Practical application of permutation test to genomewide associationstudy

• Project/Area Number: 19590332
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Human genetics
• Research Institution: The University of Tokyo
• Principal Investigator: YAMADA Ryo The University of Tokyo, 医科学研究所, 准教授 (50301106)
• Project Period (FY): 2007 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2008: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2007: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000)
• Keywords: 遺伝学 / 統計数学 / ゲノム / パーミュテーションテスト / 一塩基多型 / マルチプルテスティング

Research Abstract

ゲノムワイド疾患関連解析における統計検定上の実用的問題のひとつである多重検定問題を対象に、それをパーミュテーションテストを用いて補正するアプリケーションを実装し、公開した。

Research Products

• [Journal Article] ManganeseSuperoxide Dismutase Gene (SOD2)Polymorphism and Exudative Age-relatedMacular Degeneration in the apanese Population (2008)
  • Author(s): Gotoh N, Yamada R, Matsuda F,Yoshimura N, Iida T.
  • Journal Title: Am J Ophthalmol 146(1) Pages: 146-146
• [Journal Article] Citrullinated fibrinogen inhibitsthrombin-catalyzed fibrin polymerization (2008)
  • Author(s): Nakayama-Hamada M, Suzuki A, Furukawa H, Yamada R, Yamamoto K.
  • Journal Title: J Biochem 144(3) Pages: 393-8
• [Journal Article] SLC22A4Polymorphism and Rheumatoid ArthritisSusceptibility : A Replication Study in a Japanese Population and a Metaanalysis (2008)
  • Author(s): Okada Y, Mori M, Yamada R, Suzuki A,Kobayashi K, Kubo M, Nakamura Y,Yamamoto K.
  • Journal Title: J Rheumatol 35(9) Pages: 1273-8
• [Journal Article] A single nucleotidepolymorphism in the IRF5 promoter regionis associated with susceptibility torheumatoid arthritis in the Japanesepatients (2008)
  • Author(s): Shimane K, Kochi Y, Yamada R, Okada Y,Suzuki A, Miyatake A, Kubo M, NakamuraY, Yamamoto K.
  • Journal Title: Ann Rheum Dis.
• [Journal Article] Functional SNPs in CD244 increasethe risk of rheumatoid arthritis in aJapanese population (2008)
  • Author(s): Suzuki A, Yamada R, Kochi Y, Sawada T,Okada Y, Matsuda K, Kamatani Y, Mori M,Shimane K, Hirabayashi Y and others
  • Journal Title: Nat Genet 40(10) Pages: 1224-9
• [Journal Article] Primer : SNP-associated studies and what they canteach us (2008)
  • Author(s): Yamada R.
  • Journal Title: Nat Clin Pract Rheumatol 4(4) Pages: 210-7
• [Journal Article] An optimaldose-effect mode trend test for SNPgenotype tables (2008)
  • Author(s): Yamada R, Okada Y.
  • Journal Title: Genet Epidemiol.
• [Journal Article] An optimal dose-effect mode trend for SNP genotype tables. (2008)
  • Author(s): Yamada,R. & Okada, Y
  • Journal Title: Genet Epidemiol 33 Pages: 114-127
  • Peer Reviewed
• [Journal Article] Primer:SNP-associated studies and whay they can teach us. (2008)
  • Author(s): Yamada R.
  • Journal Title: Nature clinical practice 4 Pages: 210-217
  • Peer Reviewed
• [Journal Article] Functional SNPs inCD244 increase the risk of rheumatoid arthritis in a Japanese = (2008)
  • Author(s): Suzuki, A.;Yamada, R.;Kochi, Y.
  • Journal Title: Nat Genet. 40 Pages: 1224-1229
  • Peer Reviewed
• [Journal Article] A single nucleotide polymorphism in the IRF5 promoter region is associated with sus= (2008)
  • Author(s): Shimane, K.;Kochi,Y.;Yamada, l
  • Journal Title: Annals of the rheumatic diseases. 40(e-pub)
  • Peer Reviewed
• [Journal Article] SLG22A4 Polymorphism and Rheumatoid Arthritis Susceptibility:A Replication Study (2008)
  • Author(s): Okada, Y.;Mori, M.;Yamada, R.;
  • Journal Title: J. Rheumatol 35 Pages: 1723-1728
  • Peer Reviewed
• [Journal Article] Citrullinated fibrinogen inhibits thrombin-catalyzed fibrin polymerization. (2008)
  • Author(s): Nakayama-Hamada, M., Suzuki,
