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Szpechcinski A, Moes-Sosnowska J, Skronska P, Lechowicz U, Pelc M, Szolkowska M, Rudzinski P, Wojda E, Maszkowska-Kopij K, Langfort R, Orlowski T, Sliwinski P, Polaczek M, Chorostowska-Wynimko J. The Advantage of Targeted Next-Generation Sequencing over qPCR in Testing for Druggable EGFR Variants in Non-Small-Cell Lung Cancer. Int J Mol Sci 2024; 25:7908. [PMID: 39063150 PMCID: PMC11277480 DOI: 10.3390/ijms25147908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The emergence of targeted therapies in non-small-cell lung cancer (NSCLC), including inhibitors of epidermal growth factor receptor (EGFR) tyrosine kinase, has increased the need for robust companion diagnostic tests. Nowadays, detection of actionable variants in exons 18-21 of the EGFR gene by qPCR and direct DNA sequencing is often replaced by next-generation sequencing (NGS). In this study, we evaluated the diagnostic usefulness of targeted NGS for druggable EGFR variants testing in clinical NSCLC material previously analyzed by the IVD-certified qPCR test with respect to DNA reference material. We tested 59 NSCLC tissue and cytology specimens for EGFR variants using the NGS 'TruSight Tumor 15' assay (Illumina) and the qPCR 'cobas EGFR mutation test v2' (Roche Diagnostics). The sensitivity and specificity of targeted NGS assay were evaluated using the biosynthetic and biological DNA reference material with known allelic frequencies (VAF) of EGFR variants. NGS demonstrated a sufficient lower detection limit for diagnostic applications (VAF < 5%) in DNA reference material; all EGFR variants were correctly identified. NGS showed high repeatability of VAF assessment between runs (CV% from 0.02 to 3.98). In clinical material, the overall concordance between NGS and qPCR was 76.14% (Cohen's Kappa = 0.5933). The majority of discordant results concerned false-positive detection of EGFR exon 20 insertions by qPCR. A total of 9 out of 59 (15%) clinical samples showed discordant results for one or more EGFR variants in both assays. Additionally, we observed TP53 to be a frequently co-mutated gene in EGFR-positive NSCLC patients. In conclusion, targeted NGS showed a number of superior features over qPCR in EGFR variant detection (exact identification of variants, calculation of allelic frequency, high analytical sensitivity), which might enhance the basic diagnostic report.
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Affiliation(s)
- Adam Szpechcinski
- Department of Genetics and Clinical Immunology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (J.M.-S.); (P.S.); (U.L.); (M.P.); (J.C.-W.)
| | - Joanna Moes-Sosnowska
- Department of Genetics and Clinical Immunology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (J.M.-S.); (P.S.); (U.L.); (M.P.); (J.C.-W.)
| | - Paulina Skronska
- Department of Genetics and Clinical Immunology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (J.M.-S.); (P.S.); (U.L.); (M.P.); (J.C.-W.)
| | - Urszula Lechowicz
- Department of Genetics and Clinical Immunology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (J.M.-S.); (P.S.); (U.L.); (M.P.); (J.C.-W.)
| | - Magdalena Pelc
- Department of Genetics and Clinical Immunology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (J.M.-S.); (P.S.); (U.L.); (M.P.); (J.C.-W.)
| | - Malgorzata Szolkowska
- Department of Pathology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (M.S.); (R.L.)
| | - Piotr Rudzinski
- Clinics of Thoracic Surgery, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (P.R.); (T.O.)
| | - Emil Wojda
- III Department of Lung Diseases and Oncology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (E.W.); (M.P.)
- II Department of Lung Diseases, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland;
| | | | - Renata Langfort
- Department of Pathology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (M.S.); (R.L.)
| | - Tadeusz Orlowski
- Clinics of Thoracic Surgery, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (P.R.); (T.O.)
| | - Pawel Sliwinski
- II Department of Lung Diseases, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland;
| | - Mateusz Polaczek
- III Department of Lung Diseases and Oncology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (E.W.); (M.P.)
| | - Joanna Chorostowska-Wynimko
- Department of Genetics and Clinical Immunology, The Institute of Tuberculosis and Lung Diseases, 01-138 Warsaw, Poland; (J.M.-S.); (P.S.); (U.L.); (M.P.); (J.C.-W.)
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Bai Q, Wang J, Zhou X. EGFR exon20 insertion mutations in non-small cell lung cancer: Clinical implications and recent advances in targeted therapies. Cancer Treat Rev 2023; 120:102605. [PMID: 37703723 DOI: 10.1016/j.ctrv.2023.102605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 09/15/2023]
Abstract
The advent of targeted therapies for oncogenic mutations has led to a major paradigm shift in the management of non-small cell lung cancer (NSCLC). Molecular targets, such as epidermal growth factor receptor (EGFR)-activating mutations in the region of exons 18 through 21 are the most common oncogenic driver in NSCLC. Classical activating mutations, such as in-frame deletions in exon 19 and point mutations in exon 21 (L858R), are strong predictors for good clinical response to the approved EGFR-tyrosine kinase inhibitors (EGFR-TKIs). However, low frequency mutations occurring within exon 20 (ex20ins) have poorer responses to first/second generation EGFR-TKIs. Moreover, patients with NSCLC harboring EGFR ex20ins are known to have poorer prognosis than those with other EGFR-TKI sensitive mutations, leading to unmet clinical need of novel specific therapeutic options. Rapid changes in molecular diagnostics identifying specific causes have hastened the translation of diagnostic recommendations into clinical practice. Emergence of treatment strategies targeting EGFR ex20ins, such as newer EGFR-TKIs with increased specificity and novel approaches using bispecific monoclonal antibodies, may hold promising therapeutic options in the near future. In this review, we describe the structural, molecular characteristics, and detection strategies of EGFR ex20ins mutations and summarize the latest clinical data on approved treatments and emerging therapies for patients with NSCLC harboring EGFR ex20ins mutations. Further, we will discuss the response heterogeneity of ex20ins mutations to new drugs and acquired drug resistance mechanisms.
