Centers & Labs

RIKEN Center for Integrative Medical Sciences

Laboratory for Genotyping Development

Team Leader: Yukihide Momozawa (D.V.M., Ph.D.)
Yukihide  Momozawa(D.V.M., Ph.D.)

Our team established a high-throughput SNP genotyping system using a combined method of multiplex-PCR and the Invader assay at the era of SNP Research Center (2000-2007). Using this system, our team contributed to the establishment of the JSNP database and the success for the International HapMap Project (Phase 1). Since 2007, our team has worked as a main facility of genomic research for the BioBank Japan project and generating a large amount of SNP genotyping data for the association studies of complex diseases. Since 2013, we have focused on whole genome sequencing.
We also developed a new genotyping method for copy number variation (RETINA) and a target sequencing method to analyze specific genome regions in large samples. To take advantage of these methods, we have collaborated with NIH, Pharmacogenomics Research Network (PGRN) since 2008.
Our hope is to implement genomic medicine to optimize medical care by use of genomic information.

Main Research Field

Medicine, dentistry, and pharmacy

Related Research Fields

Agricultural sciences


  • Genome
  • Complex disease
  • Next generation sequencer
  • Rare variants

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.
  1. Huang H, Fang M, Jostins L, Umićević Mirkov M, Boucher G, Anderson CA, Andersen V, Cleynen I, Cortes A, Crins F, D'Amato M, Deffontaine V, Dmitrieva J, Docampo E, Elansary M, Farh KK, Franke A, Gori AS, Goyette P, Halfvarson J, Haritunians T, Knight J, Lawrance IC, Lees CW, Louis E, Mariman R, Meuwissen T, Mni M, Momozawa Y, Parkes M, Spain SL, Théâtre E, Trynka G, Satsangi J, van Sommeren S, Vermeire S, Xavier RJ; International Inflammatory Bowel Disease Genetics Consortium, Weersma RK, Duerr RH, Mathew CG, Rioux JD, McGovern DPB, Cho JH, Georges M, Daly MJ, Barrett JC.:
    “Fine-mapping inflammatory bowel disease loci to single-variant resolution.”
    Nature. 547, 173-178 (2017)
  2. Momozawa Y, Akiyama M, Kamatani Y, Arakawa S, Yasuda M, Yoshida S, Oshima Y, Mori R, Tanaka K, Mori K, Inoue S, Terasaki H, Yasuma T, Honda S, Miki A, Inoue M, Fujisawa K, Takahashi K, Yasukawa T, Yanagi Y, Kadonosono K, Sonoda KH, Ishibashi T, Takahashi A, Kubo M.:
    “Low-frequency coding variants in CETP and CFB are associated with susceptibility of exudative age-related macular degeneration in the Japanese population.”
    Hum Mol Genet. 25,:5027-5034 (2016)
  3. 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: 798-802 (2015)
  4. Yamazaki K, Umeno J, Takahashi A, Hirano A, Johnson TA, Kumasaka N, Morizono T, Hosono N, Kawaguchi T, Takazoe M, Yamada T, Suzuki Y, Tanaka H, Motoya S, Hosokawa M, Arimura Y, Shinomura Y, Matsui T, Matsumoto T, Iida M, Tsunoda T, Nakamura Y, Kamatani N, Kubo M.:
    “A Genome-Wide Association Study Identifies 2 Susceptibility Loci for Crohn's Disease in a Japanese Population.”
    Gastroenterology. 144: 781-8 (2013)
  5. Shiraishi K, Kunitoh H, Daigo Y, Takahashi A, Goto K, Sakamoto H, Ohnami S, Shimada Y, Ashikawa K, Saito A, Watanabe S, Tsuta K, Kamatani N, Yoshida T, Nakamura Y, Yokota J, Kubo M, Kohno T.:
    “A genome-wide association study identifies two new susceptibility loci for lung adenocarcinoma in the Japanese population.”
    Nat Genet. 44: 900-3. (2012)
  6. *Momozawa Y, Mni M, Nakamura K, Coppieters W, Almer S, Amininejad L, Cleynen I, Colombel JF, de Rijk P, Dewit O, Finkel Y, Gassull MA, Goossens D, Laukens D, Lémann M, Libioulle C, O'Morain C, Reenaers C, Rutgeerts P, Tysk C, Zelenika D, Lathrop M, Del-Favero J, Hugot JP, de Vos M, Franchimont D, Vermeire S, Louis E, Georges M.:
    “Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease.”
    Nat Genet. 43: 43-7 (2011)
  7. *Merveille AC, Davis EE, Becker-Heck A, Legendre M, Amirav I, Bataille G, Belmont J, Beydon N, Billen F, Clément A, Clercx C, Coste A, Crosbie R, de Blic J, Deleuze S, Duquesnoy P, Escalier D, Escudier E, Fliegauf M, Horvath J, Hill K, Jorissen M, Just J, Kispert A, Lathrop M, Loges NT, Marthin JK, Momozawa Y, Montantin G, Nielsen KG, Olbrich H, Papon JF, Rayet I, Roger G, Schmidts M, Tenreiro H, Towbin JA, Zelenika D, Zentgraf H, Georges M, Lequarré AS, Katsanis N, Omran H, Amselem S.:
    “CCDC39 is required for assembly of inner dynein arms and the dynein regulatory complex and for normal ciliary motility in humans and dogs.”
    Nat Genet. 43: 72-8 (2011)
  8. Arakawa S, Takahashi A, Ashikawa K, Hosono N, Aoi T, Yasuda M, Oshima Y, Yoshida S, Enaida H, Tsuchihashi T, Mori K, Honda S, Negi A, Arakawa A, Kadonosono K, Kiyohara Y, Kamatani N, Nakamura Y, Ishibashi T, Kubo M.:
    “Genome-wide association study identifies two susceptibility loci for exudative age-related macular degeneration in the Japanese population.”
    Nat Genet. 43: 1001-4 (2011)
  9. Kubo M, Hata J, Ninomiya T, Matsuda K, Yonemoto K, Nakano T, Matsushita T, Yamazaki K, Ohnishi Y, Saito S, Kitazono T, Ibayashi S, Sueishi K, Iida M, Nakamura Y, and Kiyohara Y.:
    “Nonsynonymous SNP in PRKCH encoding protein kinase c-η increases the risk of cerebral infarction”
    Nat Genet. 39, 212-217 (2007)
  10. The International HapMap Consortium.:
    “A haplotype map of the human genome”
    Nature, 437, 1299-1320 (2005)

Lab Members

Principal Investigator

Yukihide Momozawa
Team Leader

Core Members

Yusuke Iwasaki
Technical Scientist
Xiaoxi Liu
Special Postdoctoral Researcher
Tomoki Motegi
Research Associate
Sadaaki Takata
Technical Staff I
Hanae Iijima
Technical Staff II
Tomomi Aoi
Technical Staff II

Contact information

1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan

Email: momozawa [at]

Related links

Recent research results