Abstract
We performed multipoint linkage analysis of the electrophysiological trait ECB21 on chromosome 4 in the full pedigrees provided by the Collaborative Study on the Genetics of Alcoholism (COGA). Three Markov chain Monte Carlo (MCMC)-based approaches were applied to the provided and re-estimated genetic maps and to five different marker panels consisting of microsatellite (STRP) and/or SNP markers at various densities. We found evidence of linkage near the GABRB1 STRP using all methods, maps, and marker panels. Difficulties encountered with SNP panels included convergence problems and demanding computations.
Highlights
Our aims were to investigate 1) the utility of single-nucleotide polymorphisms (SNPs) versus microsatellites (STRPs), and 2) the impact of map assumptions on linkage analysis
We chose to focus our analyses on the Collaborative Study on the Genetics of Alcoholism (COGA) ECB21 trait and chromosome 4 because previous studies [1,2] had reported significant evidence for linkage of the electroencephalogram (EEG) beta wave to chromosome 4
The sex-averaged distance between STRPs 1–17 on chromosome 4 was slightly longer on the re-estimated map
Summary
Our aims were to investigate 1) the utility of single-nucleotide polymorphisms (SNPs) versus microsatellites (STRPs), and 2) the impact of map assumptions on linkage analysis. We chose to focus our analyses on the COGA ECB21 trait and chromosome 4 because previous studies [1,2] had reported significant evidence for linkage of the electroencephalogram (EEG) beta wave to chromosome 4. Multipoint linkage analysis of the full pedigree structures was performed by using MCMC techniques to implement allele-sharing, parametric LOD score, and Bayesian analysis approaches
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