Recent literature has suggested that haplotype inference through close relatives, especially nuclear families can be an alternative strategy in determining linkage phase. However, the current methods for this just make use of the information from complete nuclear families. We present a maximum likelihood method via expectation maximization (EM) algorithm using incomplete nuclear family data, consisting of only one parent and one child of only fullsibs without parents. In simulations the improved power and reliability of haplotype reconstruction with our approach, compared to the standard EM algorithm initially developed for individuals and a Bayesian method implemented in the PHASE software, is demonstrated.
Proceedings of the World Congress on Genetics Applied to Livestock Production, Volume , , 24.19, 2006
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