メンバー / Member

藤本　明洋（PhD）

藤本　明洋

所属

東京大学大学院　医学系研究科　人類遺伝学分野　教授

ひとこと

ゲノムの謎を解明してみませんか

略歴

（学歴）

2003年 九州大学・理学部・生物学科卒業（指導教官　舘田英典教授）
2005年 九州大学大学院・理学府・生物科学専攻　修士課程修了（指導教官　舘田英典教授)
2008年 東京大学大学院・医学系研究科・国際保健学専攻　博士課程修了（指導教官　徳永勝士教授）

（職歴）

2008年〜2010年 理化学研究所・次世代計算科学研究開発プログラム・データ解析融合研究チーム（特別研究員）
2010年〜2013年 理化学研究所・ゲノム医科学研究センター・情報解析研究チーム（上級研究員）
2013年〜2014年 理化学研究所・統合生命医科学研究センター・医科学数理研究グループ（上級研究員）
2014年〜2016年 理化学研究所・統合生命医科学研究センター・ゲノムシーケンス解析研究チーム（副チームリーダー）
2016年〜2019年 京都大学・医学研究科・創薬医学講座（特定准教授）
2019年〜 現職

賞罰

大正富山Award、文部科学大臣表彰 若手科学者賞、日本人類遺伝学会奨励賞、日本癌学会奨励賞、第８回理化学研究所・研究奨励賞、平成27年日本遺伝学会ベストペーパー賞、平成24年日本遺伝学会ベストペーパー賞、第２回理化学研究所・研究奨励賞、進化学会・最優秀ポスター賞受賞

業績

(*は藤本が責任著者のもの)

