Nexus Copy Number™

Category Genomics>Genetic Data Analysis/Tools

Abstract Nexus Copy Number™ is a leading software solution for DNA copy number change detection, visualization, and identification of critical phenotype-related changes in large sample populations.

Nexus Copy Number simplifies ‘genetic aberration’ analysis with an advanced and simple user interface, efficient processing for rapid and automated analysis of thousands of arrays, and a flexible design that accommodates user preferences such as custom annotation tracks, integration of custom databases [e.g. copy number variations (CNVs), genetic disorders], segmentation algorithm, and integration of miRNA and gene expression data.

With detection of copy number and LOH events and flexibility in handling almost any commercial or custom array as well as almost any organism, Nexus Copy Number is one of the only solutions you need for array based genetic aberration analysis.

With a choice of two configurations (Standard or Discovery Editions), Nexus Copy Number meets the needs of almost any investigator.

With direct integration to Nexus DB (see below...), a Cloud based highly scalable global repository, users have an unprecedented advantage to query for samples across projects they own or part of collaborations and consortiums.

Nexus Copy Number features/capabilities include:

Data type and experiment design support --

1) Platform independent - support for array platforms and associated software including Affymetrix®, Agilent®, Illumina®, Roche NimbleGen®, GenePix®, ImaGene® (see G6G Abstract Number 20128R), and more.

Affymetrix Compatibility - Nexus Copy Number is a GeneChip-compatible™ application and supports data from all Affymetrix® GeneChip® arrays (e.g. SNP 6.0, SNP 5.0, 500K, 100K, 10K, and custom arrays).

Agilent Compatibility - All Agilent CGH arrays including custom arrays are supported by Nexus Copy Number. Nexus Copy Number easily loads raw data output from Agilent’s Feature Extraction software or any other spotted array image analysis tool, such as ImaGene or GenePix.

Illumina Compatibility - BioDiscovery is a participant in the Illumina Connect Program and provides a Bead Studio plug-in allowing direct export of data from Bead Studio into Nexus Copy Number.

NimbleGen Compatibility - Roche NimbleGen has partnered with BioDiscovery to provide a complete analysis solution to their CGH array customers. Nexus Copy Number is the recommended software for copy number analysis of NimbleGen CGH arrays.

Genepix Compatibility - Nexus Copy Number is pre-configured to handle output from GenePix. All that is needed are the .GPR output files.

2) Support for almost any organism; and 3) Support for dye-swap experiments.

Processing --

1) Efficient processing for 1,000s of arrays; 2) Support for other calling algorithms; and 3) Sample QC.

Aberration detection --

1) Copy number change identification - Rank Segmentation is BioDiscovery’s proprietary algorithm based on the well accepted Circular Binary Segmentation (CBS) approach having been made robust to outliers and greatly improved in terms of performance.

2) Allelic event calling for SNP arrays (e.g. LOH) - The proprietary BioDiscovery SNPRank Segmentation algorithm takes advantage of B-allele frequency values and combines them with log ratios for segmentation of SNP array data and for performing allelic events calls such as LOH.

3) Identification of common areas and minimal common areas of aberrations - Sort and identify exact boundaries of common aberrations in a user defined frequency and easily locate the minimal common areas in a tabular format.

4) Identify statistically significant frequency peaks in a population - Calculate the frequency p-value as defined by the STAC algorithm.

Results reporting --

1) Customized sample reports - Generate aberration reports for the entire data set or for selected or individual samples. Customize sample reports with annotations you want to see (e.g. gene symbols, syndromes from the Decipher database, flanking FISH probe IDs for validation, Locus IDs, and more).

2) High resolution publication ready images.

Integration with public and custom databases --

1) Link to external databases (e.g. NCBI, UCSC, Ensemble, DECIPHER, DGV, and more).

2) Annotation tracks for genes, miRNAs, CNVs, genetic disorders - Annotation tracks integrated with the genome browser show clickable items such as genes, CNVs, and exons. Clicking on a gene provides further information from a selection of sites such as UCSC and Google.

Exon numbers can be displayed for any one of the gene’s transcript variants. Clicking on a CNV lists all overlapping CNVs at that location with hyperlinks to publications and records from the Database of Genomic Variants (DGV).

3) Custom annotation tracks; and 4) Custom CNV database support.

Data exploration --

1) Integration of phenotype/clinical data (factors) - Nexus allows addition of an unlimited number of clinical annotations/phenotypes for correlation studies.

2) Display of aberration frequency by phenotype or factor subgroups - Quickly see what factor values/phenotypes are associated with a particular aberration by viewing aberration frequency by factor subgroups.

3) Factor enrichment - Identify which phenotypes are overrepresented in another factor value of interest along with the p-value significance.

4) Ability to query all samples based on genes or genomic locations.

5) Identification of regions of statistically significant difference between sample populations - Identify the aberrant regions that are significantly different between population subgroups. In addition to tabular results, view such differences in graphical format with statistically significant differences indicated clearly.

6) Survival analysis (Kaplan Meir plots and significance values) - Study survival analysis with Kaplan Meir plots and identify survival differences that are statistically significant.

7) Clustering of samples based on genomic change - Choose from a number of clustering algorithms to group samples based on genomic aberration profiles.

8) Gene Ontology (GO) enrichment analysis - Discover statistically significant gene ontology terms affected in selected aberrant regions. Or find affected terms over the whole genome using a BioDiscovery gains and losses.

Integration of external data --

1) Gene and miRNA expression results integration - Integrate external data such as gene and miRNA expression results to correlate expression changes with copy number changes.

Nexus DB --

Nexus DB is a unique repository and data sharing system that was designed to serve a need arising from the rapid growth in application of high-resolution genome-wide technology for identification of copy number variations.

Key Features include:

1) Access data from anywhere with secure password protected login;

2) Search for samples meeting a particular query (e.g. disease state or platform);

3) Search for samples with specific aberrations (e.g. a loss at a specific genomic location);

4) Create groups and consortia to share data with colleagues across the globe;

5) Utilize the cloud computing infrastructure for virtually unlimited storage without a need for a database administrator and storage and server costs; and

6) Store processed data securely on external servers using 128-bit encryption.

Nexus Copy Number 5.1 New Features -- New features include:

1) QC Processing Steps -

2) Data Loading and Processing -

3) Visualization -

4) Annotation Databases -

5) Statistics and QC Measurements -

Note: See G6G Abstract Number 20129R for additional product info from this manufacturer.

System Requirements


Manufacturer Web Site Nexus Copy Number

Price Contact manufacturer.

G6G Abstract Number 20132B

G6G Manufacturer Number 100431