Closely linked cis-acting modifier of expansion of the CGG repeat in high risk FMR1 haplotypes

Abstract

In its expanded form, the fragile X triplet repeat at Xq27.3 gives rise to the most common form of inherited mental retardation, fragile X syndrome. This high population frequency persists despite strong selective pressure against mutation-bearing chromosomes. Males carrying the full mutation rarely reproduce and females heterozygous for the premutation allele are at risk of premature ovarian failure. Our diagnostic facility and previous research have provided a large databank of X chromosomes that have been tested for the FRAXA allele. Using this resource, we have conducted a detailed genetic association study of the FRAXA region to determine any cis-acting factors that predispose to expansion of the CGG triplet repeat. We have genotyped SNP variants across a 650-kb tract centered on FRAXA in a sample of 877 expanded and normal X chromosomes. These chromosomes were selected to be representative of the haplotypic diversity encountered in our population. We found expansion status to be strongly associated with a approximately 50-kb region proximal to the fragile site. Subsequent detailed analyses of this region revealed no specific genetic determinants for the whole population. However, stratification of chromosomes by risk subgroups enabled us to identify a common SNP variant which cosegregates with the subset of D group haplotypes at highest risk of expansion (chi(1)(2)=17.84, p=0.00002). We have verified that this SNP acts as a marker of repeat expansion in three independent samples.

FIGURE 1

FIGURE 1. Results of the preliminary association mapping analysis and an LD map of the region created using data from all 877 individuals.The LDpattern is particularly flat in the region adjacent toFRAXA (200–400 kb), indicating very high levels of LD. Aplot of the LODscore for association shows the highest evidence for association at ∼350 kb.

FIGURE 2

FIGURE 2. Unrooted phylogenetic tree representing the CCGA core haplogroup.The alleles for each of the four SNPs used to identify core groups are highlighted in blue (rs10521868, rs1805420, ATL1, FMRB).The six SNPs used in the subsequent stage of analysis are highlighted in red (rs17312728, rs1868140, and ss71651738 on the left–hand side; and rs6626286, rs12010481, and rs5904668 on the right–hand side).The black type that follows the SNP haplotype shows the DXS548–FRAXAC1–FRAXAC2 microsatellite haplotype followed by the corresponding microsatellite haplogroup and the number of observed instances of each haplotype (these data in black are for annotation purposes only and were not used in the phylogenetic analysis).The normal to expanded ratio of FRAXA chromosomes is shown for each branch.The branch onwhich the only observed primate haplotype co–occurs is identified by a green arrow. ^*Denotesmissing data.