DQ microsatellite association studies in three ethnic groups

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Abstract
Polymorphism at the level of three microsatellite markers (DQCAR, DQCARII, G51152) located in the HLA‐DQ region was characterized in 78 10th International Histocompatibility Workshop B‐cell lines, 718 random Japanese Asians, 99 Norwegian Caucasians and 95 New Guinean Aborigines with established HLA‐DRB1, ‐DQA1 and ‐DQB1 typing. DQCAR, DQCARII, and G51152 result in 13, 13, and 11 alleles respectively. All three markers were in tight linkage disequilibrium with HLA‐DRB1, ‐DQA1 and ‐DQB1. DRB1, DQA1, DQCARII, DQCAR, DQB1, and G51152 haplotypes could be defined for all subjects. In fact, DQ microsatellite typing data could predict DQA1 and DQB1 genotypes with high accuracy and may be used as a simple first pass HLA‐DQ typing method. The haplotype data was also used to determine recombination in the DRB1‐DQA1 (about 80 kb), DQA1‐DQCARII (about 4.5 kb), DQCARII‐DQCAR (about 7.5 kb), DQCAR‐DQB1 (about 1‐1.5 kb) and DQB1‐G51152 (about 20–25 kb) genomic segments and the relative rate of slippage microsatellite mutations for DQCAR, DQCARII, and G51152. This led us to conclude that recombination is more frequent in the DRB1‐DQA1 and DQCAR‐DQCARII segments, thus suggesting cross‐overs within small genomic segments are not proportional to genetic distance. We also observed that DQCAR had a higher mutation rate than DQCARII or G51152 and that 1 or 2 CA slippage mutations were arising more frequently from large size microsatellite alleles.