Quantification of ultra-rare somatic mutations using molecular barcode and risk assessment of cancer

• Project/Area Number: 16K07155
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Tumor diagnostics
• Research Institution: National Cancer Center Japan
• Principal Investigator: Yamashita Satoshi 国立研究開発法人国立がん研究センター, 研究所, ユニット長 (80321876)
• Project Period (FY): 2016-04-01 – 2019-03-31
• Project Status: Completed (Fiscal Year 2018)
• Budget Amount: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000); Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2017: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000); Fiscal Year 2016: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: 点突然変異 / 突然変異 / シークエンシング / 食道 / 口腔粘膜 / 癌 / ゲノム

Outline of Final Research Achievements

Somatic mutations with very low frequency, consisting of mostly passenger, are present even in normal tissues without expansion of clonal patches, and form a cancerization field. Recently, methods to measure such ultra-rare mutations have been developed. We established a simple method using sequencing libraries prepared from 100 copies of genomic DNA as template [Cancer Lett. 403: 152, 2017]. In this study, we analyzed normal oral tissues, and found that their mutation frequencies were similar to those of esophageal tissues. In addition, we combined the method with the molecular barcode technology to achieve more accurate analysis. We prepared sequencing libraries with molecular barcodes using a targeted DNA panel for human genomic DNA. We optimized parameters to score true mutations present only in both strands of DNA. To isolate true mutations more efficiently, further improvement in the preparation of the sequencing libraries is in progress.

Academic Significance and Societal Importance of the Research Achievements

本研究では申請者が新規に開発した超低頻度の点突然変異頻度解析法（Yamashita et al. Cancer Letters 2017, 特願2015-199342）の改良を進めた。さらに口腔、食道がん因子曝露歴（飲酒・喫煙）のある健常人の口腔粘膜から抽出したゲノムDNAについて点突然変異頻度を解析し、食道粘膜と同等の変異頻度であることを確認した。点突然変異頻度解析法については、両ストランドに同一の変異が存在する真の変異を検出することが可能で、かつ大量のリードを必要としないさらに新しい解析法が必要であると考えられた。

Research Products

• [Presentation] DNAメチル化を用いた膵癌組織中の膵癌細胞含有率の測定 (2018)
  • Author(s): 石原弘喜, 山下聡, 天野良亮, 木村健二郎, 平川弘聖, 上田貴子, 村上善基, 田守昭博, 河田則文, 萩原淳司 and 牛島俊和
  • Organizer: 第12回日本エピジェネティクス研究会年会
• [Presentation] 分子バーコードと少コピー数のテンプレートDNAを用いた超低頻度変異の定量 (2018)
  • Author(s): 山下聡, 永野玲子 and 牛島俊和
  • Organizer: 第77回日本癌学会学術総会
• [Presentation] 分子バーコードと少量の鋳型DNAを用いた超低頻度点突然変異の定量解析 (2018)
  • Author(s): 山下聡, 永野玲子 and 牛島俊和
  • Organizer: 第41回日本分子生物学会年会
• [Presentation] 正常組織におけるメチル化異常および変異は環境要因への曝露と発がんリスクを提示する (2017)
  • Author(s): 山下聡
  • Organizer: 第11回日本エピジェネティクス研究会年会
• [Presentation] Accumulation of mutations in background normal lung tissue constitutes a major lung cancer risk (2017)
  • Author(s): Kubo E, Takeshima H, Yamashita S, Ushijima T.
  • Organizer: Meeting 2017
  • Int'l Joint Research
• [Presentation] Contribution of genetic and epigenetic alteration to cancer risk is different in different tissues (2016)
  • Author(s): Satoshi Yamashita, Takayoshi Kishino, Taichi Shimazu, Hadrien Charvat, Takeshi Nakajima, Yi-Chia Lee, Masahiro Maeda, Naoko Iida, Reiko Nagano, Shoichiro Tsugane, Ming-Shiang Wu and Toshikazu Ushijima
  • Organizer: The 39th Annual Meeting of The Molecular Biology Society of Japan
  • Place of Presentation: 神奈川県横浜市
  • Year and Date: 2016-11-30
• [Presentation] Normal tissue burden by mutation and methylation provides precision cancer risk diagnosis (2016)
  • Author(s): Satoshi Yamashita, Takayoshi Kishino, Taichi Shimazu, Hadrien Charvat, Takeshi Nakajima, Yi-Chia Lee, Masahiro Maeda, Naoko Iida, Reiko Nagano, Shoichiro Tsugane, Ming-Shiang Wu and Toshikazu Ushijima
  • Organizer: The 75th Annual Meeting of the Japanese Cancer Association
  • Place of Presentation: 神奈川県横浜市
  • Year and Date: 2016-10-06