Genetics, Vol. 164, 1561-1566, August 2003, Copyright © 2003

Pedigree Data Analysis With Crossover Interference

Sharon Browninga
a Bioinformatics Research Center, North Carolina State University, Raleigh, North Carolina 27695-7566 and GlaxoSmithKline, Research Triangle Park, North Carolina 27709

Corresponding author: Sharon Browning, Five Moore Dr., MAI. A112B.1G, Research Triangle Park, NC 27709., sharon.r.browning{at}gsk.com (E-mail)

Communicating editor: S. TAVARÉ

We propose a new method for calculating probabilities for pedigree genetic data that incorporates crossover interference using the chi-square models. Applications include relationship inference, genetic map construction, and linkage analysis. The method is based on importance sampling of unobserved inheritance patterns conditional on the observed genotype data and takes advantage of fast algorithms for no-interference models while using reweighting to allow for interference. We show that the method is effective for arbitrarily many markers with small pedigrees.