Genetic variability and linkage disequilibrium within the DP region in the CEPH families

A PCR-based SSO-assay has been developed to characterize the allelic polymorphism at the HLA-DPA1 locus. To validate the performance of this assay, 77 samples were typed side by side in a blinded fashion by the SSO assay and sequencing-based typing (SBT); 100% concordance was seen between the two methods. To address questions of genetic variability and linkage disequilibrium within the class II region, 478 members of the 37 original Caucasian Centre d'Etude du Polymorphisme Humain (CEPH) families were typed for DPA1 using the SSO assay providing information on 247 independent chromosomes. Six of the eight known DPA1 alleles were detected in this population; DPA1*0103 was the most frequent allele. Analysis of the distribution of allele and haplotype frequencies using the homozygosity statistic suggests that balancing selection does not appear to be acting on the DPA1 locus nor on the functional DP heterodimer in this population. Family data permits the unambiguous assignment of haplotypes. Of the 247 independent chromosomes analyzed, 24 distinct DPA1-DPB1 haplotypes were identified with DPA1*0103-DPB1*0401 being the most common. Twelve of the 18 DPB1 alleles identified in this population have an exclusive association with one DPA1 allele. Of the remaining six DPB1 alleles, four are present at a frequency of >3% and show preferential association with just one DPA1 allele. Calculation of the normalized disequilibrium parameter (D') shows 13 DP haplotypes to be in significant positive disequilibrium. These data suggest there is strong linkage disequilibrium between the DPA1 and DPB1 loci in this Caucasoid population and provide a basis with which to study linkage disequilibrium in other ethnic groups as well as analyze the evolutionary forces which govern allelic and haplotypic variation.