A linkage disequilibrium map of the human major histocompatibility complex in Singapore Chinese: Conserved extended haplotypes and ancestral blocks

Abstract

The linkage disequilibrium (LD) structure of the human major histocompatibility complex (MHC) in the Singaporean Chinese population is described using 3 SNP maps of increasing marker density. First, the LD of the chromosome 6p was analysed in 192 individuals. These samples were then genotyped at a higher resolution across an extended MHC segment to obtain a better granularity of LD. Finally a larger set of 252 individuals was genotyped at a high resolution with 2360 SNPs across the MHC. The inclusion of HLA-homozygous individuals enabled the detailed description of conserved extended haplotypes (CEH) that stretch across more than 2.5Mb, including the A33-B58-DR3 and A2-B46-DR9 CEHs that are present at high frequency in the population. Fixed ancestral blocks not shuffled by recombination are also seen shared between HLA haplotypes of a common lineage. The results presented here provide an essential resource for understanding LD and mapping disease associations in the MHC.