Complete nanopore repeat sequencing of SCA27B (GAA- ataxia) in Japanese.

Background: Although pure GAA expansion is considered pathogenic in SCA27B, non-GAA repeat motif is mostly mixed into longer repeat sequences. This study aimed to unravel the complete sequencing of repeat expansion to elucidate its repeat motifs and pathogenicity.

Methods: We screened repeat expansion in a Japanese cohort of 460 molecularly undiagnosed adult-onset cerebellar ataxia patients and 1022 controls, together with 92 non-Japanese controls, and performed nanopore sequencing of repeat expansion.

Results: In the Japanese population, the GCA motif was predominantly observed as the non-GAA motif, whereas the GGA motif was frequently detected in non-Japanese controls. The 5'-common flanking variant was observed in all Japanese GAA repeat alleles within normal length, demonstrating its meiotic stability against repeat expansion. In both patients and controls, pure GAA repeat was up to 400 units in length, whereas non-pathogenic GAA-GCA repeat was larger, up to 900 units, but they evolved from different haplotypes, as rs534066520, located just upstream of the repeat sequence, completely discriminated them. Both (GAA) and (GAA) were enriched in patients, whereas (GAA-GCA) was similarly observed in patients and controls, suggesting the pathogenic threshold of (GAA) for cerebellar ataxia. We identified 14 patients with SCA27B (3.0%), but their single-nucleotide polymorphism genotype indicated different founder alleles between Japanese and Caucasians. The low prevalence of SCA27B in Japanese may be due to the lower allele frequency of (GAA) in the Japanese population than in Caucasians (0.15% vs 0.32%-1.26%).

Conclusions: repeat expansion has unique features of pathogenicity and allelic origin, as revealed by a single ethnic study.