As described at the AACR-NCI-EORTC International Conference on Molecular Targets and Cancer Therapeutics, a new, self-contained genetic screening platform has been developed that can be used to detect BRAF V600 mutations in melanoma and other cancers in approximately 90 minutes instead of the much longer time needed when samples are sent to a commercial high-throughput gene-screening service.
The results of the system, called MDx, were presented by Filip Janku, MD, PhD, Assistant Professor in the Department of Investigational Cancer Therapeutics at the University of Texas MD Anderson Cancer Center.
“It often takes three to four weeks to get the results back when samples are sent out for analysis, and much of that time is spent preparing the sample, including laser microdissection to isolate DNA from the tumor cells,” he said in an interview.
“In contrast, with the MDx platform, it takes about two minutes to add fresh, frozen, or paraffin-embedded tumor samples to the sample cartridge and less than 90 minutes to get the results. This platform is capable of giving you an answer in an absolutely unprecedented time frame. It is also more accurate than the standard method currently used in clinics, which could speed diagnosis and treatment.”
Developed by Biocartis, in Mechelen, Belgium, MDx can detect BRAF V600 mutations in about 90 minutes, requires no sample preparation, and is in 95 percent agreement with the standard method approved by clinical laboratory improvement amendments (CLIA), he said.
About 50 percent of melanomas, and, less frequently, other cancer types, harbor mutations in the BRAF oncogene, and more than 30 different cancer-associated BRAF mutations have been identified to date, the most common being BRAF V600 mutations.
Janku said the researchers used the platform as a proof of principle, adding that MDx should be capable of detecting a variety of other mutations, including KRAS, EGFR, and others where targeted therapies have already been approved by the U.S. Food and Drug Administration. Currently, oncologists are unable to offer such targeted therapies to patients as soon as they come to the clinic, because of the time it takes for molecular testing, he noted.
For the study, the researchers tested the MDx platform in 79 archived tumor samples with BRAF mutation status established using the CLIA-approved method. The team used formalin-fixed paraffin-embedded tumor samples (1x to 5x of 10 μm shavings) from advanced cancer patients who had tested positive for V600 mutations using fPCR-based sequencing at CLIA-certified molecular diagnostic laboratory. Agreement between the MDx platform and the certified laboratory's results were then compared, and different methods and treatment outcomes with BRAF/MEK inhibitors were also analyzed.
The CLIA-approved method was in agreement for 75 of the samples. In all, 34 samples were from melanoma patients, 20 from colorectal cancer patients, six from papillary thyroid cancer, and 15 from patients with other cancers.
A total of 49 samples were V600 mutation-positive and 30 were wild-type BRAF mutations. In 70 patients the same tissue block was used for both MDx and CLIA samples, and agreement was found in 67. “We were anticipating agreement in maybe 85 percent, but we exceeded that bar,” Janku said.
In the four samples with discrepancies, the MDx platform, but not the CLIA-approved method, detected a BRAF V600E mutation in a colon cancer sample, but not BRAF mutations in the remaining three samples that had been identified as BRAF-mutation positive by the CLIA method. Two of these three patients were treated with BRAF/MEK inhibitors, based on the CLIA results, but none responded.
In 49 patients with BRAF mutations detected by MDx, 30 were treated with BRAF/MEK inhibitors and 27 percent had a partial response.
“MDx is a fully integrated real-time PCR-based system, does not require sample preparation, and takes roughly two minutes of actual hands-on time,” Janku said. “It is a closed system and the machine can be placed anywhere. Training is relatively minimal and can be handled by anyone with laboratory training.
“Another great advantage is that specimens do not have to be archived before testing. Fresh tumor samples from a biopsy can be tested as soon as possible.”
Asked for his opinion for this article, Ryan J. Sullivan, MD, an instructor in the Division of Hematology/Oncology at Harvard Medical School, Assistant in Medicine at Massachusetts General Hospital Cancer Center, and Co-director of the Eugene Michael Egan Melanoma Translational Research Laboratory at Beth Israel Deaconess Medical Center, said, “The concept of getting quick analysis is really nice, and formalin-embedded samples provide good discrimination.
“One major issue with the way things are done now is that with biopsy samples, you first have to make blocks before sending them out for screening or doing it in-house. But most institutional high-throughput testing is not as streamlined as it could be, and sending samples out takes two to three weeks, although you can generally get more information about multiple genes.”
If we are screening for just a single gene, to be able to get the results the next day or later the same day would be really fantastic.”
However, he said, he expects there will be unanticipated problems if MDx is put into widespread use: “This is a nice start, but I would like to see it tested in a much larger group of patients—say in 1,000 patients. That way we will be able to see if there is a drop in the accuracy rate. Even so, this is raising the bar even if it does not replace conventional testing platforms of change the standards that are used.”
He said that ideally, he would like to see such a system for testing blood for the presence of oncogenes: “This is really where we need to be. I am not sure how good such a system would be, but it would help us better identify patients as candidates for certain therapies. Focusing on blood-based analysis is the wave of the future, especially because we could test patients serially and follow how well patients are doing with different treatments.”