The Study on Human Genome diversity

2011 Fiscal Year Final Research Report

• Project/Area Number: 21310126
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: 基礎ゲノム科学
• Research Institution: National Institute of Genetics
• Principal Investigator: TOYODA Atsushi 国立遺伝学研究所, 生命情報研究センター, 特任准教授 (10267495)
• Project Period (FY): 2009 – 2011
• Keywords: 個人ゲノム / 多様性 / 次世代シーケンサー

Research Abstract

Next generation sequencing offers lower cost and higher throughput than Sanger sequencing for human personal genome. To understand all genetic variants within personal genome, we carried out re-sequencing of two chromosomes(HSA21 and HSAY) separated from a human cell line and a sample from the HapMap JPT(Japanese) sets using the GAIIx sequencers. In a Japanese male genome, we identified over 3 million sequence variants(SNVs) at an average of 30-fold coverage. In addition, not only SNVs but also structural variants, such as indels and copy number variants, were detected.

Research Products

• [Journal Article] Genome analysis of the domestic dog(korean jindo) by massively parallel sequencing (2012)
  • Author(s): Kim RN, Kim DS, Choi SH, Yoon BH, Kang A, Nam SH, Kim DW, Kim JJ, Ha JH, Toyoda A, Fujiyama A, Kim A, Kim MY, Park KH, Lee KS, Park HS.
  • Journal Title: DNA Res Volume: 19(3) Pages: 275-288
  • Peer Reviewed
• [Journal Article] Genome features of "Dark-fly", a Drosophila line reared long-term in a dark environment (2012)
  • Author(s): Izutsu M, Zhou J, Sugiyama Y, Nishimura O, Aizu T, Toyoda A, Fujiyama A, Agata K, Fuse N.
  • Journal Title: PLoS One Volume: 7(3) Pages: e33288
  • Peer Reviewed
• [Journal Article] Centromere-targeted de novo ntegrations of an LTR retrotransposon of Arabidopsis lyrata (2012)
  • Author(s): Tsukahara S, Kawabe A, Kobayashi A, Ito T, Aizu T, Shin-i T, Toyoda A, Fujiyama A, Tarutani Y, Kakutani T.
  • Journal Title: Genes Dev Volume: 26(7) Pages: 705-713
  • Peer Reviewed
• [Journal Article] 1000ゲノムプロジェクトの目標と展開 (2011)
  • Author(s): 水口洋平・豊田敦
  • Journal Title: 医学のあゆみ Volume: 236 Pages: 616-622
• [Journal Article] Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data (2010)
  • Author(s): Nishito Y, Osana Y, Hachiya T, Popendorf K, Toyoda A, Fujiyama A, Itaya M, Sakakibara Y.
  • Journal Title: BMC Genomics Volume: 11 Pages: 243
  • Peer Reviewed
• [Presentation] 次世代シークエンサーを用いた全ゲノム解析 (2010)
  • Author(s): 豊田敦
  • Organizer: 日本人類遺伝学会第55回大会
  • Place of Presentation: 大宮ソニックシティホール
  • Year and Date: 2010-10-30