14. Clinical Trials - Example 5 PIK3CA H1047RΒΆ

A recent VSClinical AMP upgrade now provides a simple and efficient means to search for relevant Clinical Trials for sample biomarkers. We’ll explore this feature using additional example biomarkers starting with a PIK3CA H1047R missense variant for invasive breast carcinoma. The first step will be to browse to sample NA12877-05-Horizon_S4

sample change

Figure 14-1: Changing current sample view to sample NA12877-05-Horizon_S4.

After the sample change, you’ll notice in the Patient Tab that the Current Diagnosis/Tumor Type is set for Breast - Invasive Breast Carcinoma

patient tab

Figure 14-2: Patient Tab

Next, click on the Mutation Profile Tab to see the PIK3CA biomarker pre-selected.

PIK3CA mutation profile

Figure 14-3: Mutation Profile Tab listing the PIK3CA H1047R biomarker.

At this point you can explore the variant oncogenicity score in the Variant Tab, but the primary focus will next be in the Biomarkers Tab. Golden Helix supplies the CancerKB catalog which contains expert reviewed gene and biomarker interpretations. In the Biomarker Tab, the interpretations are not only prefilled from CancerKB but are also matching the interpretation scope for Invasive Breast Carcinoma.

PIK3CA gene int

Figure 14-4: CancerKB catalog supplies autofilled interpretations for gene and biomarker.

The bottom section of the Biomarker Tab is the assessment of available treatment options which are not only also auto-filled from CancerKB, but are also specific to the tissue type and matching H1047R mutation. The list of these drugs are in hierarchical order for matches in DrugBank, PMKB, and CIViC. This variant has multiple drugs listed such as Alpelisib and Fulvestrant which will be the focus for the clinical trial search.

PIK3CA druglist

Figure 14-5: Biomarker and tissue specific search for relevant treatment options.

Moving now to the Drug & Trial Tab, set the zipcode to 59718 (MT zipcode) click on the Alpelisib Matching Trials icon to review available trials for the drug and summary details on trial status and sites.

PIK3CA drugs & trials

Figure 14-6: New Drugs & Trials Tab in VSClinical.

A new window will pop up with clinical trial matches and the sole trial that is found is for a combination therapy study for Alpelisib with Fulvestrant which is in recruiting status for any PICK3CA mutations.

PIK3CA Trial Search

Figure 14-7: Relevant trial for Alpelisib and Fulvestrant combination therapy.

Clicking on the Sites tab, the nearest site selected to the 59718 zipcode location is in Billings, MT.

PIK3CA local search

Figure 14-8: Searching for nearby sites for the Alpelisib+Fulvestrant trial

Additionally, scrolling to the bottom of the Drug & Trials Tab users will be presented with not only summary details for the final report, but also the selection of inclusion and exclusion criteria relevant for the patient.

PIK3CA Trial Summary

Figure 14-9: Summary of selected trials and selectable inclusion criteria.

Let’s explore another clinical trial search for a different sample.