Nexus Copy Number – Accelerating Copy Number Analysis Research

Nexus Copy Number simplifies genetic aberration analysis with an elegant 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. 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 any commercial or custom array as well as any organism, Nexus Copy Number is the only solution 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 any investigator.

Nexus Copy Number - Accelerating Copy Number Analysis Research

Compare Editions



Standard Discovery

Flexible data type and experiment design support



Platform independent – support for all array platforms and associated software including Affymetrix®, Agilent®, Illumina®, Roche NimbleGen®, GenePix®, ImaGene®, and more

Support for any organism
Support for dye-swap experiments

Processing



Efficient processing for 1000s of arrays
Support for other calling algorithms

Sample QC

Aberration detection



Copy number change identification Screenshot Preview
Allelic event calling for SNP arrays (e.g. LOH) Screenshot Preview
Identification of common areas and minimal common areas of aberrations Screenshot Preview
Identify statistically significant frequency peaks in a population
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Results reporting



Customized sample reports Screenshot Preview
High resolution publication ready images

Integration with public and custom databases



Link to external databases (e.g. NCBI, Ensemble, DECIPHER)
Annotation tracks for genes, exons, miRNAs, CNVs Screenshot Preview
Custom annotation tracks
Custom CNV database support

Data exploration



Integration of phenotype/clinical data (factors) Screenshot Preview
Display of aberration frequency by phenotype or factor subgroups Screenshot Preview
Factor enrichment
Ability to query all samples based on genes or genomic locations Screenshot Preview
Identification of regions of statistically significant difference between sample populations Screenshot Preview
Identification of regions with statistically significant predictive power on numeric phenotypes Screenshot Preview
Survival analysis (Kaplan Meir plots and significance values)
Screenshot Preview
Clustering of samples based on genomic change Screenshot Preview
Gene ontology enrichment analysis Screenshot Preview

Integration of external data



Gene and miRNA expression results integration Screenshot Preview

White Papers

Recent Publications

A de-novo 7.6 Mb tandem duplication of 14q32.2-qter associated with primordial short stature with neurosecretory growth hormone dysfunction, distinct facial anomalies and mild developmental delay
Thiel CT, Dörr HG, Trautmann U, Hoyer J, Hofmann K, Kraus C, Ekici AB, Reis A, Rauch A. Eur J Med Genet. 2008 Jul-Aug; 51(4):362-7. Epub 2008 Mar 20. [PubMed]

Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia
Tom Walsh, Jon M. McClellan, Shane E. McCarthy, Anjene M. Addington, Sarah B. Pierce, Greg M. Cooper, Alex S. Nord, Mary Kusenda, Dheeraj Malhotra, Abishek Bhandari, Sunday M. Stray, Caitlin F. Rippey, Patricia Roccanova, Vlad Makarov, B. Lakshmi, Robert L. Findling, Linmarie Sikich, Thomas Stromberg , Barry Merriman, Nitin Gogtay, Philip Butler, Kristen Eckstrand, Laila Noory, Peter Gochman, Robert Long, Zugen Chen, Sean Davis, Carl Baker, Evan E. Eichler, Paul S. Meltzer, Stanley F. Nelson, Andrew B. Singleton, Ming K. Lee, Judith L. Rapoport, Mary-Claire King, Jonathan Sebat. Rare structural variants disrupt multiple genes in neurodevelopmental pathways in schizophrenia. Science, 27 March 2008. (10.1126/science.1155174). [Abstract]

Multiple sub-microscopic genomic lesions are a universal feature of chronic myeloid leukaemia at diagnosis
J S Khorashad, V A De Melo, H Fiegler, G Gerrard, D Marin, J F Apperley, J M Goldman, L Foroni and A G Reid. Leukemia (2008) 22, 1806–1807. (10.1038/leu.2008.210) [Abstract] [PubMed]

Customized Oligonucleotide Array-Based Comparative Genomic Hybridization as a Clinical Assay for Genomic Profiling of Chronic Lymphocytic Leukemia

Rachel Sargent, Dan Jones, Lynne V. Abruzzo, Hui Yao, Jaime Bonderover, Marissa Cisneros, William G. Wierda, Michael J. Keating and Rajyalakshmi Luthra. Journal of Molecular Diagnostics 2009, Vol. 11, No. 1. (10.2353/jmoldx.2009.080037) [Abstract]

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System Requirements

Platforms Supported: Windows Win2k/WinXP, OS X
Minimum: 1.0 GHz Pentium or G4, 512 MB RAM
Recommended: 2.0 GHz or faster Core 2 Duo, 1024 or more MB RAM

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