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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.

journal_name

Sci Rep

journal_title

Scientific reports

authors

Saw WY,Liu X,Khor CC,Takeuchi F,Katsuya T,Kimura R,Nabika T,Ohkubo T,Tabara Y,Yamamoto K,Yokota M,Japanese Genome Variation Consortium.,Teo YY,Kato N

doi

10.1038/srep17855

subject

Has Abstract

pub_date

2015-12-09 00:00:00

pages

17855

issn

2045-2322

pii

srep17855

journal_volume

5

pub_type

杂志文章

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