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Abstract
Patterns of linkage disequilibrium (LD) reveal the action of evolutionary processes
and provide crucial information for association mapping of disease genes. Although
recent studies have described the landscape of LD among single nucleotide polymorphisms
(SNPs) from across the human genome, associations involving other classes of molecular
variation remain poorly understood. In addition to recombination and population history,
mutation rate and process are expected to shape LD. To test this idea, we measured
associations between short-tandem-repeat polymorphisms (STRPs), which can mutate rapidly
and recurrently, and SNPs in 721 regions across the human genome. We directly compared
STRP-SNP LD with SNP-SNP LD from the same genomic regions in the human HapMap populations.
The intensity of STRP-SNP LD, measured by the average of D', was reduced, consistent
with the action of recurrent mutation. Nevertheless, a higher fraction of STRP-SNP
pairs than SNP-SNP pairs showed significant LD, on both short (up to 50 kb) and long
(cM) scales. These results reveal the substantial effects of mutational processes
on LD at STRPs and provide important measures of the potential of STRPs for association
mapping of disease genes.