PLoS Genetics (early online)
Positive Selection of a Pre-expansion CAG Repeat of the Human SCA2 Gene
Fuli Yu et al.
A region of approximately one megabase of human Chromosome 12 shows extensive linkage disequilibrium (LD) in Americans with ancestry from northern and western Europe. This strikingly large LD block was analyzed with statistical and experimental methods to determine whether natural selection could be implicated in shaping the current genome structure. Extended Haplotype Homozygosity and Relative Extended Haplotype Homozygosity (EHH/REHH) analyses on this region mapped a core region of the strongest conserved haplotype to the exon 1 of the Spinocerebellar ataxia type 2 gene (SCA2, locusID: 6311). Direct DNA sequencing of this region of the SCA2 gene revealed a significant association between a pre-expanded allele ((CAG)8CAA(CAG)4CAA(CAG)8) of CAG repeats within exon 1 and the selected haplotype of the SCA2 gene. A significantly negative Tajima's D value (-2.20, P < 0.01) on this site consistently suggested selection on the CAG repeat. This region was also interrogated in the three other populations, none of which showed signs of selection. These results suggest that a recent positive selection of the pre-expansion SCA2 CAG repeat has occurred in Europeans.