Genome-wide Distribution of Linkage Disequilibrium in Taiwan Aborigines
Linkage disequilibrium (LD) is the non-random association of alleles among loci across a chromosome. LD can be useful for mapping disease genes can extend across large distances in certain populations. However, LD patterns vary enormously among human groups due to differential population genetic forces. Prior to designing LD association studies of disease it is important to first understand the distribution of background LD (noise) in the specific population under study. We assessed the LD distribution in a Taiwan Aborigine population (Atayal) using genotype data from a genome-wide scan for gout susceptibility loci and compared LD patterns with other Austronesian populations (Palau, Samoa).
For this study we analysed a genome-wide panel of STRs (n=368) genotyped for a sample of 52 unrelated Taiwan Aborigines. ‘Ldmax’ and GOLD programmes were used to calculate the multi-allelic version of the D’ statistic graph the disequilibrium patterns.
Our analysis of all markers showed that there was a higher than expected number of marker pairs that exhibited significant background LD, and that the proportion of markers in significant LD decreased with increasing genetic distance. In addition, the proportion of markers in significant LD tended to increase across Austronesian populations from Taiwan Aborigines to Palaun to Samoan.
Our data suggest significant background LD exists in this Taiwan Aborigine tribe. It will be important to consider this noise when calculating useful levels of LD for disease association studies in this population. Moreover, the genomic LD patterns compared across different Pacific populations are consistent with the demographic histories of these populations.