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Statistical Immunology

TEL +81-6-6879-3971

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Overview

Genetic backgrounds of individuals have substantial impacts on risk of immune diseases. Statistical genetics is a research field that evaluates causality of human genetic variations on diseases, using statistical and bioinformatics approaches. Recent developments of sequencing technologies have provided human genome data of hundreds of thousands of the subjects, and successfully identified comprehensive catalogues of genetic susceptible loci of immune-related diseases. However, little is known regarding how to develop methodology to integrate large-scale human genome data with diverse biological and immunological resources. The theme of our laboratory is to develop such methods and apply to the latest large-scale disease genome and omics data. We have demonstrated that the disease risk genes were significantly enriched in overlap with the target genes of the drugs currently used for treatment of the diseases, and could be promising resources of drug repositioning. Construction of the novel analytical methodologies of statistical genetics, such as the HLA imputation method and the miRNA network-based GWAS analysis, is also the focus of our laboratory. Through such translational approaches, we would like to empirically show the value of statistical genetics to dissect disease immunology and novel drug discovery.

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Principal Investigator

Yukinori Okada Professor

Research field

Genome data analysis of the immune diseases based on statistical genetics

Education history

2005 MD, the University of Tokyo, Tokyo, Japan
2011 PhD, Graduate School of Medicine, the University of Tokyo, Tokyo, Japan

Research and career history

2005 Resident, the University of Tokyo Hospital
2010 Research Fellow of the Japan Society for the Promotion of Science
2011 Visiting Researcher, RIKEN
2012 Postdoctoral Fellow for Research Abroad of the Japan Society for the Promotion of Science
2012 Research Fellow, Brigham and Women's Hospital, Harvard Medical School
2012 Postdoctoral Fellow, the Broad Institute
2013 Tenure Track Junior Associate Professor, Tokyo Medical and Dental University
2016 Professor, Osaka University
2017 Professor, Osaka University Immunology Frontier Research Center

Prize

2012 President award of the University of Tokyo
2012 Incentive award of the Japan Society of Human Genetics
2012 49th Baelz award (second)
2013 ASHG/Charles J. Epstein Trainee Award for Excellence in Human Genetics Research – Finalist
2014 Incentive award of the Japan College of Rheumatology
2015 The Young Scientists’ Prize, the Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology
2016 Yomiuri Techno Forum Gold Medal Prize
2020 2020 JSPS Prize
2020 President award of Japan Agency for Medical Research and Development (AMED)
2022 Osaka Science Prize
2023 Ishidate-Ueno Award 2023

Members

  • Yukinori Okada Professor
    yokadasg.med.osaka-u.ac.jp

Achievements

Publications

  • Shiraishi K, Okada Y, Takahashi A, Kamatani Y, Momozawa Y, Ashikawa K, Kunitoh H, Matsumoto S, Takano A, Shimizu K, Goto A, Tsuta K, Watanabe S, Ohe Y, Watanabe Y, Goto Y, Nokihara H, Furuta K, Yoshida A, Goto K, Hishida T, Tsuboi M, Tsuchihara K, Miyagi Y, Nakayama H, Yokose T, Tanaka K, Nagashima T, Ohtaki Y, Maeda D, Imai K, Minamiya Y, Sakamoto H, Saito A, Shimada Y, Sunami K, Saito M, Inazawa J, Nakamura Y, Yoshida T, Yokota J, Matsuda F, Matsuo K, Daigo Y, Kubo M, Kohno T. Association of variations in HLA class II and other loci with susceptibility to EGFR-mutated lung adenocarcinoma. Nat Commun 7:12451 (2016).
     
  • Kanai M, Tanaka T, Okada Y. Empirical estimation of genome-wide significance thresholds based on the 1000 Genomes Project data set. J Hum Genet 61:861-866. (2016).
     
  • Okada Y, Suzuki A, Ikari K, Terao C, Kochi Y, Ohmura K, Higasa K, Akiyama M, Ashikawa K, Kanai M, Hirata J, Suita N, Teo YY, Xu H, Bae SC, Takahashi A, Momozawa Y, Matsuda K, Momohara S, Taniguchi A, Yamada R, Mimori T, Kubo M, Brown MA, Raychaudhuri S, Matsuda F, Yamanaka H, Kamatani Y, Yamamoto K. Contribution of a Non-classical HLA Gene, HLA-DOA, to the Risk of Rheumatoid Arthritis. Am J Hum Genet 99:366-374. (2016).
     
