RFLP analysis of HLA-DR and -DQ genes and their linkage relationships in the Pacific

Human genomic DNA samples from Melanesian, Micronesians, and Caucasoids of known HLA-DR type were examined with cDNA probes for HLA-DRα, -DRβ, DQα, and -DQβ chain genes. DRβ hybridizations with TaqI-digested DNA did not detect any new DR specificities in the Pacific. However, within the DR5 specificity a common DNA subtype was found in Pacific Islanders that was not seen in Caucasoids. Although, four DNA subtypes of DR5 are described. With the DQα and DQβ probes, significantly more variation could be demonstrated between populations. For example, DR2 was associated with a DQβ TaqI pattern in the Pacific that was very rare in Caucasoids and additional RFLP analysis with other enzymes showed that this pattern is probably associated with Dw12 subtype of DR2. DRw8-positive samples showed two different DQα TqaI patterns, and these correlated with DQw1 and DQw3 specificities. DRα hybridizations with BglII-digested DNA also revealed different linkage relationships of the HLA-class II region genes between Pacific and Caucasoid specimens. The different population linkage disequilibrium relationships have permitted tentative assignment of TaqI fragments to either the DRβ1 or DRβ2 genes and are highly suggestive that the DQw1 specificity is encoded by the DQα chain gene. This study shows the value of population comparisons in contributing to knowledge of the genetic organization of the genome.