Annals of Human Genetics (1999), 63:167-179. Cambridge University Press.
http://www.journals.cup.org/owa_dba/owa/issues?sjid=HGE&svid=63&siid=2
Assessing linkage disequilibrium in a complex genetic system. I. Overall
deviation from random association

H. ZHAO a1, A. J. PAKSTIS a2, J. R. KIDD a2 and K. K. KIDD a2
a1Department of Epidemiology and Public Health, Yale University School of
Medicine, New Haven CT 06520, U.S.A.
a2Department of Genetics, Yale University School of Medicine, New Haven, CT
06520, U.S.A.

Abstract

Linkage disequilibrium is an important tool both at the end stages of
positional cloning studies to map genes of particular interest and in
reconstruction of population histories. With advances in molecular biology,
complex genetic systems involving multiple highly polymorphic markers are
becoming more commonly used to study linkage disequilibrium. These systems
contain much more genetic information than simple two marker systems. In this
article, we introduce a measure to summarize the overall deviation from random
association and propose a permutation-based estimate for this measure. The
performance of the proposed estimation procedure is studied through
simulations. The methods proposed in this paper are then applied to population
data at the dopamine D2 receptor locus (DRD2) and at the homeobox B (HOXB) gene
cluster.