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Statistical genetics and big data contribute to novel cancer drug discovery

Planned Research

Project AreaConquering cancer through neo-dimensional systems understanding
Project/Area Number 15H05911
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionOsaka University (2016-2019)
Tokyo Medical and Dental University (2015)

Principal Investigator

Okada Yukinori  大阪大学, 医学系研究科, 教授 (70727411)

Co-Investigator(Kenkyū-buntansha) 鎌谷 洋一郎  京都大学, 医学研究科, 准教授 (00720880)
浦山 ケビン  国立研究開発法人国立成育医療研究センター, 社会医学研究部, 部長 (60726850)
川上 英良  国立研究開発法人理化学研究所, 科技ハブ産連本部, ユニットリーダー (30725338)
藤本 明洋  京都大学, 医学研究科, 特定准教授 (30525853)
Project Period (FY) 2015-06-29 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥71,500,000 (Direct Cost: ¥55,000,000、Indirect Cost: ¥16,500,000)
Fiscal Year 2019: ¥13,910,000 (Direct Cost: ¥10,700,000、Indirect Cost: ¥3,210,000)
Fiscal Year 2018: ¥13,910,000 (Direct Cost: ¥10,700,000、Indirect Cost: ¥3,210,000)
Fiscal Year 2017: ¥13,910,000 (Direct Cost: ¥10,700,000、Indirect Cost: ¥3,210,000)
Fiscal Year 2016: ¥13,910,000 (Direct Cost: ¥10,700,000、Indirect Cost: ¥3,210,000)
Fiscal Year 2015: ¥15,860,000 (Direct Cost: ¥12,200,000、Indirect Cost: ¥3,660,000)
Keywords遺伝統計学 / HLA imputation法 / ゲノム創薬 / ビッグデータ / 機械学習 / 横断的オミクス解析 / HLA遺伝子 / ゲノム / バイオインフォマティクス / マイクロRNA / バイオマーカー / ビッグデータ解析 / ゲノム解析
Outline of Final Research Achievements

By integrating large-scale human disease genome data with a variety of tissue-specific human epigenome resources, one can obtain substantial information on disease biology, personalized medicine, and genome drug discovery. In this project, we expanded the field of statistical genetics in Japan into a wide range of bioinformatics analyses. High-resolution mapping of the human leukocyte antigen (HLA) gene alleles using next-generation sequencing technologies elucidated detailed distributions of alleles of both classical and non-classical HLA genes in the Japanese population. Trans-layer omics analysis integrating human disease genomes and tissue-specific epigenome data highlighted hidden tissue-specificity in human diseases (e.g., contribution of regulatory T cells and central nerve system cells on Graves’ disease and obesity, respectively). Our project contributed to development of young Japanese researchers in the field of statistical genetics.

Academic Significance and Societal Importance of the Research Achievements

遺伝統計学の活用により、大規模ヒト疾患ゲノム情報の一次的なデータ処理に留まらず、疾患病態解明やゲノム創薬、個別化医療への貢献が可能になることを示すことができた。これは、遺伝統計学という学問分野の可能性を広げた成果を考えられた。「遺伝統計学・夏の学校@大阪大学」の開催と関連書籍の出版は、同分野の若手人材育成に資すると考えられた。当研究課題に参画した研究者(代表者・分担者含め計5名)が研究実施期間中に全員研究室主催者として独立を果たした点も、人材育成に貢献するものである。

Report

(6 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Annual Research Report
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • Research Products

    (35 results)

All 2020 2019 2018 2017 2016 2015 Other

All Int'l Joint Research (4 results) Journal Article (29 results) (of which Int'l Joint Research: 19 results,  Peer Reviewed: 29 results,  Open Access: 22 results,  Acknowledgement Compliant: 5 results) Presentation (1 results) (of which Int'l Joint Research: 1 results) Book (1 results)

  • [Int'l Joint Research] Harvard Medical School/Broad Institute(米国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Sanger Institute(英国)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Broad Institute/Harvard Medical School(米国)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] Sanger Institute/Cambridge University(英国)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Trans-biobank analysis with 676,000 individuals elucidates the association of polygenic risk scores of complex traits with human lifespan2020

    • Author(s)
      Sakaue S, Kanai M, Karjalainen J, Akiyama M, Kurki M, Matoba N, Takahashi A, Hirata M, Kubo M, Matsuda K, Murakami Y; FinnGen, Daly MJ, Kamatani Y, Okada Y
    • Journal Title

