Dataset Information

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

ABSTRACT: 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.

SUBMITTER: Saw WY

PROVIDER: S-EPMC4673465 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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

Saw Woei-Yuh WY Liu Xuanyao X Khor Chiea-Chuen CC Takeuchi Fumihiko F Katsuya Tomohiro T Kimura Ryosuke R Nabika Toru T Ohkubo Takayoshi T Tabara Yasuharu Y Yamamoto Ken K Yokota Mitsuhiro M Teo Yik-Ying YY Kato Norihiro N

Scientific reports 20151209

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 biological ...[more]

PMID: 26648100

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Dataset Information

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

Publications

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

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