Validation of SMA screening kits with SMN1 gene analysis in a Turkish cohort

•Quantitative Real-Time Polymerase Chain Reaction validated against MLPA for Spinal Muscular Atrophy screening.•Analysis showed high accuracy of qRT-PCR (96.2–98.7%) for detecting SMN1 gene deletions and copy number variations.•Minor discrepancies between qRT-PCR and MLPA likely due to single nucleotide polymorphisms affecting primer binding.•qRT-PCR presents as a rapid, cost-effective, and accurate method for routine SMA screening.•Enhancing molecular methodologies for rare disease screening in is important and could benefit from government funding. It is crucial to start early treatment in Spinal Muscular Atrophy (SMA) with available drugs to stop the progression of the disease, therefore making SMA screening preferable. This study assessed Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) compared to Multiplex Ligation-dependent Probe Amplification (MLPA) for detecting Spinal Muscular Atrophy (SMA) through SMN1 gene copy number analysis in a Turkish cohort. We analyzed 249 DNA samples, previously tested for SMN1 and SMN2 gene deletion via MLPA, using qRT-PCR kits from three different companies. Accuracy, sensitivity, and specificity of qRT-PCR in identifying deletions of SMN1 copy number variations. High accuracy (96.2–98.7%) achieved with qRT-PCR for detecting homozygous deletions, heterozygous deletions, and copy number variations in the SMN1 gene. Minor discrepancies between qRT-PCR and MLPA were observed, possibly due to single nucleotide polymorphisms affecting primer binding. The qRT-PCR method proved to be a rapid, cost-effective, and accurate technique, aligning well with the demands of routine SMA screening, suggesting its general suitability for application in SMA screening programs. This research highlights the importance of improving molecular methodologies and the value of collaborations between government and relevant sectors to overcome rare diseases, particularly through the enhancement of screening initiatives which is the first and most effective strategy to protect the public health.