Upgrading of an information infrastructure for Japanese genome diversity using haploid DNA materials

• Project/Area Number: 20681020
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: 基礎ゲノム科学
• Research Institution: Kyushu University
• Principal Investigator: KUKITA Yoji Kyushu University, 研究所, 研究員 (60372744)
• Project Period (FY): 2008 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥25,350,000 (Direct Cost: ¥19,500,000、Indirect Cost: ¥5,850,000); Fiscal Year 2010: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2009: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000); Fiscal Year 2008: ¥11,960,000 (Direct Cost: ¥9,200,000、Indirect Cost: ¥2,760,000)
• Keywords: ゲノム多様性 / ハプロタイプ / ゲノム / 遺伝子 / 癌

Research Abstract

We determined SNP/CNV haplotype structures by analyzing 100 complete hydatidiform moles from Japanese subjects via high-density DNA arrays. The obtained haplotype is useful as a reference for the haplotype structure of Japanese population. Furthermore, using SNP/CNV information, we analyzed one lung cancer sib-pair by whole-exome sequencing, and identified a causative CHEK2 mutation that makes the functional protein unstable.

Research Products

• [Journal Article] Conversion of a molecular classifier obtained by gene expression profiling into a classifier based on real-time PCR : a prognosis predictor for gliomas. (2010)
  • Author(s): Kawarazaki S, Taniguchi K, Shirahata M, Kukita Y, Kanemoto M, Mikuni N, Hashimoto N, Miyamoto S, Takahashi JA, Kato K.
  • Journal Title: BMC Medical Genomics 3 Pages: 52-52
  • Peer Reviewed
• [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: American Journal of Human Genetics 86 Pages: 918-928
  • NAID: 120002239171
  • Peer Reviewed
• [Journal Article] Impact of group IVA cytosolic phospholipase A2 gene polymorphisms on phenotypic features of patients with familial adenomatous polyposis. (2010)
  • Author(s): Umeno J, Matsumoto T, Esaki M, Kukita Y, Tahira T, Yanaru-Fujisawa R, Nakamura S, Arima H, Hirahashi M, Hayashi K, Iida M.
  • Journal Title: International Journal of Colorectal Disease 25 Pages: 293-301
  • Peer Reviewed
• [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, et al
  • Journal Title: American Journal of Human Genetics Volume: 86 Pages: 918-928
  • NAID: 120002239171
  • Peer Reviewed
• [Journal Article] Conversion of a molecular classifier obtained by gene expression profiling into a classifier based on real-time PCR : a prognosis predictor for gliomas. (2010)
  • Author(s): Kawarazaki S, et al
  • Journal Title: BMC Medical Genomics Volume: 3 Pages: 52-52
  • Peer Reviewed
• [Journal Article] Impact of group IVA cytosolic phospholipase A2 gene polymorphisms on phenotypic features of patients with familial adenomatous polyposis. (2010)
  • Author(s): Umeno J, et al.
  • Journal Title: International Journal of Colorectal Disease 25 Pages: 293-301
  • 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 Genetics 5
  • 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, et al.
  • Journal Title: PLoS Genetics 5
  • Peer Reviewed
• [Journal Article] Prevalence of copy-number neutral LOH in glioblastomas revealed by genomewide analysis of laser-microdissected tissues. (2008)
  • Author(s): Kuga D, Mizoguchi M, Guan Y, Hata N, Yoshimoto K, Shono T, Suzuki SO, Kukita Y, Tahira T, Nagata S, Sasaki T, Hayashi K.
  • Journal Title: Neuro Oncology 10 Pages: 995-1003