  • Takeda H, Takai A, Kumagai K, Iguchi E, Arasawa S, Eso Y, Shimizu T, Ueda Y, Taura K, Uemoto S, Kita R, Haga H, Marusawa H, Fujimoto A, Seno H. (2020) Multiregional whole-genome sequencing of hepatocellular carcinoma with nodule-in-nodule appearance reveals stepwise cancer evolution. J Pathol doi: 10.1002/path.5533. Online ahead of print.
  • Shibayama Y, Takahashi K, Yamaguchi H, Yasuda J, Yamazaki D, Rahman A, Fujimori T, Fujisawa Y, Takai S, Furukawa T, Nakagawa T, Ohsaki H, Kobara H, Wong JH, Masaki T, Yuzawa Y, Kiyomoto H, Yachida S, Fujimoto A* & Nishiyama A. (2020) Aberrant (pro)renin receptor expression induces genomic instability in pancreatic ductal adenocarcinoma through upregulation of SMARCA5/SNF2H. Commun Biol 3, 724
  • Dutta M, Nakagawa H, Kato H, Maejima K, Sasagawa S, Nakano K, Sasaki-Oku A, Fujimoto A, Mateos RN, Patil A, Tanaka H, Miyano S, Yasuda T, Nakai K, Fujita M. (2020) Whole genome sequencing analysis identifies recurrent structural alterations in esophageal squamous cell carcinoma. PeerJ 8:e9294 https://doi.org/10.7717/peerj.9294 2.
  • Fujita M, Yamaguchi R, Hasegawa T, Shimadad S, Arihiroe K, Hayashi S, Maejima K, Nakano K, Fujimoto A, Ono A, Aikata H, Ueno M, Hayami S, Tanaka H, Miyano S, Yamaue H, Chayama K, Kakimi K, Tanaka S, Imoto S, Nakagawa H (2020) Classification of primary liver cancer with immunosuppression mechanisms and correlation with genomic alterations. EBioMedicine 53:102659
  • Fujimoto A*, Fujita M,  Hasegawa T, Wong JH, Maejima K, Oku-Sasaki A, Nakano K, Shiraishi Y, Miyano S, Yamamoto G, Akagi K, Imoto S, and Nakagawa H (2020) Comprehensive Analysis of Indels in Whole-genome Microsatellite Regions and Microsatellite Instability across 21 Cancer Types. Genome Research 30:334–346
  • The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium. (2020) Pan-cancer analysis of whole genomes. Nature 578: 82-93.
  • Mizuno K, Akamatsu S, Sumiyoshi T, Wong JH, Fujita M, Maejima K, Nakano K, Ono A, Aikata H, Ueno M, Hayami S, Yamaue H, Chayama K, Inoue T, Ogawa O, Nakagawa H and Fujimoto A* (2019) eVIDENCE: a practical variant filtering for low-frequency variants detection in cell-free DNA. Sci Rep 9: 15017
  • Wong JH, Shigemizu D, Yoshii Y, Akiyama S, Tanaka A, Nakagawa H, Narumiya S, Fujimoto A* (2019)  Identification of intermediate-sized deletions and inference of their impact on gene expression in a human population. Genome Medicine 11:44
  • Sumiyoshi T, Mizuno K, Yamasaki T, Miyazaki Y, Makino Y, Okasho K, Li X, Utsunomiya N, Goto T, Kobayashi T, Terada N, Inoue T, Kamba T, Fujimoto A, Ogawa O, Akamatsu S (2019) Clinical utility of androgen receptor gene aberrations in circulating cell-free DNA as a biomarker for treatment of castration-resistant prostate cancer. Sci Rep 9: 4030
  • Nguyen DT, Nguyen HH, Nguyen TD, Nguyen TTH, Nakano K, Maejima K, Sasaki-Oku A, Nguyen VB, Nguyen DB, Le BQ, Wong JH, Tsunoda T, Nakagawa H, Fujimoto A*, Nong VH (2018) Whole Genome Sequencing of a Vietnamese Family from a Dioxin Contamination Hotspot Reveals Novel Variants in the Son with Undiagnosed Intellectual Disability. Int J Environ Res Public Health 15
  • Ton ND, Nakagawa H, Ha NH, Duong NT, Nhung VP, Hien LTT, Hue HTT, Hoang NH, Wong JH, Nakano K, Maejima K, Sasaki-Oku A, Tsunoda T, Fujimoto A*, Van Hai N. Whole genome sequencing and mutation rate analysis of trios with paternal dioxin exposure. (2018) Hum Mutat Jul 3. doi: 10.1002/humu.23585. [Epub ahead of print]
