Abstract - Text

Abstract-Text

Spinal muscular atrophy (SMA) is a severe neuromuscular disease characterized by progressive muscle weakness and atrophy due to the degeneration of spinal motor neurons, which is caused by loss of SMN1 gene function. Due to high homologies within the SMN1/SMN2 locus, analysis of the SMN1 gene is not possible by standard short-read-sequencing methods. The coding regions of SMN1 and SMN2 differ from each other by a single nucleotide in exon 7, the "gene-determining variant" (GDV). This variant inhibits correct splicing of SMN2 and leads to only 10% of functional protein production from the SMN2 gene. In 95% of cases, SMA is caused by a homozygous deletion of SMN1 on chromosome 5q13. Around 5% of individuals with SMA are compound heterozygous for an SMN1 deletion on one allele and a point mutation on the other allele (PMID: 32809522). In patients with clinical suspicion of SMA, traditional analysis by multiplex ligation probe amplification (MLPA) is performed to detect homozygous deletions in the SMN1 gene. However, patients with an atypical clinical presentation remain undiagnosed in the era of NGS WES analyses. On the basis of four cases, we present a workflow to detect homozygous SMN1 deletions and SMN1 point mutations on NGS short-read-sequencing analysis. Homozygous SMN1 deletions are detected by filtering sequence reads for the "gene-determining variant" (GDV). Point mutations are detected by aligning sequencing reads from SMN1 and SMN2 to an SMN1 reference sequence.