C.2.1 About Affymetrix CNAT

The Affymetrix GeneChip Chromosome Copy Number Analysis Tool (CNAT) is an application used with the Affymetrix GeneChip Genotyping Analysis (GTYPE) software. The CNAT Batch Analysis Tool uses cell intensity (CEL) files and GTYPE analysis results (CHP files) to create copy number analysis files (CNT files) from Affymetrix Mapping data.

GTYPE analysis supports the following DNA probe arrays:

• Affymetrix GeneChip Human Mapping 10K Array
• Affymetrix GeneChip Human Mapping 100K Array
• Affymetrix GeneChip Human Mapping 500K Array

The data must be accessed from the Affymetrix GCOS database, and therefore you must have the associated library files and the corresponding experimental information files (EXP files).

C.2.2 Creating the CNT Files

C.2.2.1 CNAT Batch Analysis Window

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The CNAT Batch Analysis Window is where the copy number analysis is run. In this window you select the sample type, the analysis type, and the CHP files that will be used for samples and references.

In CNAT, you have three analysis options: copy number analysis (CN), loss of heterozygosity (LOH) analysis, or both analyses. For copy number analysis, the output files will have the form *.cn.cnt; for loss of heterozygosity analysis, the output files with have the form *.loh.cnt. Selecting to perform both analyses will generate both types of CNT files. HelixTree does not currently support loss of heterozygosity analysis data; therefore, to create CNT files that can be used in HelixTree, you must select either Copy Number (CN) or CN & LOH.

C.2.2.2 Advanced Analysis Options

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Pressing the Advanced Analysis Options button in the CNAT Batch Analysis Window opens the Advanced Options dialog. In this dialog, you can set copy number parameters that effect the smoothing performed during the copy number analysis.

The Genomic Smoothing feature uses guassian smoothing to increase or decrease the significance of small aberrations in the data. In order for the resulting CNT files to be compatible with HelixTree, the Genomic Smoothing must be set to 0 Mb.

C.2.2.3 Performing the Analysis

After the options have been set, return to the Batch Analysis Window to start the analysis. When the analysis is running, CNAT accesses both the selected CHP files and their corresponding CEL files. The analysis results files will have the suffix *.cn.cnt and will be put in the destination folder specified in the Batch Analysis Window. These CNT files are then ready to be used in HelixTree. For instructions on how to use HelixTree to convert the CNT files to Copy Number DSF files, see section 4.4.1.2.