Yes, the analysis of genome-wide CNVs can be done in genome-edited cells for Knockout (NHEJ) experiments. A custom panel will need to be created for your editing on- and off-targets, and this can be combined with the Genome-Wide CNV Panel for these experiments. Please download our Panel Pooling Guide for guidance, and reach out to support@missionbio.com to ensure that there are no primer conflicts. The Genome Editing panel file, described here, will be needed as input for the analysis.
A diploid cell population should be spiked into each test sample before the Tapestri run. Recommended spike-in cells can be found here. Germline variant information will need to be known ahead of processing to demultiplex the spike-in cells and sample cells. After sequencing, the data should be analyzed using the Tapestri Genome Editing pipeline. The presence of the spike-in cell information in the GE pipeline will trigger the analysis of genome-wide CNVs. The readout of genome-wide CNVs in edited cells is part of the Genome Editing Knockout Report.