  • Shigemizu D, Miya F, Akiyama S, Okuda S, Boroevich KA, Fujimoto A, Nakagawa H, Ozaki K, Niida S, Kanemura Y, Okamoto N, Saitoh S, Kato M, Yamasaki M, Matsunaga T, Mutai H, Kosaki K, Tsunoda T (2018) Publisher Correction: IMSindel: An accurate intermediate-size indel detection tool incorporating de novo assembly and gapped global-local alignment with split read analysis. Sci Rep 8: 10367
  • Taniguchi H, Fujimoto A, Kono H, Furuta M, Fujita M, Nakagawa H. Loss-of-function mutations in Zn-finger DNA-binding domain of HNF4A cause aberrant transcriptional regulation in liver cancer. (2018) Oncotarget 25;9(40):26144-26156. doi: 10.18632/oncotarget.25456.
  • Wardell CP, Fujita M, Yamada T, Simbolo M, Fassan M, Karlic R, Polak P, Kim J, Hatanaka Y, Maejima K, Lawlor RT, Nakanishi Y, Mitsuhashi T, Fujimoto A, Furuta M, Ruzzenente A, Conci S, Oosawa A, Sasaki-Oku A, Nakano K, Tanaka H, Yamamoto Y, Michiaki K, Kawakami Y, Aikata H, Ueno M, Hayami S, Gotoh K, Ariizumi SI, Yamamoto M, Yamaue H, Chayama K, Miyano S, Getz G, Scarpa A, Hirano S, Nakamura T, Nakagawa H. (2018) Genomic characterization of biliary tract cancers identifies driver genes and predisposing mutations. J Hepatol 68:959-969. doi: 10.1016/j.jhep.2018.01.009.
  • Shirai K, Matsuda F, Nakabayashi R, Okamoto M, Tanaka M, Fujimoto A, Shimizu M, Shinozaki K, Seki M, Saito K, Hanada K (2017) A Highly Specific Genome-Wide Association Study Integrated with Transcriptome Data Reveals the Contribution of Copy Number Variations to Specialized Metabolites in Arabidopsis thaliana Accessions. Mol Biol Evol 34: 3111-3122
  • Fujita M, Matsubara N, Matsuda I, Maejima K, Oosawa A, Yamano T, Fujimoto A, Furuta M, Nagano K, Oku-Sasaki A, Tanaka H, Shiraishi Y, Mateos RN, Sakai K, Miyano S, Tomita N, Hirota S, Ikeuchi H, and Nakagawa N. (2017) Genomic landscape of colitis-associated cancer indicates the impact of chronic inflammation and its stratification by mutations in RNF43 and Wnt signaling. Oncotarget 12:969-981. doi: 10.18632/oncotarget.22867.
  • Furuta M, Ueno M, Fujimoto A, Hayami S, Yasukawa S, Kojima F, Arihiro K, Kawakami Y, Wardell CP, Shiraishi Y, Tanaka H, Nakano K, Maejima K, Sasaki-Oku A, Tokunaga N, Boroevich KA, Abe T, Aikata H, Ohdan H, Goto K, Kubo M, Tsunoda T, Miyano S, Chayama K, Yamaue H, Nakagawa H. (2017) Whole genome sequencing discriminate hepatocellular carcinoma with intrahepatic metastasis from multicentric tumors. J Hepatic 66:363-373
  • Alexandrov LB, Ju YS, Haase K, Van Loo P, Martincorena I, Nik-Zainal S, Totoki Y, Fujimoto A, Nakagawa H, Shibata T, Campbell PJ, Vineis P, Phillips DH, Stratton MR. (2016) Mutational signatures associated with tobacco smoking in human cancer. Science 354:618-622.
  • Fujimoto A*, Okada Y, Boroevich KA, Tsunoda T and Taniguchi H, and Nakagawa H. (2016) Systematic analysis of mutation distribution in three dimensional protein structures identifies cancer driver genes. Sci Rep 6, Article number: 26483
  • Fujimoto A, Furuta M (equal contribution), Totoki Y (equal contribution), Tsunoda T (equal contribution), Kato M (equal contribution), Shiraishi Y, Tanaka H, Taniguchi H, Kawakami Y, Ueno M, Gotoh K, Ariizumi S, Wardell CP, Hayami S, Nakamura T, Aikata, Arihiro K, Boroevich KA, Abe T, Nagano K, Maejima K, Sasaki-Oku A, Oshawa A, Shibuya T, Nakamura H, Hama N, Hosoda F, Arai Y, Shashi S, Urushidate T, Nagae G, Yamamoto S, Ueda H, Tatsuno K, Ojima H, Hiraoka N, Okusakan T, Kubo M, Marubashi S, Yamada T, Hirano S, Yamamoto M, Ohdan H, Shimada K, Ishikawa O, Yamane H, Chayama K, Miyano S, Aburatani H, Shibata T, and Nakagawa H. (2016) Whole genome mutational landscape and characterization of non-coding and structural mutations in liver cancer. Nat Genet 48: 500-509
