Novel detection of restriction fragment length polymorphisms in the human major histocompatibility complex

Cosmid genomic DNA clones have been used as hybridization probes in genomic Southern blot analysis to define restriction fragment length polymorphisms (RFLPs) in the major histocompatibility complex (MHC). Using 14 different enzymes and three overlapping cosmid clones we have detected six RFLPs in a 100 kilobase (kb) segment of DNA in the class III region extending centromeric of the TNFA gene toward HLA-DR. Four of the five RFLPs, defined using the enzymes Taq I, Rsa I, Hinc II, and Hind III, and detected by the cosmid clone cosM7B, map to a 29 kb segment of DNA that includes all of the recently described G2 (BAT2) gene and a large portion of the 3' end of the G3 (BAT3) gene. The different RFLP variants were established by analyzing the DNA from three informative families and a panel of 51 HLA-homozygous typing cell lines. CosM7B detects Taq I variants of 4.3 kb, and 2.9 kb or 2.8 kb, Rsa I variants of 2.9 kb or 2.4 kb, Hinc II variants of 5.8 kb or 3.8 kb and 1.4 kb, and a Hind III variant of 4.8 kb, while cosOT2 detects Taq I variants of 4.5 kb or 4 kb. The distribution of the Rsa I, Hinc II and Taq I RFLPs detected by cosM7B, and the Taq I RFLP detected with cosOT2, within the panel of cell line DNAs was assessed by Southern blotting. The 4.3 kb Taq I variant was observed in only one cell line with the extended haplotype HLA-A29, C-, B44, SC30, DR4. The other RFLPs, however, occurred much more frequently. The 2.8 kb Taq I variant was observed in 20% of haplotypes, the 2.9 kb Rsa I variant was observed in 42% of haplotypes, and the 5.8 kb Hinc II variant was observed in 12% of haplotypes analyzed. The 4.5 kb Taq I variant detected by the overlapping cosmid cosOT2 was present in 21% of haplotypes. Analysis of the RFLP variants with each other revealed seven different haplotypic combinations. Three of the haplotypic combinations were each subdivided into two subsets on the basis of the Nco I RFLP variant they carried at the TNF-B locus. These haplotypic combinations potentially allow differentiation among different extended haplotypes such as HLA-B8, SC01, DR3, HLA-B18, F1C30, DR3, and HLA-B44, FC31, DR7. The RFLPs detected by the cosmid clones thus provide new tools which will be useful in the further genetic analysis of the MHC class III region.