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Audience
This webinar is geared towards those requiring copy number results from low coverage sequencing results (shallow/targeted) and/or from normal coverage WGS/WES results. Shawn Anderson headshot.jpg


Speaker information
Shawn Anderson
Research Scientist
Vancouver Prostate Centre

Join us as Shawn Anderson from the Vancouver Prostate Centre discusses how BioDiscovery’s Nexus Copy Number software has played a crucial role in many discoveries and subsequent publications.  A challenge encountered with retrospective tumor cohorts is the lack of benign tissue as a copy number reference for baseline and ploidy calling.  BioDiscovery’s new BAM (multiscale reference) algorithm has proven to be an invaluable tool for addressing this challenge. The algorithm, available in the newly released Nexus Copy Number 9.0, 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. 

Background: 
The Vancouver Prostate Centre’s (VPC) Laboratory for Advanced Genome Analysis uses both array-based and next generation sequencing platforms to support clinical research to identify drivers of cancer progression and actionable targets in the development of novel therapies.

Challenge:
Deriving CN from WES of patient derived xenografts and primary prostate tumors lacking benign tissue samples

Solution:
Using Nexus Copy Number 9.0 to

  1. create a robust pooled reference with the BAM (multiscale reference) algorithm
  2. adjust copy number baseline ploidy