Linkage Disequilibrium and Association Analysis

This chapter considers allelic association to be association occurring between alleles at different loci. Allelic association can occur between linked or unlinked loci. There are many different measures of linkage disequilibrium. Studies examining association between single-nucleotide polymorphisms (SNPs) have demonstrated that linkage disequilibrium may be organized in distinct regions of strong linkage disequilibrium, with little association occurring between SNPs in different regions. Association tests with quantitative traits use continuous measures, such as weight or height, and test the correlation between genotypes and the trait values in the sample. Case–control studies can provide estimates of important measures of association and impact. Family-based studies ensure that cases and controls are appropriately matched by using family-based controls. Testing for association between genetic markers and a quantitative trait can be used in fine-mapping the quantitative trait loci in the same way that we use association tests to look for genes for dichotomous traits.