Genetics in medicine : official journal of the American College of Medical Genetics · 2026
Copy Number Variant Detection by Exome/Genome Sequencing Versus Chromosomal Microarray: A Comparative Study of Over 9,000 Clinical Cases.
СтатьяНазвание и аннотация: Перевод в очереди
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Poll Sarah R, Facio Flavia M, McWalter Kirsty, Lopes Patricia C, Lindy Amanda, Friedman Bethany, Kelly Kirsten, Trimmier Olivia, Juusola Jane, Kruszka Paul, Wang Wei, Dyer Lisa, Shi Lisong, Johnson Britt, Douglas Ganka
Аннотация
PURPOSE: Copy number variants (CNVs) are implicated in many health conditions. Chromosomal microarray (CMA) has traditionally been the first-tier test for CNV detection. However, exome and genome sequencing (ES/GS) can identify CNVs alongside other variant types. This study compared CNV detection using CMA versus ES/GS in a large clinical cohort.
METHODS: CNV calls from CMA and ES/GS were analyzed in a diverse cohort of over 9,000 individuals tested in a high-throughput clinical laboratory. Concordance between platforms was evaluated, with discordant findings reviewed to determine their nature and causes.
RESULTS: ES/GS showed >99% concordance with CMA. CMA results not detected on ES/GS were typically CNV <3 exons, CNV outside regions of interest, or low-level mosaicism. Interestingly, 0.68% of cases had a CNV reported by ES/GS only, usually CNVs below the CMA detection limit. The additional CNV detection of CMA after ES/GS was ≤1%. When considering non-CNV findings, the added yield of ES/GS was >41%.
CONCLUSION: ES/GS matched or exceeded CMA performance for CNV detection and identified additional variant types. These findings support the adoption of ES/GS as first-tier tests for CNV detection, streamlining diagnostic workflows, and improving diagnostic rate by capturing both small and large structural variants with high accuracy.
METHODS: CNV calls from CMA and ES/GS were analyzed in a diverse cohort of over 9,000 individuals tested in a high-throughput clinical laboratory. Concordance between platforms was evaluated, with discordant findings reviewed to determine their nature and causes.
RESULTS: ES/GS showed >99% concordance with CMA. CMA results not detected on ES/GS were typically CNV <3 exons, CNV outside regions of interest, or low-level mosaicism. Interestingly, 0.68% of cases had a CNV reported by ES/GS only, usually CNVs below the CMA detection limit. The additional CNV detection of CMA after ES/GS was ≤1%. When considering non-CNV findings, the added yield of ES/GS was >41%.
CONCLUSION: ES/GS matched or exceeded CMA performance for CNV detection and identified additional variant types. These findings support the adoption of ES/GS as first-tier tests for CNV detection, streamlining diagnostic workflows, and improving diagnostic rate by capturing both small and large structural variants with high accuracy.