Analyzing Affymetrix GeneChip SNP 6 Copy Number Data in Partek (Allele Specific)

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1 Analyzing Affymetrix GeneChip SNP 6 Copy Number Data in Partek (Allele Specific) This example data set consists of 8 tumor/normal pairs provided by Ian Campbell. Each pair of samples has one blood normal sample and one fresh frozen tumor sample. The samples were genotyped with a subset of the 270 HapMap samples available from Affymetrix. This tutorial will illustrate how to: Create Allele Specific Copy Number Identify regions of allelic imbalance Visualize the results with other data Note: It is recommended that you go through the Pattern Visualization System chapter in the Partek On-line Help before going through this tutorial if you have not done so. In addition, this tutorial covers specific information; for general information covering a variety of subjects, see the Partek On-line Help. The data and most library files for this experiment can be downloaded from Affymetrix s Support Materials and Data Resource Center; however, links to the necessary files can be found on the Partek tutorials page, found by selecting Help > On-line Tutorials in the Partek main menu. For this example, put the unzipped Data files (.CEL and sample information files) in the folder C:\Partek Example Data\SNP6. Put the unzipped Library Files (.cdf, annot.csv) C:\ Microarray Libraries\Affymetrix\SNP6. Please refer to the suggested guidelines on where to store these files on your computer in the Guidelines for Storing Affymetrix Library Files section of Chapter 4 of the Partek On-line Help. Estimating and Analyzing Allele Specific Copy Number Select Allele Specific Copy Number from the Workflows drop-down menu on the right side of the main window (Figure 1) Analyzing Affymetrix GeneChip SNP 6 Copy Number Data in Partek 1

2 Figure 1: Selecting the Allele Specific Copy Number option within the Partek GS main window Select Load Intensity Data. You will be asked to import CEL files or load an existing file as shown in Figure 2. Load the data from the file provided or import from CEL files. For instruction on importing from CEL files, see the SNP 6.0 HapMap tutorial. Figure 2: Loading allele intensity Next, select Load Genotype Data from the workflow. Load the genotypes from the provided file. Two spreadsheets will be loaded in the main window as shown in Figure 3 Analyzing Affymetrix GeneChip SNP 6 Copy Number Data in Partek 2

3 Figure 3: Viewing the spreadsheet after loading allele intensity and genotype spreadsheets Select Create Allele Specific Copy Number from the workflow; the dialog shown in Figure 4 will appear. Select the File column in each respective spreadsheet for the Unique sample column. This column should be unique for every sample and have the same value for both spreadsheets Select the Reference column as Tumor from the drop down menu. Choose N for the Reference category. These two fields will specify which samples are used as our normal references Select SubjectID from the Paired subject column drop down menu. This will match the normal references to the study samples Click OK. When complete, a new spreadsheet will be created containing allele specific copy number for the heterozygous calls in the normal sample Analyzing Affymetrix GeneChip SNP 6 Copy Number Data in Partek 3

4 Figure 4: Configuring the Allele Specific Copy Number Dialog From the Analysis section of the workflow, select Detect Allelic Imbalances The created spreadsheet will contain regions that have similar allele imbalance scores defined as (Max Min) / (Max + Min). A spreadsheet will be created containing all regions for all samples with the mean imbalance. We will filter the regions with the lowest proportion. Select the Interactive filter from the main window toolbar. Choose Proportion from the drop down Column menu. We will filter own most of the lowest mode from the results. Set the Min value to The filters will adjust as shown in Figure 5. Analyzing Affymetrix GeneChip SNP 6 Copy Number Data in Partek 4

5 Figure 5: Reviewing the filtered allele imbalance spreadsheet Select Plot Allele Specific Copy Number from the Visualization section of the workflow. From the Detected Regions drop down menu, select the imbalance spreadsheet. If you have total copy number estimates or other data, you can specify them here to be visualized as well. The dialog should appear as in Figure 6 Select OK Figure 6: Configuring the multiple track visualization Select a region in the bottom heat map. This will show the allele specific copy number for the sample as shown in Figure 7. Analyzing Affymetrix GeneChip SNP 6 Copy Number Data in Partek 5

6 Figure 7: Viewing the allele specific copy number for detected region End of Tutorial This is the end of the mapping SNP 6.0 allele specific copy number tutorial. If you need additional assistance with this data set, you can call our technical support staff at or our technical support staff at Copyright 2007 by Partek Incorporated. All Rights Reserved. Reproduction of this material without expressed written consent from Partek Incorporated is strictly prohibited. Analyzing Affymetrix GeneChip SNP 6 Copy Number Data in Partek 6