Using NextGENe Software for Copy Number Variation (CNV) Analysis

There are various programs available to assist researchers/clinicians in their bioinformatic analyses, but how do you know which one is most suited to your needs?

nextgene-logo.pngNextGENe software includes a sophisticated algorithm for copy-number variation (CNV) detection from a wide variety of diploid genome projects, including whole-exome and targeted sequencing panels.

There are three options for CNV analysis within NextGene:

  1. The NextGENe CNV tool. Validated for Clinical applications is used to compare a single sample with a single control or group of controls. The CNV tool can be used for targeted panels and Whole Exome Sequencing (WES).
  2. NextGENe software's Batch CNV tool can be used to compare several samples to one another, no controls. It has been shown to be concordant with a Sanger/MLPA® combo approach. The method is ideal for CNV panels such as NimbleGen Seq Cap targeted panels and other chemistries with low noise.
  3. NextGENe software's Sensitive Aneuploidy Detection (SAD) tool is designed for chromosome copy number detection in Whole Genome Sequencing (WGS) and for cell free DNA (cfDNA) applications such as non-invasive prenatal testing (NIPT).



As an example, "Clinical Validation of Copy Number Variant Detection from Targeted Next-Generation Sequencing Panels" (Kerkhof et al., Journal of Molecular Diagnostics, 2017, 19:905-920) shows the utility of NextGene for CNV analysis. The aim of the study was to "clinically validate a novel CNV detection algorithm using targeted clinical NGS gene panel data."

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