Design and implementation of a novel mapping technique for single-nucleotide polymorphism genotypes using Textile Plot

• Project/Area Number: 21790342
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Human genetics
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: KUMASAKA Natsuhiko The Institute of Physical and Chemical Research, 統計解析研究チーム, 研究員 (80525527)
• Project Period (FY): 2009 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2010: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2009: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
• Keywords: Data Visualization / 鎖不平衡 / 集団構造 / JAVA / ゲノムワイド関連解析 / Hardy-Weinberg平衡 / ハプロタイプ / 自然選択 / 連鎖不平衡 / 一塩基多型 / データビジュアリゼーション / ハプロタイプ解析 / Genome-wide Association Study / 優性選択 / JAVA言語

Research Abstract

Textile Plot is a novel visualization technique and multivariate data analysis tool in statistics. We applied it to single-nucleotide polymorphism genotype data to develop a novel mapping technique of linkage disequilibrium, selection footprints and disease genes. We provided a population genetic perspective of the plot along with a software environment implemented in JAVA language. We also performed disease gene mappings in an association study of chronic hepatitis B and a comparative study of Crohn's disease and ulcerative colitis in Japanese.

Research Products

• [Journal Article] HLA-Cw*1202-B*5201-DRB1*1502 haplotype confers distinct effects on ulcerative colitis and Crohn's disease in Japanese. (2011)
  • Author(s): Okada, Y., Yamazaki, K., Umeno, J., Takahashi, A., Kumasaka, N., Ashikawa, K., Aoi, T., Takazoe, M., Matsui, T., Hirano, A., Matsumoto, T., Kamatani, N., Nakamura, Y., Yamamoto, K.Kubo, M.
  • Journal Title: Gastroenterology(peer review, accepted : June 6, 2011) doi:10.1053/gastro.(in press.) Pages: 48-48
• [Journal Article] The Textile Plot : a new linkage disequilibrium dis-play of multiple-single nucleotide polymorph-ism genotype data. (2010)
  • Author(s): Kumasaka N, Nakamura Y, Kamatani N
  • Journal Title: PLoS ONE(peer review, published : April 27, 2010) 5(4):e10207.doi:10.1371/journal. pone. Pages: 10207-10207
• [Journal Article] The Textile Plot : A New Linkage Disequilibrium Display of Multiple-Single Nucleotide Polymorphism Genotype Data (2010)
  • Author(s): Kumasaka, N.
  • Journal Title: PLoS One Volume: 5(4)
  • Peer Reviewed
• [Presentation] LD mapping of disease gene and haplotype analysis on textile plot (2009)
  • Author(s): Kumasaka, N., Kamatani, N.
  • Organizer: The American Society of Human Genetics 59th Annual Meeting
  • Place of Presentation: Honolulu.
  • Year and Date: 2009-10-22
• [Presentation] LD Mapping of Disease Gene and Haplotype Analysis on Textile Plot (2009)
  • Author(s): 熊坂夏彦
  • Organizer: アメリカ人類遺伝学会
  • Place of Presentation: Honolulu, Hawaii
  • Year and Date: 2009-10-22
• [Remarks] ホームページ等
  • URL: http://kumasakanatsuhiko.jp/projects/
• [Remarks]
  • URL: http://www.stat.math.keio.ac.jp/TextilePlot/genetics
• [Remarks]
  • URL: http://stat.math.keio.ac.jp/TextilePlot/Genetics/