Analysis of spinal muscular atrophy-like patients by targeted resequencing

Background Several effective therapies have been developed for spinal muscular atrophy (SMA), but there are multiple diseases that show SMA-like symptoms, necessitating efficient differential genetic diagnostic methods. Advancements in next-generation sequencing (NGS) technology have facilitated the successful diagnosis of many undiagnosed genetic diseases. Here, we applied NGS along with conventional methods for the molecular diagnosis of undiagnosed patients with lower motor neuron (LMN) symptoms who were initially suspected to have SMA. Methods We enrolled 157 patients with LMN symptoms who visited the Institute of Medical Genetics, Tokyo Women’s Medical University, between 2005 and 2016. We excluded 86 patients diagnosed with SMA after confirming the causative SMN1 gene deletion or variants. Finally, we examined 12 undiagnosed patients from eight families by targeted resequencing using NGS. Variants were selected on the basis of literature search and databases, and mutations in a gene where loss of function is a known mechanism of disease were considered as pathogenic. Candidate variants were validated by Sanger sequencing. Results We detected novel variants for three patients from two families. Patients 1 and 2 (siblings) showed compound heterozygous TTN variants (c.6621delG, p.W2207Cfs*28 and c.23718T>A, p.F7906L), while patient 3 displayed compound heterozygous KIF1A variants of (c.3871C>T, p.R1291C and c.3898G>A, p.V1300M). Conclusions We detected appropriate variants using our approach of obtaining candidate pathogenic variants by targeted resequencing through NGS and narrowed down the variants in light of patient clinical symptoms. We successfully identified novel causative variants in three undiagnosed patients, which indicated the effectiveness of our approach.