Closing the Gap - Detection of 5q-Spinal Muscular Atrophy by Short-Read Next-Generation Sequencing and Unexpected Results in a Diagnostic Patient Cohort

Abstract

Background: The importance of early diagnosis of 5q-Spinal muscular atrophy (5q-SMA) has heightened as early intervention can significantly improve clinical outcomes. In 96% of cases, 5q-SMA is caused by a homozygous deletion of SMN1. Around 4 % of patients carry a SMN1 deletion and a single-nucleotide variant (SNV) on the other allele. Traditionally, diagnosis is based on multiplex ligation probe amplification (MLPA) to detect homozygous or heterozygous exon 7 deletions in SMN1. Due to high homologies within the SMN1/SMN2 locus, sequence analysis to identify SNVs of the SMN1 gene is unreliable by standard Sanger or short-read next-generation sequencing (srNGS) methods. Objective: The objective was to overcome the limitations in high-throughput srNGS with the aim of providing SMA patients with a fast and reliable diagnosis to enable their timely therapy. Methods: A bioinformatics workflow to detect homozygous SMN1 deletions and SMN1 SNVs on srNGS analysis was applied to diagnostic whole exome and panel testing for suggested neuromuscular disorders (1684 patients) and to fetal samples in prenatal diagnostics (260 patients). SNVs were detected by aligning sequencing reads from SMN1 and SMN2 to an SMN1 reference sequence. Homozygous SMN1 deletions were identified by filtering sequence reads for the ,, gene-determining variant“ (GDV). Results: 10 patients were diagnosed with 5q-SMA based on (i) SMN1 deletion and hemizygous SNV (2 patients), (ii) homozygous SMN1 deletion (6 patients), and (iii) compound heterozygous SNVs in SMN1 (2 patients). Conclusions: Applying our workflow in srNGS-based panel and whole exome sequencing (WES) is crucial in a clinical laboratory, as otherwise patients with an atypical clinical presentation initially not suspected to suffer from SMA remain undiagnosed.

Molecular Mechanisms in the Design of Novel Targeted Therapies for Neurodegenerative Diseases

“…This, in turn, results in the formation of the exonic splicing silencing element (ESS), to which the A1/A2 splicing factor can bind [ 87 , 89 ]. This leads to the translation of the transcript into a dysfunctional SMNΔ7 protein, which is subsequently degraded via a proteasome-associated pathway [ 90 , 91 , 92 , 93 ]. Accordingly, due to this molecular mechanism, current applied therapies mainly consist of the modification of the splicing phase or the correction of the SMN2 gene in the exon 7 region [ 87 , 88 , 89 ].…”

“…Regarding targeting the SMN1 gene, on the other hand, the only drug approved to date is onasemnogene abeparvovec [ 87 , 92 ]. The viral carrier used in this instance is a recombinant adeno-associated serotype 9 virus (AAV9) that carries a complementary DNA (cDNA) transgene of the SMN1 gene, which encodes a fully functional protein [ 87 , 91 , 92 , 93 ]. The advantage of this system is the fact that the viral vector targets the motor neuron cell.…”

“…The advantage of this system is the fact that the viral vector targets the motor neuron cell. It is administered in the form of suspension via intravascular infusions [ 91 , 92 , 93 ].…”

“…Spinal muscular atrophy may manifest at any stage of life, from infancy to adulthood [ 92 ]. Despite relatively good diagnostics focusing on molecular testing using polymerase chain reaction (PCR)-based methods and methods based on short-read sequencing, treatment options are mainly limited to the three FDA-approved pharmaceuticals [ 92 , 93 ]. Due to this, new solutions in the field of genetic engineering and pharmaceutics are being sought to develop alternative methods of treating SMA with the highest possible efficacy.…”

The First Decade of Journal of Neuromuscular Diseases: Supporting and Advancing the Rapidly Evolving Field of Translational Research

“…Special thanks to our social media editors, Emily O’Connor (until 2021) and Grace McMacken, who racked up 2347 Facebook followers and 1837 Twitter/X followers to date. The latest feature, our podcast highlighted two exciting publications in 2023, the first one by Carsten Bönnemann on the challenges of gene therapy [ 16 ], the second one by Angela Abicht on advancements in genomic diagnosis of SMA [ 17 ]. Podcasts, articles in press and back issues are available on our website ( https://www.iospress.com/catalog/journals/journal-of-neuromuscular-diseases ).…”