Development of statistical methods for detecting gene-gene interactions from large-scale genomic data

• Project/Area Number: 25330054
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Research Field: Statistical science
• Research Institution: Japanese Foundation for Cancer Research
• Principal Investigator: USHIJIMA Masaru 公益財団法人がん研究会, ゲノムセンター, 研究員 (60328565)
• Co-Investigator(Renkei-kenkyūsha): MATSUURA Masaaki 帝京大学, 大学院公衆衛生学研究科, 教授 (40173794) ; MIKI Yoshio 東京医科歯科大学, 難治疾患研究所, 教授 (10281594)
• Research Collaborator: DAN Shingo がん研究会, がん化学療法センター, 副部長 (70332202)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2014: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2013: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
• Keywords: 多重検定 / SNP / ゲノムワイド関連解析 / 遺伝子間相互作用 / マイクロアレイ / クラスタリング / 遺伝子発現解析 / SNP解析 / 多重検定法 / False Discovery Rate

Outline of Final Research Achievements

We developed a statistical method for detecting gene-gene interactions using simple statistics from genome-wide SNP data. This program is about 20 times faster than the program we developed previously. In addition, we developed analytical programs which detect gene-gene interactions from microarray data and three-way interactions from SNP data in the similar way. As an application of our method, we performed Lasso clustering to the breast cancer microarray data to detect a novel subtype and related genes.

Research Products

• [Journal Article] 抗がん剤副作用予測システム (2015)
  • Author(s): 松浦正明，牛嶋大
  • Journal Title: 血液内科 Volume: 70 Pages: 533-538
  • NAID: 40020439698
• [Presentation] Development of Lasso clustering method with application to basal-like breast cancer microarray data (2016)
  • Author(s): Ushijima M, Miyaguchi K, Mori S, Miki Y, Matsuura M.
  • Organizer: 10th AACR-JCA joint conference
  • Place of Presentation: HYATT Regency, Maui, HW
  • Year and Date: 2016-02-17
• [Presentation] Lasso クラスタリング法の開発とbasal-like 乳がんマイクロアレイデータへの応用 (2015)
  • Author(s): 牛嶋大, 宮口健, 森誠一, 三木義男, 松浦正明
  • Organizer: 第74回日本癌学会学術総会
  • Place of Presentation: 名古屋国際会議場
  • Year and Date: 2015-10-09
• [Presentation] Lasso clustering method for classification of cancer subtypes using microarray data (2014)
  • Author(s): Masaru Ushijima, Shinto Eguchi, Osamu Komori, Yoshio Miki, Masaaki Matsuura
  • Organizer: 27th International Biometric Conference
  • Place of Presentation: Florence, Italy
  • Year and Date: 2014-07-07 – 2014-07-11
• [Presentation] Development of clustering-based gene selection method with application to breast cancer subtype data (2013)
  • Author(s): 牛嶋 大、三木義男、松浦正明
  • Organizer: 第72回日本癌学会学術総会
  • Place of Presentation: パシフィコ横浜