Gene order and gene distances in the HLA region studied by the haplotype method

The present report describes a method to establish gene order and gene distances in chromosomal regions where several genes are located closely together. The method is applied to the study of the complement loci in the HLA complex on chromosome 6 in man. The method is based on allelic association, i.e. alleles of closely linked loci are nonrandomly associated on haplotypes. A haplotype which yields information has a frequency higher than would be expected from the frequencies of each of its alleles. They occur, moreover, with a frequency which makes them the main source of the least frequent of the alleles in the combinations. Other haplotype combinations involving this allele (these alleles) are most likely the results of recombinational events involving a main haplotype. Such crossovers may therefore, on certain conditions, be used for gene mapping purposes. Some basic rules for the use of the method are given. A total of 701 haplotypes involving the short arm of chromosome 6 have been studied. Typings have been performed with regard to HLA-A, -B, -C, -D/-DR, C4, C2 and Bf. The study confirms previous localization of the complement loci between HLA-D and -B. The investigation suggests the order HLA-D-Bf-C4-C2-HLA-B. There is, moreover, slight evidence in favour of a localization of the C4A gene on the HLA-B side of C4B. Given an HLA-A-HLA-B distance of 0.8 cM, suggested relative distances are: HLA-D-Bf:0.44 cM, Bf-C4:0.04 cM, C4-C2:0.11 cM, and C2-HLA-B:0.12 cM.