Claire Bocciarelli1, Justine Cohen1, Romain Pelletier2, Jeanne Tran Van Nhieu1, Jonathan Derman1, Loetitia Favre3, Anaïs Bourgogne4, Isabelle Monnet5, Christos Chouaid5, Anaïs Pujals6. 1. Assistance Publique-Hôpitaux de Paris, Department of Pathology, Centre Hospitalier Universitaire Henri-Mondor, 94010 Créteil, France. 2. Assistance Publique-Hôpitaux de Paris, Department of Pathology, Centre Hospitalier Universitaire Henri-Mondor, 94010 Créteil, France; Université Paris-Est Créteil, Faculté de Médecine, Créteil, France. 3. Assistance Publique-Hôpitaux de Paris, Department of Pathology, Centre Hospitalier Universitaire Henri-Mondor, 94010 Créteil, France; Université Paris-Est Créteil, Faculté de Médecine, Créteil, France; Inserm U955, Institut Mondor de Recherche Biomédicale, Créteil, France. 4. Centre Hospitalier Intercommunal de Créteil, Department of Pathology, Créteil, France. 5. Centre Hospitalier Intercommunal de Créteil, Department of Pneumology, Créteil, France. 6. Assistance Publique-Hôpitaux de Paris, Department of Pathology, Centre Hospitalier Universitaire Henri-Mondor, 94010 Créteil, France; Université Paris-Est Créteil, Faculté de Médecine, Créteil, France; Inserm U955, Institut Mondor de Recherche Biomédicale, Créteil, France. Electronic address: anais.pujals@aphp.fr.
Abstract
INTRODUCTION: During the last few years, detection of epidermal growth-factor-receptor (EGFR)-activating mutations has become a routine part of clinical practice because of their importance in choosing the optimal treatment strategy for non-small-cell lung cancers (NSCLCs). The emergence of third-generation EGFR-tyrosine-kinase inhibitors required the implementation of sensitive methods to detect the subclonal EGFRT790M mutation. Clinical implications make it essential to rapidly search for the T790M mutation, which is a real challenge for laboratories. The aim of this study was to compare performances of next-generation sequencing (NGS), one of the most frequently used molecular biology methods, and Idylla EGFR-Mutation Assay (henceforth Idylla), a fully automated real-time polymerase chain reaction (PCR) that is increasingly used in pathology laboratories, to detect the EGFRT790M mutation using DNA. METHODS: This retrospective study used 47 DNA samples extracted from NSCLC biopsies that previous NGS identified as: 29 harboring EGFR and T790M resistance mutations, 11 EGFR-activating mutation without T790 M and 7 wild-type EGFR. EGFRT790M limit-of-detection (LOD) experiments used a commercial DNA known to harbor that mutation. RESULTS: Idylla detected primary EGFR-activating mutations and the T790 M mutation in 97.5 % and 65.5 % of the cases, respectively. The results of this retrospective analysis and LOD experiments showed that the Idylla should only be used to detect EGFR mutations in samples with > 25 ng of DNA and > 10 % tumor cells. CONCLUSIONS: Idylla was able to rapidly detect EGFR-activating mutations but detecting subclone mutations, like T790M, with < 25 ng of good-quality DNA or < 10 % tumor cells (variant allele frequency below the assay's validated LOD) was not always reliable.
INTRODUCTION: During the last few years, detection of epidermal growth-factor-receptor (EGFR)-activating mutations has become a routine part of clinical practice because of their importance in choosing the optimal treatment strategy for non-small-cell lung cancers (NSCLCs). The emergence of third-generation EGFR-tyrosine-kinase inhibitors required the implementation of sensitive methods to detect the subclonal EGFRT790M mutation. Clinical implications make it essential to rapidly search for the T790M mutation, which is a real challenge for laboratories. The aim of this study was to compare performances of next-generation sequencing (NGS), one of the most frequently used molecular biology methods, and Idylla EGFR-Mutation Assay (henceforth Idylla), a fully automated real-time polymerase chain reaction (PCR) that is increasingly used in pathology laboratories, to detect the EGFRT790M mutation using DNA. METHODS: This retrospective study used 47 DNA samples extracted from NSCLC biopsies that previous NGS identified as: 29 harboring EGFR and T790M resistance mutations, 11 EGFR-activating mutation without T790 M and 7 wild-type EGFR. EGFRT790M limit-of-detection (LOD) experiments used a commercial DNA known to harbor that mutation. RESULTS: Idylla detected primary EGFR-activating mutations and the T790 M mutation in 97.5 % and 65.5 % of the cases, respectively. The results of this retrospective analysis and LOD experiments showed that the Idylla should only be used to detect EGFR mutations in samples with > 25 ng of DNA and > 10 % tumor cells. CONCLUSIONS: Idylla was able to rapidly detect EGFR-activating mutations but detecting subclone mutations, like T790M, with < 25 ng of good-quality DNA or < 10 % tumor cells (variant allele frequency below the assay's validated LOD) was not always reliable.
Authors: Amir Momeni-Boroujeni; Paulo Salazar; Tao Zheng; Nana Mensah; Ivelise Rijo; Snjezana Dogan; JinYuan Yao; Christine Moung; Chad Vanderbilt; Jamal Benhamida; Jason Chang; William Travis; Natasha Rekhtman; Marc Ladanyi; Khedoudja Nafa; Maria E Arcila Journal: J Mol Diagn Date: 2020-12-18 Impact factor: 5.568