  • Alioto TS, Buchhalter I, Derdak S, Hutter B, Eldridge MD, Hovig E, Heisler LE, Beck TA, Simpson JT, Tonon J, Sertier S, Patch AS, Jäger N, Ginsbach P, Drews R, Paramasivam N, Kabbe R, Chotewutmontri S, Diessl N, Previti C, Schmidt S, Brors B, Feuerbach L, Heinold, Gröbner S, Korshunov A, Tarpey PS, Butler AP, Hinton J, Jones D, Menzies A, Raine K, Shepherd R, Stebbings L, Teague JW, Ribeca P, Giner FC, Beltran S, Raineri E, Dabad M, Heath SC, Gut M, Denroche RE, Harding NJ, Yamaguchi TN, Fujimoto A, Nakagawa H, Quesada V, Valdés-Mas R, Nakken S, Vodák D, Bower L, Lynch A, Anderson CL, Waddell N, Pearson JV, Grimmond SM, Peto M, Spellman P, He M, Kandoth C, Lee S, Zhang J, Létourneau L, Ma S, Seth S, Torrents D, Xi L, Wheeler DA, López-Otín C, Campo E, Campbell PJ, Boutros PC, Puente XS, Gerhard DS, Pfister SM, McPherson JD, Hudson TJ, Schlesner M, Lichter P, Eils P, Jones DTW, and Gut IG. (2015) A comprehensive assessment of somatic mutation detection in cancer using whole genome sequencing. Nature Comms 6, Article number: 10001
  • Ono A, Fujimoto A, Yamamoto Y, Akamatsu S, Nobuhiko H, Imamura M, Kawaoka T, Tsuge M, Abe H, Hayes CN, Miki D, Furuta M, Tsunoda T, Miyano S, Kubo M, Aikata H, Ochi H, Kawakami Y, Arihiro K, Ohdan H, Nakagawa H, Chayama K (2015) Circulating tumor DNA analysis for liver cancers and its usefulness as a liquid biopsy. Cellular and Molecular Gastroenterology and Hepatology 1: 516-534
  • Shigemizu D, Aiba T, Nakagawa H, Ozaki K, Miya F, Satake W, Toda T, Miyamoto Y, Fujimoto A, Suzuki Y, Kubo M, Tsunoda T, Shimizu W, and Tanaka T (2015) Exome analyses of long QT syndrome reveal candidate pathogenic mutations in calmodulin-interacting gene. PLoS One 10: e0130329
  • Nakagawa H, Wardell CP , Furuta M, Taniguchi H, Fujimoto A (2015) Cancer whole-genome sequencing: present and future. Oncogene 34:5943-5950
  • Fujimoto A, Furuta M (equal contribution), Shiraishi Y, Nguyen H, Shigemizu D, Gotoh K, Kawakami Y, Nakamura T, Ueno M, Ariizumi S, Shibata T, Abe T, Boroevich KA, Nakano K, Sasaki A, Kitada R, Maejima K, Tanaka H, Shibuya T, Ojima H, Shimada K, Hayami S, Shigekawa Y, Aikata H, Arihiro K, Ohdan H, Marubashi S, Yamada T, Ishikawa O, Kubo M, Hirano S, Yamamoto M, Yamaue H, Chayama K, Miyano S, Tsunoda T, and Nakagawa H (2015) Whole-genome mutational landscape of liver cancers displaying biliary phenotype reveals hepatitis impact and molecular diversity. Nat Comms 6, Article number: 6120
  • Shiraishi Y, Fujimoto A, Furuta M, Tanaka H, Chiba K, Boroevich KA, Abe T, Kawakami Y, Ueno M, Gotoh K, Ariizumi S, Shibuya T, Nakano K, Sasaki A, Maejima K, Kitada R, Hayami S, Shigekawa Y, Marubashi S, Yamada T, Kubo M, Ishikawa O, Aikata H, Arihiro K, Ohdan H, Yamamoto M, Yamaue H, Chayama K, Tsunoda T, Miyano S, and Nakagawa H (2014) Integrated analysis of whole genome and transcriptome sequencing reveals diverse transcriptomic aberrations driven by somatic genomic changes in liver cancers. PLoS One 9: e114263
  • Takezawa Y, Kato K, Oota H, Caulfield T, Fujimoto A, Honda S, Kamatani N, Kawamura S, Kawashima K, Kimura R, Matsumae H, Saito A, Savage PE, Seguchi N, Shimizu K, Terao S, Yamaguchi-Kabata Y, Yasukouchi A, Yoneda M, Tokunaga K (2014) Human genetic research, race, ethnicity and the labeling of populations: recommendations based on an interdisciplinary workshop in Japan. BMC Med Ethics 15: 33