  • Fujimoto A, Okada Y, Boroevich KA, Tsunoda T, Taniguchi H, Nakagawa H. Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes. Sci Rep 6:26483. (2016).
     
  • Okada Y, Muramatsu T, Suita N, Kanai M, Kawakami E, Iotchkova V, Soranzo N, Inazawa J, Tanaka T. Significant impact of miRNA-target gene networks on genetics of human complex traits. Sci Rep 6:22223. (2016).
     
  • Okada Y, Raj T, Yamamoto K. Ethnically shared and heterogeneous impacts of molecular pathways suggested by the genome-wide meta-analysis of rheumatoid arthritis. Rheumatology (Oxford) 55:186-189 (2016).
     
  • Okada Y, Momozawa Y, Ashikawa K, Kanai M, Matsuda K, Kamatani Y, Takahashi A, Kubo M. Construction of a population-specific HLA imputation reference panel and its application to Graves' disease risk in Japanese. Nat Genet 47:798-8022 (2015).
     
  • Okada Y, Wu D, Trynka G, Raj T, Terao C, Ikari K, Kochi Y, Ohmura K, Suzuki A, Yoshida S, Graham RR, Manoharan A, Ortmann W, Bhangale T, Denny JC, Carroll RJ, Eyler AE, Greenberg JD, Kremer JM, Pappas DA, Jiang L, Yin J, Ye L, Su DF, Yang J, Xie G, Keystone E, Westra HJ, Esko T, Metspalu A, Zhou X, Gupta N, Mirel D, Stahl EA, Diogo D, Cui J, Liao K, Guo MH, Myouzen K, Kawaguchi T, Coenen MJ, van Riel PL, van de Laar MA, Guchelaar HJ, Huizinga TW, Dieudé P, Mariette X, Bridges SL Jr, Zhernakova A, Toes RE, Tak PP, Miceli-Richard C, Bang SY, Lee HS, Martin J, Gonzalez-Gay MA, Rodriguez-Rodriguez L, Rantapää-Dahlqvist S, Arlestig L, Choi HK, Kamatani Y, Galan P, Lathrop M; RACI consortium; GARNET consortium, Eyre S, Bowes J, Barton A, de Vries N, Moreland LW, Criswell LA, Karlson EW, Taniguchi A, Yamada R, Kubo M, Liu JS, Bae SC, Worthington J, Padyukov L, Klareskog L, Gregersen PK, Raychaudhuri S, Stranger BE, De Jager PL, Franke L, Visscher PM, Brown MA, Yamanaka H, Mimori T, Takahashi A, Xu H, Behrens TW, Siminovitch KA, Momohara S, Matsuda F, Yamamoto K, Plenge RM. Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature 506:376-381 (2014).
     
  • Okada Y, Han B, Tsoi LC, Stuart PE, Ellinghaus E, Tejasvi T, Chandran V, Pellett F, Pollock R, Bowcock AM, Krueger GG, Weichenthal M, Voorhees JJ, Rahman P, Gregersen PK, Franke A, Nair RP, Abecasis GR, Gladman DD, Elder JT, de Bakker PI, Raychaudhuri S. Fine mapping major histocompatibility complex associations in psoriasis and its clinical subtypes. Am J Hum Genet 95:162-172 (2014).
     
  • Okada Y, Kim K, Han B, Pillai NE, Ong RT, Saw WY, Luo M, Jiang L, Yin J, Bang SY, Lee HS, Brown MA, Bae SC, Xu H, Teo YY, de Bakker PI, Raychaudhuri S. Risk for ACPA-positive rheumatoid arthritis is driven by shared HLA amino acid polymorphisms in Asian and European populations. Hum Mol Genet 23:6916-6926 (2014).
     
