TY - JOUR
T1 - HLA and SNP haplotype mapping in the Japanese population
AU - Kitajima, H.
AU - Sonoda, M.
AU - Yamamoto, K.
N1 - Funding Information:
This work was supported by KAKENHI (22133003) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT).
PY - 2012/10
Y1 - 2012/10
N2 - 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.
AB - 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.
KW - HLA
KW - disease susceptibility
KW - linkage disequilibrium
KW - tag SNP
KW - tag SNP haplotype
UR - http://www.scopus.com/inward/record.url?scp=84867744818&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84867744818&partnerID=8YFLogxK
U2 - 10.1038/gene.2012.35
DO - 10.1038/gene.2012.35
M3 - Article
C2 - 22914434
AN - SCOPUS:84867744818
SN - 1466-4879
VL - 13
SP - 543
EP - 548
JO - Genes and Immunity
JF - Genes and Immunity
IS - 7
ER -
