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Imoto K, Yamamoto H, Ohkawa C, Shimada N, Ikuzawa R, Takeda H, Ohhara T, Kojima Y, Furuya N, Motoyoshi A, Migita O, Kuga A, Keira T, Wakamatsu H, Sato T, Oike N, Koike J, Yamano Y, Sunakawa Y. An approach for improvement of the accuracy of cancer gene panel testing. Int J Clin Oncol 2024; 29:571-581. [PMID: 38472663 DOI: 10.1007/s10147-024-02483-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 01/22/2024] [Indexed: 03/14/2024]
Abstract
BACKGROUND Tissue-based comprehensive genomic profiling (CGP) is increasingly being employed for genotype-directed therapies in patients with advanced cancer. However, tissue availability may limit their potential applications. In Japan, the cost of cancer gene panel tests is covered by public insurance for patients diagnosed with advanced solid tumors once in their lifetime. Therefore, it is essential to improve the success rate (reportability) and accuracy of CGP tests. The purpose of this study was to identify the factors associated with efficient and accurate CGP testing using relevant information obtained from real-world data. METHODS This study included 159 samples analyzed using tumor-only panel FoundationOne® CDx cancer genome profiling (F1CDx) and 85 samples analyzed using matched-pair panel OncoGuide™ NCC Oncopanel system (NCCOP) at St. Marianna University Hospital. Sample characteristics (fixation conditions, storage period, histology, tumor cell ratio, and genomic tumor cell content), CGP performance, and quality control status were evaluated across all 244 tested samples. RESULTS In 237/244 samples (97.1%), CGP testing results were successfully obtained [F1CDx, 99.4% (158/159) and NCCOP, 92.9% (79/85)]. An increased number of fibroblasts, inflammatory cells, and necrotic tumor cells, long-term storage, and/or prolonged fixation of tissue sections were involved in the unreported results and/or qualified CGP results. In addition, a negative correlation between median insert size values and ΔΔCq was observed in the NCCOP system. CONCLUSION We identified various factors associated with efficient and accurate CGP testing using relevant information obtained from real-world data, suggesting that thorough selection and preparation of tissue sections could optimize CGP and maximize useful information.
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Affiliation(s)
- Kiyomi Imoto
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
| | - Hiroyuki Yamamoto
- Department of Bioinformatics, St. Marianna University Graduate School of Medicine, 2-16-1 Sugao, Miyamae-ku, Kawasaki, Kanagawa, 216-8511, Japan.
- Department of Gastroenterology, St. Marianna University School of Medicine, Kawasaki, Japan.
| | - Chie Ohkawa
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Naoki Shimada
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Ryo Ikuzawa
- Department of Pathology, St. Marianna University Hospital, Kawasaki, Japan
| | - Hiroyuki Takeda
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Tatsuru Ohhara
- Department of Obstetrics and Gynecology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yasuyuki Kojima
- Department of Breast and Endocrine Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Naoki Furuya
- Department of Respiratory Medicine, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Ai Motoyoshi
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
- Department of Breast and Endocrine Surgery, St. Marianna University School of Medicine, Kawasaki, Japan
- Department of Clinical Genetics, St. Marianna University Hospital, Kawasaki, Japan
| | - Ohsuke Migita
- Department of Clinical Genetics, St. Marianna University Hospital, Kawasaki, Japan
| | - Asami Kuga
- Department of Clinical Genetics, St. Marianna University Hospital, Kawasaki, Japan
| | - Takayuki Keira
- Department of Pharmacy, St. Marianna University Hospital, Kawasaki, Japan
| | | | - Tomoo Sato
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
| | - Nobuyuki Oike
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Junki Koike
- Department of Pathology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yoshihisa Yamano
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
- Department of Neurology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Yu Sunakawa
- Center for Genomic Medicine, St. Marianna University Hospital, Kawasaki, Japan
- Department of Clinical Oncology, St. Marianna University School of Medicine, Kawasaki, Japan
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