Creating CNCHP Files using Affymetrix Genotyping Console 2.0

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C.3.1 About Affymetrix Genotyping Console

AffymetrixR○ Genotyping ConsoleTM (GTC) is an application used to calculate genotype calls and to generate copy number data. Genotyping Console uses cell intensity (CEL) files and genotypeing analysis results (CHP files) to create copy number analysis files (CNCHP files) from Affymetrix Mapping data.

GTC supports the copy number analysis of the following DNA probe arrays:

  • Affymetrix GeneChipR○ Human Mapping 100K Array
  • Affymetrix GeneChipR○ Human Mapping 500K Array
  • Affymetrix GeneChipR○ Genome Wide SNP 6.0 Array

GTC also supports genotype analysis of the Genome Wide SNP 5.0 Array; however, as of the release of Genotyping Console 2.0, the software does not support copy number analysis of the SNP 5.0 Array.

C.3.2 Generating CNCHP Files for the Mapping 100k and Mapping 500k Arrays

C.3.2.1 Setting Analysis Configurations

To perform copy number analysis of Mapping 100K or Mapping 500K data for analysis in HelixTree, first set the analysis parameters using the menu Edit->Copy Number / LOH Configurations->New Configuration....

After selecting the array type, a dialog will open where 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 CNCHP files to be compatible with HelixTree, the Genomic Smoothing must be set to 0 Mb.

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Figure C.3: Setting up the copy number configuration for 500K analysis in Affymetrix○R Genotyping ConsoleTM
C.3.2.2 Starting the Analysis

Start the copy number analysis by using Workspace->Intensity Data->Perform Copy Number / LOH Analysis....

In the first window, select the sample type and the analysis type. HelixTree does not currently support paired sample analysis or LOH analysis. Select the Unpaired Sample Analysis sample type and the Copy Number (CN) analysis type.

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Figure C.4: Selecting the sample and analysis type for 500K copy number analysis in Affymetrix○R Genotyping ConsoleTM

In the next window, select from the first drop down list the analysis configuration where the Genomic Smoothing was set to 0 Mb. By clicking the Advanced> button, you can verify the settings. Verify the output path and the batch name for the analysis.

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Figure C.5: Selecting the analysis options for 500K copy number analysis in Affymetrix○R Genotyping ConsoleTM

In the following window, select the CEL files that will be used for samples and references, select the enzyme’s shared attribute, and begin the analysis.

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Figure C.6: Selecting sample and reference files for 500K copy number analysis in Affymetrix○R Genotyping ConsoleTM

When the analysis is complete, a *.CN4.cnchp file will be created for each sample. Those files will be located in the directory given by the selected output path and batch name. The *.CN4.cnchp files are ready to be converted to a copy number DSF using the CNCHP file parsing tool in HelixTree (See 4.4.1.3).

C.3.3 Generating CNCHP Files for the Genome Wide SNP 6.0 Array

C.3.3.1 Setting Analysis Configurations

To perform copy number analysis of Genome Wide SNP 6.0 data for analysis in HelixTree, first set the analysis parameters using the menu Edit->Copy Number / LOH Configurations->New Configuration....

After selecting the array type, a dialog will open where you can set parameters that effect the copy number analysis. Click on Advanced to view the advanced settings. For copy number analysis in HelixTree, the data should not have any smoothing applied. In the SmoothSignal Graph Output, set both the Smoothing Guassian Window and the Smoothing Sigma Multiplier to 0. Under Smoothing Parameters select Skip any smoothing.

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Figure C.7: Setting up analysis configurations for SNP 6.0 copy number analysis in Affymetrix○R Genotyping ConsoleTM
C.3.3.2 Starting the Analysis

Genotyping Console uses a *.ppw reference model file for copy number analysis of SNP 6.0 array data. GTC allows you to use a reference model file provided by Affymetrix. You may also select to create your own reference model file with samples selected from your Genotyping Console Workspace. To start the copy number analysis using your own reference samples, select Workspace->Intensity Data->Create Copy Number / LOH Reference Model File and Perform Analysis.... To start the analysis using the reference model provided or a reference model you previously created, select Workspace->Intensity Data->Perform Copy Number / LOH Analysis....

In the first window, select from the first drop down list the analysis configuration where the smoothing was deactivated. By clicking the Advanced> button, you can verify the settings. Verify the output path and the batch name for the analysis.

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Figure C.8: Selecting the analysis options for SNP 6.0 copy number analysis in Affymetrix○R Genotyping ConsoleTM

If you selected to create a reference model, the following window will prompt for the samples to be used in the reference model. Select the reference samples and a save location for the reference model. Copy number results will be generated for each of the samples in the reference set. If you selected not to create a reference model, the window will prompt for the samples to be analyzed. You must also select the reference model file you wish to use for this analysis.

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Figure C.9: Selecting samples to create a reference model file for SNP 6.0 copy number analysis in Affymetrix○R Genotyping ConsoleTM

When the analysis is complete, a *.CN5.cnchp file will be created for each sample. Those files will be located in the directory given by the selected output path and batch name. The *.CN5.cnchp files are ready to be converted to a copy number DSF using the CNCHP file parsing tool in HelixTree (See 4.4.1.3).

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