  • 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: International Journal of Cancer 122 Pages: 1820-1826
  • Peer Reviewed
• [Journal Article] Prevalence of copy number neutral LOH in glioblastomas revealed by genome-wide analysis of laser-microdissected tissues (2008)
  • Author(s): Kuga D., et.al.
  • Journal Title: Neuro-Oncology 10 Pages: 995-1003
  • Peer Reviewed
• [Journal Article] Narrowing the regions of allelic losses of chromosome 1p36 in meningioma tissues by an improved SSCP analysis (2008)
  • Author(s): Guan Y, et.al.
  • Journal Title: International Journal of Cancer 122 Pages: 1820-1826
  • Peer Reviewed
• [Presentation] 全エキソン配列解析による同胞がん罹患症例の原因遺伝子変異の探索 (2010)
  • Author(s): 久木田洋児
  • Organizer: 第33回日本分子生物学会年会第83回日本生化学学会合同大会
  • Place of Presentation: 神戸
  • Year and Date: 2010-12-07
• [Presentation] A definitive haplotype map derived from homozygous genomes as a basis for disease gene study (2010)
  • Author(s): Tahira T, et al
  • Organizer: The American Society of Human Genetics 60th Annual Meeting
  • Place of Presentation: 米国・ワシントンDC
  • Year and Date: 2010-11-04
• [Presentation] Conversion of a molecular classifier for gliomas based on gene expression profiling into diagnostic test on real-time PCR (2010)
  • Author(s): Kawarazaki S, et al
  • Organizer: 第69回日本癌学会学術総会
  • Place of Presentation: 大阪
  • Year and Date: 2010-09-24
• [Presentation] Assessment of the correlation between MGMT promotor methylation and clinical outcome of Glioblastoma patients (2010)
  • Author(s): Kanemoto M, et al
  • Organizer: 第69回日本癌学会学術総会
  • Place of Presentation: 大阪
  • Year and Date: 2010-09-24
• [Presentation] CNV/SNP haplotype map determined using completc hydatidiform moles carrying haploidgenomes (2009)
  • Author(s): Hayashi K, et al.
  • Organizer: Cold Spring Harbor Laboratory Meeting "Personal Genomes"
  • Place of Presentation: 米国・ニューヨーク
  • Year and Date: 2009-09-16
• [Presentation] Detection of human copy number variations using complete hydatidiform moles carrying haploid genomes. (2008)
  • Author(s): Kukita Y.
  • Organizer: 58st Annual Meeting of the American Society of Human Genetics.
  • Place of Presentation: 米国・フィラデルフィア
  • Year and Date: 2008-11-14
• [Presentation] Detection of human copy number variations using complete hydatidiform moles carrying haploid genomes (2008)
  • Author(s): Kukita Y, et.al.
  • Organizer: 58st Annual Meeting of the American Society of Humar Genetics
  • Place of Presentation: 米国・フィラデルフィア
  • Year and Date: 2008-11-14
• [Presentation] Detection of human copy number variations using a collection of complete hydatidiform moles : a strategy of CNV-detection using human haploid genomes. (2008)
  • Author(s): Kukita Y.
  • Organizer: Cold Spring Harbor Laboratory Meeting "The Biology of Genomes"
  • Place of Presentation: 米国・ニューヨーク
  • Year and Date: 2008-05-08
• [Presentation] Detection of human copy number variations using a collection of complete hydatidiform moles : a strategy of CNV-detection using human haploid genomes (2008)
  • Author(s): Kukita Y, et.al.
  • Organizer: Cold Spring Harbor Laboratory Meeting " The Biology of Genomes"
  • Place of Presentation: 米国・ニューヨーク
  • Year and Date: 2008-05-08
• [Remarks] データベース
• [Remarks] D-HaploDB(全胞状奇胎ゲノムDNAを用いて直接決定した日本人集団ゲノムのハプロタイプのデータベース
  • URL: http://orca.gen.kyushu-u.ac.jp
• [Remarks]
  • URL: http://orca.gen.kyushu-u.ac.jp
• [Remarks]
  • URL: http://orca.gen.kyushu-u.ac.jp
• [Remarks]
  • URL: http://orca.gen.kyushu-u.ac.jp