Estimating and testing linkage disequilibrium from sib data

We consider estimation and testing of linkage equilibrium from genotypic data on a random sample of sibs, such as monozygotic and dizygotic twins. We compute the maximum likelihood estimator with an EM‐algorithm and a likelihood ratio statistic that takes the family structure into account. As we are interested in applying this to twin data we also allow observations on single children, so that monozygotic twins can be included. We allow non‐zero recombination fraction between the loci of interest, so that linkage disequilibrium between both linked and unlinked loci can be tested. The EM‐algorithm for computing the maximum likelihood estimator of the haplotype frequencies and the likelihood ratio test‐statistic, are described in detail. It is shown that the usual estimators of haplotype frequencies based on ignoring that the sibs are related are inefficient, and the likelihood ratio test for testing that the loci are in linkage disequilibrium.