A team from India developed a comprehensive and simple protocol for long-range targeted amplification of GAA repeats in the FXN gene that could solve a suspected case of late-onset spinocerebellar ataxia as Friedreich ataxia (FA) in a time- and cost-effective manner.
The new approach used the Oxford Nanopore Technologies MinION platform, which allowed the team to correctly estimate the length of an expanded intronic region of up to 1100 GAA repeats in the FXN gene of patients with FA. The mean coverage was approximately 2600×.
The GC content of sequence reads ranged from 42% to 45% and the percentage of mapped reads per sample ranged from 12% to 47%.
“LRseq [long-read sequencing] as offered by the ONT offers many unprecedented advantages over the former [ie, short-read sequencing]. Besides their rapidly shrinking costs and improved read quality, LRseq platforms provide additional manoeuvring with respect to the bioinformatics analysis pipelines,” the study’s authors said. “This is of special significance in diseases attributable to complex expanded alleles with multiple repeat interruptions.”
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This new approach also offers reproducibility and scalability as it may allow for low-cost sequencing of up to 96 samples on a single ONT flow cell in less than 24 hours.
Therefore, it shows potential to integrate an eventual diagnostic pipeline, for the precise estimation of GAA repeat length adds value to the identification of FXN-GAA repeat sequence and configuration when approaching difficult to solve, late-onset cases of cerebellar ataxias.
Conventionally, PCR, coupled with triplet repeat-primed PCR, is used to detect FXN-GAA repeats, whereas Southern blot is used to detect GAA length.
The pilot study recently published in Brain Communications enrolled 12 subjects with FA with GAA repeats ranging from approximately 120 to 1100.
Reference
Uppili B, Sharma P, Ahmad I, et al. Sequencing through hyperexpanded Friedreich’s ataxia-GAA repeats by nanopore technology: implications in genotype-phenotype correlation. Brain Commun. Published online March 29, 2023. doi:10.1093/braincomms/fcad020
