Linkage Disequilibrium between Chromosomes in the Human Genome : Test Statistics and Rapid Computation

Linkage disequilibrium (LD) refers to the statistical dependency of the DNA content at nearby locations of the chromosome. Numerous approaches to analyze genome data rely on the well documented fact that LD decays monotonously with the distance of the studied loci. This decay, though noisy and modi ed by a number of factors, can be attributed to the recombination process, a major source of genetic variation in diploid organisms. In this work we take first steps toward analyzing the extent of LD between very distant loci, even loci from different chromosomes. This is in contrast to traditional "genome-wide" analyses which merely study the LD within each chromosome separately. We design several measures of LD, and use them for analyzing the HapMap data. We also consider LD between supermarkers determined by haplotype clusters in windows of a few SNPs. We report on suggestive pairs of loci where unusually large correlations are observed within all ethnic groups. We describe how the computations can be arranged in a way that enables an all-pairs analysis of the data, that is, all pairs of loci across all the 22 autosomal chromosomes. This kind of "genome times genome" analysis is computationally very burdensome due to the sheer number of possible pairs. We show ways to make it feasible