Liquid biopsy sequencing for liver cancer and pancreatic tumor

• Project/Area Number: 15H04814
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Gastroenterology
• Research Institution: Institute of Physical and Chemical Research
• Principal Investigator: Nakagawa Hidewaki 国立研究開発法人理化学研究所, 統合生命医科学研究センター, チームリーダー (50361621)
• Co-Investigator(Kenkyū-buntansha): 山上 裕機 和歌山県立医科大学, 医学部, 教授 (20191190)
• Co-Investigator(Renkei-kenkyūsha): Kawakami Yoshiiku 広島大学, 医学部, 講師 (70403516) ; Fujimoto Akihiro 国立研究開発法人理化学研究所, 統合生命医科学研究センター, 副チームリーダー (30525853) ; Wardell Chris 国立研究開発法人理化学研究所, 統合生命医科学研究センター, 研究員 (70748805)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥17,550,000 (Direct Cost: ¥13,500,000、Indirect Cost: ¥4,050,000); Fiscal Year 2017: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2016: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000); Fiscal Year 2015: ¥6,890,000 (Direct Cost: ¥5,300,000、Indirect Cost: ¥1,590,000)
• Keywords: Liquid biopsy / シークエンス / 肝臓がん / 膵臓がん / IPMT / 膵液 / がんゲノム / cfDNA / 膵腫瘍 / liquid biopsy / 膵がん / 癌 / ゲノム / 病理学 / ゲノム診断 / がん

Outline of Final Research Achievements

Exome sequencing of the cfDNAs (cell-free DNAs) in pancreatic juices from 37 IPMT patients and a half of samples were found to have KRAS or GNAS mutations and some had mutations of TP53 and RNF43. Loss of 17p13 and amplification of 8q24 were found in the pancreatic juice cfDNAs. We identified some genomic markers in pancreatic juices associated with histological grade of IPMT. We also deeply sequenced 100 liver cancer genes of plasma cfDNA from seven liver cancer patients after constructing new NGS libraries installed with molecular barcoding system. We improved the algorism to obtain the consensus reads and read filtering from these data, and succeed in calling somatic variants with more than 1% of VAF (variant allele frequency) in cfDNA. But less than 1% VAF is still difficult to discriminate from PCR and sequencing errors.

Research Products

• [Int'l Joint Research] ヴェローナ大学(イタリア)
• [Int'l Joint Research] ブロード研究所/ハーバード大学+MIT(米国)
• [Journal Article] Genomic Characterization of Biliary Tract Cancers Identifies Driver Genes and Predisposing Mutations (2018)
  • Author(s): Wardell CP, Fujita M, Yamada T, Simbolo M, Fassan M, Karlic R, Polak P, Kim J, Hatanaka Y, Maejima K, Lawlor RT, Nakanishi Y, Mitsuhashi T et al
  • Journal Title: J Hepatol Volume: - Issue: 5 Pages: 959-969
  • DOI: 10.1016/j.jhep.2018.01.009
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Whole genome sequencing discriminates hepatocellular carcinoma with intrahepatic metastasis from multi-centric tumors (2017)
  • Author(s): Furuta M, Ueno M, Fujimoto A, Hayami S, Yasukawa S, Kojima F, Arihiro K, Kawakami Y, Wardell CP, Shiraishi Y, Tanaka H, Nakano K, Maejima K, Sasaki-Oku A, Tokunaga N, Boroevich KA, Abe T, Aikata H, Ohdan H, Gotoh K, Kubo M, Tsunoda T, Miyano S, Chayama K, Yamaue H, Nakagawa H
  • Journal Title: J Hepatol Volume: 66(2) Issue: 2 Pages: 363-373
  • DOI: 10.1016/j.jhep.2016.09.021
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] がん診断の新たなマテリアルcfDNA (2016)
  • Author(s): 西塚哲、谷上賢瑞、八谷剛史、中川英刀
  • Journal Title: 実験医学 Volume: 34 Pages: 948-952
• [Journal Article] 臨床現場からのctDNAサンプル抽出まで (2016)
  • Author(s): 西塚哲、谷上賢瑞、八谷剛史、中川英刀
  • Journal Title: 実験医学 Volume: 34 Pages: 1319-1324
• [Journal Article] Whole genome mutational landscape and characterization of non-coding and structural mutations in liver cancer. (2016)
  • Author(s): Fujimoto A et al.
  • Journal Title: Nat Genet Volume: 48 Issue: 5 Pages: 500-509
  • DOI: 10.1038/ng.3547
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Circulating tumor DNA analysis for liver cancers and its usefulness as a liquid biopsy. (2015)
  • Author(s): Ono A, Fujimoto A, Yamamoto Y, Akamatsu S, Nobuhiko H, Imamura M, Kawaoka T, Tsuge M, Abe H, Hayes CN, Miki D, Furuta M, Tsunoda T, Miyano S, Kubo M, Aikata H, Ochi H, Kawakami Y, Arihiro K, Ohdan H, Nakagawa H, Chayama K
  • Journal Title: Cellular and Molecular Gastroenterology and Hepatology Volume: 1 Issue: 5 Pages: 516-534
  • DOI: 10.1016/j.jcmgh.2015.06.009
  • Peer Reviewed / Int'l Joint Research
• [Presentation] Cell-free DNAのシークエンス解析の課題 (2017)
  • Author(s): 中川 英刀
  • Organizer: NGS現場の会
  • Invited
• [Presentation] Cell-free DNA analysis for liver cancer and pancreatic cancer as a liquid biopsy for precision monitoring and diagnosis (2016)
  • Author(s): Hidewaki Nakagawa
  • Organizer: AGBT Precison Medicine
  • Place of Presentation: Phoenix, USA
  • Year and Date: 2016-09-23
  • Int'l Joint Research
• [Presentation] Sequencing analysis of plasma and pancreatic juice cell-free DNAs for cancer diagnosis (2016)
  • Author(s): 中川 英刀
  • Organizer: 第75回日本癌学会学術総会
  • Place of Presentation: パシフィコ横浜 （神奈川県、横浜）
  • Invited
• [Presentation] Cancer genome profiling by NGS of archives and liquid biopsy samples (2015)
  • Author(s): 中川 英刀
  • Organizer: 日本がん学会総会
  • Place of Presentation: 名古屋国際会議場（名古屋）
  • Year and Date: 2015-10-08
  • Int'l Joint Research / Invited