The Sensitivity and Rationality of Pairwise Linkage Disequilibrium Measures – a Practical Analysis

Linkage disequilibrium (LD) measures are primary elements involved in the kinds of definitions for haplotype block structure. According to the report on a high-resolution analysis of the haplotype structure by Daly at.al., we reformatted their data, which has a range of 500 kb on chromosome 5q31 using 103 single nucleotide polymorphisms (SNPs) in a European-derived population, calculated the pairwise LD and graphically displayed it. It can be clearly noticed that the haplotype blocks reported in the original work were approximately the same as the regions produced by LD measure r. Meanwhile, the measure D′ shows lower sensitivity compared with r. Under such scenario, we should reconsider the application of LD: these known LD measures may not be applicable to arbitrary data sets and researchers have to make particular modification to the definition of LD or choose the most suitable one from kinds of the measures.