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Copyright 2008 by the Genetics Society of America DOI: 10.1534/genetics.108.089912

Summary: Copyright 2008 by the Genetics Society of America
DOI: 10.1534/genetics.108.089912
Identity-by-Descent Estimation and Mapping of Qualitative Traits in
Large, Complex Pedigrees
Mark Abney1
Department of Human Genetics, University of Chicago, Chicago, Illinois 60637
Manuscript received April 4, 2008
Accepted for publication May 2, 2008
Computing identity-by-descent sharing between individuals connected through a large, complex
pedigree is a computationally demanding task that often cannot be done using exact methods. What I
present here is a rapid computational method for estimating, in large complex pedigrees, the probability
that pairs of alleles are IBD given the single-point genotype data at that marker for all individuals. The
method can be used on pedigrees of essentially arbitrary size and complexity without the need to divide
the individuals into separate subpedigrees. I apply the method to do qualitative trait linkage mapping
using the nonparametric sharing statistic Spairs. The validity of the method is demonstrated via simulation
studies on a 13-generation 3028-person pedigree with 700 genotyped individuals. An analysis of an asthma
data set of individuals in this pedigree finds four loci with P-values ,103
that were not detected in prior
analyses. The mapping method is fast and can complete analyses of $150 affected individuals within this


Source: Abney, Mark - Department of Human Genetics, University of Chicago


Collections: Computer Technologies and Information Sciences; Biology and Medicine