Detection of Copy Number Variation (CNV) from Next-generation Sequencing (NGS) data

Comparative genomic hybridization array (aCGH) is currently considered the gold standard for copy number variation analysis. However, in recent years, several robust algorithms have been developed to detect CNVs from next-generation sequencing data (sometimes referred to as CNV-by-NGS). This allows for detection of both sequence variants and CNVs through a single assay, which is now available at EGL.

This methodology involves comparative analysis of NGS read depth (coverage) of the targeted regions of genes on a panel to detect CNVs. The clinical sensitivity and specificity of CNV-by-NGS are highly sequence dependent and are comparable to that of aCGH. The assay is highly sensitive for CNVs of 500 base pairs or larger and those containing at least 3 exons. Smaller (< 500 base pairs) CNVs and those that involving only 1 or 2 exons may or may not be detected depending on the sequence context, size of exon(s) involved and depth of coverage.

Most NGS panel tests offered by EGL now include this analysis at no additional cost. Tests that include this complementary CNV analysis are indicated as such in their test names on the webpage and in the requisition form. Please see the test webpage for more details on each test.

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