Bayesian oligogenic analysis of quantitative and qualitative traits in general pedigrees
Article first published online: 12 OCT 2001
Copyright © 2001 Wiley-Liss, Inc.
Volume 21, Issue 3, pages 224–242, November 2001
How to Cite
Uimari, P. and Sillanpää, M. J. (2001), Bayesian oligogenic analysis of quantitative and qualitative traits in general pedigrees. Genet. Epidemiol., 21: 224–242. doi: 10.1002/gepi.1031
- Issue published online: 12 OCT 2001
- Article first published online: 12 OCT 2001
- Manuscript Accepted: 11 DEC 2000
- Manuscript Received: 24 APR 2000
- Academy of Finland. Grant Numbers: 40225, 42780
- posterior distribution;
- Markov chain Monte Carlo
A Bayesian method for multipoint oligogenic analysis of quantitative and qualitative traits is presented. This method can be applied to general pedigrees, which do not necessarily have to be “peelable” and can have large numbers of markers. The number of quantitative/qualitative trait loci (QTL), their map positions in the genome, and phenotypic effects (mode of inheritances) are all estimated simultaneously within the same framework. The summaries of the estimated parameters are based on the marginal posterior distributions that are obtained through Markov chain Monte Carlo (MCMC) methods. The method uses founder alleles together with segregation indicators in order to determine the genotypes of the trait loci of all individuals in the pedigree. To improve mixing properties of the sampler, we propose (1) joint sampling of map position and segregation indicators, (2) omitting data augmentation for untyped or uninformative markers (homozygous parent), and (3) updating several markers jointly within a single block. The performance of the method was tested with two replicate GAW10 data sets (considering two levels of available marker information). The results were concordant and similar to those presented earlier with other methods. These analyses clearly illustrate the utility and wide applicability of the method. Genet. Epidemiol. 21:224–242, 2001. © 2001 Wiley-Liss, Inc.