After extensive development and testing, we are finally ready for the release of Nexus Copy Number 9.0. This new version will help our customers immensely with a new method to get copy number results from NGS data, among the many other new features and improvements.
The new method is called BAM (multiscale reference). It derives copy number results from whole genome sequencing (WGS), whole exome sequencing (WES), and targeted panel sequencing data. This method builds a reference file out of a pool of BAM files that are either from normal samples or from unrelated experimental samples. The reference building process uses a Hidden Markov Model to segment the genome into “target” areas using the reads in targeted regions and the “backbone” areas using the off-target reads. Coarse binning is utilized in the “backbone” areas that provide copy number base line as well as large copy number events and fine binning is used in “target” areas to provide high resolution copy number detection in targeted regions. The BAM files of the individual experimental samples are loaded against the reference file to generate log ratios and B-allele frequencies (BAFs), so that copy number and loss of heterozygosity (LOH) calls can be made. Shallow WGS sequencing (low pass WGS) data widely used in PGS (Pre-implantation Genetic Screening) can also be successfully analyzed using this method. An example showing the whole genome log ratio distribution of PGS WGS is displayed below (monosomy 5 and 14, as well as a one copy gain on chromosome 13).
Other important features include display of the B-allele frequencies plot (BAF plot) in the BAM ngCGH (matched) method, the NGS pair matched CNV analysis method in Nexus Copy Number. This enables cancer researchers to re-center the log ratio plot based on diploid regions which can be easily located with the help of the BAF plot.
An interesting addition in version 9.0 is the ability for users to change the colors of the copy number calls. Even though it has been mostly agreed upon that blue color represents CN Gain and red color is for CN Loss, some researchers still prefer the old fashion way to swap the colors for these two events. We have enabled this function to give people the choice.
Nexus Copy Number 9.0 is now available for customers via the Early Access Program. If you are interested in having a taste of it before the final release, please contact us.