Oncotarget

Research Papers:

Cross-platform comparison for the detection of RAS mutations in cfDNA (ddPCR Biorad detection assay, BEAMing assay, and NGS strategy)

Jessica Garcia, Julien Forestier, Eric Dusserre, Anne-Sophie Wozny, Florence Geiguer, Patrick Merle, Claire Tissot, Carole Ferraro-Peyret, Frederick S. Jones, Daniel L. Edelstein, Valérie Cheynet, Claire Bardel, Gaelle Vilchez, Zhenyu Xu, Pierre Paul Bringuier, Marc Barritault, Karen Brengle-Pesce, Marielle Guillet, Marion Chauvenet, Brigitte Manship, Marie Brevet, Claire Rodriguez-Lafrasse, Valérie Hervieu, Sébastien Couraud, Thomas Walter and Léa Payen _

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Oncotarget. 2018; 9:21122-21131. https://doi.org/10.18632/oncotarget.24950

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Abstract

Jessica Garcia1,2,3,4, Julien Forestier5, Eric Dusserre1,3,4, Anne-Sophie Wozny1,3, Florence Geiguer1,3,4, Patrick Merle6,7, Claire Tissot8, Carole Ferraro-Peyret2,9, Frederick S. Jones10, Daniel L. Edelstein10, Valérie Cheynet4,11, Claire Bardel12,18, Gaelle Vilchez4, Zhenyu Xu13, Pierre Paul Bringuier2,9, Marc Barritault1,9, Karen Brengle-Pesce4,11, Marielle Guillet14, Marion Chauvenet15, Brigitte Manship2, Marie Brevet3,9,16, Claire Rodriguez-Lafrasse1,4, Valérie Hervieu9, Sébastien Couraud3,16,17, Thomas Walter2,5 and Léa Payen1,2,3,4

1Laboratoire de Biochimie et Biologie Moléculaire, Groupe Hospitalier Sud, Hospices Civils de Lyon, Lyon, France

2University of Lyon, Claude Bernard University, Cancer Research Center of Lyon, INSERM U1052, CNRS UMR5286, Lyon, France

3Hospices Civils de Lyon Cancer institute, CIRculating CANcer (CIRCAN) program, Pierre Bénite, France

4Laboratoire Commun de Recherche Hospices Civils de Lyon – BioMérieux, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Pierre Bénite Cedex, France

5Service d’oncologie médicale, Hôpital E. Herriot, Hospices Civils de Lyon, Lyon, France

6Service de Pneumologie et oncologie thoracique, CHU G Montpied, Clermont-Ferrand, France

7Université d’Auvergne, UMR INSERM 1240, Clermont-Ferrand, France

8Service de Pneumologie et cancérologie thoracique, CHU de Saint Etienne, Saint Etienne, France

9Service d’Anatomopathologie, Groupement Hospitalier Est, Hospices Civils de Lyon, Lyon, France

10Medical Scientific Affairs, Sysmex Inostics, Inc., Mundelein, IL, USA

11BioMérieux SA medical diagnostic Department, Centre Hospitalier Lyon Sud, Hospices Civils de Lyon, Lyon, France

12Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558, Villeurbanne, France

13SOPHiA GENETICS SA, Headquarters, CH-1025 Saint Sulpice, Switzerland

14Service de gastro-entérologie, Hôpital de la Croix-Rousse, Hospices Civils de Lyon, Lyon

15Hépatogastroentérologie et oncologie digestive, Groupement hospitalier Sud, Hospices civils de Lyon, Pierre Bénite, France

16EMR 3738 Ciblage Thérapeutique en Oncologie, Faculté de médecine Lyon Sud, Université Lyon 1, Université de Lyon, Oullins

17Service de Pneumologie aigue spécialisée et cancérologie thoracique, Groupement hospitalier sud, Institut de Cancérologie des Hospices Civils de Lyon, Pierre Bénite, France

18Service de Biostatistique–bioinformatique et plateforme NGS-CHU Lyon, Hospices Civils de Lyon, Lyon, France

Correspondence to:

Léa Payen, email: lea.payen-gay@chu-lyon.fr

Keywords: circulating-free DNA; digital PCR; NGS; liquid biopsy; colon and lung cancer

Received: November 03, 2017     Accepted: February 27, 2018     Published: April 20, 2018

ABSTRACT

CfDNA samples from colon (mCRC) and non-small cell lung cancers (NSCLC) (CIRCAN cohort) were compared using three platforms: droplet digital PCR (ddPCR, Biorad); BEAMing/OncoBEAM™-RAS-CRC (Sysmex Inostics); next-generation sequencing (NGS, Illumina), utilizing the 56G oncology panel (Swift Biosciences). Tissue biopsy and time matched cfDNA samples were collected at diagnosis in the mCRC cohort and during 1st progression in the NSCLC cohort. Excellent matches between cfDNA/FFPE mutation profiles were observed. Detection thresholds were between 0.5–1% for cfDNA samples examined using ddPCR and NGS, and 0.03% with BEAMing. This high level of sensitivity enabled the detection of KRAS mutations in 5/19 CRC patients with negative FFPE profiles. In the mCRC cohort, comparison of mutation results obtained by testing FFPE to those obtained by testing cfDNA by ddPCR resulted in 47% sensitivity, 77% specificity, 70% positive predictive value (PPV) and 55% negative predictive value (NPV). For BEAMing, we observed 93% sensitivity, 69% specificity, 78% PPV and 90% NPV. Finally, sensitivity of NGS was 73%, specificity was 77%, PPV 79% and NPV 71%.

Our study highlights the complementarity of different diagnostic approaches and variability of results between OncoBEAM™-RAS-CRC and NGS assays. While the NGS assay provided a larger breadth of coverage of the major targetable alterations of 56 genes in one run, its performance for specific alterations was frequently confirmed by ddPCR results.


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