Researchers Develop Assay to Accurately Determine SMN Copy Number in SMA Patients

Patrícia Silva, PhD avatar

by Patrícia Silva, PhD |

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A study recently published in the journal Molecular Genetics and Genomic Medicine reported a new assay to assess the copy number of specific genes linked to spinal muscular atrophy (SMA) pathogenesis and disease severity. The study was led by researchers at the Nemours/Alfred I. duPont Hospital for Children and is entitled “SMN1 and SMN2 copy numbers in cell lines derived from patients with spinal muscular atrophy as measured by array digital PCR”.

SMA is a rare, devastating motor neuron disease and one of the leading genetic causes of pediatric mortality, occurring in approximately 1 in every 6,000 to 10,000 newborns. It is characterized by the degeneration of nerves controlling muscles and voluntary movement, resulting in muscle weakness, atrophy, paralysis and eventually death. SMA is the result of a mutation or deletion in a gene called survival of motor neuron 1 (SMN1) that results in low levels of the SMN protein. The disease has currently no approved treatment.

Besides SMN1, there is another protein variant – SMN2. This variant is mainly produced as an unstable and shortened version of the SMN protein due to a single nucleotide difference in the exon 7 of the gene, and therefore cannot compensate for SMN1 loss. There is a considerable variation in the copy number of SMN2 among SMA patients, where in general, a high SMN2 copy number is associated with a milder disease. An accurate determination of SMN2 copy number may therefore be clinically relevant.

The goal of the study was to develop a method to determine the copy numbers of SMN1 and SMN2 in DNA samples. The research team developed an assay for this purpose using an array-based digital PCR (dPCR) system. PCR (polymerase chain reaction) is a molecular biology method that can amplify DNA generating thousands to millions of copies.

Researchers reported that their dPCR assay could accurately and reliably determine the number of SMN1 and SMN2 copies in DNA samples from cell lines derived from SMA patients. Furthermore, through their dPCR assay, researchers confirmed that there is a strong inverse correlation between disease severity and the copy number of SMN2.

The research team concluded that the array digital PCR developed is a practical assay that can accurately determine the copy numbers of SMN1 and SMN2 genes in samples from SMA patients, and confirmed the prognostic value of SMN2 copy number.