APPLICATION CATEGORY - CHROMOSOMAL COPY NUMBER

Identification of chromosomal amplifications or deletions can be correlated with disease-associated phenotypic conditions. Software applications within this class allow researchers to leverage Affymetrix arrays to identify differences in chromosomal copy number thus providing insights into fields such as cancer biology.

Developers interested in creating tools in this application class should review the resources available here.

BioDiscovery Nexus CGH
BioDiscovery | Support | Nexus CGH | Online Demo | Download Evaluation

Nexus CGH allows scientist to perform copy number analysis and visualization across large data sets having thousands of samples and millions of probes per sample. The software supports many platforms including Affymetrix SNP array data. Nexus CGH provides an intuitive and interactive user interface allowing rapid identification of critical regions of genomic change in the entire population or sub-groups (e.g. different disease states). The publication quality visualization tools are coupled with sophisticated statistical analysis for identification of areas of minimal overlap, statistically significant regions between two populations, clustering of samples based on genomic profiles, over representation of GO terms in regions of genomic instability, and much more. Nexus CGH is unlike any other tool for copy number analysis on the market taking advantage of BioDiscovery's decade long experience in developing pioneering software for the microarray market.

Exemplar Copy Number
Sapio Sciences | Technical Specs | Support | Sales

Exemplar's Copy Number Module is the first complete implementation of the Copy Number algorithm outside of the CNAT tool. The Copy Number module has the following features:

Golden Helix's Copy Number Analysis Module (CNAM)
HelixTree | CNAM | Download | Webinars | Tutorials | Support | Golden Helix, Inc.

The Golden Helix Copy Number Analysis Module (CNAM) is an advanced software application which provides the high accuracy needed for whole genome copy number assocation studies.

CNAM provides a powerful set of novel methods and workflows for detecting copy number variations (CNVs) and performing association analysis on both CNV covariates and log ratios directly. It employs a proprietary optimal segmenting algorithm that can detect CNVs with astonishing accuracy. In fact, its unique multivariate method can detect CNVs at single marker resolution! You can also use CNAM to normalize log ratios against a reference set of your choice and correct for batch effects and stratification in your data using an Eigenstrat-based principal component analysis method.

Affymetrix Compatibility
CNAM substantially replicates the Affymetrix workflow for converting CEL files to log ratios. This includes:

This can be done for 500k, SNP 5.0, and SNP 6.0 arrays. Further, it is relatively high speed and works for thousands of samples. (2,000 samples can be processed overnight.) If preferred, CNAM can also read CNT and CNCHP files from Affymetrix's CNAT Batch Analysis and Genotyping Console Software 2.0 Software tools.

View a recent Affymetrix webcast from February 2008 for an overview of whole genome copy number (and SNP) association using Golden Helix software and Affymetrix arrays.

Partek® Genomics Suite

Partek | Technical Specs | Support | Sales | Download | Partek Genomics Suite

Partek Genomics Suite is an integrated statistical and visual analysis solution for GeneChip® experiments, optimized for fast and memory-efficient processing of large, ultra high-dimensional data. Statistical and visual features make it easy to detect regions of insertions and deletions on the genome. The Partek Genome Browser™ provides dot plots, box & whiskers, profiles, and gene summaries to show the level of insertion/deletion, and the number of affected individuals. All graphs can be exported in publication-quality vector graphic format. Partek GS has seamless integration with CNAT version 3 output files and CEL files, and automatically associates annotations to all results, providing hyperlinks to NetAffx and other internet databases.

View a recent Partek webinar from October 2007, illustrating a complete workflow to identify regions of amplification and deletion using the Affymetrix Copy Number platform.