Study: NGS May Be a Superior Method of Detecting SMN1 Gene Copy Number

As uptake of next-generation sequencing (NGS) continues across various diseases and conditions, new research suggests the method is more reliable than traditional methods for detecting SMN1 gene copy number in patients with spinal muscular atrophy (SMA).

The researchers of the study, published in Scientific Reports, said the screening method could offer a simplified way to detect the gene copy number without a need for extra testing, and provide a high cost performance, as the study also showed NGS could reduce test costs.

“It is recommended by the [American College of Obstetrics and Gynecology] and [American College of Medical Genetics] that all women and all couples regardless of race or ethnicity undergo carrier screening for SMA, a common severe genetic disease worldwide,” highlighted the researchers. “Thus, the selection of a suitable method is vitally important. Therefore, good performance should be the first priority.”

Among the 3 methods used across 478 samples included in the study, NGS yielded the most favorable results, including when compared with multiplex ligation probe amplification (MLPA), which is typically considered the gold standard for molecular analysis for SMA. According to the researchers, their study is the first to analyze the retest rate of the traditional screening method.

Compared with MLPA (6.69%) and quantitative polymerase chain reaction (qPCR) (5%)—another common method used for SMN1 gene copy number screening—NGS had the lowest retest rate at 2.74%, meaning less samples had to be retested in order to get definitive results.

The analysis also demonstrated NGS had higher precision and specificity. Leveraging the classifications determined by MLPA as a reference, which were consistent with previous diagnostic results, researchers tested the ability of NGS and qPCR to identify 0 copy, 1 copy, and ≥2 copies of SMN1. Across all 3 of these measures, NGS demonstrated a sensitivity, specificity, and precision of 100%. Using qPCR, sensitivity was 100%, 97.52%, and 94.30%, respectively; specificity was 98.63%, 95.48%, and 100% respectively; and precision was 72.72%, 88.72%, and 100%, respectively.

Of the samples, 71 were used to determine repeatability of NGS and qPCR. While reproducibility was sufficient among homozygous deletion samples for qPCR, results were insufficient among heterozygous deletion and nondeletion samples. Meanwhile, NGS showed favorable repeatability, which the researchers said suggests that NGS can be used not just to detect homozygous deletion for diagnosing SMA but to also analyze heterozygous deletion for carrier screening.

Besides the 3 methods studied, there are other methods that be used for SMN1 copy number detection, wrote the researchers. “The droplet digital PCR is another emerging technique for SMN1 copy number assay. Although, the improved digital PCR technology has been reported, the most are operational complexity and the related equipment and reagents are expensive. At present, it is mostly used as a validation method for positive results and has not been adopted extensively for carrier screening of SMA,” they concluded.

Reference:

Zhao S, Wang Y, Xin X, et al. Next generation sequencing is a highly reliable method to analyze exon 7 deletion of survival motor neuron 1 (SMN1) gene. Sci Rep. Published online January 7, 2022. doi: 10.1038/s41598-021-04325-1