      Nat Med

      Volume: 26 Issue: 4 Pages: 542-548

    • DOI

      10.1038/s41591-020-0785-8

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Dimensionality reduction reveals fine-scale structure in the Japanese population with consequences for polygenic risk prediction2020

    • Author(s)
      Sakaue S, Hirata J, Kanai M, Suzuki K, Akiyama M, Lai Too C, Arayssi T, Hammoudeh M, Al Emadi S, Masri BK, Halabi H, Badsha H, Uthman IW, Saxena R, Padyukov L, Hirata M, Matsuda K, Murakami Y, Kamatani Y, Okada Y
    • Journal Title

      Nat Commun

      Volume: 11 Issue: 1 Pages: 1569-1569

    • DOI

      10.1038/s41467-020-15194-z

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] GWAS of 165,084 Japanese individuals identified nine loci associated with dietary habits.2020

    • Author(s)
      Matoba N, Akiyama M, Ishigaki K, Kanai M, Takahashi A, Momozawa Y, Ikegawa S, Ikeda M, Iwata N, Hirata M, Matsuda K, Murakami Y, Kubo M, Kamatani Y, Okada Y
    • Journal Title

      Nat Hum Behav

      Volume: 4 Issue: 3 Pages: 308-346

    • DOI

      10.1038/s41562-019-0805-1

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population2020

    • Author(s)
      Kishikawa T, Maeda Y, Nii T, Motooka D, Matsumoto Y, Matsushita M, Matsuoka H, Yoshimura M, Kawada S, Teshigawara S, Oguro E, Okita Y, Kawamoto K, Higa S, Hirano T, Narazaki M, Ogata A, Saeki Y, Nakamura S, Inohara H, Kumanogoh A, Takeda K, Okada Y.
    • Journal Title

      Annals of the Rheumatic Diseases

      Volume: 79(1) Issue: 1 Pages: 103-111

    • DOI

      10.1136/annrheumdis-2019-215743

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Next-generation sequencing identifies contribution of both class I and II HLA genes on susceptibility of multiple sclerosis in Japanese2019

    • Author(s)
      Ogawa, Kotaro; Okuno, Tatsusada; Hosomichi, Kazuyoshi; Hosokawa, Akiko; Hirata, Jun; Suzuki, Ken; Sakaue, Saori; Kinoshita, Makoto; Asano, Yoshihiro; Miyamoto, Katsuichi
    • Journal Title

      Journal of neuroinflammation

      Volume: 16 Issue: 1 Pages: 162-162

    • DOI

      10.1186/s12974-019-1551-z

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Empirical evaluation of variant calling accuracy using ultra-deep whole-genome sequencing data.2019

    • Author(s)
      Kishikawa T, Momozawa Y, Ozeki T, Mushiroda T, Inohara H, Kamatani Y, Kubo M, Okada Y.
    • Journal Title

      Sci Rep

      Volume: 9 Issue: 1 Pages: 1784-1784

    • DOI

      10.1038/s41598-018-38346-0

    • NAID

      120006818699

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genetic and phenotypic landscape of the major histocompatibilty complex region in the Japanese population.2019

    • Author(s)
      Hirata J, Hosomichi K, Sakaue S, Kanai M, Nakaoka H, Ishigaki K, Suzuki K, Akiyama M, Kishikawa T, Ogawa K, Masuda T, Yamamoto K, Hirata M, Matsuda K, Momozawa Y, Inoue I, Kubo M, Kamatani Y, Okada Y.
    • Journal Title

      Nat Genet

      Volume: 51 Issue: 3 Pages: 470-480

    • DOI

      10.1038/s41588-018-0336-0

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] A Transethnic Mendelian Randomization Study Identifies Causality of Obesity on Risk of Psoriasis.2019

    • Author(s)
      Ogawa K, Stuart PE, Tsoi LC, Suzuki K, Nair RP, Mochizuki H, Elder JT, Okada Y.
    • Journal Title

      J Invest Dermatol

      Volume: 115 Issue: 6 Pages: 1397-1400

    • DOI

      10.1016/j.jid.2018.11.023

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] eLD: entropy-based linkage disequilibrium index between multiallelic sites.2018

    • Author(s)
      Okada Y
    • Journal Title

      Hum Genome Var.

