An exploration of sex-specific linkage disequilibrium on chromosome X in Caucasians from the COGA study

Miranda E Cox,Joel K Campbell,Carl D Langefeld

doi:10.1186/1471-2156-6-s1-s81

Miranda E Cox, Joel K Campbell + Show 1 more

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https://doi.org/10.1186/1471-2156-6-s1-s81

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Journal: BMC genetics	Publication Date: Dec 1, 2005
Citations: 7	License type: cc-by

Affiliation: Wake Forest University

Abstract

This paper explores the decay of linkage disequilibrium (LD) on the autosomes and chromosome X. The extent of marker-marker LD is important for both linkage and association studies. The analysis of the Caucasian sample from the Collaborative Study on the Genetics of Alcoholism study revealed the expected negative relationship between the magnitude of the marker-marker LD and distance (cM), with the male and female subgroups exhibiting similar patterns of LD. The observed extent of LD in females was less across the pseudoautosomal markers relative to the heterosomal region of chromosome X. Marked differences in LD patterns were also observed between chromosomes X and the 22 autosomes in both males and females.

Highlights

In the human genome, alleles at two loci on the same chromosome often show stochastic dependence
Dense genetic linkage maps have revealed a high rate of recombination in pseudoautosomal region 1 (PAR1) [1], prompting comparisons between linkage disequilibrium (LD) patterns in PAR1 and the heterosomal region on chromosome X
Data used for our analyses were obtained from the Collaborative Study on the Genetics of Alcoholism (COGA)

Summary

Introduction

Alleles at two loci on the same chromosome often show stochastic dependence This nonrandom pair-wise allelic association, or linkage disequilibrium (LD), is both interesting evolutionarily in its own right and a powerful tool in the mapping of genes for complex genetic traits. The two pseudoautosomal regions on chromosomes X and Y (PAR1 and PAR2) are approximately 2.6 and 0.4 Mb respectively, and are located at the tips of the sex chromosomes. Within these regions pairing and recombination may occur between X and Y as it naturally does in the autosomes or between two X chromosomes in females. The purpose of this paper is to explore the rate of decay in LD as a function of distance between males and females both across and within autosomal and sex chromosomes

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