Clinical and genetic diagnostic challenges in presumed hereditary ataxia

Cerebellar ataxia is present in many different genetic disorders, such as autosomal-dominant spinocerebellar ataxias (SCA), autosomal-recessive ataxias and mitochondriopathy [1]. With the growing use and possibilities of genetic diagnostics, many overlaps between neurogenetic disorders and highly variable clinical manifestations have been identified. For instance, many genes that were previously assigned to either hereditary ataxia or hereditary spastic paraplegia (HSP) have now been associated with both ataxia and HSP [2]. In line with clinical heterogeneity, the genetic causes of hereditary cerebellar ataxia are manifold. Genetic alterations include single nucleotide variants (SNVs), copy number variations (CNVs), structural variants (SVs), mitochondrial DNA (MT-DNA) variants and frequently short tandem repeat (STR) expansions [3]. SNVs, CNVs and, if included, MT-DNA variants can be readily detected in parallel using diagnostic state-of-the-art sequencing: short-read whole exome (WES) and whole genome sequencing (WGS) [4, 5]. In contrast, STR expansions are more challenging to detect due to the limitation of short-reads to 100-150 bp as many repeat expansions exceed this length by far. Nonetheless, bioinformatic tools have been developed to enable the detection of repeat expansions in short-read WGS data [6]. Several studies demonstrated the benefit of repeat expansion detection with ExpansionHunter also in WES data for loci in or near coding regions [7, 8]. However, due to limited read length, short-read sequencing can usually only be used as a screening test for repeat expansion detection and a second method is necessary. In contrast, long-read sequencing (LRS) allows accurate and comprehensive genotyping of repeat expansions and identification of methylation changes.