Comprehensive Genomic Analysis Leading to Personalized Therapies

CureDaisyOrg

Author: CureDaisy.org 

I recently had a very informative meeting with Foundation Medicine.  Foundation Medicine is a cancer diagnostics company at the forefront of bringing comprehensive genomic a analysis to routine cancer care.  Foundation Medicine’s clinical laboratory services help physicians and their patients tailor therapy based on each tumor’s molecular subtype.  I met with both Dr. Gary Palmer, SVP Medical Affairs and Commercial Development, and Dr. Vincent Miller, SVP Clinical Development.   My goal for the meeting was to further understand the specific services provided by Foundation Medicine in the area of whole body genome sequencing; and, further understand the potential therapeutic options for Daisy’s specific cancer that such tests could present.

I

 

It was encouraging to get Dr. Palmer’s affirmation that we are on the right track by researching and seeking to meet with both oncology and research experts in the field of personalized medicine.  Dr. Palmer said that personalized medicine is gathering steam.  As opposed to treating cancer patients with non-targeted-one-size-fits-all therapies, personalized cancer therapies offer the chance to confront cancer by the same route that it attacks the body.  This confrontation happens at the genomic level based on identifying and targeting the molecular alterations associated with the cancerous cells.

Scientists are identifying these molecular alterations by utilizing the same technology that was used a decade ago to decode the human genome. By sequencing the genomes of cancer cells and tumors, scientists can describe the molecular subtype and understand why some patients respond to certain therapies and others do not.

Dr. Palmer pointed to Daisy’s current therapy of Tamoxifen and Lupron as being a giant step toward providing personalized medicine to breast cancer patients that have estrogen/proestrogen positive cancer.  Daisy’s therapy specifically targets the estrogen receptor in her cancer cells.

 

 
Today there are not very many FDA approved drugs for cancer targets, however Dr. Palmer did point to various breakthroughs made this year in providing targeted therapies for melanoma as an example that progress and innovation are beginning to rapidly accelerate.

 

I wanted to also understand how Foundation Medicine’s testing methods were different from the OncoMap testing done at Dana Farber.   Both are tumor-based tests that looks at alterations/mutations in cancer cells.  Oncomap looks at 238 mutations in 17 oncogenes.  Thus the test is relatively binary – you either have these same mutations in your cancer cells or not.  Foundation Medicine takes a different approach. Through next generation sequencing, they look for aberrations in 182 different genes that are known to be influential in cancer biology.  ”From a gene perspective, potential mutations are in the thousands” stated Dr. Palmer.

 

The next obvious question I had is what then can we do with what this information?  Foundation Medicine categorizes tumor mutations into 3 categories:

1. Information about specific mutations that leads to an FDA approved therapies.
2. Information about specific mutations that leads to a clinical trail.  This is a relatively large category that is most relevant to Daisy.  Specifically, we would use this information to identify new drug trials that have shown some effectiveness against Daisy’s specific cancer target.
3. Information about specific mutations that lead to plausibly actionable treatments.  For example, we may find that an FDA-approved drug that has proven to be effective for a specific gene alteration in colon cancer, could also be effective for the same gene alteration in Breast Cancer.   Dr. Palmer stated that historically Doctors have not looked at breast and colon cancer as the same, however scientists are beginning to uncover, through whole body genome sequencing, similar mutations are occurring in different tumor types.  This will ultimately lead doctors into a “pathway” type of treatment approach.  20 years from now we may not talk about breast or colon cancer, it is likely we will be talking about a specific mutation-type and treat it with a personalized therapy targeted to that specific mutation.

The goal for both Foundation Medicine’s genome test and Dana Farber’s OncoMap test is to ultimately give the oncologist every potential treatment option with every potential gene alteration.  Knowing Daisy’s specific gene alterations could give us a head start in identifying a clinical trial that can begin to treat her specific cell mutation.  Daisy is currently scheduled to undertake OncoMap testing at the beginning of next year.

 

Foundation Medicine was approved by the State of Massachusetts in September of this year to begin collecting clinical tissue samples for their genome test.  The list price for the test is $5,800 and needs to be ordered by a physician.  The results of the test take a couple of weeks to process.  Foundation Medicine is still uncertain as to how much insurance companies will be willing to contribute to their test.