Eun Kyung Kim1, Kyung A Kim2, Chang Young Lee3, Sangwoo Kim4, Sunhee Chang5, Byoung Chul Cho6, Hyo Sup Shim7. 1. Department of Pathology, National Health Insurance Service Ilsan Hospital, Goyang, Gyeonggi, Republic of Korea. 2. Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea. 3. Department of Cardiovascular and Thoracic Surgery, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea. 4. Severance Biomedical Science Institute, Yonsei University College of Medicine, Seoul, Republic of Korea. 5. Department of Pathology, Ilsan Paik Hospital, Inje University, Goyang, Gyeonggi, Republic of Korea. 6. Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, Seoul, Republic of Korea. 7. Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, Republic of Korea. Electronic address: shimhs@yuhs.ac.
Abstract
BACKGROUND: Recent studies revealed MET exon 14 skipping (METex14) as a biomarker that predicts the response to MET inhibitors in non-small-cell lung cancer (NSCLC). However, METex14 genomic alterations exhibit a highly diverse sequence composition, posing a challenge for clinical diagnostic testing. This study aimed to find a reasonable diagnostic assay for METex14 and identify its clinicopathologic implications. MATERIALS AND METHODS: We performed a comprehensive analysis of METex14 in 414 EGFR/KRAS/ALK/ROS1-negative (quadruple negative) surgically resected NSCLCs. We used real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Sanger sequencing for the first assay, followed by next-generation sequencing (NGS; hybrid-capture targeted DNA/RNA sequencing). Clinicopathologic implications of the METex14 group were analyzed in a total of 880 NSCLCs. RESULTS: METex14 was confirmed in 13 (3.1%) patients by DNA- and RNA-NGS. After comparison of assay results, qRT-PCR and NGS demonstrated the highest concordance rate. The mean variant allele frequency was 10.5% and 49% in DNA- and RNA-NGS, respectively. DNA-NGS revealed various lengths of indel and substitutions around and in exon 14. Moreover, METex14 was associated with adenocarcinoma (4.8%; 11/230) or sarcomatoid carcinoma (9.5%; 2/21), old age, never-smokers, and early stage of disease. CONCLUSIONS: METex14 occurs in about 3% of NSCLCs and has characteristic clinicopathologic features. NGS should be the first assay of choice as a multiplex testing. Sanger sequencing can detect METex14, but sensitivity can be hampered by large deletions or low allele frequency. qRT-PCR, an mRNA-based method, is sensitive and specific and can be appropriate for screening METex14 as a single gene testing.
BACKGROUND: Recent studies revealed MET exon 14 skipping (METex14) as a biomarker that predicts the response to MET inhibitors in non-small-cell lung cancer (NSCLC). However, METex14 genomic alterations exhibit a highly diverse sequence composition, posing a challenge for clinical diagnostic testing. This study aimed to find a reasonable diagnostic assay for METex14 and identify its clinicopathologic implications. MATERIALS AND METHODS: We performed a comprehensive analysis of METex14 in 414 EGFR/KRAS/ALK/ROS1-negative (quadruple negative) surgically resected NSCLCs. We used real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) and Sanger sequencing for the first assay, followed by next-generation sequencing (NGS; hybrid-capture targeted DNA/RNA sequencing). Clinicopathologic implications of the METex14 group were analyzed in a total of 880 NSCLCs. RESULTS: METex14 was confirmed in 13 (3.1%) patients by DNA- and RNA-NGS. After comparison of assay results, qRT-PCR and NGS demonstrated the highest concordance rate. The mean variant allele frequency was 10.5% and 49% in DNA- and RNA-NGS, respectively. DNA-NGS revealed various lengths of indel and substitutions around and in exon 14. Moreover, METex14 was associated with adenocarcinoma (4.8%; 11/230) or sarcomatoid carcinoma (9.5%; 2/21), old age, never-smokers, and early stage of disease. CONCLUSIONS: METex14 occurs in about 3% of NSCLCs and has characteristic clinicopathologic features. NGS should be the first assay of choice as a multiplex testing. Sanger sequencing can detect METex14, but sensitivity can be hampered by large deletions or low allele frequency. qRT-PCR, an mRNA-based method, is sensitive and specific and can be appropriate for screening METex14 as a single gene testing.
Authors: Joon Young Hur; Bo Mi Ku; Joon Ho Shim; Hyun Ae Jung; Jong-Mu Sun; Se-Hoon Lee; Jin Seok Ahn; Keunchil Park; Myung-Ju Ahn Journal: In Vivo Date: 2020 May-Jun Impact factor: 2.155