A method for adjusting allele frequencies in the case of microsatellite allele drop-out

A new method is proposed to adjust allele frequencies when allelic drop-out is common. This method assumes Hardy-Weinberg equilibrium (HWE), and treats the problematic alleles as a one-locus two-allele system with dominance. By assuming that the homozygote frequency of the 'recessive' allele is measured correctly, we can back calculate the allele frequency of the 'dominant' allele, and adjust the heterozygote frequency accordingly. The drawback is that multilocus genotypes cannot be constructed and tests that use deviations from Hardy-Weinberg such as tests for bottlenecks become impossible. An example is given where a large homozygote excess (F-IS = 0.44) is adjusted to a reasonable level (F-IS = 0.046). The effect of scoring error was set in relation to sampling error and while F-IS values can be seriously biased, F-ST values are not necessarily so, if scoring error and sample size are both low. As sample size increases, the effect of scoring error increases.