Copy Number Variation (CNV) Analysis
NextGENe software provides three options for CNV for the various needs of molecular genetics laboratories:
- The NextGENe CNV tool. Validated for Clinical applications is used to compare a single sample with either a single control or group of controls. The CNV tool can be used for targeted panels and Whole Exome Sequencing (WES). Since it relies on normalized coverage values, adequate base coverage is important. Both the sample and control (control group) should be run with the same chemistry and similar run conditions.
- NextGENe software’s Batch CNV tool can be used to compare several samples to one another, but without controls. It has been shown to be concordant with a Sanger/MLPA® combo approach. When used as a screening function, the Batch CNV Tool has been shown to significantly reduce costs, while greatly enhancing analysis efficiency in laboratories performing MLPA.
The method is ideal for CNV panels such as NimbleGen Seq Cap targeted panels and other chemistries with low noise, (minimal effect on sensitivity/specificity – WES may be too noisy). The tool can simultaneously analyze up to 228 total data points, for example 24 samples with each targeting 11 Mbps.
- NextGENe software’s Sensitive Aneuploidy Detection (SAD) tool is designed for chromosome copy number detection in Whole Genome Sequencing (WGS) for cell-free DNA (cfDNA) applications, such as non-invasive prenatal testing (NIPT). The tool is streamlined for simple operation and the normalization process allows for detection of aneuploidies, even those with a high background of non-aneuploid data. Due to the level of normalization required, this tool uses a modeling control group of at least 30 samples generated by the same chemistry.
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