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BioDiscovery, Inc.'s Nexus Copy Number 6 Significantly Improves Analysis of Cancer Samples with New ASCAT Processing

8/31/2011 1:38:34 PM

EL SEGUNDO, CA, August 31, 2011 – BioDiscovery, Inc. a leader in integrated software solutions for genomics data analysis from high-throughput microarray and Next-Gen sequencing technologies announced today inclusion of the Allele Specific Copy number Analysis of Tumors (ASCAT) algorithm to its latest version of Nexus Copy Number software (ver. 6.0), the leading platform independent and user friendly application for DNA analysis. The ASCAT algorithm was developed by scientists at Radium Hospital in Oslo and was recently published in Proceedings of the National Academy of Sciences U.S.A. (Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16910-5). The approach utilizes the allelic information generated by SNP array platforms to estimate the sample ploidy as well as percentage of “normal” contamination in tumor samples, factors that are very important in using such data in cancer research. The Nexus implementation of ASCAT is platform independent and quite efficient. The processing can be performed on Affymetrix arrays (including the new OncoScan™ FFPE product), as well as on Illumina arrays.

“Nexus Copy Number is widely used in the cancer community and several notable cancer centers were the first groups to implement the software. Copy number analysis of cancer samples poses many challenges as the samples tend to be heterogeneous making it difficult to ascertain the ‘real’ aberrant events” said Dr. Soheil Shams, CEO of BioDiscovery. “Among several new tools for analysis of cancer samples in version 6 of Nexus Copy Number, an important addition is the ASCAT processing which helps address such issues. Using both the B-allele frequency and the log ratio values, ASCAT processing extracts the ploidy information allowing users to see how many copies of a chromosome are present as well as the percent of contamination of normal samples in the tumor cell population. This vital additional information makes it much easier for the researcher to make sense of the complicated aberration profiles that are generally derived from cancer samples.”

“We initially developed ASCAT to be able to analyze our own SNP array data, as at the time, no methods existed that could correctly interpret high-throughput genomics data of primary tumors”, said Dr. Peter Van Loo, one of the key developers of ASCAT. “We believe many researchers would benefit from using a method such as ASCAT, and the inclusion of ASCAT into Nexus Copy Number makes it available for all in an easy-to-use way.”

Nexus Copy Number can integrate and process together, in a single project, data from commercial array platforms such as Agilent, Affymetrix, Illumina, Roche NimbleGen, Next Gen read depth, as well as custom arrays. With its free access to a web-based repository for querying, and storing genomic data from any location across the globe, Nexus Copy Number is a powerful solution for large groups such as special consortia. The software is applicable to many types of studies from focused projects of a cytogeneticist to large scale cancer or GWAS studies. BioDiscovery is attuned to such different needs and offers the product in a flexible and modular system to allow users to create configurations that are suited to their needs.

About BioDiscovery, Inc.

BioDiscovery is a leader in the development of advanced microarray bioinformatics software and services that enable its customers to revolutionize drug discovery and diagnostics by efficiently managing, integrating, and analyzing data generated using high-throughput microarray technology. Contact BioDiscovery: 310-414-8100 or

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