Incorporating genotypes of relatives into a test of linkage disequilibrium

American Journal of Human Genetics
L Excoffier, M Slatkin

Abstract

Genetic data from autosomal loci in diploids generally consist of genotype data for which no phase information is available, making it difficult to implement a test of linkage disequilibrium. In this paper, we describe a test of linkage disequilibrium based on an empirical null distribution of the likelihood of a sample. Information on the genotypes of related individuals is explicitly used to help reconstruct the gametic phase of the independent individuals. Simulation studies show that the present approach improves on estimates of linkage disequilibrium gathered from samples of completely independent individuals but only if some offspring are sampled together with their parents. The failure to incorporate some parents sharply decreases the sensitivity and accuracy of the test. Simulations also show that for multiallelic data (more than two alleles) our testing procedure is not as powerful as an exact test based on known haplotype frequencies, owing to the interaction between departure from Hardy-Weinberg equilibrium and linkage disequilibrium.

References

Dec 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·R Chakraborty, K M Weiss

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Citations

Jan 9, 2009·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Myounghai Kwak, Paul Gepts
Jan 16, 1999·Current Opinion in Biotechnology·J D Terwilliger, K M Weiss
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Dec 4, 2004·Genetic Epidemiology·Sharon R BrowningMichael J Wagner

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