Interpreting Foundation One results

Hello, Pingmama. Actually, this is not the right thread, but let's see if we can help. This thread is about genetic testing to see if a person has, in their whole body, a genetic mutation that puts them at greater risk than average for breast cancer. But Foundation one is a genomic test of the cancer only; that is, a test for mutations in the tumor. The results can suggest which treatment drugs may work and which ones may not work.

Did your mom have Foundation One CDx which uses tissue from a biopsy, or Foundation One Liquid which uses a blood test? Will the doctor give your mom a copy of the report? Will he/she make an appointment so your mom can ask more questions? What stage breast cancer does she have?

There is information for patients on the company's web site. Click on “Patients".

https://www.foundationmedicine.com/patients#resources

So that was the liquid biopsy that detects circulating tumor cells in the blood and analyses them for mutations. When I had one of my liquid biopsies from a similar company (Guardant), the scientist explained that the reason not many mutations were detected was probably that there was a low volume of tumor, or because I was on chemo. So my guess is that the doctor means that with treatment, in your mom's case radiation, there will be less cancer detected in the blood and more mutations will have “no data". But that still confuses me, because if the doctor is talking about is whole breast radiation following lumpectomy, the tumor would have been removed already.

Did the doctor recommend this test? In my experience these tests are used for patients on continuous treatment for metastatic breast cancer, to help choose the next treatment when one stops working. But I can see how it might be useful in choosing adjuvant chemo or a targeted therapy to go along with hormonal therapy for early stage breast cancer. What mutations and suggested treatments show on the report?

What treatment has your mom had already, and what has been recommended? Did she have the Oncotype DX test to determine whether chemo is indicated?

Pingmama, that is not the main page. At the top right it says “Appendix. Variants of Unknown Significance” Unknown Significance means we do not know if these variants are harmful (pathogenic, deleterious) or not. So doctors typically do not make any recommendations based on them. Scientists do keep collecting data on people with these VUS, and sometimes they are eventually able to say whether the mutation is or is not pathogenic. I think most turn out not to be. But you may want to talk to a genetic counselor at a cancer center about these in order to keep an eye on this. The reason is that two of the mutations found in your mom’s tumor, ATM and CHEK2, can be not only in the tumor, but in all cells of the body; that is, a germline mutation. See the list at the top of this topic. A pathogenic germline mutation means the person may be at increased risk for various cancers, depending on the particular gene, and if so should have extra screening, etc. I found out about a harmful mutation in my family because it first showed up on my Foundation One report, but was a mutation that is often germline, not just in tumors (somatic mutation). This led us to get genetic testing, and the family members who have the mutation are taking steps to prevent and find any cancer early.

I am glad to hear your mom’s PAM50 showed her low risk and able to skip chemo. It sounds like she is on track with treatment. I am still not sure why Foundation One was ordered for her. If you can find the main pages, we can talk about them.

(Keep in mind that I am only an educated patient, not a doctor.)

The first page says “No reportable genomic alterations" and “No biomarker or genomic findings". That sounds like they found nothing other than those VUS, doesn't it? I do not find this surprising as your mom's tumor has been removed so presumably there is not much tumor DNA in her blood at this point, and also this is an early stage cancer. The fewer mutations, the better. As breast cancer progresses, it tends to acquire more mutations. (Over the years each of my genomic tests of metastatic breast cancer has shown more mutations than the previous test.)

The second page appears to be a list of the genes their test looks at.

The third page is too blurry for me to read well, but it seems to be technical specifications about the test.

So it looks to me like there isn't much to be done with this test as far as your mom's treatment. Do confirm this with the doctor.

P.S. In the future you can ask the doctor to have Foundation One tell you if anything more has been learned about those three VUS. I think that is called re-curating.