Pathogen detetcion in liver cancer by sequencing analysis

• Project/Area Number: 25670375
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Gastroenterology
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: NAKAGAWA Hidewaki 独立行政法人理化学研究所, 統合生命医科学研究センター, チームリーダー (50361621)
• Co-Investigator(Renkei-kenkyūsha): SHIRAISHI Yuichi 東京大学, 医科学研究所, 助教 (70516880) ; FUJIMOTO Akihiro 独立行政法人理化学研究所, 統合生命医科学研究センター, 副チームリーダー (30525853) ; FURUTA Mayuko 独立行政法人理化学研究所, 統合生命医科学研究センター, 特別研究員 (00647183)
• Project Period (FY): 2013-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000); Fiscal Year 2014: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2013: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
• Keywords: ゲノム / 肝がん / 病原体 / 肝炎 / シークエンス

Outline of Final Research Achievements

We performed RNA-Seq analysis of 240 liver cancers. After excluding sequences aligned to the human reference genome and human transcriptome sequences, the unaligned sequences were de novo assembled by Abyss. By referring 200bp~ contigs to NCBI　Nucleotide Collection, we identified some bacteria and virus sequences in liver cancer and hepatitis tissues. Psudomonas, Lactobacillus, Flavobacterium, Acinetobactor, and Staphylococcus epidermidis were identified and we validated the presence of Psudomonas by PCR. Furthermore, HBV, HCV, and AAV sequences were also identified.

Research Products

• [Journal Article] Whole-genome mutational landscape of liver cancers displaying biliary phenotype reveals hepatitis impact and molecular diversity (2015)
  • Author(s): Fujimoto A, Furuta M, Shiraishi Y, Shigemizu D, Abe T, Boroevich KA, Nakano K, Yamamoto Y, Tanaka H, Shibuya T, Shibata T, Kubo M, Chayama K, Miyano S, Tsunoda T, Nakagawa H, 他
  • Journal Title: Nature Communications Volume: 6 Issue: 1 Pages: 6120-6120
  • DOI: 10.1038/ncomms7120
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers (2014)
  • Author(s): Shiraishi Y, Fujimoto A, Furuta M, Chayama K, Tsunoda T, Miyano S, and Nakagawa H, 他
  • Journal Title: PLoS One Volume: 9 Issue: 12 Pages: e114263-e114263
  • DOI: 10.1371/journal.pone.0114263
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] Rearrnagements and non-coding mutations detected in liver cancers by whole geneme sequencing (2015)
  • Author(s): Hidewaki Nakagawa
  • Organizer: 10th ICGC Scientific Workshop
  • Place of Presentation: Verona, Italy
  • Year and Date: 2015-02-15 – 2015-02-17
  • Invited
• [Presentation] Whole genome sequencing analysis of liver cancer and personalized cancer medicine (2013)
  • Author(s): Hidewaki Nakagawa
  • Organizer: Genomic Research Asia
  • Place of Presentation: Singapore
  • Invited
• [Presentation] Whole genome sequencing analysis of liver cancer, forwarding to personalized medicine (2013)
  • Author(s): Hidewaki Nakagawa
  • Organizer: 0th Yonsei Cancer Research Annual International Symposium
  • Place of Presentation: Seoul, Korea
  • Invited
• [Presentation] Whole genome sequencing analysis of liver cancer, forwarding to personalized medicine (2013)
  • Author(s): Hidewaki Nakagawa
  • Organizer: BGI 8th International Conference on Genomics
  • Place of Presentation: Shenzen, China
  • Invited
• [Presentation] Whole genome signatures of liver cancer and personalized medicine (2013)
  • Author(s): Hidewaki Nakagawa
  • Organizer: 12th Roche Round Asia Oncology Forum
  • Place of Presentation: Seoul, Korea
  • Invited