Analysis of allele-specific expression and its correlation with haplotypes

• Project/Area Number: 18310131
• 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: Kyushu University
• Principal Investigator: TAHIRA Tomoko Kyushu University, 生体防御医学研究所, 助教 (50155230)
• Co-Investigator(Kenkyū-buntansha): HAYASHI Kenshi 九州大学, 生体防御医学研究所, 特任教授 (00019671)
• Project Period (FY): 2006 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥18,310,000 (Direct Cost: ¥15,400,000、Indirect Cost: ¥2,910,000); Fiscal Year 2008: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000); Fiscal Year 2007: ¥6,630,000 (Direct Cost: ¥5,100,000、Indirect Cost: ¥1,530,000); Fiscal Year 2006: ¥5,700,000 (Direct Cost: ¥5,700,000)
• Keywords: ゲノム / 遺伝子発現 / SNP

Research Abstract

ゲノム上の発現調節領域に存在する多型はアレル依存的発現をもたらす。これを検出するため2つのアレルに対応するcDNAの量比をSSCP法により定量する方法を確立し、さらに、DNAタイピング用マイクロアレイにより解析する条件を検討した。1次スクリーニングにはマイクロアレイによるゲノムワイド解析を、2次スクリーニングには測定精度のよいSSCP法を利用することが効率的であると結論した。また、転写因子結合配列の挿入欠失多型を含むハプロタイプと発現との強い関連を見出した。

