Topic: Research

The role of a Customer Success Manager in Biotech: customer focus for positive outcomes

With a continued focus on customers, BioDiscovery moves from a sales and support departmental structure to a holistic team filled with Customer Success Managers.

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.

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.

Nexus Copy Number – Casting a Wide Net

Nexus Copy Number has been used to work on a variety of organisms, including canines, monkeys, plants, humans, and more. View these highlighted publications.

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).

Using CoNIFER to Detect Copy Number Variations from Exome Sequencing Data

CoNIFER can be used to discover CNVs that might be missed by standard practices. Look at our considerations when evaluating the CoNIFER algorithm.

Estimating Copy Number From Log Ratios

Take a look at some common questions that customers have about using Nexus, and receive some advice on calculating the actual copy number of samples in Nexus.

From Raw Data to Copy Number Calls – Data processing workflow in Nexus Copy Number

Take a look at how Nexus Copy Number handles the different “Raw Data” and the three steps to analyzing the data.

Estimation of Aberrant Cell Percentage in Tumor Normal Cell Mixture

Cancer samples usually contain a mixture of tumor and normal cells. Take a look at this formula for calculating a one-copy loss event.