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Genomic imprinting and maternal effects are two epigenetic factors that havebeen increasingly explored for their roles in the etiology of complex diseases.This is part of a concerted effort to find the "missing heritability."Accordingly, statistical methods have been proposed to detect imprinting andmaternal effects simultaneously based on either a case-parent triads design ora case-mother/control-mother pairs design. However, existing methods arefull-likelihood based and have to make strong assumptions concerning matingtype probabilities (nuisance parameters) to avoid overparametrization. In thispaper we propose to augment the two popular study designs by combining them andincluding control-parent triads, so that our sample may contain a mixture ofcase-parent/control-parent triads and case-mother/control-mother pairs. Bymatching the case families with control families of the same structure andstratifying according to the familial genotypes, we are able to derive apartial likelihood that is free of the nuisance parameters. This rendersunnecessary any unrealistic assumptions and leads to a robust procedure withoutsacrificing power. Our simulation study demonstrates that our partiallikelihood method has correct type I error rate, little bias and reasonablepower under a variety of settings.

Robust partial likelihood approach for detecting imprinting and maternal effects using case-control families