Comparison of novel and existing methods for detection of linkage disequilibrium using parent-child trios in the GAW12 genetic isolate simulated data

A novel method for joint detection of association caused by linkage disequi librium (LD) and estimation of both recombination fraction and linkage dise quilibrium parameters was compared to several existing implementations of t he transmission/disequilibrium test (TDT) and modifications of the TDT in t he simulated genetic isolate data from Genetic Analysis Workshop 12. The fi rst completely genotyped trio of affected child and parents was selected fr om each family in each replicate so that the TDT tests are valid tests of l inkage and association, rather than being only valid as tests for linkage. In general, power to detect LD using the genome-wide scan markers was inade quate in the individual replicate samples, but the power was better when an alyzing several SNP markers in candidate gene 1. ((C)) 2001 Wiley-Liss, Inc .