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Abstract:
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With the advent of genome-wide SNPs, the use of HWD for gene mapping warrants further study. Its utility is related to homozygosity mapping. Deviations from HWE, resulting in reduced heterozygosity, may also result in increased IBD in individuals with a recessive disease and whose alleles are copies of an ancestral one. However, simply examining homozygosity is not sufficient because it may simply be due to a high MAF or allozygosity (not autozygosity). Sophisticated methods have been developed to differentiate between these two types of homozygosity, however, the standard approach is to count the number of contiguous SNPs for which cases are all homozygous. We propose scanning the genome for autozygosity, not just homozygosity, to evaluate differences in autozygosity and allele frequencies between cases and controls. Simulation studies and analyses of real data are given.
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