Detection of Japanese Structural Variation Using Definitive Haplotype Data Obtained from Complete Hydatidiform Moles.

2009 Fiscal Year Final Research Report

• Project/Area Number: 20710147
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: 基礎ゲノム科学
• Research Institution: Kyushu University
• Principal Investigator: HIGASA Koichiro Kyushu University, 統計解析研究チーム, 研究員 (10419583)
• Project Period (FY): 2008 – 2009
• Keywords: ゲノム / 進化 / ハプロタイプ / 構造多型

Research Abstract

We determined true Japanese haplotypes by genotyping 100 complete hydatidiform moles (CHM), each carrying a genome derived from a single sperm. We then assessed how inferred haplotypes can differ from true haplotypes, and found that, at various genomic regions, especially the MHC locus, the expansion of extended haplotype homozygosity (EHH), which is a measure of positive selection, is obscured when inferred Asian haplotype data is used to detect the expansion. We also show that the true haplotype data is useful not only to assess and improve the accuracy of phasing of Asian genotypes, but also to detect structural variation of Japanese genome.

Research Products

• [Journal Article] A definitive haplotype map as determined by genotyping duplicated haploid genomes finds a predominant haplotype preference at copy number variation events. (2010)
  • Author(s): Kukita Y, Yahara K, Tahira T, Higasa K, Sonoda M, Yamamoto K, Kato K, Wake N, Hayashi K.
  • Journal Title: Am. J. Hum. Genet. (in press)
  • Peer Reviewed
• [Journal Article] Evaluation of haplotype inference using definitive haplotype data obtained from complete hydatidiform moles, and its significance for the analyses of positively selected regions. (2009)
  • Author(s): Higasa K, Kukita Y, Kato K, Wake N, Tahira T, Hayashi K.
  • Journal Title: PLoS Genet. 5(5) Pages: e1000468
  • Peer Reviewed
• [Journal Article] Narrowing of the regions of allelic losses of chromosome 1p36 in meningioma tissues by an improved SSCP analysis. (2008)
  • Author(s): Guan Y, Hata N, Kuga D, Yoshimoto K, Mizoguchi M, Shono T, Suzuki SO, Tahira T, Kukita Y, Higasa K, Yokoyama N, Nagata S, Iwaki T, Sasaki T, Hayashi K.
  • Journal Title: Int J Cancer 15,122(8) Pages: 1820-6
  • Peer Reviewed
• [Presentation] 胞状奇胎から得られた確定ハプロタイプに基づく推定ハプロタイプの評価と自然選択解析への影響 (2009)
  • Author(s): 日笠幸一郎、久木田洋児、田平知子、林健志
  • Organizer: 日本人類遺伝学会、第54回大会
  • Place of Presentation: 日本・東京
  • Year and Date: 2009-09-23
• [Presentation] Impact of definitive haplotypes on genetical analysis. (2008)
  • Author(s): Higasa K, Kukita Y, Tahira T, Hayashi K
  • Organizer: 58th Annual Meeting of the American Society of Human Genetics
  • Place of Presentation: Pennsylvania, USA
  • Year and Date: 2008-11-14
• [Presentation] Impact of definitive haplotypes for detecting recent positive selection. (2008)
  • Author(s): Higasa K, Kukita Y, Tahira T, Hayashi K
  • Organizer: Cold Spring Harbor Laboratory Meeting on The Biology of Genomes
  • Place of Presentation: New York, USA
  • Year and Date: 2008-05-08
• [Book] Methods Mol Biol.(Estimation of SNP allele frequencies by SSCP analysis of pooled DNA) (2009)
  • Author(s): Tahira T, Kukita Y, Higasa K, Okazaki Y, Yoshinaga A, Hayashi K.
  • Total Pages: 193-207
• [Remarks]
  • URL: http://qsnp.gen.kyushu-u.ac.jp/
• [Remarks]
  • URL: http://finch.gen.kyushu-u.ac.jp/