2018 Fiscal Year Research-status Report
Establishment of Japan circulating tumor DNA cancer screening panel
| Project/Area Number |
18K15332
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| Research Institution | Japanese Foundation for Cancer Research |
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Principal Investigator |
LOW SIEWKEE 公益財団法人がん研究会, がんプレシジョン医療研究センター 免疫ゲノム医療開発プロジェクト, 研究員 (40634720)
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| Project Period (FY) |
2018-04-01 – 2020-03-31
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| Keywords | liquid biopsy / ctDNA |
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| Outline of Annual Research Achievements |
The proposal aims to establish a circulating tumor DNA (ctDNA) cancer screening panel to evaluate the mutation profiles focusing on Japan top 10 most frequent cancer. Firstly, cancer genome database was established by gathering data from TCGA and COSMIC databases. The frequency of the hotspot mutations in cancer related genes were assessed. The ctDNA panel was designed and established by incorporating 33 cancer-related gene covering 1,542 hotspot mutations. Next generation sequencing (NGS) condition was optimized to have average overall depth of 50,000x. Standard control samples with known mutation and mutation frequency were used to perform NGS. The correlation r2 value of the mutation frequency is about 0.95 between the NGS data and standard control. 4 ctDNA samples were assessed.
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| Current Status of Research Progress |
Current Status of Research Progress
2: Research has progressed on the whole more than it was originally planned.
Reason
The customized ctDNA amplicon-based panel is designed and established. Other parameters such as individual amplicon depth and molecular barcode tagging efficiency of the panel was evaluated as measurement of quality control. The panel was tested by using standard control and ctDNA samples from patients.
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| Strategy for Future Research Activity |
After the establishment of the customized ctDNA panel, more ctDNA samples from various cancer types will be assessed. Comparison will be performed between NGS results generated from this customized panel and current market available panel. The efficacy, limit of detection, sensitivity and specificity of the panel will be evaluated.
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[Presentation] The establishment and optimization of customized circulating tumor DNA cancer screening panel2018
Author(s)
Siew-Kee Low, Tomoko Shibayama, Satoshi Nagayama, Eisaku Miyauchi, Kazuma Kiyotani, Takayuki Kobayashi, Shinji Ohno, Takayuki Ueno, Masakazu Ichinose, Masashi Ueno, Shunji Takahashi and Yusuke Nakamura
Organizer
77th Annual Meeting of the Japanese Cancer Association
