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 amplified_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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