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

Molecular Biology & Genetics

Research Subjects

  • Genome wide analysis of complex disease
  • Development of a novel genome analysis method

Selected Publications

Papers with an asterisk(*) are based on research conducted outside of RIKEN.
  1. 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)
  2. 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, Louis Bridges Jr S, 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; the RACI consortium; the 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: 376-81 (2014)
  3. The AMD Gene Consortium, Fritsche LG, Chen W, Schu M, Yaspan BL, Yu Y, Thorleifsson G, Zack DJ, Arakawa S, Cipriani V, Ripke S, Igo RP Jr, Buitendijk GH, Sim X, Weeks DE, Guymer RH, Merriam JE, Francis PJ, Hannum G, Agarwal A, Armbrecht AM, Audo I, Aung T, Barile GR, Benchaboune M, Bird AC, Bishop PN, Branham KE, Brooks M, Brucker AJ, Cade WH, Cain MS, Campochiaro PA, Chan CC, Cheng CY, Chew EY, Chin KA, Chowers I, Clayton DG, Cojocaru R, Conley YP, Cornes BK, Daly MJ, Dhillon B, Edwards AO, Evangelou E, Fagerness J, Ferreyra HA, Friedman JS, Geirsdottir A, George RJ, Gieger C, Gupta N, Hagstrom SA, Harding SP, Haritoglou C, Heckenlively JR, Holz FG, Hughes G, Ioannidis JP, Ishibashi T, Joseph P, Jun G, Kamatani Y, Katsanis N, N Keilhauer C, Khan JC, Kim IK, Kiyohara Y, Klein BE, Klein R, Kovach JL, Kozak I, Lee CJ, Lee KE, Lichtner P, Lotery AJ, Meitinger T, Mitchell P, Mohand-Saïd S, Moore AT, Morgan DJ, Morrison MA, Myers CE, Naj AC, Nakamura Y, Okada Y, Orlin A, Ortube MC, Othman MI, Pappas C, Park KH, Pauer GJ, Peachey NS, Poch O, Priya RR, Reynolds R, Richardson AJ, Ripp R, Rudolph G, Ryu E, Sahel JA, Schaumberg DA, Scholl HP, Schwartz SG, Scott WK, Shahid H, Sigurdsson H, Silvestri G, Sivakumaran TA, Smith RT, Sobrin L, Souied EH, Stambolian DE, Stefansson H, Sturgill-Short GM, Takahashi A, Tosakulwong N, Truitt BJ, Tsironi EE, Uitterlinden AG, van Duijn CM, Vijaya L, Vingerling JR, Vithana EN, Webster AR, Wichmann HE, Winkler TW, Wong TY, Wright AF, Zelenika D, Zhang M, Zhao L, Zhang K, Klein ML, Hageman GS, Lathrop GM, Stefansson K, Allikmets R, Baird PN, Gorin MB, Wang JJ, Klaver CC, Seddon JM, Pericak-Vance MA, Iyengar SK, Yates JR, Swaroop A, Weber BH, Kubo M, Deangelis MM, Léveillard T, Thorsteinsdottir U, Haines JL, Farrer LA, Heid IM, Abecasis GR.:
    “Seven new loci associated with age-related macular degeneration.”
    Nat Genet. 45: 433-9 (2013)
  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

Keiko Yamazaki
Research Scientist
Yusuke Iwasaki
Technical Scientist
Xiaoxi Liu
Postdoctoral Researcher
Kyota Ashikawa
Technical Staff I
Hanae Iijima
Technical Staff II
Sadaaki Takata
Technical Staff II
Tomomi Aoi
Technical Staff II
Chihiro Inai
Technical Staff II

Contact information

E308,
1-7-22 Suehiro-cho, Tsurumi-ku,
Yokohama City, Kanagawa,
230-0045, Japan

Email: yukihide.momozawa [at] riken.jp

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