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논문KCI 등재

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

임승택|장원진|박경화|이종원|강은주|조성심|김정선|임태규|김혜숙|김유정|이수현|최정윤|김주원|조장호|안미선|임아름|김영생|박지현|신상원|이영우|정희준|김열홍|최윤지|성재숙
대한암학회 (Korean Cancer Association)|2022.01|Cancer Research and Treatment|제54권 제1호|pp. 30-39|DOI 10.4143/crt.2021.218

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키워드

Precision medicinePathologyHigh-throughput nucleotide sequencingMolecularTargetable gene alteration
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초록

Purpose: K-MASTER project is a Korean national precision medicine platform that screened actionable mutations by analyzing next-generation sequencing (NGS) of solid tumor patients. We compared gene analyses between NGS panel from the K-MASTER project and orthogonal methods. Materials and methods: Colorectal, breast, non-small cell lung, and gastric cancer patients were included. We compared NGS results from K-MASTER projects with those of non-NGS orthogonal methods (KRAS, NRAS, and BRAF mutations in colorectal cancer [CRC]; epidermal growth factor receptor [EGFR], anaplastic lymphoma kinase [ALK] fusion, and reactive oxygen species 1 [ROS1] fusion in non-small cell lung cancer [NSCLC], and Erb-B2 receptor tyrosine kinase 2 (ERBB2) positivity in breast and gastric cancers). Results: In the CRC cohort (n=225), the sensitivity and specificity of NGS were 87.4% and 79.3% (KRAS); 88.9% and 98.9% (NRAS); and 77.8% and 100.0% (BRAF), respectively. In the NSCLC cohort (n=109), the sensitivity and specificity of NGS for EGFR were 86.2% and 97.5%, respectively. The concordance rate for ALK fusion was 100%, but ROS1 fusion was positive in only one of three cases that were positive in orthogonal tests. In the breast cancer cohort (n=260), ERBB2 amplification was detected in 45 by NGS. Compared with orthogonal methods that integrated immunohistochemistry and in situ hybridization, sensitivity and specificity were 53.7% and 99.4%, respectively. In the gastric cancer cohort (n=64), ERBB2 amplification was detected in six by NGS. Compared with orthogonal methods, sensitivity and specificity were 62.5% and 98.2%, respectively. Conclusion: The results of the K-MASTER NGS panel and orthogonal methods showed a different degree of agreement for each genetic alteration, but generally showed a high agreement rate.

Abstract

Purpose: K-MASTER project is a Korean national precision medicine platform that screened actionable mutations by analyzing next-generation sequencing (NGS) of solid tumor patients. We compared gene analyses between NGS panel from the K-MASTER project and orthogonal methods. Materials and methods: Colorectal, breast, non-small cell lung, and gastric cancer patients were included. We compared NGS results from K-MASTER projects with those of non-NGS orthogonal methods (KRAS, NRAS, and BRAF mutations in colorectal cancer [CRC]; epidermal growth factor receptor [EGFR], anaplastic lymphoma kinase [ALK] fusion, and reactive oxygen species 1 [ROS1] fusion in non-small cell lung cancer [NSCLC], and Erb-B2 receptor tyrosine kinase 2 (ERBB2) positivity in breast and gastric cancers). Results: In the CRC cohort (n=225), the sensitivity and specificity of NGS were 87.4% and 79.3% (KRAS); 88.9% and 98.9% (NRAS); and 77.8% and 100.0% (BRAF), respectively. In the NSCLC cohort (n=109), the sensitivity and specificity of NGS for EGFR were 86.2% and 97.5%, respectively. The concordance rate for ALK fusion was 100%, but ROS1 fusion was positive in only one of three cases that were positive in orthogonal tests. In the breast cancer cohort (n=260), ERBB2 amplification was detected in 45 by NGS. Compared with orthogonal methods that integrated immunohistochemistry and in situ hybridization, sensitivity and specificity were 53.7% and 99.4%, respectively. In the gastric cancer cohort (n=64), ERBB2 amplification was detected in six by NGS. Compared with orthogonal methods, sensitivity and specificity were 62.5% and 98.2%, respectively. Conclusion: The results of the K-MASTER NGS panel and orthogonal methods showed a different degree of agreement for each genetic alteration, but generally showed a high agreement rate.

참고문헌 (30)