      Volume: 5 Issue: 1 Pages: 29-29

    • DOI

      10.1038/s41439-018-0030-x

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genetic analysis of quantitative traits in the Japanese population links cell types to complex human diseases2018

    • Author(s)
      Kanai M, Akiyama M, Takahashi A, Matoba N, Momozawa Y, Ikeda M, Iwata N, Ikegawa S, Hirata M, Matsuda K, Kubo M, Okada Y, Kamatani Y
    • Journal Title

      Nat Genet

      Volume: 50 Issue: 3 Pages: 390-400

    • DOI

      10.1038/s41588-018-0047-6

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Statist ical genetics and its application to neuroimmunology2018

    • Author(s)
      Ogawa K, Okada Y
    • Journal Title

      Clin Exp Neurol

      Volume: 9 Issue: 1 Pages: 7-12

    • DOI

      10.1111/cen3.12445

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Variants at HLA-A, HLA-C, and HLA-DQB1 confer risk of psoriasis vulgaris in Japanese.2018

    • Author(s)
      Hirata J, --- Saeki H, et al
    • Journal Title

      J Invest Dermatol

      Volume: 138 Issue: 3 Pages: 542-548

    • DOI

      10.1016/j.jid.2017.10.001

    • NAID

      120007134453

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Genome-wide association study identifies 112 new loci for body mass index in the Japanese population2017

    • Author(s)
      Akiyama M, Okada Y, Kanai M, Takahashi A, Momozawa Y, Ikeda M, Iwata N, Ikegawa S, Hirata M, Matsuda K, Iwasaki M, Yamaji T, Sawada N, Hachiya T, Tanno K, Shimizu A, Hozawa A, Minegishi N, Tsugane S, Yamamoto M, Kubo M and Kamatani Y
    • Journal Title

      Nat Genet

      Volume: 49 Issue: 10 Pages: 1458-1462

    • DOI

      10.1038/ng.3951

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Polygenic burdens on cell-specific pathways underlie the risk of rheumatoid arthritis2017

    • Author(s)
      Ishigaki Kazuyoshi、Kochi Yuta、Suzuki Akari、Tsuchida Yumi、Tsuchiya Haruka、Sumitomo Shuji、Yamaguchi Kensuke、Nagafuchi Yasuo、Nakachi Shinichiro、Kato Rika、Sakurai Keiichi、Shoda Hirofumi、Ikari Katsunori、Taniguchi Atsuo、Yamanaka Hisashi、Miya Fuyuki、Tsunoda Tatsuhiko、et al.、Yamamoto Kazuhiko
    • Journal Title

      Nature Genetics

      Volume: 49 Issue: 7 Pages: 1120-1125

    • DOI

      10.1038/ng.3885

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The Rheumatoid Arthritis Risk Variant CCR6DNP Regulates CCR6 via PARP-1.2016

    • Author(s)
      Li G, Cunin P, Wu D, Diogo D, Yang Y, Okada Y, Plenge RM, Nigrovic PA
    • Journal Title

      PLoS Genet

      Volume: 12 Issue: 9 Pages: e1006292-e1006292

    • DOI

      10.1371/journal.pgen.1006292

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Trans-ethnic Fine Mapping Highlights Kidney-Function Genes Linked to Salt Sensitivity.2016

    • Author(s)
      Mahajan A, Rodan AR, Le TH, Gaulton KJ, Haessler J, ..., Okada Y, Laurie CC, Morris AP, Franceschini N
    • Journal Title

      Am J Hum Gen

      Volume: 99 Issue: 3 Pages: 636-646

    • DOI

      10.1016/j.ajhg.2016.07.012

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Association of variations in HLA class II and other loci with susceptibility to EGFR-mutated lung adenocarcinoma.2016

    • Author(s)
      Shiraishi K, Okada Y 他44名 Inazawa J 38番目
    • Journal Title

      Nat Commun.

      Volume: 7 Issue: 1 Pages: 12451-12451

    • DOI

      10.1038/ncomms12451

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Contribution of a Non-classical HLA Gene, HLA-DOA, to the Risk of Rheumatoid Arthritis2016

    • Author(s)
      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
    • Journal Title

      Am J Hum Genet

      Volume: 99 Issue: 2 Pages: 366-374

    • DOI

      10.1016/j.ajhg.2016.06.019

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Genetic risk of extranodal natural killer T-cell lymphoma: a genome-wide association study.2016

    • Author(s)
      Li Z, Xia Y, Feng LN, Chen JR, Li HM, Cui J, Cai QQ, Sim KS, ..., Okada Y, Raychaudhuri S, Lim ST, Tan W, Peng RJ, Khor CC, Bei JX
    • Journal Title

      Lancet Oncol

      Volume: 17 Issue: 9 Pages: 1240-1247

    • DOI

      10.1016/s1470-2045(16)30148-6

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Empirical estimation of genome-wide significance thresholds based on the 1000 Genomes Project data set2016

