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An algorithm for sampling descent graphs in large complex pedigrees efficiently

Published online by Cambridge University Press:  25 June 2003

JOHN M. HENSHALL  and
BRUCE TIER
JOHN M. HENSHALL
Affiliation:
CSIRO Livestock Industries, J. M. Rendel Laboratory, Rockhampton, QLD, Australia
BRUCE TIER
Affiliation:
Animal Genetics and Breeding Unit
AGBU is a joint institute of NSW Agriculture and The University of New England.
, University of New England, Australia

Abstract

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No exact method for determining genotypic and identity-by-descent probabilities is available for large complex pedigrees. Approximate methods for such pedigrees cannot be guaranteed to be unbiased. A new method is proposed that uses the Metropolis–Hastings algorithm to sample a Markov chain of descent graphs which fit the pedigree and known genotypes. Unknown genotypes are determined from each descent graph. Genotypic probabilities are estimated as their means. The algorithm is shown to be unbiased for small complex pedigrees and feasible and consistent for moderately large complex pedigrees.

Type
Research Article
Information
Genetics Research , Volume 81 , Issue 3 , June 2003 , pp. 205 - 212
Copyright
© 2003 Cambridge University Press