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Linkage and association studies in complex diseases are used to identify and fine map disease loci. The process of identifying the aetiological polymorphism, the molecular variant responsible for the linkage and association of the chromosome region with disease, is complicated by the low penetrance of the disease variant, the linkage disequilibrium between physically-linked polymorphic markers flanking the disease variant, and the possibility that more than one polymorphism in the most associated region is aetiological. It is important to be able to detect additional disease determinants in a region containing a cluster of genes, such as the major histocompatibility complex (MHC) region on chromosome 6p21. Some methods have been developed for detection of additional variants, such as the Haplotype Method, Marker Association Segregation Chi-squares (MASC) Method, and the Homozygous Parent Test. Here, the Extended Transmission/Disequilibrium Test is adapted to test for association conditional on a previously associated locus. This test is referred to as the Conditional Extended TDT (CETDT). We discuss the advantages of the CETDT compared to existing methods and, using simulated data, investigate the effect of polymorphism, inheritance, and linkage disequilibrium on the CETDT.

Original publication

DOI

10.1017/S0003480000008095

Type

Journal article

Journal

Ann Hum Genet

Publication Date

05/2000

Volume

64

Pages

207 - 213

Keywords

Genetic Diseases, Inborn, Genetic Markers, Genetic Predisposition to Disease, Genetic Testing, Genotype, Homozygote, Humans, Likelihood Functions, Linkage Disequilibrium, Models, Genetic, Quantitative Trait, Heritable