Untangling the SMN locus in spinal muscular atrophy: insights from long-read sequencing

Spinal muscular atrophy (SMA) is a severe hereditary neuromuscular disorder with highly variable severity, ranging from profound muscle weakness and need for ventilation at birth to adult onset with mild symptoms and normal life expectancy. SMA results from absence of the SMN1 gene, leading to shortage of SMN protein. The ‘backup’ gene SMN2 resembles SMN1, but produces less protein. The number of SMN2 copies correlates with severity but does not explain all disease variation. No less than three therapies that replace SMN1 or enhance SMN2 have become available since 2017, but treatment responses vary. This thesis aims to advance understanding of SMA genetics to improve prognostic accuracy and treatment decisions.

The SMN locus, the genetic region that contains the SMN genes, is difficult to analyze using conventional short-read sequencing due to extensive duplications. We therefore applied long-read sequencing to characterize its structure. We confirm that SMN1 loss can occur through deletion or conversion into SMN2. In three patients, we fully resolved the SMN locus and found that the same SMN1 deletion recurs in multiple individuals. We also examined DNA methylation of SMN2, which proved not to be a reliable predictor of severity or treatment response.

Finally, we studied SMA carrier status. Parents of SMA patients are typically carriers with one SMN1 copy. In a rare case where both parents had two SMN1 copies, we used a combination of conventional methods and long-read sequencing to show that one parent was a silent carrier and that a new deletion occurred in the other parent, resulting in a low recurrence risk.

In conclusion, this thesis provides novel insights into SMA genetics with important implications for prognosis and therapy.