  1. Collins FS, "A new initiative on precision medicine", N Engl J Med, 372, pp.793~795 (2015)
  2. Kummar S, "Application of molecular profiling in clinical trials for advanced metastatic cancers", J Natl Cancer Inst, 107, pp.djv003~ (2015)
  3. Allegra CJ, "Extended RAS gene mutation testing in metastatic colorectal carcinoma to predict response to anti-epidermal growth factor receptor monoclonal antibody therapy : American Society of Clinical Oncology provisional clinical opinion update 2015", J Clin Oncol, 34, pp.179~185 (2016)
  4. Amado RG, "Wild-type KRAS is required for panitumumab efficacy in patients with metastatic colorectal cancer", J Clin Oncol, 26, pp.1626~1634 (2008)
  5. MacConaill LE, "Existing and emerging technologies for tumor genomic profiling", J Clin Oncol, 31, pp.1815~1824 (2013)
  6. Shao D, "A targeted next-generation sequencing method for identifying clinically relevant mutation profiles in lung adenocarcinoma", Sci Rep, 6, pp.22338~ (2016)
  7. Hagemann IS, "Clinical next-generation sequencing in patients with non-small cell lung cancer", Cancer, 121, pp.631~639 (2015)
  8. 이영우, "Clinical Application of Targeted Deep Sequencing in Metastatic Colorectal Cancer Patients: Actionable Genomic Alteration in K-MASTER project", Cancer Research and Treatment, 53(1), pp.123~130 (2021), 대한암학회[DOI]
  9. Cha YJ, "Screening of ROS1 rearrangements in lung adenocarcinoma by immunohistochemistry and comparison with ALK rearrangements", PLoS One, 9, pp.e103333~ (2014)
  10. Sung JS, "Detection of somatic variants and EGFR mutations in cell-free DNA from non-small cell lung cancer patients by ultra-deep sequencing using the ion ampliseq cancer hotspot panel and droplet digital polymerase chain reaction", Oncotarget, 8, pp.106901~106912 (2017)
  11. Yang SR, "Integrated genomic characterization of ERBB2", HER2 alterations in invasive breast carcinoma : a focus on unusual FISH groups, 2020, pp.33, 1546~1556
  12. Jing C, "Nextgeneration sequencingbased detection of EGFR, KRAS, BRAF, NRAS, PIK3CA, Her2 and TP53 mutations in patients with nonsmall cell lung cancer", Mol Med Rep, 18, pp.2191~2197 (2018)
  13. Arsenic R, "Comparison of targeted next-generation sequencing and Sanger sequencing for the detection of PIK3CA mutations in breast cancer", BMC Clin Pathol, 15, pp.20~ (2015)
  14. Sakai K, "Extended RAS and BRAF mutation analysis using next-generation sequencing", PLoS One, 10, pp.e0121891~ (2015)
  15. 박은향, "Detection of Targetable Genetic Alterations in Korean Lung Cancer Patients: A Comparison Study of Single-Gene Assays and Targeted Next-Generation Sequencing", Cancer Research and Treatment, 52(2), pp.543~551 (2020), 대한암학회
  16. Franczak C, "Uncommon mutational profiles of metastatic colorectal cancer detected during routine genotyping using next generation sequencing", Sci Rep, 9, pp.7083~ (2019)
  17. Nambiar M, "How does DNA break during chromosomal translocations?", Nucleic Acids Res, 39, pp.5813~5825 (2011)
  18. Beadling C, "A multiplexed amplicon approach for detecting gene fusions by next-generation sequencing", J Mol Diagn, 18, pp.165~175 (2016)
  19. Cheng DT, "Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets(MSK-IMPACT) : a hybridization capture-based next-generation sequencing clinical assay for solid tumor nolecular oncology", J Mol Diagn, 17, pp.251~264 (2015)
  20. Davies KD, "Comparison of molecular testing modalities for detection of ROS1 rearrangements in a cohort of positive patient samples", J Thorac Oncol, 13, pp.1474~1482 (2018)
  21. Nong L, "Comparison of next-generation sequencing and immunohistochemistry analysis for targeted therapy-related genomic status in lung cancer patients", J Thorac Dis, 11, pp.4992~5003 (2019)
  22. WolffAC, "Human epidermal growth factor receptor 2 testing in breast cancer : American Society of Clinical Oncology", College of American Pathologists clinical practice guideline focused update, 2018, pp.36, 2105~2122
  23. Krumm N, "Copy number variation detection and genotyping from exome sequence data", Genome Res, 22, pp.1525~1532 (2012)
  24. Amarasinghe KC, "CoNVEX : copy number variation estimation in exome sequencing data using HMM", BMC Bioinformatics, 14(Suppl 2), pp.S2~ (2013)
  25. Grasso C, "Assessing copy number alterations in targeted, amplicon-based next-generation sequencing data", J Mol Diagn, 17, pp.53~63 (2015)
  26. Ross DS, "Next-generation assessment of human epidermal growth factor receptor 2(ERBB2)amplification status : clinical validation in the context of a hybrid capture-based, comprehensive solid tumor genomic profiling assay", J Mol Diagn, 19, pp.244~254 (2017)
  27. Niu D, "Evaluation of next generation sequencing for detecting HER2 copy number in breast and gastric cancers", Pathol Oncol Res, 26, pp.2577~2585 (2020)
  28. Hosonaga M, "HER2 heterogeneity is associated with poor survival in HER2-positive breast cancer", Int J Mol Sci, 19, pp.2158~ (2018)
  29. Wakatsuki T, "Clinical impact of intratumoral HER2 heterogeneity on trastuzumab efficacy in patients with HER2-positive gastric cancer", J Gastroenterol, 53, pp.1186~1195 (2018)
  30. McGranahan N, "Clonal heterogeneity and tumor evolution : past, present, and the future", Cell, 168, pp.613~628 (2017)

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