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Adaptation of the extended transmission/disequilibrium test to distinguish disease associations of multiple loci: the Conditional Extended Transmission/Disequilibrium Test

Published online by Cambridge University Press:  23 October 2000

B. P. C. KOELEMAN
Affiliation:
Wellcome Trust Centre for Molecular Mechanisms in Disease, University of Cambridge, UK Current address: Department of Immunohematology and Bloodbank, Leiden University Medical Center, PO Box 9600 Leiden, The Netherlands
F. DUDBRIDGE
Affiliation:
Wellcome Trust Centre for Molecular Mechanisms in Disease, University of Cambridge, UK
H. J. CORDELL
Affiliation:
Wellcome Trust Centre for Molecular Mechanisms in Disease, University of Cambridge, UK
J. A. TODD
Affiliation:
Wellcome Trust Centre for Molecular Mechanisms in Disease, University of Cambridge, UK
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Abstract

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.

Type
Research Article
Copyright
© University College London 2000

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