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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References
Cheng ML, Berger MF, Hyman DM et al (2018) Clinical tumour sequencing for precision oncology: time for a universal strategy. Nat Rev Cancer 18:527–528
Beaubier N, Bontrager M, Huether R et al (2019) Integrated genomic profiling expands clinical options for patients with cancer. Nat Biotechnol 37:1351–1360
Takeda H, Imoto K, Umemoto K et al (2022) Clinical utility of genomic profiling tests in patients with advanced gastrointestinal cancers. Target Oncol 17:177–185
Umemoto K, Yamamoto H, Oikawa R et al (2022) The molecular landscape of pancreatobiliary cancers for novel targeted therapies from real-world genomic profiling. J Natl Cancer Inst 114:1279–1286
Foundation Medicine: FoundationOne® CDx Technical Information. https://www.google.com/search?client=firefox-b-d&q=FoundationOne%C2%AECDx+Technical+Information. Accessed 1 July 2023
Sunami K, Ichikawa H, Kubo T et al (2019) Feasibility and utility of a panel testing for 114 cancer-associated genes in a clinical setting: a hospital-based study. Cancer Sci 110:1480–1490
Woodhouse R, Li M, Hughes J et al (2020) Clinical and analytical validation of FoundationOne® Liquid CDx, a novel 324-Gene cfDNA-based comprehensive genomic profiling assay for cancers of solid tumor origin. PLoS ONE 15:e0237802
Ebi H, Bando H (2019) Precision oncology and the universal health coverage system in Japan. JCO Precis Oncol 3:1–12
Jennings LJ, Arcila ME, Corless C et al (2017) Guidelines for validation of next-generation sequencing-based oncology panels: a joint consensus recommendation of the Association for Molecular Pathology and College of American Pathologists. J Mol Diagn 19:341–365
Brown NA, Elenitoba-Johnson KSJ (2020) Enabling precision oncology through precision diagnostics. Annu Rev Pathol 15:97–121
Fujii T, Uchiyama T, Matsuoka M et al (2020) Evaluation of DNA and RNA quality from archival formalin-fixed paraffin-embedded tissue for next-generation sequencing—retrospective study in Japanese single institution. Pathol Int 70:602–611
Tomlins SA, Hovelson DH, Suga JM et al (2021) Real-world performance of a comprehensive genomic profiling test optimized for small tumor samples. JCO Precis Oncol 5:1312
Kanai Y, Nishihara H, Miyagi Y et al (2018) The Japanese Society of Pathology Guidelines on the handling of pathological tissue samples for genomic research: standard operating procedures based on empirical analyses. Pathol Int 68:63–90
Hatanaka Y, Kuwata T, Morii E et al (2021) The Japanese Society of Pathology Practical Guidelines on the handling of pathological tissue samples for cancer genomic medicine. Pathol Int 71:725–740
Imoto K, Sunakawa Y (2023) The role of clinical laboratory technicians in genomic medicine. JSLH 24:49–59
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Imoto, K., Yamamoto, H., Ohkawa, C. et al. An approach for improvement of the accuracy of cancer gene panel testing. Int J Clin Oncol 29, 571–581 (2024). https://doi.org/10.1007/s10147-024-02483-6
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DOI: https://doi.org/10.1007/s10147-024-02483-6