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Affiliation(s)
- Qianming Bai
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Institute of Pathology, Fudan University, Shanghai, China
| | - Jialei Wang
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Department of Thoracic Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, China; Institute of Thoracic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Xiaoyan Zhou
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China; Institute of Pathology, Fudan University, Shanghai, China.
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Pujol N, Heeke S, Bontoux C, Boutros J, Ilié M, Hofman V, Marquette CH, Hofman P, Benzaquen J. Molecular Profiling in Non-Squamous Non-Small Cell Lung Carcinoma: Towards a Switch to Next-Generation Sequencing Reflex Testing. J Pers Med 2022; 12:1684. [PMID: 36294823 PMCID: PMC9605324 DOI: 10.3390/jpm12101684] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/05/2022] Open
Abstract
Molecular diagnosis of lung cancer is a constantly evolving field thanks to major advances in precision oncology. The wide range of actionable molecular alterations in non-squamous non-small cell lung carcinoma (NS-NSCLC) and the multiplicity of mechanisms of resistance to treatment resulted in the need for repeated testing to establish an accurate molecular diagnosis, as well as to track disease evolution over time. While assessing the increasing complexity of the molecular composition of tumors at baseline, as well as over time, has become increasingly challenging, the emergence and implementation of next-generation sequencing (NGS) testing has extensively facilitated molecular profiling in NS-NSCLC. In this review, we discuss recent developments in the molecular profiling of NS-NSCLC and how NGS addresses current needs, as well as how it can be implemented to address future challenges in the management of NS-NSCLC.
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Affiliation(s)
- Nina Pujol
- Centre Antoine-Lacassagne, Department of Radiation Oncology, Côte d’Azur University, 06000 Nice, France
| | - Simon Heeke
- Department of Thoracic/Head and Neck Medical Oncology, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Christophe Bontoux
- Laboratory of Clinical and Experimental Pathology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Biobank BB-0033-00025, 06000 Nice, France
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
| | - Jacques Boutros
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
- Department of Pulmonary Medicine and Thoracic Oncology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, 06000 Nice, France
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Biobank BB-0033-00025, 06000 Nice, France
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
| | - Véronique Hofman
- Laboratory of Clinical and Experimental Pathology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Biobank BB-0033-00025, 06000 Nice, France
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
| | - Charles-Hugo Marquette
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
- Department of Pulmonary Medicine and Thoracic Oncology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, 06000 Nice, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, Biobank BB-0033-00025, 06000 Nice, France
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
| | - Jonathan Benzaquen
- CNRS UMR 7284, INSERM U1081, Institute of Research on Cancer and Aging, Côte d’Azur University, 06000 Nice, France
- Department of Pulmonary Medicine and Thoracic Oncology, Côte d’Azur University, Pasteur 1 Hospital, Centre Hospitalier Universitaire de Nice, FHU OncoAge, 06000 Nice, France
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Real-world evidence of the intrinsic limitations of PCR-based EGFR mutation assay in non-small cell lung cancer. Sci Rep 2022; 12:13566. [PMID: 35945330 PMCID: PMC9363455 DOI: 10.1038/s41598-022-17394-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/25/2022] [Indexed: 01/09/2023] Open
Abstract
Detection of driver gene mutations is important in advanced NSCLC. The cobas EGFR mutation test is a mutant allele-specific real-time PCR assay with limitation owing to its primer design. Next-generation sequencing-based assay has a higher mutation detection coverage; however, its clinical impact remains unclear. We retrospectively collected the records of stage IV NSCLC patients with wild-type EGFR tested by cobas test. FoundationOne CDx was used for comprehensive genomic profiles. We then evaluated the missed EGFR mutations by the cobas test. We studied 62 patients. The median age was 60 (range: 35–86 years). Most patients were male and 58.1% were smokers. 91.9% were adenocarcinomas. Of the 62 samples, 7 (11.3%) were detected with EGFR mutations by NGS. Among these overlooked EGFR mutations, five were exon 20 insertions, and two were exon 19 deletions. Two patients received EGFR TKIs and showed durable response with PFS 5.9 months and 10.1 months, respectively. Using NGS as the standard, the false-negative rate of the cobas EGFR mutation test was 11.3%—in a population with a high prevalence of EGFR mutations. The most overlooked mutations were exon 20 insertions. A comprehensive EGFR mutation assay can provide significant benefits to patients with NSCLC.
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