This section will instruct you on how to download and install the HelixTree DSF Plug-In to be used with Illumina BeadStudio. You will also be guided through the export of your genotype or copy number analysis data from BeadStudio into HelixTree’s proprietary sparse data storage format (DSF) files. Please note, these instructions only apply for BeadStudio version 3.0 or greater. A breif discussion on how to import the data into HelixTree will also be provided.

D.3.1 Installation of the HelixTree Plug-In

Before beginning the installation, make sure all instances of BeadStudio are not running.

To install the HelixTree DSF Plug-in into Illumina BeadStudio, you must first download the plug-in installer from http://www.goldenhelix.com/download/bin/HelixTreeBeadStudioPlugin.exe.

When the download has completed, open the installer and click Next to continue the installation. The second window will ask for a directory to extract the plug-in to; by default, the location is the standard BeadStudio installion directory:

C:\Program Files\Illumina\BeadStudio 2.0

Click Next and the installation will be finished. Three plug-ins will be made available with this installation: a DSF export plugin for exporting SNP call data or copy number LogR ratios (section D.3.2), an import bookmark file plug-in that allows you to view copy number segmenting results generated in HelixTree (section 25.8.1), and a segment means import plug-in that allows you to view copy number segment means data calculated in HelixTree (section D.3.4).

D.3.2 Exporting DSF Data from BeadStudio

D.3.2.1 The BeadStudio Report Wizard

To export a HelixTree DSF, a BeadStudio project must be open. From BeadStudio, open the report wizard by selecting Analysis->Reports->Report Wizard. See figure D.1.

From the Report Wizard, select Custom Report and, from the dropdown menu, select HelixTree DSF Export from Golden Helix, Inc. Click Next.

Figure D.8: Selecting the report type in the BeadStudio Reports Wizard

Select the sample groups that you wish to include in your report and click Next.

Figure D.9: Selecting sample groups in the BeadStudio Reports Wizard

If you have excluded samples inside the BeadStudio project the following window will appear. In this window you must instruct BeadStudio on how to handle these excluded samples. BeadStudio offers to remove the samples from the report or to zero the samples so they are present but do not show data.

Note: BeadStudio will not zero Log R ratio data (see section D.3.2.2) even for samples that have been excluded from the data set. If the Log R ratio data for these samples is not wanted in the report, select remove them from the report.

Click Next.

Figure D.10: Selecting how to handle excluded samples in the BeadStudio Reports Wizard

The following window may appear if you have applied filters to your data inside BeadStudio. Select whether or not you want to include the hidden SNPs in your report, and click Next to continue through the wizard.

Figure D.11: Selecting whether or not to include hidden SNPs in the BeadStudio Reports Wizard

Select the Output Path and a Report Name. These parameters will determine the final DSF file name and directory location. Click Finish.

Figure D.12: Setting the Output Path and the Report Name in the BeadStudio Reports Wizard

D.3.2.2 The HelixTree DSF Export Window

After going through the BeadStudio Report Wizard, a BeadStudio progress bar will appear. After a brief moment, the HelixTree DSF Export window will open. In this window you must select the output options that determine what type of data you wish to export in DSF format.

Figure D.13: Setting the DSF export options in the HelixTree DSF Export Window

There are two DSF output options to choose from: SNP Call Data and Log R Ratios for Copy Number Analysis. If you choose to export SNP Call Data, you must also choose which strand type you want to use for base pair translations, which is used when importing a DSF file into HelixTree. Top is recommended.

The Output DSF File is displayed at the bottom of the window. The file name is set by the output directory chosen in the BeadStudio Report Wizard and can not be changed in this window.

You may also deselect individual chromosomes to be left out of the DSF file. Pressing the Pick Chromosomes button will open the Chromosome Picker where you can select or deselect specific chromosomes. Only chromosomes initially included in the report will be available in the Chromosome Picker.

Click OK in the HelixTree DSF Export window to begin the export.

D.3.3 Importing the DSF file into HelixTree

The method that should be used to import the data into HelixTree will depend on if you selected to export SNP Call Data or Log R Ratios for Copy Number Analysis from the HelixTree DSF Plug-In.

If the data that was exported from BeadStudio was SNP Call Data, the data should be imported using File->Import Data->Import DSF. For details about this import process, see Importing DSF Files (section 4.3.4). When the import is complete, a dialogue box will appear letting you know that your file included base pairs in the A,B format. Click Yes if you want convert it to standard genetic base pairs or No if you want keep the existing format.

If the data that was exported from BeadStudio was Log R Ratios, the data must be imported using CNV->Copy Number Anlysis. This method opens the Copy Number Analysis Import Tool, and for a discussion on how to use this tool, see section 25.3.

D.3.4 Using the BeadStudio Create Column Plug-in

After analyzing BeadStudio Log R ratio data using the HelixTree Copy Number Analysis Import Tool, you may import the resulting segment means data back into BeadStudio as a data column for further analysis. To do so, export the LogRRatio Segments Dataset spreadsheet created from the copy number analysis as a CSV file (25.4).

In BeadStudio, open a project containing the same data that was segmented in HelixTree. From the main window, select from the menu bar Analysis->Create Plugin Column...

Figure D.14: Selecting Create Column Plugin from BeadStudio

If the HelixTree plug-in was installed correctly, the HelixTree Segment Mean Import algorithm should be available in the window that opens. Select the HelixTree algorithm and click Next.

Figure D.15: Plugin Column Importer in BeadStudio showing the available HelixTree Segment Mean Column Import algorithm.

After a few moments, you will be prompted for the CSV data file that contains the segment mean data. Be sure to select "Segment Mean" as the data to import and click OK.

Figure D.16: Prompt for the CSV file containing segment means data.

When the data has finished loading, you should see the Segment Mean column in the BeadStudio Data Table.