Mechanisms and Biomarkers Group, Lyon Cedex, France. Laboratorio de Genómica, Instituto Nacional de Cancerología, Tlalpan, México. Unidad de Biomedicina, FES-Iztacala, UNAM, México.
authors.forename: Felipe
authors.initials: F
authors.lastname: Vaca-Paniagua
authors.affiliation: International Agency for Research on Cancer, Section of Mechanisms of Carcinogenesis, Molecular Mechanisms and Biomarkers Group, Lyon Cedex, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Villar
authors.affiliation: International Agency for Research on Cancer, Genetic Cancer Susceptibility Group, Lyon Cedex, France.
authors.forename: Javier
authors.initials: J
authors.lastname: Oliver
authors.affiliation: 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.
authors.forename: Tibor
authors.initials: T
authors.lastname: Schuster
authors.affiliation: The Jean Dausset Foundation - CEPH, Paris, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Blanché
authors.affiliation: Department of Respiratory Medicine, Hôpital Louis Pradel, Hospices Civils de Lyon, Lyon, France. Claude Bernard University Lyon 1, Lyon (Bron), France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Girard
authors.affiliation: Department of Pulmonology, Paris - Saint Joseph Hospital, and Sorbonne Paris Cité university, France.
authors.forename: Jean
authors.initials: J
authors.lastname: Trédaniel
authors.affiliation: Pulmonology Unit, University Hospital of Tours, France and François Rabelais University, Respiratory Diseases Study Centre, Tours, France.
authors.forename: Laurent
authors.initials: L
authors.lastname: Guilleminault
authors.affiliation: Francois Baclesse Cancer Institute, Caen, France.
authors.forename: Radj
authors.initials: R
authors.lastname: Gervais
authors.affiliation: Department of Chest, Strasbourg University Hospital, Strasbourg, France.
authors.forename: Nathalie
authors.initials: N
authors.lastname: Prim
authors.affiliation: Department of Pulmonology, Saint Joseph-Saint Luc Hospital, Lyon, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Vincent
authors.affiliation: Department of Respiratory Department, Percy Military Hospital, Clamart, France.
authors.forename: Jacques
authors.initials: J
authors.lastname: Margery
authors.affiliation: Department of Pulmonology, Mâcon Hospital, Mâcon, France.
authors.forename: Sébastien
authors.initials: S
authors.lastname: Larivé
authors.affiliation: Thoracic Oncology, Dijon University Hospital, Dijon, France.
authors.forename: Pascal
authors.initials: P
authors.lastname: Foucher
authors.affiliation: Department of Oncology, Montélimar Hospital, Montélimar, France.
authors.forename: Bernard
authors.initials: B
authors.lastname: Duvert
authors.affiliation: International Agency for Research on Cancer, Genetic Cancer Susceptibility Group, Lyon Cedex, France.
authors.forename: Maxime
authors.initials: M
authors.lastname: Vallee
authors.affiliation: International Agency for Research on Cancer, Genetic Cancer Susceptibility Group, Lyon Cedex, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Le Calvez-Kelm
authors.affiliation: International Agency for Research on Cancer, Genetic Cancer Susceptibility Group, Lyon Cedex, France.
authors.forename: James
authors.initials: J
authors.lastname: McKay
authors.affiliation: Intergroupe Francophone de Cancérologie Thoracique, Paris, France.
authors.forename: Pascale
authors.initials: P
authors.lastname: Missy
authors.affiliation: Intergroupe Francophone de Cancérologie Thoracique, Paris, France.
authors.forename: Franck
authors.initials: F
authors.lastname: Morin
authors.affiliation: Pulmonology and Thoracic Oncology Unit and UMR 1086 Inserm "Cancers and Préventions," Caen University Hospital, Caen, France.
authors.forename: Gérard
authors.initials: G
authors.lastname: Zalcman
authors.affiliation: International Agency for Research on Cancer, Section of Mechanisms of Carcinogenesis, Molecular Mechanisms and Biomarkers Group, Lyon Cedex, France.
authors.forename: Magali
authors.initials: M
authors.lastname: Olivier
authors.affiliation: Department of Pulmonology, Lyon Sud University Hospital, Hospices Civils de Lyon, Lyon, France. Lyon Sud Faculty of Medicine, Lyon 1 University, Pierre Bénite Cedex, France.
authors.forename: Pierre-Jean
authors.initials: PJ
authors.lastname: Souquet
mesh_terms: D000328:Adult; D000368:Aged; D014408:Biomarkers, Tumor / Q000097:blood / Q000235:genetics; D058534:Class I Phosphatidylinositol 3-Kinases; D004252:DNA Mutational Analysis; D004273:DNA, Neoplasm / Q000097:blood; D066246:ErbB Receptors / Q000097:blood / Q000235:genetics*; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008175:Lung Neoplasms / Q000097:blood / Q000235:genetics* / Q000473:pathology; D008875:Middle Aged; D009360:Neoplastic Cells, Circulating / Q000473:pathology; D019869:Phosphatidylinositol 3-Kinases / Q000235:genetics*; D011518:Proto-Oncogene Proteins / Q000097:blood / Q000235:genetics*; D048493:Proto-Oncogene Proteins B-raf / Q000097:blood / Q000235:genetics*; D016283:Proto-Oncogene Proteins p21(ras); D018719:Erb-b2 Receptor Tyrosine Kinases / Q000097:blood / Q000235:genetics*; D012907:Smoking; D018631:ras Proteins / Q000097:blood / Q000235:genetics*
chemical_list: D014408:Biomarkers, Tumor; D058534:Class I Phosphatidylinositol 3-Kinases; D004273:DNA, Neoplasm; D066246:ErbB Receptors; D019869:Phosphatidylinositol 3-Kinases; D011518:Proto-Oncogene Proteins; D048493:Proto-Oncogene Proteins B-raf; D016283:Proto-Oncogene Proteins p21(ras); D018719:Erb-b2 Receptor Tyrosine Kinases; D018631:ras Proteins; C117307:KRAS protein, human; C484760:PIK3CA protein, human; C512478:EGFR protein, human; C508053:ERBB2 protein, human; C482119:BRAF protein, human