Reconstituting the frequency spectrum of ascertained single-nucleotide polymorphism data

Most of the available SNP data have eluded valid population generic analysis because most population genetical methods do not correctly accommodate the special discovery process used to identify SNPS. Most of the available SNP data have allele frequency distributions dial are biased by die ascertainment protocol. We here show how this problem can be corrected by obtaining maximum-likelihood estimates of the true allele frequency distribution. In simple cases, the NIL estimate of the true allele frequency distribution can be obtained analytically, but in other cases computational methods based on numerical optimization or the EM algorithm must be used. We illustrate the new correction method by analyzing some previously published SNP data from the SNP Consortium. Appropriate treatment of SNP ascertainment is vital to our ability to make correct inferences from the data of die International HapMap Project.