title: The transmission disequilibrium test and imprinting effects test based on case-parent pairs.
abstract: The transmission disequilibrium test (TDT) based on case-parents trios is a powerful tool in linkage analysis and association studies. When only one parent is available, the 1-TDT is applicable in the absence of imprinting. In the presence of imprinting, a statistic is proposed, based on case-mother pairs and case-father pairs to test for linkage when association is present as well as to test for association when linkage is present. The recombination fractions are allowed to be sex-specific in this test statistic. Meanwhile, a statistic based on case-parent pairs is proposed to test for imprinting. Both test statistics can be extended to include families with more than one affected offspring. A number of simulation studies are conducted to investigate the validity of the proposed tests. The effects of different ratios of the numbers of case-mother pairs and case-father pairs on the powers of the proposed tests are studied through simulation. The results show that the optimal ratio is 1:1. How to combine case-parents, case-mother pairs, and case-father pairs jointly in testing for linkage, association, and imprinting is addressed.
authors.affiliation: Department of Statistics and Actuarial Science, The University of Hong Kong, Pokfulam Road, Hong Kong, China.
authors.forename: Yue-Qing
authors.initials: YQ
authors.lastname: Hu
authors.forename: Ji-Yuan
authors.initials: JY
authors.lastname: Zhou
authors.forename: Fengzhu
authors.initials: F
authors.lastname: Sun
authors.forename: Wing K
authors.initials: WK
authors.lastname: Fung
mesh_terms: D003198:Computer Simulation; D005220:Fathers; D005260:Female; D005821:Genetic Techniques; D018392:Genomic Imprinting; D006801:Humans; D015810:Linkage Disequilibrium; D008297:Male; D008957:Models, Genetic; D009035:Mothers; D010290:Parents