Diagnosis of challenging spinal muscular atrophy cases with long-read sequencing

Spinal Muscular Atrophy (SMA) is an autosomal recessive neuromuscular disorder primarily caused by the deletion or mutation of the Survival Motor Neuron 1 (SMN1) gene. This study assesses the diagnostic potential of Long-Read Sequencing (LRS) in three SMA patients. For Patient 1, who has a heterozygous SMN1 deletion, LRS unveiled a missense mutation in SMN1 exon 5. In Patient 2, an Alu/Alu-mediated rearrangement covering the SMN1 promoter and exon 1 was identified through a blend of Multiplex Ligation-Dependent Probe Amplification (MLPA), LRS, and Gap-PCR. The third patient, born to a consanguineous family, bore four copies of hybrid SMN genes. LRS determined the genomic structures, indicating two distinct hybrids of SMN2 exon 7-SMN1 exon 8. However, a discrepancy was found between the SMN1-SMN2 ratio interpretations by LRS (0:2) and MLPA (0:4), which suggested a limitation of LRS in SMA diagnosis. In conclusion, this newly adapted long PCR-based third-generation sequencing introduces an additional avenue for SMA diagnosis.