Methods of genome-wide gene-gene interaction analysis

• Project/Area Number: 22590300
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Human genetics
• Research Institution: Yamagata University
• Principal Investigator: TAMIYA Gen 山形大学, 医学部, 教授 (10317745)
• Co-Investigator(Kenkyū-buntansha): UEKI Masao 山形大学, 医学部, 助教 (10515860)
• Project Period (FY): 2010 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000); Fiscal Year 2012: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2011: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2010: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
• Keywords: SNP-GWAS / SNPs / ゲノムワイド関連解析 / モデル選択 / 変数選択 / 遺伝子×遺伝子相互作用 / 高次元変数選択 / 量的形質

Research Abstract

We propose utilizing a model selection strategy for an exhaustive interaction analysis in whole GWA data. Our new software, EPISIS, implements the ‘sure independence screening', which has two major parts, screening and variable selection;EPISIS can complete an exhaustive search for all possible SNP by SNP interactions innon-filtered GWA data within several days under common computing environments. Ourfast program is applied to find novel genetic components in GWA data from WTCCC (Wellcome Trust Case-Control Consortium).

Research Products

• [Journal Article] Association of breast-fed neonatal hyperbilirubinemia with UGT1A1 polymorphisms: 211G>A (G71R) mutation becomes a risk factor under inadequate feeding (2013)
  • Author(s): Sato H, Uchida T, Toyota K, Kanno M, Hashimoto T, Watanabe M, Nakamura T, Tamiya G, Aoki K, Hayasaka K.
  • Journal Title: J Hum Genet Volume: 58(1) Issue: 1 Pages: 7-10
  • DOI: 10.1038/jhg.2012.116
  • NAID: 10031145893
  • Peer Reviewed
• [Journal Article] Constructinga contemporary gene-environmental cohort: study design of the Yamagata Molecular Epidemiological Cohort Study (2013)
  • Author(s): Yamagata University Genomic CohortConsortium. Tamiya G、UekiM, 他57名
  • Journal Title: J Hum Genet Volume: 58(1) Issue: 1 Pages: 54-56
  • DOI: 10.1038/jhg.2012.128
  • Peer Reviewed
• [Journal Article] Association of melanogenesis genes with skin color variation among Japanese females (2013)
  • Author(s): Abe Y, Tamiya G, Nakamura T, Hozumi Y, Suzuki T.
  • Journal Title: J Dermatol Sci Volume: 69(2) Issue: 2 Pages: 167-172
  • DOI: 10.1016/j.jdermsci.2012.10.016
  • Peer Reviewed
• [Journal Article] Generation of a Monoclonal Antibody Specifically Reacting with Neuron-specific TATA-Box Binding Protein-Associated Factor 1 (N-TAF1) (2013)
  • Author(s): Makino S, Masuda C, Ando S, Tamiya G, Tooyama I.
  • Journal Title: Antibodies Volume: 2 Issue: 1 Pages: 1-8
  • DOI: 10.3390/antib2010001
  • Peer Reviewed
• [Journal Article] Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis (2013)
  • Author(s): Ueki M, Tamiya G.
  • Journal Title: BMC Bioinformatics Volume: 13 Issue: 1 Pages: 72-72
  • DOI: 10.1186/1471-2105-13-72
  • Peer Reviewed
• [Journal Article] Improved statistics for genome-wide interaction analysis (2012)
  • Author(s): Ueki M, Cordell HJ.
  • Journal Title: PLoS Genet Volume: 8(4) Issue: 4 Pages: e1002625-e1002625
  • DOI: 10.1371/journal.pgen.1002625
  • Peer Reviewed
• [Journal Article] HLA-A*0206 with TLR3 Polymorphisms Exerts More than Additive Effects in Stevens-Johnson Syndrome with Severe Ocular Surface Complications (2012)
  • Author(s): Ueta M, Tokunaga K, Sotozono C, Sawai H, Tamiya G, Inatomi T, Kinoshita S
  • Journal Title: PLoS One, Peer-Reviewed papers Volume: 7(8) Issue: 8 Pages: e43650-e43650
  • DOI: 10.1371/journal.pone.0043650
  • Peer Reviewed
• [Journal Article] Epistatic interaction between Toll-like receptor 3 (TLR3) and prostaglandin E receptor 3 (PTGER3) genes (2012)
