Use Case: Investigating Comorbidities of Breast Cancer in Authorized PIC-SURE

In this section, the functionalities of Authorized PIC-SURE will be described in the context of a scientific use case. Specifically, let’s say I am interested in investigating some comorbidities of breast cancer in women with BRCA1 and BRCA2 gene variants, such as hypertension and COPD.

I have already been authorized to access the Women’s Health Initiative (WHI) study and am interested in a single cohort: women with breast cancer and variants of the BRCA1 and BRCA2 genes. I want to select hypertension-related variables of interest, check the distributions of some variables, and export all the data to an analysis workspace.

First, let's apply our variable filters for the WHI study.

1. Search "breast cancer" in Authorized PIC-SURE.

2. Filter to participants with breast cancer by clicking the filter icon next to the variable of interest. Select values to filter your variable on and click "Add Filter to Query".

   

   Adding a filter to the 'BREAST' variable from Women's Health Initiative Study.
3. Click the "Genomic Filtering" button to begin a filter on genomic variants.

4. Select "BRCA1" and "BRCA2" genes of "High" and "Medium" severity. Click "Apply genomic filter".

Applying a genomic filter on high or medium severity variants of the BRCA1 and BRCA2 genes.

6. Now, let’s filter to participants who have and do not have COPD. Similar to before, we will search ‘COPD’. After selecting the variable of interest, we can filter to the desired values before adding the filter to our query. Notice how the total number of participants in our cohort changes.

7. Search “hypertension”.

8. Add variables to data export by clicking the select variables icon in the Actions column next to the variable of interest. The icon next to the variables selected for export will change to the checkmark icon.

9. Notice how the number of variables changed in the Data Summary box.

Adding 'hypertension' variables ('HTNTRT', 'HYPT', 'HYPTPILL', and 'HYPTPILN') for export from Women's Health Initiative Study

10. Open the Select and Package Data tool in the Tool Suite. The variables shown in this table are those which will be available in your data export; you can remove variables as necessary.

Select and Package Data modal

12. Click "Package Data" when you are ready.

13. Once the data is packaged, you can select either "Save Dataset ID", “Export to Seven Bridges” or “Export to Terra”. Copy over the personalized user token and dataset ID use the PIC-SURE API and export your data to an analysis workspace.