Pathogen detetcion in liver cancer by sequencing analysis

2014 Fiscal Year Final Research Report

• 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
• Keywords: ゲノム / 肝がん / 病原体

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.

Free Research Field

がんゲノム