  • Author(s): Ueta M, Tamiya G, Tokunaga K, Sotozono C, Ueki M, Sawai H, Inatomi T, Matsuoka T, Akira S, Narumiya S, Tashiro K, Kinoshita S
  • Journal Title: J Allergy Clin Immunol Peer-Reviewed papers Volume: 129(5) Issue: 5 Pages: 1413-1416
  • DOI: 10.1016/j.jaci.2012.01.069
  • Peer Reviewed
• [Journal Article] UBR5 Gene Mutation Is Associated with Familial Adult Myoclonic Epilepsy in a Japanese Family (2012)
  • Author(s): Kato T, Tamiya G, Koyama S, Nakamura T, Makino S, Arawaka S, Kawanami T, Tooyama I.
  • Journal Title: ISRN Neurol Volume: 2012 Pages: 508308-508308
  • DOI: 10.5402/2012/508308
  • Peer Reviewed
• [Journal Article] Sustained expression of a neuron-specific isoform of the Taf1 gene in development stages and aging in mice (2012)
  • Author(s): Jambaldorj J, Makino S, Munkhbat B, Tamiya G.
  • Journal Title: Biochem Biophys Res Commun Volume: 425(2) Issue: 2 Pages: 273-277
  • DOI: 10.1016/j.bbrc.2012.07.081
  • Peer Reviewed
• [Journal Article] Ultrahigh-dimensional variable selection method for whole-genome gene-gene interaction analysis (2012)
  • Author(s): Ueki M, Tamiya G
  • Journal Title: BMC Bioinformatics Volume: (in press)
  • Peer Reviewed
• [Journal Article] Epistatic interaction between TLR3 and PTGER3 genes (2012)
  • Author(s): Ueta U, Tamiya G, Tokunaga T, Sotozono C, Ueki M, Sawai H, Inatomi T, Matsuoka T, Akira S, Narumiya S, Tashiro K, Kinoshita S
  • Journal Title: J Allergy Clin Immunol Volume: (in press)
  • Peer Reviewed
• [Journal Article] Automatic grouping using smooth-threshold estimating equations (2011)
  • Author(s): Ueki, M., Kawasaki, Y.
  • Journal Title: Electronic Journal of Statistics Volume: 5 Issue: none Pages: 309-328
  • DOI: 10.1214/11-ejs608
  • Peer Reviewed
• [Journal Article] Impaired Glucose Metabolism Slows Executive Function Independent of Cerebral Ischemic Lesions in Japanese Elderly: The Takahata Study (2011)
  • Author(s): Takahashi Y, Iseki C, Wada M, Momma T, Ueki M, Kawanami T, Daimon M, Suzuki K, et al
  • Journal Title: Internal Medicine Volume: 50 Issue: 16 Pages: 1671-1678
  • DOI: 10.2169/internalmedicine.50.4871
  • NAID: 130000969367
  • ISSN: 0918-2918, 1349-7235
  • Peer Reviewed
• [Journal Article] Polymorphism of proinflammatory cytokine genes and albuminuria in the Japanese general population: the Takahata study (2011)
  • Author(s): Mashima Y, Konta T, Kudo K, Suzuki K, Ikeda A, Ichikawa K, Shibata Y, Watanabe T, Tamiya G, Kato T, Kawata S, Kubota I.
  • Journal Title: Nephrol Dial Transplant Volume: 26(12) Issue: 12 Pages: 3902-3907
  • DOI: 10.1093/ndt/gfr105
  • Peer Reviewed
• [Journal Article] ゲノムコホート研究の理論的側面 (2011)
  • Author(s): 田宮元,植木優夫,中村智洋
  • Journal Title: HORMONE FRONTIERINGYNECOLOGY Volume: 18(1) Pages: 27-34
  • URL: http://m-review.co.jp/magazine/detail/J17_18_01
  • Peer Reviewed
• [Journal Article] Impaired Glucose Metabolism Slows Executive Function Independent of Cerebral Ischemic Lesions in Japanese Elderly : The Takahata Study (2011)
  • Author(s): Takahashi Y, Iseki C, Wada M, Momma T, Ueki M, Kawanami T, Daimon M, Suzuki K, Tamiya G, Kato T
  • Journal Title: Internal Med Volume: 50(16) Pages: 1671-1678
  • NAID: 130000969367
  • Peer Reviewed
• [Journal Article] Impair Polymorphism of proinflammatory cytokine genes and albuminuria in the Japanese general population : the Takahata study (2011)
  • Author(s): Mashima Y, Konta T, Kudo K, Suzuki K, Ikeda A, Ichikawa K, Shibata Y, Watanabe T, Tamiya G, Kato T, Kawata S, Kubota I
  • Journal Title: Internal Med Volume: 26(12) Pages: 3902-3907
  • Peer Reviewed
• [Journal Article] Boosting local quasi-likelihood estimators (2010)
  • Author(s): Ueki M, Fueda K.
  • Journal Title: Ann Inst StatMath Volume: 62(2) Issue: 2 Pages: 235-248
