Testing for linkage disequilibrium using SAS/GENETICS and SAS/STAT

Testing for the presence of linkage disequilibrium (LD) and measuring its value is important in statistical genetics. LD deals with the correlation of genetic variation at two or more loci in the genome within a given population. PROC ALLELE in SAS/GENETICS provides a variety of pair-wise LD measures that are related to the well-known Pearson correlation r. Different statistical tests of linkage disequilibrium are performed using PROC ALLELE. PROC HAPLOTYPE offers LD test statistics for multiple loci. In this paper, we clarify differences between LD measures obtained using PROC ALLELE and show how the HAPLO=OPTION of this procedure interacts with the linkage disequilibrium calculations and tests. Moreover, we compare PROC CORR and PROC ALLELE in terms of correlation coefficients of genotypic data.