AmplideX Kit Accurately Identifies Variants Linked to Spinal Muscular Atrophy

Gary J. Latham, PhD

Recently published results from a multisite evaluation study of the AmplideX PCR/CE SMA Plus Kit showed that the screening test accurately identifies genetic variations associated with spinal muscular atrophy (SMA).^1,2

Senior author Gary J. Latham, PhD, chief scientific officer, Asuragen, and colleagues developed and evaluated the single-tube polymerase chain reaction (PCR)/capillary electrophoresis (CE) assay system that quantifies SMN1/2 copy numbers and genotypes 3 additional clinically relevant variants. They performed a validation analysis with human cell lines and whole blood representing varying SMN1/2 copies on 4 capillary electrophoresis instrument models.

In total, 468 clinical DNA samples were tested. The results were greater than or equal too 98.3% concordant with consensus SMN1/2 exon 7 copy numbers, determined using multiplex ligation-dependent probe amplification and droplet digital PCR, and 100% concordant with Sanger sequencing for the 3 variants.²

“Existing methods for identifying relevant variants in the SMN1 and SMN2 genes are often cumbersome, complex, and time-consuming,” Latham said in a statement.¹ “We believe this kit – which analyzes all variants in a single reaction – will be important for expanding the availability of reliable results to all populations.”

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Copy number values were 98.6% (SMN1) and 97.1% (SMN2) concordant to each laboratory’s own reference results. Notably, all known carriers (n = 81) and affected individuals (n = 47) were correctly identified.

The kit presents a possible advantage compared with current screening methods as it produces results in less than 4 hours and requires only 60 minutes of hands-on-time. The assay shares a common workflow with other assays in the AmplideX product portfolio and is optimized for use on widely established laboratory equipment.

The multiplexed, scalable design allows analysis of single-nucleotide variants, small indels, and copy-number changes from a single PCR reaction and has the ability to differentiate between 0,1,2,3, and 4 or more copies for both SMN1 and SMN2.

"Breakthrough molecular medicines for SMA have raised the bar for more informative and timely SMA diagnostic assays even as labs have been overwhelmed by testing for the COVID-19 pandemic,” Vivianna M. Van Deerlin, MD, PhD, director, Molecular Pathology Laboratory, and professor of pathology and laboratory medicine, Pennsylvania Perelman School of Medicine, said in a statement.¹ “Our validation results demonstrate that the AmplideX Kit not only produces quality results, but it does so using a fast, flexible format that can be easily implemented – at a time when efficient assays and lab operations are more important than ever.”

Latham and colleagues have published a number of research studies using the kit demonstrating its efficacy as a validated screening tool for SMA. At the 2019 Association for Molecular Pathology (AMP) Annual Meeting, combined copy number data for 130 samples from 2 sites showed 98.4% agreement for SMN1 and 95.3% for SMN2. Furthermore, internal testing with 71 samples with verified gene duplication and disease modifier status showed 100% agreement with the reference methods.³

REFERENCES

1. Multisite study demonstrates utility of Asuragen Kit for identifying variants linked to spinal muscular atrophy. News release. Bio-Techne Corporation. May 10, 2021. Accessed May 17, 2021. https://www.prnewswire.com/news-releases/multisite-study-demonstrates-utility-of-asuragen-kit-for-identifying-variants--linked-to-spinal-muscular-atrophy-301287054.html

2. Milligan JN, Larson JL, Filipovic-Sadic S, et al. Multisite evaluation and validation of a sensitive diagnostic and screening system for spinal muscular atrophy that reports SMN1 and SMN2 copy number, along with disease modifier and gene duplication variants. J Mol Diagn. doi: 10.1016/j.moldx.2021.03.004

3. Zhu H, Filipovic-Sadic S, Church M, et al. A rapid diagnostic and screening system for spinal muscular atrophy that reports copy number changes, single nucleotide variants and small indels. Presented at 2019 AMP Annual Meeting.