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Originally published as Genetics Published Articles Ahead of Print on June 18, 2005.
Genetics, Vol. 171, 791-801, October 2005, Copyright © 2005
doi:10.1534/genetics.105.042705
A Novel Markov Chain Monte Carlo Approach for Constructing Accurate Meiotic Maps
Andrew W. George1
Program in Public Health Genetics, University of Iowa, Iowa City, Iowa 52242
1 Address for correspondence: Program in Public Health Genetics, 2186 Westlawn Bldg., University of Iowa, Iowa City, IA 52242.
E-mail: andrew-george{at}uiowa.edu
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 article, a new Markov chain Monte Carlo (MCMC) approach that solves both these computational problems is presented. 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 those of CRI-MAP.
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