DNA variation in a 5-Mb region of the X chromosome and estimates of sex-specific/type-specific mutation rates

We describe a new approach for the study of human genome variation, based o n our solid-phase fluorescence chemical mismatch-cleavage method. Multiplex screening rates greater than or equal to 80 kb/36-lane gels are achieved, and accuracy of mismatch location is within +/-2 bp. The density of differe nces between DNA from any two humans is sufficiently low and the estimate o f their position is accurate enough, to avoid sequencing of most polymorphi c sites when defining their allelic state. Furthermore, highly variable seq uences, such as microsatellites, are distinguished easily, so that separate consideration can be given to loci that do and do not fit the definition o f infinite mutation sites. We examined a 5-Mb region of Xq22 to define the haplotypes of 23 men (9 Europeans, 9 Ashkenazim, and 5 Pygmies) by referenc e to DNA from one Italian man. Fifty-eight 1.5-kb segments revealed 102 seg regating sites. Seven of these-are shared by all three groups, two by Pygmi es and Europeans, two by Pygmies and Ashkenazim, and 19 by Ashkenazim and E uropeans. Europeans are the least polymorphic, and Pygmies are the most pol ymorphic. Conserved allelic associations were recognizable within 40-kb DNA segments, and so was recombination in the longer intervals separating such segments; The men showed only three segregating sites in a 16.5-kb unique region of the Y chromosome. Divergence between X- and Y-chromosome sequence s of humans and chimpanzees indicated higher male mutation rates for differ ent types of mutations. These rates for the X chromosomes were very similar to those estimated for the X-linked factor IX gene in the U.K. population.