  • Shigemizu D, Fujimoto A (equal contribution), Akiyama S, Abe T, Nakano K, Boroevich KA, Yamamoto Y, Furuta M, Kubo M, Nakagawa H, Tsunoda T (2013) A practical method to detect SNVs and indels from whole genome and exome sequencing data. Sci Rep 3: 2161
  • Sato Y, Yoshizato T, Shiraishi Y, Maekawa S, Okuno Y, Kamura T, Shimamura T, Sato-Otsubo A, Nagae G, Suzuki H, Nagata Y, Yoshida K, Kon A, Suzuki Y, Chiba K, Tanaka H, Niida A, Fujimoto A, Tsunoda T, Morikawa T, Maeda D, Kume H, Sugano S, Fukayama M, Aburatani H, Sanada M, Miyano S, Homma Y, Ogawa S (2013) Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet 45: 860-867
  • Fujimoto A, Totoki Y (equal contribution), Abe T, Boroevich KA, Hosoda F, Nguyen HH, Aoki M, Hosono N, Kubo M, Miya F, Arai Y, Takahashi H, Shirakihara T, Nagasaki M, Shibuya T, Nakano K, Watanabe-Makino K, Tanaka H, Nakamura H, Kusuda J, Ojima H, Shimada K, Okusaka T, Ueno M, Shigekawa Y, Kawakami Y, Arihiro K, Ohdan H, Gotoh K, Ishikawa O, Ariizumi SI, Yamamoto M, Yamada T, Chayama K, Kosuge T, Yamaue H, Kamatani N, Miyano S, Nakagama H, Nakamura Y, Tsunoda T, Shibata T and Nakagawa H (2012) Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat Genet 44: 760-76
  • Fujimoto A, Nakagawa H, Hosono N, Nakano K, Abe T, Boroevich KA, Nagasaki M, Yamaguchi R, Shibuya T, Kubo M, Miyano S, Nakamura Y, Tsunoda T (2010) Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing. Nat Genet 42: 931–936
  • The International Cancer Genome Consortium (2010) International network of cancer genome projects. Nature 464: 993-998
  • Fujimoto A, Nishida N, Kimura R, Miyagawa T, Yuliwulandari R, Batubara L, Mustofa MS, Samakkarn U, Settheetham-Ishida W, Ishida T, Morishita Y, Tsunoda T, Tokunaga K, Ohashi J (2009) FGFR2 is associated with hair thickness in Asian populations. J Hum Genet 54: 461-465
  • Miyagawa T, Nishida N, Ohashi J, Kimura R, Fujimoto A, Kawashima M, Koike A, Sasaki T, Tanii H, Otowa T, Momose Y, Nakahara Y, Gotoh J, Okazaki Y, Tsuji S, Tokunaga K (2008) Appropriate data cleaning methods for genome-wide association study. J Hum Genet 53: 886-893
  • Miyagawa T, Kawashima M, Nishida N, Ohashi J, Kimura R, Fujimoto A, Shimada M, Morishita S, Shigeta T, Lin L, Hong SC, Faraco J, Shin YK, Jeong JH, Okazaki Y, Tsuji S, Honda M, Honda Y, Mignot E, Tokunaga K (2008) Variant between CPT1B and CHKB associated with susceptibility to narcolepsy. Nat Genet 40: 1324-1328
  • Fujimoto A, Ohashi J, Nishida N, Miyagawa T, Morishita Y, Tsunoda T, Kimura R, Tokunaga K (2008) A replication study confirmed the EDAR gene to be a major contributor to population differentiation regarding head hair thickness in Asia. Hum Genet 124: 179-185
  • Fujimoto A, Kimura R, Ohashi J, Omi K, Yuliwulandari R, Batubara L, Mustofa MS, Samakkarn U, Settheetham-Ishida W, Ishida T, Morishita Y, Furusawa T, Nakazawa M, Ohtsuka R, Tokunaga K (2008) A scan for genetic determinants of human hair morphology: EDAR is associated with Asian hair thickness. Hum Mol Genet 17: 835-843
  • Fujimoto A, Kado T, Yoshimaru H, Tsumura Y, Tachida H (2008) Adaptive and slightly deleterious evolution in a conifer, Cryptomeria japonica. J Mol Evol 67: 201-210
  • Kimura R, Fujimoto A, Tokunaga K, Ohashi J (2007) A practical genome scan for population-specific strong selective sweeps that have reached fixation. PLoS One 2: e286
  • Kado T, Fujimoto A, Giang LH, Tuan M, Hong PN, Harada K, Tachida H (2004) Genetic structure of natural populations of three mangrove species, Avicennia marina, Kandelia candel and Lumnitzera racemosa, in Vietnam revealed by maturase sequences of plastid DNA. Plant Species Biology 19: 91-99

