Topic: Nexus Copy Number

Combined CNV and SNV detection from NGS panels in a clinical setting – a single test system is within reach!

Dr. Darine Villela and colleagues in Dr. Carla Rosenber's lab at the University of Sau Paulo, Brazil sought to find an integrated solution to combine two tests into one – one that was cost effective and easy to adopt in a clinical setting. They noted that there are several tools for CNV analysis from sequencing data, but the homemade tools are designed for a specific pipeline, are not user-friendly and require a high degree of bioinformatics expertise. They knew they needed a solution that would be easy to implement in a clinical lab and chose a commercial target enrichment kit and BioDiscovery’s Nexus Copy Number for analysis.

How does clustering work in Nexus Copy Number?

When studying genomic data, we are often looking for similarities and differences among a group of samples. We try to see if there are any patterns and whether the samples group together into subsets based on gain and loss profiles. One way to do this is with a clustering function. clustering.pngIn Nexus Copy Number, clustering is done by clicking on the "Cluster" button on the "Results" tab.

Customer publication: functional analysis of CNA in sporadic colorectal cancer showcases Nexus Copy Number's statistical analysis tools

Most are well-aware of Nexus Copy Number’s strengths in detection of copy number from different technologies and this often overshadows the many other powerful features of Nexus Copy Number. A recent customer publication illustrates nicely the power of these additional analysis tools. Here I’m going to walk through a recent customer publication highlighting the areas where the authors used these powerful research tools available within Nexus Copy Number.

Patent application for methods for prognosticating brain tumors uses Nexus Copy Number and TCGA Premier

Cedar Sinai Medical Center in Los Angeles, CA has filed a patent for a method for prognosticating patient survival based on the ZEB1 gene. The application also describes methods for selecting therapies based on analysis of ZEB1 and several other genes.

Mosaic copy number aberrations in healthy individuals

Nexus Copy Number has helped many researchers to detect and interpret the profiles from cancer samples where contamination by normal cells is quite common.

Advances in Comparative Genomics and Genome Mapping

More and more plant and animal genomes are being sequenced and mapped - ANY organism with a mapped genome can be analyzed for copy number analysis using Nexus Copy Number.

What are systematic correction files?

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.

For CNV analysis, how do I combine data from different sources into a single Nexus Copy Number project?

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).

Looking for more information about integrating analysis of copy number, sequence variant and gene expression data?

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.

Can I Get Quality Copy Number Results from NGS data?

We have come a long way in a short amount of time with NGS (next-generation sequencing) technologies. Learn more about the benefits here!