Test for Imprinting Effects on the X-Chromosome

Abstract

Genomic imprinting is an epigenetic phenomenon that the expression of an allele copy depends on its parental origin. This mechanism has been found to play an important role in many diseases. Methods for detecting imprinting effects have been developed primarily for autosomal markers. However, no method is available in the literature to test for imprinting effects on the X chromosome. Therefore, it is necessary to suggest methods for detecting such imprinting effects. In this talk, the parental-asymmetry test on X the chromosome (XPAT) is first developed to test for imprinting for qualitative traits in the presence of association, based on family trios each with both parents and their affected daughter. Then, we propose 1-XPAT to tackle parent-daughter pairs, each with one parent and his/her affected daughter. By simultaneously considering family trios and parent-daughter pairs, CXPAT is constructed to test for imprinting. Further, we extend the proposed methods to accommodate complete (with both parents) and incomplete (with one parent) nuclear families having multiple daughters of which at least one is affected. Simulations are conducted to assess the performance of the proposed methods under different settings. Simulation results demonstrate that the proposed methods control the size well, irrespective of the inbreeding coefficient in females being zero or nonzero. By incorporating incomplete nuclear families, C-XPAT is more powerful than XPAT using only complete nuclear families. For practical use, these proposed methods are applied to analyze the rheumatoid arthritis data.