    • 総説

  • 藤本明洋 肝癌の全ゲノムシークエンス解析. 医学のあゆみ 2018年8月4日号
  • 藤本明洋 ゲノムシークエンスデータの情報解析. 生物物理 58(3),001-003 (2018）
  • 藤本明洋 進化遺伝学とがんゲノム解析. 実験医学 増刊 2018年
  • 藤本明洋 全ゲノムシークエンス. 炎症と免疫 2015年7月号
  • 藤本明洋, 中川 英刀 肝癌のゲノム解析と発癌メカニズムの解明. Medical Science Digest 2014年11月号
  • 藤本明洋 がんのゲノム解析. 血管医学 2014年9月号
  • 藤本明洋, 角田達彦, 中川英刀 肝がんの網羅的ゲノム解析. 医学のあゆみ 2014年6月7日号
  • 藤本明洋 全ゲノムシークエンス. 医学のあゆみ 2014年5月3日号 （創刊3000号記念 キーワード解説）
  • 藤本明洋 毛髪の太さと関連するEDAR遺伝子多型――集団間分化と毛髪形態の進化史. 医学のあゆみ 2014年4月26日号
  • 藤本明洋 次世代シークエンサーを用いた遺伝的多様性の包括的解析とゲノム人類学への応用. 医学のあゆみ 2014年3月22日号
  • 藤本明洋, 角田達彦, 中川英刀 肝腫瘍の全ゲノム解析 肝胆膵 2014年3月号
  • 藤本明洋, 中川英刀, 角田逹彦 次世代シークエンサーを用いた日本人ゲノム解読による遺伝的多様性の包括的解析. 最新医学 2012年67巻1号
  • 藤本明洋, 中川英刀, 角田逹彦 次世代シークエンサーを用いた日本人ゲノム解読による遺伝的多様性の包括的解析. 生体の科学 2011年12月号

    • 翻訳

  • Serena Nik-Zainal がんゲノムの新たな特徴の発見. 実験医学 2014年32巻12号

    • Akihiro Fujimoto (PhD)

    Dr.Akihiro Fujimoto is a professor of Department of Human Genetics, Graduate School of Medicine, University of Tokyo. He received his Ph.D from the University of Tokyo in 2008. He joined RIKEN institute and carried out analysis of the first Japanese whole genome and liver cancer genomes. He currently interest is identification of genetic variations and somatic mutations, and inference of their functional impacts.

    Current address

    Department of Human Genetics
    Graduate School of Medicine
    The University of Tokyo
    7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033
    Japan

    Education

    March, 2008 Ph. D., Department of Human Genetics, University of Tokyo
    March, 2005 M. S., Department of Biological Science, Kyushu University
    March, 2003 B. A., Department of Biological Science, Kyushu University

    Employment

    2019- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo (Professor)
    2016-2019 Department of Drug Discovery Medicine, Graduate School of Medicine, Kyoto University (Associate Professor)
    2014-2016 Centre for Integrative Medical Sciences, RIKEN (Deputy Team Leader)
    2013-2014 Centre for Integrative Medical Sciences, RIKEN (Senior Researcher)
    2011-2013 Center for Genomic Medicine, RIKEN (Senior Researcher)
    2010-2011 Center for Genomic Medicine, RIKEN (Special Postdoctoral Researcher)
    2008-2010 Data Analysis Fusion Team, Computational Science Research Program, RIKEN (Special Postdoctoral Researcher)

    Message

    We welcome motivated individuals who are interested in unlocking the secrets of the human genome and make meaningful contributions to human health.