Detection of Targetable Genetic Alterations in Korean Lung Cancer Patients: A Comparison Study of Single-Gene Assays and Targeted Next-Generation Sequencing

Abstract

PurposeEpidermal growth factor receptor (<i>EGFR</i>), anaplastic lymphoma kinase (<i>ALK</i>), and ROS proto-oncogene 1 (<i>ROS1</i>) are ‘must-test’ biomarkers in the molecular diagnostics of advanced-stage lung cancer patients. Although single-gene assays are currently considered the gold standard for these genes, next-generation sequencing (NGS) tests are being introduced to clinical practices. We compared the results of current diagnostics and aimed to suggest timely effective guidance for their clinical use. Materials and MethodsPatients with lung cancer who received both conventional single-gene assays and subsequent targeted NGS testing were enrolled, and the results of their tests were compared. ResultsA total of 241 patients were enrolled, and the <i>EGFR</i> real-time polymerase chain reaction, <i>ALK</i> fluorescence <i>in situ</i> hybridization (FISH), and <i>ROS1</i> FISH assays exhibited 92.9%, 99.6%, and 99.5% concordance with the NGS tests, respectively. The discordant cases were mostly false-negatives of the single-gene assays, probably due to technical limitation. Of 158 cases previously designated as wild-type, <i>EGFR</i>, <i>ALK</i>, and <i>ROS1</i> alterations were identified in 10.1%, 1.9%, and 1.3%, respectively, and other targetable alterations were identified in 36.1% of the cases. Of patients with additionally identified actionable alterations, 32.6% (31/95) received matched therapy with a clinical benefit of 48.4% (15/31). ConclusionEven though the conventional and NGS methods were concordant in the majority of cases, NGS testing still revealed a considerable number of additional <i>EGFR</i>, <i>ALK</i>, and <i>ROS1</i> alterations, as well as other targetable alterations, in Korean advanced-stage lung cancer patients. Given the high frequency of <i>EGFR</i> and other targetable mutations identified in the present study, NGS testing is highly recommended in the diagnosis of Korean lung cancer patients.

Comparison of the Data of a Next-Generation Sequencing Panel from K-MASTER Project with That of Orthogonal Methods for Detecting Targetable Genetic Alterations

“…The concordance rate for EGFR mutation between NGS and PCR was 83.9% in this study and 92.9% in another study conducted in Korea [15].…”

Real-world Treatment Patterns in Patients with EGFR Mutation-positive NSCLC Receiving a First-Line, First- or Second-generation EGFR Tyrosine Kinase Inhibitor in South Korea and Taiwan

“…Epidermal growth factor receptor (EGFR) mutations (EGFRm) are observed in a greater proportion of patients with non-small cell lung cancer (NSCLC) from Asian populations (32-60%) compared with non-Asian populations (10-30%) [1][2][3]. In addition, the prevalence of EGFRm in patients with NSCLC from South Korea and Taiwan has been reported to range from 27-51% [4][5][6] and 34-53% [7][8][9], respectively.…”

Genetic Markers in Lung Cancer Diagnosis: A Review

“…The molecular diagnostics of lung cancer, similarly to NGS applications purposes, is explored in two areas—for research purposes, to find novel druggable mutations, and in clinical practice to diagnose and select eligible patients for specific tyrosine kinase inhibitor (TKI) therapy [ 18 , 55 ]. Before the development of NGS, our understanding of the molecular pathology of lung cancer was based on such techniques as mismatch repair detection, the sequencing of candidate genes, single nucleotide polymorphism (SNP) arrays, and gene expression analysis.…”

“…The National Comprehensive Cancer Network Guidelines recommends testing a panel of genes for NSCLC, which consists of epidermal growth factor ( EGFR ) mutations, anapestic lymphoma kinase ( ALK ) rearrangements, and c-ros oncogene 1 ( ROS1 ) rearrangements. These biomarkers are considered the “must-tests” biomarkers in lung cancer patient diagnosis and are analyzed by single-gene assays such as PCR, immunohistochemistry (IHC), and FISH [ 20 , 55 , 56 , 57 , 58 , 59 , 60 ]. Sanger sequencing, qPCR, ddPCR, IHC, and FISH are regarded as the gold standard techniques of molecular analysis in clinical practice, while tumor-only sequencing, matched-tumor, and normal-tissue sequencing are the gold standards in somatic mutation detection [ 18 , 61 ].…”

“…In the study by Park et al (2020) [55], the researchers have compared single-gene assays, such as real-time PCR, IHC, and FISH (considered as the gold standard for selecting eligible patients for EGFR-, ALK-, and ROS1-specific TKI therapy) to targeted NGS. Considering the NGS results as the final outcome, EGFR PCR revealed a sensitivity of 80.3% and specificity of 99.4%, ALK FISH showed a 71.4% sensitivity and 100% specificity, and ROS1 FISH showed a 100% sensitivity and 99.5% specificity.…”