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doi:10.1534/genetics.105.042705
A more recent version of this article appeared on October 1, 2005.
REGULAR RESEARCH PAPERS |
A novel MCMC approach for constructing accurate meiotic maps
Andrew W George 1*
1 The University of Iowa
* To whom correspondence should be addressed. E-mail: andrew-george{at}uiowa.edu.
Submitted on February 28, 2005
Revised on May 18, 2005
Accepted on 18 May 2005
Mapping markers from linkage data continues to be a task performed in many genetic epidemiological studies. Data collected in a study may be used to refine published map estimates and a study may use markers that do not appear in any published map. Furthermore, inaccuracies in meiotic maps can seriously bias linkage findings. To make best use of the available marker information, multilocus linkage analyses are performed. However, two computational issues greatly limit the number of markers currently mapped jointly; the number of candidate marker orders increases exponentially with marker number and computing exact multilocus likelihoods on general pedigrees is computationally demanding. In this paper, a new Markov chain Monte Carlo (MCMC) approach is presented that solves both these computational problems. The MCMC approach allows many markers to be mapped jointly using data observed on general pedigrees with unobserved individuals. The performance of the new mapping procedure is demonstrated through the analysis of simulated and real data. The MCMC procedure performs extremely well, even when there are millions of candidate orders, and gives results superior to CRI-MAP.
Key Words: Bayesian linkage analysis, General pedigrees, Genetic maps, Markov chain Monte Carlo
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