For
case-parents data, the information from offspring can be used to reduce the
uncertainty of parents’ haplotype. In this article we develop likelihood ratio
test to compare haplotype frequencies in transmitted and non-transmitted group.
The maximum likelihood estimate of the haplotype frequencies for the family
data is obtained via expectation-maximization (EM) algorithm. Our proposed
method can handle the uncertainty of haplotypes and missing data. The
simulations show that the method is more powerful to test association between haplotype and
traits than TRANSMIT. We also demonstrated the method to detect the association
between Megsin gene and immunoglobulin A nephropathy.
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