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HLA and SNP haplotype mapping in the Japanese population

Genes & Immunity volume 13, pages 543–548 (2012)Cite this article

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Abstract

The genes that encode the human leukocyte antigen (HLA) class I and II molecules are highly polymorphic and located in the major histocompatibility complex (MHC) region, where there is a high density of immune-related genes. Numerous studies have identified disease susceptibility in this region; however, interpretation of the results is complicated because of the strong linkage disequilibrium (LD) among HLA alleles and single-nucleotide polymorphisms (SNPs). In this study, we evaluated the correlation between the HLA alleles of 6 loci (HLA-A, C, B, DRB1, DQB1 and DPB1) and 6502 SNPs within 8 Mb of the extended MHC region using 92 Japanese subjects to identify SNP single loci or haplotypes that tag HLA alleles. We found a total of 39 HLA alleles that showed strong LD (r2⩾0.8) with SNPs, including 11 non-synonymous SNPs in non-HLA genes. In addition, we identified several SNP haplotypes in strong LD (r2⩾0.8) with eight HLA alleles, which do not possess tag SNPs. Our detailed list of tag SNPs and haplotypes could be utilized for a better understanding of the results obtained by association studies in the Japanese population and for the characterization of the differences in LD structures between races.

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Acknowledgements

This work was supported by KAKENHI (22133003) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT).

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  1. Division of Genome Analysis, Research Center for Genetic Information, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan

    H Kitajima, M Sonoda & K Yamamoto

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  1. H Kitajima
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Correspondence to K Yamamoto.

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Kitajima, H., Sonoda, M. & Yamamoto, K. HLA and SNP haplotype mapping in the Japanese population. Genes Immun 13, 543–548 (2012). https://doi.org/10.1038/gene.2012.35

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