Skip the CMA, Exome-Wide CNV Analysis Now Available at PreventionGenetics

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Genetic variants of least 50 base pairs that differ in copy number (i.e., deletions or duplications) from the reference sequence are commonly called copy number variants (CNVs). Detection of CNVs is an important diagnostic tool for rare disorders. Pathogenic CNVs are common in specific disorders, such as microdeletion and microduplication syndromes and neurodevelopmental disorders. For example, in people affected with autism or intellectual disability, around 10-15% will carry a pathogenic CNV. CNVs occur frequently in certain genes as well, such as DMD, in which 65-80% of pathogenic variants are CNVs (Darras et al. 2018).

Chromosomal microarray (CMA) has become the standard of care for detecting CNVs in patients with intellectual disability, autism, and multiple congenital anomalies. However, at PreventionGenetics, we have demonstrated through our validation studies that CNV detection via exome sequencing is at least as sensitive and often more sensitive than CMA. This newer option provides the opportunity to bypass standard CMA testing and test patients for both sequencing variants and CNVs in a single test, leading to lower costs and reduced turnaround time (Reddy et al. 2012; Sahoo et al. 2017). 

Panel tests + Exome-Wide CNV 
At PreventionGenetics, all next generation sequencing (NGS) panels include CNV detection for the genes within the panel. We are now pleased to announce an expanded option for PGxome-based defined and custom panels: Exome-Wide CNV Analysis. PreventionGenetics’ Exome-Wide CNV Analysis uses exome sequencing data to identify chromosomal imbalances similar to those detected by CMA. The genes from the selected panel receive the same CNV analysis as previously offered (CNVs of four or more exons are detected with sensitivity greater than 95%); with the Exome-Wide CNV Analysis added, the remainder of the exome is analyzed for CNVs as well. The Exome-Wide CNV Analysis method will identify aneuploidy, triploidy, unbalanced rearrangements, and known microdeletion and microduplication syndromes, as well as unique CNV events. This test targets deletions larger than 250 kb and duplications larger than 500 kb. Since the scope is not limited to the genes in the specific panel ordered, potentially important CNVs across the entire exome are able to be detected.

The cost for Exome-Wide CNV Analysis is $250, which is added to the price of the panel. To confirm if this option is available, visit the panel-specific test descriptions and look for the exome-wide CNV badge: 

Whole Exome Sequencing + Exome-Wide CNV
PreventionGenetics’ Exome-Wide CNV Analysis is automatically included with all exome tests (including PGxome, Neonatal Crisis Panel, and ASD-ID Comprehensive Panel). With comparable CNV detection available using this method, the ability of whole exome sequencing (WES) to detect small variants in addition to large variants provides a definitive advantage over CMA. A recent paper by Clark et al. found patients were about eight times more likely to receive a diagnosis from WES or whole genome sequencing (WGS) than CMA. The clinical utility from the WES or WGS results was also greater than the CMA results (Clark et al. 2018).

With our new Exome-Wide CNV Analysis, PreventionGenetics invites you to skip the CMA and get everything you need for your patient in a single test! 


Clark et al. 2018. PubMed ID: 30002876
Darras et al. 2018. PubMed ID: 20301298
Iafrate et al. 2004. PubMed ID: 15286789
Reddy et al. 2012. PubMed ID: 23215556
Sahoo et al. 2017. PubMed ID: 27337029
Sebat et al. 2004. PubMed ID: 15273396