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Sci Rep. 2015 Dec 9;5:17855. doi: 10.1038/srep17855.

Mapping the genetic diversity of HLA haplotypes in the Japanese populations.

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Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549.
Life Sciences Institute, National University of Singapore, Singapore 117456.
NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore 117456.
Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672.
Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan 162-8655.
Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan 565-0871.
Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan 903-0215.
Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan 693-8501.
Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan 162-8655.
Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan 606-8501.
Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan 830-0011.
Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Japan 464-8651.
Department of Statistics and Applied Probability, National University of Singapore, Singapore.


Japan has often been viewed as an Asian country that possesses a genetically homogenous community. The basis for partitioning the country into prefectures has largely been geographical, although cultural and linguistic differences still exist between some of the districts/prefectures, especially between Okinawa and the mainland prefectures. The Major Histocompatibility Complex (MHC) region has consistently emerged as the most polymorphic region in the human genome, harbouring numerous biologically important variants; nevertheless the presence of population-specific long haplotypes hinders the imputation of SNPs and classical HLA alleles. Here, we examined the extent of genetic variation at the MHC between eight Japanese populations sampled from Okinawa, and six other prefectures located in or close to the mainland of Japan, specifically focusing at the haplotypes observed within each population, and what the impact of any variation has on imputation. Our results indicated that Okinawa was genetically farther to the mainland Japanese than were Gujarati Indians from Tamil Indians, while the mainland Japanese from six prefectures were more homogeneous than between northern and southern Han Chinese. The distribution of haplotypes across Japan was similar, although imputation was most accurate for Okinawa and several mainland prefectures when population-specific panels were used as reference.

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