Markov Chain Monte Carlo Linkage Analysis: Effect of Bin Width on the Probability of Linkage

We analyzed part of the Genetic Analysis Workshop (GAW) 12 simulated data using Monte Carlo Markov chain (MCMC) methods that are implemented in the computer program Loki. The MCMC method reports the “probability of linkage” (PL) across the chromosomal regions of interest. The point of maximum PL can...

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Bibliographic Details
Published in:Genetic epidemiology 2001, Vol.21 (S1), p.S700-S705
Main Authors: Slager, S.L., Juo, S.H., Durner, M., Hodge, S.E.
Format: Article
Language:English
Subjects:
Chromosome Mapping - statistics & numerical data
Chromosomes, Human, Pair 1
Humans
Lod Score
Loki
Markov Chains
Mathematical Computing
MCMC
Models, Genetic
Monte Carlo Method
Probability
quantitative trait
Quantitative Trait, Heritable
Software
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Summary:We analyzed part of the Genetic Analysis Workshop (GAW) 12 simulated data using Monte Carlo Markov chain (MCMC) methods that are implemented in the computer program Loki. The MCMC method reports the “probability of linkage” (PL) across the chromosomal regions of interest. The point of maximum PL can then be taken as a “location estimate” for the location of the quantitative trait locus (QTL). However, Loki does not provide a formal statistical test of linkage. In this paper, we explore how the bin width used in the calculations affects the max PL and the location estimate. We analyzed age at onset (AO) and quantitative trait number 5, Q5, from 26 replicates of the general simulated data in one region where we knew a major gene, MG5, is located. For each trait, we found the max PL and the corresponding location estimate, using four different bin widths. We found that bin width, as expected, does affect the max PL and the location estimate, and we recommend that users of Loki explore how their results vary with different bin widths. © 2001 Wiley‐Liss, Inc.
ISSN:0741-0395
1098-2272
DOI:10.1002/gepi.2001.21.s1.s700