Analysis of GAA repeat interruptions in a large panel of Friedreich ataxia patient DNA samples

Friedreich ataxia (FRDA) is a multi-system autosomal recessive inherited disorder primarily caused by homozygous GAA repeat expansion mutations within intron 1 of the frataxin (FXN) gene. The GAA repeat expansions may be pure (GAA)n in sequence or may be interrupted with regions of non-GAA sequence, such as (GAAGGA)n. To our knowledge there has been no large-scale study of FRDA patient DNA samples to determine the frequency of interruptions in GAA repeat expansions. Therefore, we have investigated a large panel of 258 FRDA patient and carrier DNA samples using GAA repeat PCR amplification and MboII restriction enzyme digestion, together with GAA repeat TP-PCR analysis. Our results demonstrate that the vast majority (87%) of FRDA GAA repeat expansions do not contain significant sequence changes that would result in abnormal MboII digestion profiles, indicating that they are primarily pure GAA repeats. However, a large number of samples (65%) do show small sequence variations at the 3' end of the GAA repeat sequence as detected by TP-PCR. These results have specific implications in our understanding of FRDA disease progression and the more general understanding of trinucleotide repeat disease characteristics.