Haplotype and interspersion analysis of the FMR1 CGG repeat identifies two different mutational pathways for the origin of the fragile X syndrome

To understand the origins of the fragile X syndrome and factorspredisposing alleles to instability and hyperexpansion, we have comparedthe haplotype (using markers FRAXAC1, FRAXAC2, and DXS548) and AGGinterspersion patterns of the FMR1 CGG repeat for 214 normal and 16premutation chromosomes. Association testing between interspersion patternand haplotype reveals a highly significant (P < 0.002) non- randomdistribution, indicating that all three markers are useful in phylogeneticreconstruction of mutational change. Parsimony analysis of the FMR1 CGGrepeat substructure predicts that loss of AGG interruptions has occurredindependently on many haplotypes associated with the fragile X syndrome,partially explaining the haplotype diversity of this disease. Amonghaplotypes found in linkage disequilibrium with the fragile X mutation, twodifferent modes of mutation and predisposition to instability have beenidentified. One pathway has involved the frequent and recurrent loss of AGGinterruptions from rare asymmetrical ancestral array structures.Intergenerational transmission studies suggest that these predisposedchromosomes progress relatively rapidly to the disease state. In contrast,the second mutational pathway involves a single haplotype which hasmaintained two AGG interruptions. Parsimony analysis of CGG repeatsubstructure within this haplotype suggests that larger alleles have beengenerated by gradual increments of CGG repeats distal to the most 3'interruption. Pedigree analysis of the intergenerational stability ofalleles of this haplotype confirms a gradual progression toward instabilitythresholds. As a result, a large reservoir of chromosomes carrying largerepeats on this haplotype exists. These chromosomes are predisposed todisease. The present data support a model in which there are at least twodifferent mutational pathways predisposing alleles to instability andhyperexpansion associated with the fragile X syndrome.