  • DOI: 10.1007/s10463-008-0173-5
  • NAID: 40017001998
  • Peer Reviewed
• [Journal Article] Automatic grouping using smooth-threshold estimating equations.
  • Author(s): Ueki M, Kawasaki Y
  • Journal Title: Electronic Journal of Statistics Volume: 印刷中
  • Peer Reviewed
• [Presentation] Genome-wide gene-gene interaction analysis based on ultrahigh-dimensional variable selection (2012)
  • Author(s): Ueki M.
  • Organizer: 5th International Conference of the ERCIM WG on COMPUTING & STATISTICS (ERCIM 2012)(招待講演)
  • Place of Presentation: オビエドカンファレンスセンター(オビエド・スペイン)
• [Presentation] Molecular evolution of IZUMO1 and CD9; genes involved in reproductive fitness (2012)
  • Author(s): Tamiya G.
  • Organizer: International Symposium on the Mechanisms of Sexual Reproduction in Animals and Plant. Joint Meeting of the 2nd Allo-Authentication Meeting and the5th Egg-Coat Meeting (MCBEEC)
  • Place of Presentation: ホテル名古屋ガーデンパレス(名古屋)
• [Presentation] 役に立つ集団遺伝学 (2012)
  • Author(s): 田宮元
  • Organizer: 第5回生殖研究若手の会
  • Place of Presentation: 東京大学三崎臨海実験所(神奈川)
• [Presentation] adaptiveデザインのゲノム疫学研究への適用 (2012)
  • Author(s): 中村智洋
  • Organizer: 日本人類遺伝学会第57回大会
  • Place of Presentation: 京王プラザホテル(東京)
• [Presentation] 高次元変数選択法によるゲノムワイド遺伝子-遺伝子および遺伝子-環境相互作用解析法 (2012)
  • Author(s): 植木優夫
  • Organizer: 日本人類遺伝学会第57回大会
  • Place of Presentation: 京王プラザホテル(東京)
• [Presentation] Genome-wide gene-gene interaction analysis based on ultrahigh-dimensional variable selection (2012)
  • Author(s): Ueki M
  • Organizer: 5th International Conference of the ERCIM WG on COMPUTING & STATISTICS (ERCIM 2012)
  • Place of Presentation: オビエドカンファレンスセンター（オビエド・スペイン）
  • Invited
• [Presentation] Molecular evolution of IZUMO1 and CD9; genes involved in reproductive fitness．International Symposium on the Mechanisms of Sexual Reproduction in Animals and Plants. (2012)
  • Author(s): Tamiya G
  • Organizer: Joint Meeting of the 2nd Allo-Authentication Meeting and the 5th Egg-Coat Meeting (MCBEEC)
  • Place of Presentation: ホテル名古屋ガーデンパレス（名古屋）
• [Presentation] 役に立つ集団遺伝学 (2012)
  • Author(s): 田宮 元
  • Organizer: 第5回生殖研究若手の会
  • Place of Presentation: 東京大学三崎臨海実験所（神奈川）
• [Presentation] adaptiveデザインのゲノム疫学研究への適用 (2012)
  • Author(s): 中村 智洋
  • Organizer: 日本人類遺伝学会第57回大会
  • Place of Presentation: 京王プラザホテル（東京）
• [Presentation] 高次元変数選択法によるゲノムワイド遺伝子-遺伝子および遺伝子-環境相互作用解析法 (2012)
  • Author(s): 植木 優夫
  • Organizer: 日本人類遺伝学会第57回大会
  • Place of Presentation: 京王プラザホテル（東京）
• [Presentation] Variable Selection in Discrete Choice Models (2010)
  • Author(s): Kawasaki Y.
  • Organizer: American Statistical Association
  • Place of Presentation: カナダプレイス(バンクーバー・カナダ)
• [Presentation] A machine learning approach for genome-wide interaction analysis (2010)
  • Author(s): Ueki M.
  • Organizer: the 60th annual meeting of the American Society for Human Genetics
  • Place of Presentation: D.C.コンベンションセンター(ワシントン D.C.・アメリカ)
• [Presentation] Neuron-specific enhanced expression of TAF1 and its isoform (2010)
  • Author(s): Makino S.
  • Organizer: the 60th annual meeting of the AmericanSociety for Human Genetics
  • Place of Presentation: D.C.コンベンションセンター(ワシントン D.C.・アメリカ)
• [Presentation] A machine learning approach for genome-wide interaction analysis.Was hington;November 2010 (2010)
  • Author(s): eki M, Tamiya G
  • Organizer: 米国人類遺伝学会
  • Place of Presentation: ワシントジDC
• [Remarks]
  • URL: http://www.genetix-h.com/~AMERI/index.html
• [Remarks]
  • URL: http://www.genetix-h.com/~AMERI/
• [Patent(Industrial Property Rights)] 遺伝子間相互作用解析システム、その方法及びプログラム (2012)
  • Inventor(s): 植木優夫, 田宮元
  • Industrial Property Rights Holder: NTTデータ株式会社
  • Industrial Property Number: 2012-040646
  • Filing Date: 2012-02-27