2023 ACMG Annual Clinical Genetics Meeting Digital Edition: Poster Gallery-Clinical Implementation of Carrier Screening and Diagnostic Testing for Spinal Muscular Atrophy using PCR/Capillary Electrophoresis assay

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The document discusses the clinical implementation of carrier screening and diagnostic testing for Spinal Muscular Atrophy (SMA) using PCR/capillary electrophoresis assay. SMA is an autosomal recessive neuromuscular disorder characterized by muscle weakness and atrophy. The SMN1 and SMN2 genes play a critical role in SMA, and variations in their copy number and sequencing variants are associated with the onset and severity of the disease.<br /><br />Multiple laboratory methods are available for testing SMN1 and SMN2, including MLPA, qPCR, ddPCR, PCR/CE, NGS, and long-read sequencing. The PCR/CE method offers high accuracy, short turnaround time, simple setup, moderate to high throughput, and relatively low cost, making it suitable for routine clinical testing.<br /><br />A validation study was conducted using 74 samples, including reference material samples, clinical blood samples, and proficiency testing samples. The assay demonstrated analytical accuracy, sensitivity, and specificity above 99% for copy number detection and variant genotyping. Triplicate testing showed consistent results, indicating robust repeatability and reproducibility. The assay also achieved clinical sensitivity, specificity, and accuracy greater than 99% for both diagnostic and carrier screening purposes.<br /><br />The PCR/CE assay is cost-effective and provides a short turnaround time, making it suitable for clinical SMA carrier screening and diagnostic testing. The assay uses PCR/CE to detect SMN1 and SMN2 copy numbers and genotypes of three variants. The normalized ratios of target genes to endogenous control are used to calculate the copy number, which is then reported as 0, 1, 2, 3, or ≥4 copies. The current bin setting effectively covers most samples, with ratios falling within the appropriate copy number bins.<br /><br />Overall, the PCR/CE-based SMA assay offers an accurate and efficient method for clinical testing of SMA, both for carrier screening and diagnostic purposes. The assay has been validated for analytical and clinical performance, demonstrating high sensitivity, specificity, and accuracy.

Asset Subtitle

Presenting Author - Wanqiong Qiao, PhD; Co-Author - Chandler Ho, BS; Co-Author - Litz Villanueva, MS; Co-Author - Caitlin Hale, MS; Co-Author - Lei Chen, BS; Co-Author - Linda Liao, MS; Co-Author - Caitlin Reavey, PhD; Co-Author - Huanzhi Shi, MS; Co-Author - Nathan Hammond, PhD; Co-Author - Shana White, MS;

Meta Tag

Methodology

Neuroscience

Variant Detection

Co-Author Chandler Ho, BS

Co-Author Litz Villanueva, MS

Co-Author Caitlin Hale, MS

Co-Author Lei Chen, BS

Co-Author Linda Liao, MS

Co-Author Caitlin Reavey, PhD

Co-Author Huanzhi Shi, MS

Co-Author Nathan Hammond, PhD

Co-Author Shana White, MS

Presenting Author Wanqiong Qiao, PhD

Keywords

carrier screening

diagnostic testing

Spinal Muscular Atrophy

PCR/capillary electrophoresis assay

neuromuscular disorder

SMN1 gene

SMN2 gene

copy number variations

sequencing variants

laboratory methods