De novo approach to find differentially appearing genome sequence patterns from the two NGS datasets.

2016 Fiscal Year Final Research Report

• Project/Area Number: 26540159
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Life / Health / Medical informatics
• Research Institution: Waseda University (2016); National Institute of Advanced Industrial Science and Technology (2014-2015)
• Principal Investigator: Kana Shimizu 早稲田大学, 理工学術院, 准教授 (60367050)
• Project Period (FY): 2014-04-01 – 2017-03-31
• Keywords: 次世代シークエンサー / アルゴリズム / アラインメントフリー / ゲノム配列 / パターン

Outline of Final Research Achievements

High-throughput sequencing technology enables to determine various genomes for a same species. Given such a variety of genomes, it is more natural to consider all of such variations. However, majority of analysis method conducts mapping against only a single reference genome in first, which leads to loss of important information caused by mis-mapping. In order to capture individual data’s feature, we developed new approach to analyze NGS data by comparing two different NGS data sets directly and discovering sequence patterns which appears either of the two datasets and do not appear in the other. The proposed approach can be applied to various problems such as finding breakpoints in cancer genomes.

Free Research Field

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