Large-scale Genomic Cohort Study by Deep Learning
| Project/Area Number |
16K08638
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Multi-year Fund |
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| Section | 一般 |
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| Research Field |
Human genetics
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| Research Institution | Tohoku University |
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Principal Investigator |
TAMIYA Gen 東北大学, 東北メディカル・メガバンク機構, 教授 (10317745)
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| Co-Investigator(Kenkyū-buntansha) |
植木 優夫 国立研究開発法人理化学研究所, 革新知能統合研究センター, 研究員 (10515860)
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| Project Period (FY) |
2016-04-01 – 2019-03-31
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| Project Status |
Completed (Fiscal Year 2018)
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| Budget Amount *help |
¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000)
Fiscal Year 2018: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2016: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
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| Keywords | 遺伝統計学 / 人類遺伝学 / コホート研究 / 遺伝子×環境相互作用 / 深層学習 / ゲノム / 遺伝学 / 機械学習 |
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| Outline of Final Research Achievements |
In large-scale genomic cohort studies, we have several hundreds or over thousand phenotype data from tens of thousands participants: health exam results, diseases outcome, blood test and imaging data, if any, metabolomics and proteomics data. The high dimensionality and correlation structure may become an obstacle in the statistical detection of the effect among genes, environments and their interactions. In this study, we utilized a framework of deep learning to flexibly extract features from the high dimensional data as health status variable that overcome the obstacle to be deciphering these effect.
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| Academic Significance and Societal Importance of the Research Achievements |
現在、深層学習の研究は人工知能分野で活発に行われ、すでに多くのアルゴリズムが工夫され公開されている。本研究は、このような最先端の枠組みを遺伝学・ゲノム医学分野に応用して、大規模ゲノムコホートデータ解析の限界を克服し、より網羅的な遺伝統計学的分析手法を開発しているところが特色・独創的な点である。これにより、大規模ゲノムコホートデータを網羅的に用いた因子間相互作用解析手法が開発され、妥当な計算機資源で実行可能なソフトウェアとして整備される。このようなソフトウェアは、限られた研究施設でなくとも解析の実行を可能にし、大規模ゲノムコホート研究でのジレンマを打破するブレークスルーになると期待される。
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Report
(4 results)
Research Products
(45 results)
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[Journal Article] Respiratory resistance among adults in a population-based cohort study in Northern Japan.2019
Author(s)
Miura E, Tsuchiya N, Igarashi Y, Arakawa R, Nikkuni E, Tamai T, Tabata M, Ohkouchi S, Irokawa T, Ogawa H, Takai-Igarashi T, Suzuki Y, Kuriyama S, Tamiya G, Hozawa A, Yamamoto M, Kurosawa H.
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Journal Title
Respiratory Investigation
Volume: 印刷中
Issue: 3
Pages: 30226-0
DOI
Related Report
Peer Reviewed
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[Journal Article] Ethylene-gibberellin signaling underlies adaptation of rice to periodic flooding2018
Author(s)
T Kuroha, K Nagai, R Gamuyao, D R Wang, T Furuta, M Nakamori, T Kitaoka, K Adachi, A Minami, Y Mori, K Mashiguchi, Y Seto, S Yamaguchi, M Kojima, H Sakakibara, J Wu, K Ebana, N Mitsuda, M Ohme-Takagi, S Yanagisawa, M Yamasaki, R Yokoyama, K Nishitani, T Mochizuki, G Tamiya, S R McCouch, and M Ashikari
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Journal Title
Science
Volume: 361
Issue: 6398
Pages: 181-186
DOI
NAID
Related Report
Peer Reviewed / Open Access / Int'l Joint Research
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[Journal Article] Evaluation of reported pathogenic variants and their frequencies in a Japanese population based on a whole-genome reference panel of 2,049 individuals2018
Author(s)
Y Yamaguchi-Kabata, J Yasuda, O Tanabe, Y Suzuki, H Kawame, N Fuse, M Nagasaki, Y Kawai, K Kojima, F Katsuoka, S Saito, I Danjoh, I Motoike, R Yamashita, S Koshiba, D Saigusa, G Tamiya, S Kure, N Yaegashi, Y Kawaguchi, F Nagami, S Kuriyama, J Sugawara, N Minegishi, A Hozawa, T Takai-Igarashi, K Kinoshita, M Yamamoto.
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Journal Title
Journal of Human Genetics.
Volume: 63
Issue: 2
Pages: 213-230
DOI
Related Report
Peer Reviewed / Open Access
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[Journal Article] Genome-wide meta-analysis in Japanese populations identifies novel variants at the TMC6-TMC8 and SIX3-SIX2 loci associated with HbA1c.2017
Author(s)
Hachiya T, Komaki S, Hasegawa Y, Ohmomo H, Tanno K, Hozawa A, Tamiya G, Yamamoto M, Ogasawara K, Nakamura M, Hitomi J, Ishigaki Y, Sasaki M, Shimizu A.
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Journal Title
Sci Rep.
Volume: 7
Issue: 1
Pages: 16147-16147
DOI
Related Report
Peer Reviewed / Open Access
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[Journal Article] Security controls in an integrated Biobank to protect privacy in data sharing: rationale and study design2017
Author(s)
Takai-Igarashi T, Kinoshita K, Nagasaki M, Ogishima S, Nakamura N, Nagase S, Nagaie S, Saito T, Nagami F, Minegishi N, Suzuki Y, Suzuki K, Hashizume H, Kuriyama S, Hozawa A, Yaegashi N, Kure S, Tamiya G, Kawaguchi Y, Tanaka H, Yamamoto M
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Journal Title
BMC Med Inform Decis Mak
Volume: 17
Issue: 1
Pages: 100-100
DOI
Related Report
Peer Reviewed / Open Access
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