    • Author(s)
      Kanai M, Tanaka T, Okada Y
    • Journal Title

      J Hum Genet

      Volume: 61 Issue: 10 Pages: 861-866

    • DOI

      10.1038/jhg.2016.72

    • NAID

      40020966136

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes2016

    • Author(s)
      Fujimoto A, Okada Y, Boroevich KA, Tsunoda T, Taniguchi H, Nakagawa H
    • Journal Title

      Sci Rep

      Volume: 6 Issue: 1 Pages: 26483-26483

    • DOI

      10.1038/srep26483

    • NAID

      120005774574

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Significant impact of miRNA-target gene networks on genetics of human complex traits.2016

    • Author(s)
      Okada Y, Muramatsu T, Suita N, Kanai M, Kawakami E et al.
    • Journal Title

      Sci Rep

      Volume: 6 Issue: 1 Pages: 22223-22223

    • DOI

      10.1038/srep22223

    • Related Report
      2016 Annual Research Report 2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Genome-wide association studies in the Japanese population identify seven novel loci for type 2 diabetes.2016

    • Author(s)
      Imamura M, ・・Yamauchi T,・・ Shojima N, ・・Kadowaki T
    • Journal Title

      Nat Commun.

      Volume: 7 Issue: 1 Pages: 10531-10531

    • DOI

      10.1038/ncomms10531

    • NAID

      120006889946

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] High-density genotyping of immune-related loci identifies new SLE risk variants in individuals with Asian ancestry2016

    • Author(s)
      76.Imamura M, Takahashi A, Yamauchi T, Hara K, Yasuda K, ... Okada Y et al.
    • Journal Title

      Nat Genet

      Volume: 48 Issue: 3 Pages: 323-330

    • DOI

      10.1038/ng.3496

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Ethnically shared and heterogeneous impacts of molecular pathways suggested by the genome-wide meta-analysis of rheumatoid arthritis.2016

    • Author(s)
      Okada Y, Raj T, Yamamoto K.
    • Journal Title

      Rheumatology

      Volume: 22 Issue: 1 Pages: 186-189

    • DOI

      10.1093/rheumatology/kev314

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Anti-citrullinated peptide/protein antibody (ACPA)-negative RA shares a large proportion of susceptibility loci with ACPA-positive RA: a meta-analysis of genome-wide association study in a Japanese population.2015

    • Author(s)
      Terao C, Ohmura K, Kochi Y, Ikari K, Okada Y, Shimizu M, , Kubo M, Yamada R, Taniguchi A, Yamanaka H, Momohara S, Yamamoto K, Mimori T, Matsuda F.
    • Journal Title

      Arthritis Res Ther

      Volume: 17 Issue: 1 Pages: 104-104

    • DOI

      10.1186/s13075-015-0623-4

    • NAID

      120005749954

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Partitioning heritability by functional annotation using genome-wide association summary statistics2015

    • Author(s)
      Finucane HK, Bulik-Sullivan B, Gusev A, Trynka G, Reshef Y, ... Okada Y et al.
    • Journal Title

      Nat Genet

      Volume: 47 Issue: 11 Pages: 1228-1235

    • DOI

      10.1038/ng.3404

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Widespread non-additive and interaction effects within HLA loci modulate the risk of autoimmune diseases.2015

    • Author(s)
      Lenz TL, Deutsch AJ, Han B, Hu X, Okada Y et al.
    • Journal Title

      Nat Genet

      Volume: 47 Issue: 9 Pages: 1085-1090

    • DOI

      10.1038/ng.3379

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Directional dominance on stature and cognition in diverse human populations2015

    • Author(s)
      Joshi PK, Esko T, Mattsson H, Eklund N, Gandin I, ... Okada Y et al.
    • Journal Title

      Nature

      Volume: 523 Issue: 7561 Pages: 459-462

    • DOI

      10.1038/nature14618

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] Identification of the risk HLA variants of Graves' disease by applying the HLA imputation method to large scale Japanese genome-wide association study data2015

    • Author(s)
      Okada Y, Momozawa Y, Ashikawa K, Kanai M, Matsuda K et al.
    • Organizer
      17th Asia Pacific League of Associations for Rheumatology Congress
    • Place of Presentation
      Chennai, India
    • Year and Date
      2015-09-05
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Book] ゼロから実践する 遺伝統計学セミナー2020

    • Author(s)
      岡田 随象
    • Total Pages
      247
    • Publisher
      羊土社
    • ISBN
      9784758120920
    • Related Report
      2019 Annual Research Report

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Published: 2015-07-02   Modified: 2022-11-04  

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