Identifying Therapeutically Relevant Genetic Abnormalities in Cancer Patients

I just came across an example of a new type of cancer genomic test. Foundation Medicine has developed a test that utilizes tumor biopsies to detect the presence of therapeutically relevant gene abnormalities (see: High-Speed DNA Scans Help Most Lung Cancer Patients, Study Finds). Below is an excerpt from the article:

More than half of lung and colon cancer patients may benefit from high-speed tests that detect DNA flaws doctors can target with existing medicines, a study found. Researchers used a gene test made by closely held Foundation Medicine...to sequence 145 cancer-associated genes in 40 colon tumor samples and 24 lung tumors. They found that 53 percent of colon tumors and 71 percent of lung tumors had mutations that may be attacked with cancer medicines on the market or in human trials....In some cases, the results revealed what drugs wouldn’t work against the tumors. The study from researchers at Foundation Medicine and the Dana-Farber Cancer Institute in Boston, shows the value of using DNA sequencing machines to optimize treatment by matching drugs against specific gene abnormalities inside a patient’s tumor....The researchers also spotted a previously unknown genetic flaw in 2 percent of 561 lung tumors tested. The flaw activates a growth-boosting protein targeted by [the] Pfizer...kidney- cancer drug Sutent, hinting that the treatment from the New York-based drugmaker may also work in these lung patients....

Here's more information about the test from the web page of Foundation Medicine (see: For Physicians, Our Approach):

Foundation Medicine has developed a molecular diagnostics test that analyzes routine clinical [tumor] specimens for somatic alterations in relevant cancer-related genes. It provides valuable information needed to inform treatment decisions based on an individual patient’s molecular cancer subtype....Our test is designed to capture molecular information for all solid tumor types, therefore alleviating the uncertainty associated with appropriate selection of genomic tests for patients, and subsequent interpretation of multiple sets of information. Using DNA extracted from cancer biopsy tissue, our test examines a wide range of specifically targeted cancer-related genes for all potential somatic alterations....Our broad approach, which captures any relevant alterations in one test, is made possible by using massively parallel sequencing. Although many alterations may be identified, our proprietary analytics specify the small number (average 2-3) of somatic alterations that are reportable and actionable for each patient....Test performance requires a very small amount of cancer tissue such as that typically obtained from surgical resection, core needle biopsy, or fine needle aspirate (FNA). [The test] uses routine clinical pathological specimens, typically formalin-fixed paraffin embedded (FFPE) tumor tissue....Foundation Medicine’s comprehensive cancer genomics test will be launched nationally mid-2012.

Very quickly, a few points jump out at me from the description of this new test:

• I have stated in previous notes that I prefer the term targeted therapy over personalized medicine (see: Genetic Testing to Cull Out the "Un-Right Patient" as a Candidate for a Particular Drug Therapy;  A "New" Twist on Personalized Medicine: Genetically Targeted Therapy). This more specific term is used frequently in the Foundation Medicine web site. The discovery of "actionable and reportable" genetic tumor flaws is clearly the goal of  this new approach.
• As noted above, the test, in a research study, has detected a "previously unknown genetic flaw in 2 percent of 561 lung tumors tested." We are thus now seeing the emergence of a type of test will become routine for hospitalized cancer patients and that will also generate a list of new targets for biotech drugs. In other words, new information will now be moving "bed to bench."
• Finally, we are witnessing a genomic test that will change over time as new drugs come to market and as the the list of actionable cancer genes expands. In other words, such a test done today will be different than the "same" test a few months ago. A patient's tumor will also need to be genomically tested periodically to confirm that the patient is being treated optimally.

Comments

[alpha male characteristics]

"by matching drugs against specific gene abnormalities inside a patient’s tumor" This is good as it very difficult to know what specific treatment will be best for a patient while not damaging the entire tissue. Treatment of cancer has been a challenge worth investing in.