NGS-Based Assay Shows Feasibility, Potential Cost Savings in Newborn SMA Screening

Leveraging next-generation sequencing (NGS) for newborn screening (NBS) of spinal muscular atrophy (SMA) may be a robust alternative to current screening assays while yielding cost savings, suggest study findings published in Frontiers in Genetics.

Current screening methods for SMA include analyzing dried blood spot samples in a real-time polymerase chain reaction (RT-PCR) or digital droplet PCR for homozygous SMN1 exon 7 deletion. In this new study, researchers examined the use of an NGS-based assay among samples from over 2500 newborns in Australia. Similar to the PCR-based assays, the NGS assay screened for exon 7 deletion.

“Screening for SMA using RT-PCR is one method used by NBS programs, but this approach may lead to high rates of false positive results in certain assays, whereas we had no false positive results after screening 2552 samples,” wrote the researchers. “One reason for this may be that current RT-PCR assays use only 1 locus to discriminate between SMN1 and SMN2 sequences. We found NGS to have 100% specificity for SMA screening when 3 loci are used to assign a sequencing to read to SMN1 or SMN2.”

The researchers found the sensitivity and specificity of the assay to be 100%. The group also included 12 positive and 4 negative samples as controls, and this showed that the positive samples were correctly identified to be positive for homozygous deletion and the negative samples were categorized as either a carrier or as not harboring exon 7 deletion. Across all samples, the failure rate was 0%.

The assay was integrated into the country’s existing NBS program using hybridization-based capture with a customized bioinformatics algorithm and purpose designed high throughput reporting software.

“One challenge with expanding NBS is the cost of implementing single disease assays into existing programs,” described the researchers. “NGS allows multiplex testing for potentially hundreds of conditions, which improves the cost-effectiveness of testing. Other conditions currently screened using biochemical assays or other conditions that meet Jungner and Wilson criteria for screening for which there is currently no screening test available warrant investigation as candidate conditions for inclusion in an NGS assay.”

The group noted that although the overall cost for implementing NGS testing would be more than implementing current PCR-based testing, the assay may be more cost-effective overall because it screens for multiple conditions. The entire NGS panel used in the study included 176 genes, which amounting to a cost of less than $80 per patient or less than $1 per condition. Current PCR-based testing for SMA amounts to approximately $5 per patient.

Reference

Shum BOV, Henner I, Cairns A, et al. Technical feasibility of newborn screening for spinal muscular atrophy by next-generation DNA sequencing. Front Geneti. Published online January 12, 2023. doi:10.3389/fgene.2023.1095600