Creating a list of regions

In this tutorial, the experimental goal is to identify regions with copy number changes in multiple patients. To do this, we will create a list containing deleted and amplified regions across the genome shared by 8 or more samples.

• Select Create Region List from the Copy Number Analysis section of the Copy Number workflow

• Select Specify New Criteria

We want to include all the amplified regions across the genome shared by at least 8 samples in our first criteria (Figure 1).

• Set Name to Amplified

• Set Spreadsheet to 2/segmentation/summary (segment-analysis)

• Set Column to 6. Total Amplifications using the drop-down menu

• Deselect the box next to Include values less than or equal to

• Set Include values greater than or equal to value to 8

The # pass should be 86, indicating that 86 regions meet the criteria.

• Select OK

Figure 1. Configuring the Amplified criteria

• Select Save to save the list

• Select OK to confirm that you would like to save Amplified as a list

• Select Close to exit the List Creator dialog

Amplified is now open in the Analysis tab as a child spreadsheet of segmentation. Although this list contains regions amplified in 8 or more samples, some samples may also contain deletions in the same regions. For downstream analysis, we may want to filter out these regions to create a final list with only amplified regions. Here, we will use the interactive filter.

• Select the Amplified spreadsheet

• Select to open the interactive filter

• Set the Column drop-down list to 8. Total Deletions

• Type 0 in the Max box

• Select Enter on your keyboard

This will apply a filter excluding any region with deletions (Figure 2).

Figure 2. Interactive filter excluding regions with deletions.

The yellow and black bar on the right-hand side of the spreadsheet indicates the porportion of rows that have been filtered. Next, we can save the filtered list.

• Right-click the Amplified spreadsheet in the spreadsheet trees

• Select Clone... from the pop-up menu

• Set the Name of the new spreadsheet to amplified_only

• Set Create new spreadsheet as a child of spreadsheet to 2/segmentation (segmentation.txt)

• Select OK

The new spreadsheet is a temporary file. To keep the spreadsheet, we need to save it.

• Select amplified_only in the spreadsheet tree

• Select

• Set the file name as a****mplified_only

• Select Save

The amplified_only spreadsheet contains 60 rows and includes regions that were amplified in 8 or more samples and not deleted in any sample.

To create a list of regions only deleted in 8 or more samples, repeat the above steps for deleted regions. You should create a final list, deleted_only, with 92 regions.

Next, we can merge the two lists to create a spreadsheet with both deleted and amplified regions.

• Select File from the main taskbar

• Select Merge Spreadsheets...

• Select the Append Rows tab

• Select **2/segmentation/**deleted_only (deleted_only) from the First Spreadsheet drop-down menu

• Select 2/segmentation/amplified_only (amplified_only) from the Second Spreadsheet drop-down menu

• Name the merged spreadsheet amplified_or_deleted using the Specify Output File (Figure 3)

• Select OK

Figure 3. Merging amplified and deleted spreadsheets

• Select the new spreadsheet, amplified_or_deleted in the spreadsheet tree

• Select to save the spreadsheet

This spreadsheet, amplified_or_deleted, will be used as the basis for the downstream steps in this analysis.

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