MCMC-based linkage analysis for complex traits on general pedigrees: multipoint analysis with a two-locus model and a polygenic component
Article first published online: 22 NOV 2006
© 2006 Wiley-Liss, Inc.
Volume 31, Issue 2, pages 103–114, February 2007
How to Cite
Sung, Y. J., Thompson, E. A. and Wijsman, E. M. (2007), MCMC-based linkage analysis for complex traits on general pedigrees: multipoint analysis with a two-locus model and a polygenic component. Genet. Epidemiol., 31: 103–114. doi: 10.1002/gepi.20194
- Issue published online: 10 JAN 2007
- Article first published online: 22 NOV 2006
- Manuscript Accepted: 4 OCT 2006
- Manuscript Received: 23 JUN 2006
- NIH. Grant Numbers: GM46255, HD35465
- Markov chain Monte Carlo;
- quantitative trait locus;
- large pedigree;
- lod score;
We describe a new program lm_twoqtl, part of the MORGAN package, for parametric linkage analysis with a quantitative trait locus (QTL) model having one or two QTLs and a polygenic component, which models additional familial correlation from other unlinked QTLs. The program has no restriction on number of markers or complexity of pedigrees, facilitating use of more complex models with general pedigrees. This is the first available program that can handle a model with both two QTLs and a polygenic component. Competing programs use only simpler models: one QTL, one QTL plus a polygenic component, or variance components (VC). Use of simple models when they are incorrect, as for complex traits that are influenced by multiple genes, can bias estimates of QTL location or reduce power to detect linkage. We compute the likelihood with Markov Chain Monte Carlo (MCMC) realization of segregation indicators at the hypothesized QTL locations conditional on marker data, summation over phased multilocus genotypes of founders, and peeling of the polygenic component. Simulated examples, with various sized pedigrees, show that two-QTL analysis correctly identifies the location of both QTLs, even when they are closely linked, whereas other analyses, including the VC approach, fail to identify the location of QTLs with modest contribution. Our examples illustrate the advantage of parametric linkage analysis with two QTLs, which provides higher power for linkage detection and better localization than use of simpler models. Genet. Epidemiol. © 2006 Wiley-Liss, Inc.