OncoScan Console 1.3 is the original analysis software for OncoScan CNV and OncoScan CNV Plus assays.

Chromosomal Analysis Suite (ChAS) software is our most up-to-date analysis software with improved functionality and content, updated security, and the most current library files. ChAS is the preferred analysis software for OncoScan CNV and CNV Plus assays.

Visit the ChAS webpage to learn more.

Key features of OncoScan Console 1.3 Software

  • Runs TuScan analysis algorithm to determine copy number for samples processed using OncoScan CNV and OncoScan CNV Plus assays
    • Provides copy number in log and linear scale
    • Algorithmically identifies diploid regions and uses them to properly center the log ratios
    • Identifies regions of loss of heterozygosity (LOH) including regions of copy neutral LOH
    • In some cases, provides an estimate of the percent of aberrant cells in the sample and estimates the copy number change in just the aberrant cell population
    • For OncoScan CNV Plus Assay, run Affymetrix' somatic mutation algorithm to identify the presence of key somatic mutations
  • Displays relevant QC metrics, including the ability to apply custom thresholds to identify outlier samples
  • Uses "signature SNPs" to identify potential errors in channel identification and sample pairing during analysis set-up
  • Supports the download of the necessary analysis and annotation files from NetAffx

Technical documentation

Manuals
Quick reference cards
Sample data
Additional support
NetAffx alignment files
Current NetAffx annotation files

Note: NetAffx Annotation Files are intended for use in automated analysis. Some are not compatible with all spreadsheet applications. Please use the NetAffx Analysis Center to limit download data to your probesets of interest. Annotation CSV files for the exon arrays are split into a probeset level annotation file and a transcript cluster level annotation file; exon array CSV files are compatible with ExACT.

Citations

Comparative transcriptional profiling of orange fruit in response to the biocontrol yeast Kloeckera apiculata and its active compounds
Liu, P.; Chen, K.; Li, G. F.; Yang, X. P.; Long, C. A. BMC Genomics 17(), NPG, 2016 PubMed

A novel comparative pattern analysis approach identifies chronic alcohol mediated dysregulation of transcriptomic dynamics during liver regeneration
Kuttippurathu, L.; Juskeviciute, E.; Dippold, R. P.; Hoek, J. B.; Vadigepalli, R. BMC Genomics 17(), NPG, 2016 PubMed

Anti-VP6 VHH: An Experimental Treatment for Rotavirus A-Associated Disease
Maffey, L.; Vega, C. G.; Mino, S.; Garaicoechea, L.; Parreno, V. Plos One 11(9), NPG, 2016 PubMed

A cross-modal genetic framework for the development and plasticity of sensory pathways
Frangeul, L.; Pouchelon, G.; Telley, L.; Lefort, S.; Luscher, C.; Jabaudon, D. Nature 538(7623), 96-8, 2016 PubMed

Phenotypic and Molecular Alterations in the Mammary Tissue of R-Spondin1 Knock-Out Mice during Pregnancy
Chadi, S.; Polyte, J.; Lefevre, L.; Castille, J.; Ehanno, A.; Laubier, J.; Jaffrezic, F.; Le Provost, F. Plos One 11(9), NPG, 2016 PubMed

Required products

For Research Use Only. Not for use in diagnostic procedures.