Journal
GENES AND IMMUNITY
Volume 13, Issue 7, Pages 543-548Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/gene.2012.35
Keywords
HLA; tag SNP; tag SNP haplotype; disease susceptibility; linkage disequilibrium
Categories
Funding
- KAKENHI from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) [22133003]
Ask authors/readers for more resources
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 (r(2) >= 0.8) with SNPs, including 11 non-synonymous SNPs in non-HLA genes. In addition, we identified several SNP haplotypes in strong LD (r(2) >= 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.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available