Q.  Hello Dr. Weisenthal.  My oncologist has ordered what she calls a gene test to help in planning my treatments.  I have read your website and I understand it is not what you do at your laboratory.  The test seems expensive to me but I am more curious to learn if the test will be useful in choosing chemotherapy drugs.   

A.  Two of the most widely used genetic sequencing tests — FoundationOne and Guardant360 — have shown "widely discordant" results in the same patients, according to a small online study published in JAMA Oncology. The FoundationOne test sequences clinical tumor samples to characterize the exons of 315 cancer-associated genes and introns from 28 genes involved in rearrangements. The Guardant360 test uses cell-free circulating DNA from blood to sequence 70 genes.

The study evaluated nine patients with breast cancer (n = 5), pancreatic cancer, thymic carcinoma, lung cancer and salivary gland cancer (n = 1 for each).  The results of this study were quite revealing. One patient had no identified genetic alteration using either sequencing test. But among the remaining eight patients harbored 45 alterations, only 10 (22%) of which were concordant between FoundationOne and Guardant360 platforms.

In two (25%) of the other eight patients, there was absolutely no concordance among the described alterations. And although total of 36 drugs were recommended for the eight patients, only nine (24%) of these drugs were recommended for the same patients by both platforms. Notably, in five patients (more than 50%), there was no overlap whatsoever between the drugs recommended by the FoundationOne test and those recommended by the Guardant360 test.

The researchers concluded that the output from genetic testing can differ markedly depending on which genetic test is applied. Furthermore, they stated that these findings are clinically relevant because both the FoundationOne and the Guardant360 tests are performed on thousands of cancer patients each year. 

Here is a link to the original study article: http://www.healio.com/hematology-oncology/breast-cancer/news/in-the-journals/%7B7ad8fdf6-0661-4d67-a0b2-773251903520%7D/genetic-sequencing-tests-show-widely-discordant-results