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Cancers (Basel). 2018 Mar 21;10(4). pii: E88. doi: 10.3390/cancers10040088.

Use of the Ion PGM and the GeneReader NGS Systems in Daily Routine Practice for Advanced Lung Adenocarcinoma Patients: A Practical Point of View Reporting a Comparative Study and Assessment of 90 Patients.

Author information

1
Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice Cedex 2, France. heeke.s@chu-nice.fr.
2
Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice Cedex 2, France. HOFMAN.V@chu-nice.fr.
3
Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. HOFMAN.V@chu-nice.fr.
4
Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. HOFMAN.V@chu-nice.fr.
5
Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice Cedex 2, France.
6
Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France.
7
Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France.
8
Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. LESPINET-FABRE.V@chu-nice.fr.
9
Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. lalvee.s@chu-nice.fr.
10
Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. bordone.o@chu-nice.fr.
11
Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. ribeyre.camille@gmail.com.
12
Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. TANGA.V@chu-nice.fr.
13
Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice Cedex 2, France. benzaquen.j@chu-nice.fr.
14
Department of Pulmonary Medicine and Oncology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. benzaquen.j@chu-nice.fr.
15
Department of Pulmonary Medicine and Oncology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France.
16
Department of Thoracic Surgery, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. cohen.c@chu-nice.fr.
17
Department of Thoracic Surgery, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. mouroux.j@chu-nice.fr.
18
Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice Cedex 2, France. marquette.c@chu-nice.fr.
19
Department of Pulmonary Medicine and Oncology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. marquette.c@chu-nice.fr.
20
Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice Cedex 2, France. ilie.m@chu-nice.fr.
21
Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. ilie.m@chu-nice.fr.
22
Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. ilie.m@chu-nice.fr.
23
Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice Cedex 2, France. hofman.p@chu-nice.fr.
24
Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. hofman.p@chu-nice.fr.
25
Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice Cedex 1, France. hofman.p@chu-nice.fr.

Abstract

Background: With the integration of various targeted therapies into the clinical management of patients with advanced lung adenocarcinoma, next-generation sequencing (NGS) has become the technology of choice and has led to an increase in simultaneously interrogated genes. However, the broader adoption of NGS for routine clinical practice is still hampered by sophisticated workflows, complex bioinformatics analysis and medical interpretation. Therefore, the performance of the novel QIAGEN GeneReader NGS system was compared to an in-house ISO-15189 certified Ion PGM NGS platform. Methods: Clinical samples from 90 patients (60 Retrospectively and 30 Prospectively) with lung adenocarcinoma were sequenced with both systems. Mutations were analyzed and EGFR, KRAS, BRAF, NRAS, ALK, PIK3CA and ERBB2 genes were compared and sampling time and suitability for clinical testing were assessed. Results: Both sequencing systems showed perfect concordance for the overlapping genes. Correlation of allele frequency was r² = 0.93 for the retrospective patients and r² = 0.81 for the prospective patients. Hands-on time and total run time were shorter using the PGM system, while the GeneReader platform provided good traceability and up-to-date interpretation of the results. Conclusion: We demonstrated the suitability of the GeneReader NGS system in routine practice in a clinical pathology laboratory setting.

KEYWORDS:

GeneReader; Ion PGM; lung adenocarcinoma; molecular pathology; next-generation sequencing

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