Research Products

• [Journal Article] Estimation of SNP allele frequencies by SSCP analysis of pooled DNA (2009)
  • Author(s): Tahira T, et al
  • Journal Title: Methods in Molecular Biology 578(in press)
• [Journal Article] Association of polymorphisms in complement component C3 gene with susceptibility to systemic lupus erythematosus (2008)
  • Author(s): Miyagawa, H, Yamai, M, Sakaguchi, D, Kiyohara, C, Tsukamoto, H, Kimoto, Y, Nakamura, T, Lee, J-H, Tsai, C-Y, Chiang, B-L, Nagasawa, K, Harada, M, Tahira, T, Hayashi, K, and Horiuchi, T.
  • Journal Title: Rheumatology 47 Pages: 158-164
  • 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 Oncl. 10 Pages: 995-1003
  • Peer Reviewed
• [Journal Article] (2008)
  • Author(s): Qin M, et. al.
  • Journal Title: Human Genetics 122 Pages: 615-623
  • Peer Reviewed
• [Journal Article] Association of polymorphisms in complement component C3 gene with susceptibility to systemic lupus erythematosus (2008)
  • Author(s): Miyagawa H, et. al.
  • Journal Title: Rheumatology 47 Pages: 158-164
  • Peer Reviewed
• [Journal Article] Moderate reduction of Norrin signaling activity associated with the causative missense mutations identified in patients with familial exudative vitreoretinopathy (2007)
  • Author(s): Qin, M, Kondo, H, Uno, H, Tahira, T, and Hayashi, K
  • Journal Title: Human Genetics 122 Pages: 615-623
  • Peer Reviewed
• [Journal Article] D-HaploDB : a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples (2007)
  • Author(s): Higasa, K, Miyatake, K, Kukita, Y, Tahira, T, and Hayashi, K.
  • Journal Title: Nucleic Acids Res. 35
  • Peer Reviewed
• [Journal Article] D-HaploDB : a database of definitive haplotypes determined by genotyping complete hydatidiform mole samples. (2007)
  • Author(s): Higasa K et al.
  • Journal Title: Nucleic Acids Res. 35
• [Journal Article] Novel mutations in Norrie disease gene in Japanese patients with Norrie disease and familial exudative vitreoretinopathy. (2007)
  • Author(s): Kondo H et al.
  • Journal Title: Invest Ophthalmol Vis Sci. 48 Pages: 1276-1282
• [Journal Article] QSNPlite, a software system for quantitative analysis of SNPs based on capillary array SSCP analysis (2006)
  • Author(s): Tahira, T, Okazaki, Y, Miura, K, Yoshinaga, A, Masumoto, K, Higasa, K, Kukita, Y, and Hayashi, K.
  • Journal Title: Electrophoresis 27 Pages: 3869-3878
  • Peer Reviewed
• [Journal Article] Optimization of capillary array electrophoresis single-strand conformation polymorphism analysis for routine molecular diagnostics. (2006)
  • Author(s): Jespersgaard, C, Larsen, LA, Baba, S, Kukita, Y, Tahira, T, Christiansen, M, Vuust, J, Hayashi, K, and Andersen, PS.
  • Journal Title: Electrophoresis 27 Pages: 3816-3822
  • Peer Reviewed
• [Journal Article] Novel OPA1 mutations identified in Japanese pedigrees with optic atrophy. (2006)
  • Author(s): Qin M et al.
  • Journal Title: Molecular Vision 12 Pages: 485-491
• [Journal Article] Optimization of capillary array electrophoresis single-strand conformation polymorphism analysis for routine molecular diagnostics. (2006)
  • Author(s): Jespersgaard C et al.
  • Journal Title: Electrophoresis 27 Pages: 3816-3822
• [Journal Article] QSNPlite, a software system for quantitative analysis of SNPs based on capillary array SSCP analysis. (2006)
  • Author(s): Tahira T et al.
  • Journal Title: 27 Pages: 3869-3878
• [Journal Article] Estimation of SNP allele frequencies by SSCP analysis of pooled DNA
  • Author(s): Tahira T, Kukita Y, Higasa K, Okazaki Y, Yoshinaga A, Hayashi K.
  • Journal Title: Methods in Molecular Biology (in press)
• [Presentation] DNAプールのマイクロアレイ解析および定量的SSCP解析による全身性エリテマトーデス(SLE)疾患感受性遺伝子の大規模探索 (2008)
  • Author(s): 田平知子, 他
  • Organizer: 第31回日本分子学会年会
  • Place of Presentation: 神戸
  • Year and Date: 2008-12-09
• [Presentation] DNAプールのマイクロアレイ解析および定量的SSCP解析による全身性エリテマトーデス(SLE)疾患感受性遺伝子の大規模探索 (2008)
  • Author(s): 田平知子, et al.
  • Organizer: 第31回日本分子生物学会年会
  • Place of Presentation: 神戸
  • Year and Date: 2008-12-09
• [Presentation] Identification of loci for systemic lupus erythematosus by pooling-based genome-wide association study (2008)
  • Author(s): Tahira T, et al.
  • Organizer: 57th Annual Meeting of the American Society of Human Genetics
  • Place of Presentation: Philadelphia, U.S.A.
  • Year and Date: 2008-11-12
• [Presentation] Identification of loci for systemic lupus erythematosus by pooling-based genome-wide association study. (2008)
  • Author(s): Tahira T, et al.
  • Organizer: 58th Annual Meeting of the American Society of Human Genetics
  • Place of Presentation: フィラデルフィア, 米国
  • Year and Date: 2008-11-12
• [Presentation] DNAプールのDNA-chip解析による全身性エリテマトーデス(SLE)疾患感受性遺伝子の大規模探索 (2007)
  • Author(s): 田平知子, 他
  • Organizer: 第30回日本分子学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2007-12-13
• [Presentation] Pooling-based genomewide association study identifies loci for systemic lupus erythematosus (2007)
  • Author(s): Tahira T, et al.
  • Organizer: 7th Annual Meeting of the American Society of Human Genet
  • Place of Presentation: San Diego, USA
  • Year and Date: 2007-10-26
• [Presentation] Pooling-based genomewide association study identifies loci for systemic lupus erythematosus (2007)
  • Author(s): Tahira T, et. al.
  • Organizer: 57th Annual Meeting of the American Society of Human Genetics
  • Place of Presentation: San Diego, USA
  • Year and Date: 2007-10-26
• [Presentation] IRF5遺伝子多型の全身性エリテマトーデス感受性への関与 : アジア人集団を用いた解析 (2007)
  • Author(s): 田平知子, 他
  • Organizer: 第51回日本リウマチ学会総会・学術集会
  • Place of Presentation: 横浜
  • Year and Date: 2007-04-26
• [Presentation] Precise estimation of allele frequencies in pooled DNA based on capillary array SSCP analysis (2006)
  • Author(s): Tahira T, et.al.
  • Organizer: The 8th international meeting on human genome variation and complex genome analysis.
  • Place of Presentation: Hong Kong, SAR, China
  • Year and Date: 2006-09-15
• [Remarks] 「dbQSNP」データベース
  • URL: http://qsnp.gen.kyushu-u.ac.jp/
• [Remarks] 「D-HaploDB」データベース
  • URL: http://orca.gen.kyushu-u.ac.jp/
• [Remarks] 「D-HaploDB」データベース
  • URL: http://qsnp.gen.kyushu-u.ac.jp/placeSSCP/
• [Remarks]
  • URL: http://qsnp.gen.kyushu-u.ac.jp/
• [Remarks]
  • URL: http://orca.gen.kyushu-u.ac.jp/
• [Remarks]
  • URL: http://qsnp.gen.kyushu-u.ac.jp/placeSSCP/qsnplite/