We have presented here an evaluation of the usefulness of estimated kinship coefficients to account for cryptic relatedness in a population-based association study. Such cryptic relatedness may occur even when there is no population structure and when pedigree information is available. For example, the pedigrees may not fully describe the actual relatedness among individuals, such as when individuals share a long common genetic background history, or in other situations such as the presence of non-paternity or unreported adoption. We showed that the use of whole-genome scan markers to estimate relationships and to determine an appropriate variance correction reduces the false positive rate that otherwise results from use of the data without such a correction.
