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Chromosome Copy Number Analysis Tool (CNAT)

The Affymetrix Chromosome Copy Number Analysis Tool 4.0 (CNAT 4.0) implements a new algorithm developed to identify genome-wide chromosomal gains and losses and loss of heterozygosity (LOH) using high-density SNP oligonucleotide arrays and the whole-genome sampling assay (WGSA). Similar to the previous version, CNAT 4.0 is integrated into the Affymetrix GeneChip® Genotyping Analysis Software (GTYPE) to allow genotype calling and copy number calculations to be performed within one software application.

CNAT 4.0 Benefits

  • Support for all GeneChip Mapping Arrays: Mapping 10K, 50K, 100K, 250K and 500K
  • Four workflows: Copy number for paired tumor/normal samples, copy number for un-paired samples, LOH for paired tumor/normal samples and LOH for un-paired sample
  • Normal references available:
    • 48 HapMap Samples
    • Additional HapMap samples are available on the HapMap and GEO websites (Accession Number GSE5173)
  • Sample data sets available
  • PCR fragment size and GC content normalization (Nannya, et al. CancerRes; 65(14), 6071-79 (2005).)
  • Allele-specific copy number estimation on paired tumor/normal samples
  • Hidden Markov Model (HMM) for copy number and LOH
  • Graphical display of data: Copy number, HMM states and Loss of Heterozygosity (LOH)
  • Direct Export to Affymetrix' Integrated Genome Browser (IGB)
  • Export data in wiggle format for uploading into UCSC browser
    • IGB and UCSC genome browsers enable the identification of disease genes and biomarkers

Copy Number Analysis Tool Download

The Copy Number Analysis Tool is currently available as a Microsoft Windows installer package:

Download Copy Number Analysis Tool 4.0.1 (zip 14 MB)  * Posted on 3/28/2007

The details of the updated copy number data analysis workflow using CNAT 4.0 are described in a workflow document.

Further details can be found in the CNAT 4.0 user guide. CNAT is an Affymetrix Tool and subject to the Affymetrix Tool Support Policy.