Affiliation:
1. Division of Diagnostic Medical Genetics Department of Pathology and Lab Medicine Mount Sinai Hospital Toronto Ontario Canada
2. Institute of Health Policy Management, and Evaluation Dalla Lana School of Public Health University of Toronto Toronto Ontario Canada
3. Department of Laboratory Medicine and Pathobiology Temerty Faculty of Medicine University of Toronto Toronto Ontario Canada
4. Department of Molecular Genetics Temerty Faculty of Medicine University of Toronto Toronto Ontario Canada
5. Prenatal Diagnosis and Medical Genetics Program Department of Obstetrics and Gynecology Mount Sinai Hospital Toronto Ontario Canada
Abstract
AbstractObjectiveChromosomal microarray (CMA), while considered the gold standard for detecting copy number variants (CNVs) in prenatal diagnostics, has its limitations, including the necessity to replace aging microarray equipment, low throughput, a static design, and an inefficient multi‐day workflow. This study evaluates the feasibility of low‐pass genome sequencing (LP‐GS) as a potential replacement for CMA in prenatal diagnostics.MethodsWe comprehensively compared LP‐GS at 10x and 5x average depths with CMA in a prenatal laboratory. We examined parameters, including concordance, sensitivity, specificity, workflow efficiency, and cost‐effectiveness.ResultsWe found a high degree of agreement between LP‐GS and CMA for detecting CNVs and absence of heterozygosity. Furthermore, compared to CMA, LP‐GS increased workflow efficiency and proved to be cost‐neutral at 10x and cost‐effective at 5x.ConclusionOur study suggests that LP‐GS is a promising alternative to CMA in prenatal diagnostics, offering advantages, including a more efficient workflow and scalability for larger testing volumes. Importantly, for clinical laboratories that have adopted next‐generation sequencing in a separate capacity, LP‐GS facilitates a unified NGS‐centric approach, enabling workflow consolidation. By offering a single, streamlined platform for detecting a broad range of genetic variants, LP‐GS may represent a critical step toward enhancing the diagnostic capabilities of prenatal laboratories.
Cited by
2 articles.
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