Abstract
This paper provides a brief overview of software currently available for the genetic analysis of quantitative traits in humans. Programs that implement variance components, Markov Chain Monte Carlo (MCMC), Haseman-Elston (H-E) and penetrance model-based linkage analyses are discussed, as are programs for measured genotype association analyses and quantitative trait transmission disequilibrium tests. The software compared includes LINKAGE, FASTLINK, PAP, SOLAR, SEGPATH, ACT, Mx, MERLIN, GENEHUNTER, Loki, Mendel, SAGE, QTDT and FBAT. Where possible, the paper provides URLs for acquiring these programs through the internet, details of the platforms for which the software is available and the types of analyses performed.
Highlights
Localisation and characterisation of quantitative trait loci (QTLs) and causal polymorphisms influencing complex phenotypes are of major importance in statistical genetic analyses
Variance components approaches model the covariance among family members as a function of unspecified aggregate additive genetic effects, effects due to a hypothetical gene in the region being tested for linkage, and a residual component that is uncorrelated among individuals and is sometimes described as an environmental component.[1,38,40]
The H –E model has been extended to model the full variance –covariance matrix within a family.[48]. This latest version of the H –E is very similar to a variance component approach, the primary difference being that the various components are generally estimated by regression rather than maximum likelihood
Summary
Localisation and characterisation of quantitative trait loci (QTLs) and causal polymorphisms influencing complex phenotypes are of major importance in statistical genetic analyses. The most commonly used methods for quantitative trait linkage analysis in humans are the variance components and H – E approaches.
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