  • Okada Y, Diogo D, Greenberg JD, Mouassess F, Achkar WA, Fulton RS, Denny JC, Gupta N, Mirel D, Gabriel S, Li G, Kremer JM, Pappas DA, Carroll RJ, Eyler AE, Trynka G, Stahl EA, Cui J, Saxena R, Coenen MJ, Guchelaar HJ, Huizinga TW, Dieudé P, Mariette X, Barton A, Canhão H, Fonseca JE, de Vries N, Tak PP, Moreland LW, Bridges SL Jr, Miceli-Richard C, Choi HK, Kamatani Y, Galan P, Lathrop M, Raj T, De Jager PL, Raychaudhuri S, Worthington J, Padyukov L, Klareskog L, Siminovitch KA, Gregersen PK, Mardis ER, Arayssi T, Kazkaz LA, Plenge RM. Integration of sequence data from a Consanguineous family with genetic data from an outbred population identifies PLB1 as a candidate rheumatoid arthritis risk gene. PLoS One 9:e87645 (2014).
     
  • Okada Y. From the era of genome analysis to the era of genomic drug discovery: a pioneering example of rheumatoid arthritis. Clin Genet 86:432-440 (2014).
     
  • Okada Y, Plenge RM. Editorial: entering the age of whole-exome sequencing in rheumatic diseases: novel insights into disease pathogenicity. Arthritis Rheum 65:1975-1979 (2013).
     
  • Okada Y, Sim X, Go MJ, Wu JY, Gu D, Takeuchi F, Takahashi A, Maeda S, Tsunoda T, Chen P, Lim SC, Wong TY, Liu J, Young TL, Aung T, Seielstad M, Teo YY, Kim YJ, Lee JY, Han BG, Kang D, Chen CH, Tsai FJ, Chang LC, Fann SJ, Mei H, Rao DC, Hixson JE, Chen S, Katsuya T, Isono M, Ogihara T, Chambers JC, Zhang W, Kooner JS, Albrecht E, Yamamoto K, Kubo M, Nakamura Y, Kamatani N, Kato N, He J, Chen YT, Cho YS, Tai ES, Tanaka T. Meta-analysis identifies multiple loci associated with kidney function-related traits in east Asian populations. Nat Genet 44:904-909 (2012).
     
  • Okada Y, Terao C, Ikari K, Kochi Y, Ohmura K, Suzuki A, Kawaguchi T, Stahl EA, Kurreeman FA, Nishida N, Ohmiya H, Myouzen K, Takahashi M, Sawada T, Nishioka Y, Yukioka M, Matsubara T, Wakitani S, Teshima R, Tohma S, Takasugi K, Shimada K, Murasawa A, Honjo S, Matsuo K, Tanaka H, Tajima K, Suzuki T, Iwamoto T, Kawamura Y, Tanii H, Okazaki Y, Sasaki T, Gregersen PK, Padyukov L, Worthington J, Siminovitch KA, Lathrop M, Taniguchi A, Takahashi A, Tokunaga K, Kubo M, Nakamura Y, Kamatani N, Mimori T, Plenge RM, Yamanaka H, Momohara S, Yamada R, Matsuda F, Yamamoto K. Meta-analysis identifies nine new loci associated with rheumatoid arthritis in the Japanese population. Nat Genet 44:511-516 (2012).
     
  • Okada Y, Kubo M, Ohmiya H, Takahashi A, Kumasaka N, Hosono N, Maeda S, Wen W, Dorajoo R, Go MJ, Zheng W, Kato N, Wu JY, Lu Q, Tsunoda T, Yamamoto K, Nakamura Y, Kamatani N, Tanaka T. Common variants at CDKAL1 and KLF9 are associated with body mass index in east Asian populations. Nat Genet 44:302-306 (2012).
     
  • Okada Y, Shimane K, Kochi Y, Tahira T, Suzuki A, Higasa K, Takahashi A, Horita T, Atsumi T, Ishii T, Okamoto A, Fujio K, Hirakata M, Amano H, Kondo Y, Ito S, Takada K, Mimori A, Saito K, Kamachi M, Kawaguchi Y, Ikari K, Mohammed OW, Matsuda K, Terao C, Ohmura K, Myouzen K, Hosono N, Tsunoda T, Nishimoto N, Mimori T, Matsuda F, Tanaka Y, Sumida T, Yamanaka H, Takasaki Y, Koike T, Horiuchi T, Hayashi K, Kubo M, Kamatani N, Yamada R, Nakamura Y, Yamamoto K. A genome-wide association study identified AFF1 as a susceptibility locus for systemic lupus eyrthematosus in Japanese. PLoS Genet 8:e1002455 (2012).
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