Practical guidelines to manage discordant situations of SMN2 copy number in patients with spinal muscular atrophy

Abstract

ObjectiveAssessment of SMN2 copy number in patients with spinal muscular atrophy (SMA) is essential to establish careful genotype-phenotype correlations and predict disease evolution. This issue is becoming crucial in the present scenario of therapeutic advances with the perspective of SMA neonatal screening and early diagnosis to initiate treatment, as this value is critical to stratify patients for clinical trials and to define those eligible to receive medication. Several technical pitfalls and interindividual variations may account for reported discrepancies in the estimation of SMN2 copy number and establishment of phenotype-genotype correlations.MethodsWe propose a management guide based on a sequence of specified actions once SMN2 copy number is determined for a given patient. Regardless of the method used to estimate the number of SMN2 copies, our approach focuses on the manifestations of the patient to recommend how to proceed in each case.ResultsWe defined situations according to SMN2 copy number in a presymptomatic scenario of screening, in which we predict the possible evolution, and when a symptomatic patient is genetically confirmed. Unexpected discordant cases include patients having a single SMN2 copy but noncongenital disease forms, 2 SMN2 copies compatible with type II or III SMA, and 3 or 4 copies of the gene showing more severe disease than expected.ConclusionsOur proposed guideline would help to systematically identify discordant SMA cases that warrant further genetic investigation. The SMN2 gene, as the main modifier of SMA phenotype, deserves a more in-depth study to provide more accurate genotype-phenotype correlations.

Genomic Variability in the Survival Motor Neuron Genes (SMN1 and SMN2): Implications for Spinal Muscular Atrophy Phenotype and Therapeutics Development

“…Patients with milder forms of SMA have higher SMN2 copy numbers than severe SMA patients. SMN2 copy number is being used as a prognostic tool to guide therapeutic strategies and care plans for SMA patients across the spectrum of phenotype severity [ 95 , 96 ]. The variability in SMN2 copy number within the SMA patient population and its relationship to disease severity makes it an ideal target for therapeutics development.…”

“…Nusinersin and risdiplam act by increasing exon 7 inclusion in SMN2 transcripts while onasemnogene abeparvovec replaces full-length SMN mRNA and protein. Since there is a strong relationship between SMN2 copy number and disease severity, accurate and rapid measurements of SMN2 copy number are often used to identify treatment options and regimens for children with SMA [ 96 , 153 , 154 ]. Accurate and rapid measurement of SMN2 CN is particularly essential to guide decisions around timing and treatment choice for SMA infants identified by newborn screening.…”

The Importance of Digging into the Genetics of SMN Genes in the Therapeutic Scenario of Spinal Muscular Atrophy

“…Wu et al (2017) demonstrated that this transition decreases the affinity of the RNA-binding protein HuR, which acts as a splicing repressor, increasing in~20% the SMN2 exon 7 inclusion [38]. Despite the rare frequency of at least c.859G>C variant (0.8%, 11/1345) [41], a recent SMA practical guideline recommends the evaluation of both variants in discordant SMA patients presenting a better-than-expected phenotype [42].…”

“…In MLPA and RT-PCR based on SYBR Green, DNA quality is crucial to achieve reliable results, and moreover, both methods can be affected by variants in the target region of primers or probes, leading to a misinterpretation of the SMN2_CN. In addition, control samples or references are needed in all the approaches since they are based on indirect quantification, and therefore the right choice of these controls is decisive to establish the correct SMN2_CN [42]. This fact is reflected in the work of Schorling et al (2019), in which 20 SMA patients were retested for their SMN2 dosage using new DNA samples and 45% of the results were discrepant in comparison with the initial ones [55].…”

“…Retesting of cohorts with discrepancies (i.e., [33][34][35]) would be interesting to confirm if some of the results are due to problems with SMN2_CN determination or clinical misclassification of patients. In fact, a guideline is proposed to manage the discordant situations that are present in SMA patients [42].…”