OncoScan Console 1.3 Software provides quality control (QC) and data summaries for OncoScan FFPE Assay Kit and OncoScan CNV FFPE Assay Kit.

Key features

  • Runs TuScan analysis algorithm to determine copy number for samples processed using OncoScan™ FFPE Assay Kit
    • Provides copy number in log2 and linear scale
    • Algorithmically identifies diploid regions and uses them to properly center the log2 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 FFPE Assay Kit, run Affymetrix' somatic mutation algorithm to identify the presence of key somatic mutations
  • Displays the relevant QC metrics for OncoScan FFPE Assay Kit, 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

Download information and instructions

GeneChip™ Command Console (AGCC) requires library files to scan OncoScan arrays. Download the desired AGCC library file package to the Command Console workstation, extract the zip archive, and install the needed files by running the AGCC library installer.

Recommended system requirements
Processor 3+ GHz Intel™ Pentium™ Quad Core
64-bit Win7 or 64-bit Win8 operating system and web browser Windows™ 7 Professional SP1 or Windows 8.1 Professional and Internet Explorer™ 9.0 or above
Available disk space 250 GB HD + data storage
Free disk space required at install >5 GB
RAM 16 GB

Minimum system requirements
Processor 2+ GHz Intel Pentium Dual-Core
64-bit Win7 or 64-bit Win8 operating system and web browser Windows 7 Professional SP1 or Windows 8.1 Professional and Internet Explorer 9.0 or above
Available disk space 150 GB HD + data storage
Free disk space required at install >5 GB
RAM 8 GB

Technical documentation

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.

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