  • Journal Title: J. Biochem. 140 Pages: 393-398
  • Peer Reviewed
• [Journal Article] Manganese Superoxide Dismutase Gene (SOD2) Polymorphism and vExudative Age-re (2008)
  • Author(s): Gotoh, N., Yamada, R., Matsuda,
  • Journal Title: Am. J. Ophthalmol. 146 Pages: 146-146
  • Peer Reviewed
• [Journal Article] Lessons from a Genomewide AssociationStudy of Rheumatoid Arthritis (2007)
  • Author(s): Yamamoto K.& Yamada R.
  • Journal Title: N Engl Jmed 357 Pages: 1250-1251
• [Journal Article] Mechanisms of disease : genetics ofrheumatoid arthritis--ethnic differences indisease-associated genes (2007)
  • Author(s): Yamada R.& Yamamoto K.
  • Journal Title: Nat Clin PractRheumatol 3
• [Journal Article] Citrullination bypeptidylarginine deiminase in rheumatoidarthritis (2007)
  • Author(s): Suzuki, A., Yamada, R.& Yamamoto, K.
  • Journal Title: Ann N Y Acad Sci. 1108 Pages: 323-39
• [Journal Article] A novelmethod to express SNP-based geneticheterogeneity, and its use to measurelinkage disequilibrium for multiple SNPs, Dg, and to estimate absolute maximum ofhaplotype frequency (2007)
  • Author(s): Ryo Yamada, F.Matsuda.
  • Journal Title: Genetic Epidemiology 31 Pages: 709-726
• [Journal Article] A novel method to express SNP-based genetic heterogeneity, Ψ, and its use to measure linkage disequilibrium for multiple SNPs, Dg, and to estimate absolute maximum of haplotype frequency (2007)
  • Author(s): Ryo Yamada, F. Matsuda
  • Journal Title: Genetic Epidemiology 31 Pages: 709-726
  • Peer Reviewed
• [Journal Article] Lessons from a Genomewide Association Study of Rheumatoid Arthritis. (2007)
  • Author(s): Yamamoto, K. Yamada, R.
  • Journal Title: New England Journal of Medicine 357 Pages: 1250-1251
  • Peer Reviewed
• [Journal Article] Mechanisms of disease: genetics of rheumatoid arthritis-ethnic differences in disease-associated genes. (2007)
  • Author(s): Yamada, R. Yamamoto, K.
  • Journal Title: Nature Clinical Practice Rheumatology 3 Pages: 644-650
  • Peer Reviewed
• [Presentation] An Optimal Dose-effect Mode Trend Testfor SNP Genotype Tables (2008)
  • Author(s): Yamada R., Hirosawa K. and Okada Y.
  • Organizer: Human Genome Variation Meeting
  • Place of Presentation: Toronto, Canada
• [Presentation] Genomic Control for Fisher's Exact Test (2008)
  • Author(s): Okada, Y. and Yamada R.
  • Organizer: Human Genome Meeting 2008
  • Place of Presentation: Hyderabad, India
• [Presentation] An Optimal Dose-effect Mode Trend Test for SNP Genotype Tables OMTT (2008)
  • Author(s): Yamada, R., Hirosawa, K., and Oka
  • Organizer: Human Genome Variation Meeting 2008
  • Place of Presentation: Toronto, Canada
• [Presentation] SNP-pair Tetrahedron: Geometric Presentation of Haplotype Space of Pairwise SNPs (2007)
  • Author(s): Ryo Yamada
  • Organizer: International Genetic Epidemiology Meeting (2007)
  • Place of Presentation: York, Great Britain
  • Year and Date: 2007-08-09
• [Presentation] SNP-pair Tetrahedron : Geometric Presentation of Haplotype Space of Pairwise SNPs (2007)
  • Author(s): Ryo Yamada
  • Organizer: International Genetic Epidemiology Meeting
  • Place of Presentation: York, Great Britain
• [Presentation] 集団構造化補正、Genomic Control法のフィッシャー正確確率検定への応用 (2007)
  • Author(s): 岡田随象・山本一彦・山田亮
  • Organizer: 日本人類遺伝学会
  • Place of Presentation: 東京
• [Presentation] 一塩基多型(SNP)を用いた有意検定における (2007)
  • Author(s): 廣澤 桂, 山田亮, 松田文彦
  • Organizer: 観測ジェノタイプ情報の組み込みに関する検討日本人類遺伝学会
  • Place of Presentation: 東京
• [Remarks]
  • URL: http://func-gen,hgc.ip/wiki/index.php/
• [Remarks]
  • URL: http://func-gen.hgc.jp/
• [Remarks]
  • URL: http://func-gen.hgc.jp/