Population survey of the human FMR1 CGG repeat substructure suggests biased polarity for the loss of AGG interruptions

Both sequence length and sequence content are important parameters in determining stability of the fragile x syndrome CGG repeat. In order to estimate the incidence of uninterrupted CGG repeats in the general population and to gain insight into the mechanisms responsible for the loss and acquisition of AGG interruptions, 406 randomly selected FMR1 CGG repeat alleles from four broad ethnic groups were assayed for AGG punctuation. Among the 79 different classes of alleles detected, long uninterrupted tracts of pure repeats were rare in the general population, with only 1/406 or 0.25% found at the instability threshold (34–37 pure CGG repeats). There was no significant difference (P >0.05) in the distribution of alleles with long (>20) pure repeat tracts among the different ethnic groups, suggesting that different ethnic groups should be equally susceptible to the development of this disease. Analysis of an additional 43 alleles with total repeat lengths between 35 and 50 repeats, revealed that highly interrupted CGG repeat alleles (>2 AGG interruptions) occur preferentially at modal repeat lengths in the population, providing confirmatory evidence that the presence of AGG interruptions confers stability. A consideration of length variation of the most 3′ tract of pure repeats revealed a bimodal distribution pattern with maxima at approximately 10 and 20 repeats. Only unimodal distribution with maxima at 9 or 10 were observed for the 5′ tract and middle CGG tract within the FMR1 CGG repeat substructure. These results suggest that the loss of the most 3′ AGG interruption or its conversion to CGG is a common event in the human population, occurring by a mechanism which preserves overall repeat length. This bias for the loss of the distal-most AGG interruption likely plays an important part in predisposing human alleles to the development of the fragile x syndrome.