Users of Nexus Copy Number know that the software can analyze data from microarray and NGS to get copy number results. However, not everyone is aware that it can also load NGS sequence variants from a .vcf file and integrate them with the copy number events.
Sometimes a wave-like pattern is seen in the probe distribution across chromosomes. This artifact can affect the accuracy of calls. Systematic correction based on GC content of the probe sequence and its neighborhood can be applied to minimize this problem.
NxClinical allows for the upload of annotation information in the form of Sample Attributes. These pre-defined fields allow for inclusion of any and all information.
You already know that Nexus Copy Number is a versatile software for genomic data analysis that can load and process data from different technologies (arrays, NGS), manufacturers (Agilent, Affymetrix, Illumina…), and modalities (copy number, sequence variants, gene expression, methylation).
In this webinar we discussed how to prepare, upload and process copy number, expression and sequence variant results for the same samples within a cancer cohort.
Our Nexus Copy Number software for years provided the ability to integrate sequence variants and gene expression results with copy number allowing identifications of genomic hotspots.