Effect of misspecification of gene frequency on the two-point LOD score

22Citations
Citations of this article
7Readers
Mendeley users who have this article in their library.

This article is free to access.

Abstract

In this study, we used computer simulation of simple and complex models to ask: (1) What is the penalty in evidence for linkage when the assumed gene frequency is far from the true gene frequency? (2) If the assumed model for gene frequency and inheritance are misspecified in the analysis, can this lead to a higher maximum LOD score than that obtained under the true parameters? Linkage data simulated under simple dominant, recessive, dominant and recessive with reduced penetrance, and additive models, were analysed assuming a single locus with both the correct and incorrect dominance model and assuming a range of different gene frequencies. We found that misspecifying the analysis gene frequency led to little penalty in maximum LOD score in all models examined, especially if the assumed gene frequency was lower than the generating one. Analysing linkage data assuming a gene frequency of the order of 0.01 for a dominant gene, and 0.1 for a recessive gene, appears to be a reasonable tactic in the majority of realistic situations because underestimating the gene frequency, even when the true gene frequency is high, leads to little penalty in the LOD score.

Cite

CITATION STYLE

APA

Pal, D. K., Durner, M., & Greenberg, D. A. (2001). Effect of misspecification of gene frequency on the two-point LOD score. European Journal of Human Genetics, 9(11), 855–859. https://doi.org/10.1038/sj.ejhg.5200724

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free