Allele frequency estimation from data on relatives

Given genetic marker data on unrelated individuals, maximum-likelihood allele-frequency estimates and their standard errors are easily calculated from sample proportions. When marker phenotypes are observed on relatives, this method cannot be used without either discarding a subset of the data or incorrectly assuming that all individuals are unrelated. Here, I describe a method for allele frequency estimation for data on relatives that is based on standard methods of pedigree analysis. This method makes use of all available marker information while correctly taking into account the dependence between relatives. I illustrate use of the method with family data for a VNTR polymorphism near the apolipoprotein B locus.