Liquid biopsy can rapidly and accurately detect mutations in two key genes in non-small cell lung tumors, according to a new study.1 Researchers at Dana-Farber Cancer Institute, Boston, and other institutions have demonstrated the test’s potential as a clinical tool for identifying patients who can benefit from drugs targeting those mutations.
The blood test proved so reliable in the study that the Dana-Farber/Brigham and Women’s Cancer Center (DF/BWCC) recently became the first medical facility in the country to offer it to all patients with non-small cell lung cancer (NSCLC), either at the time of first diagnosis or of relapse following previous treatment.
NSCLC is the most common form of lung cancer, diagnosed in more than 200,000 people in the United States each year, according to the American Cancer Society.2 An estimated 30% of NSCLC patients have mutations in either of the genes included in the study, and can often be treated with targeted therapies.
Technically known as rapid plasma genotyping, the liquid biopsy technique tested in the study involves taking a test tube of blood, which contains free-floating DNA from cancer cells, and analyzing that DNA for mutations or other abnormalities. The technique, which provides a “snapshot” of key genetic irregularities in a tumor, is a common research tool for probing the molecular make-up of different kinds of cancers.
“We see plasma genotyping as having enormous potential as a clinical test, or assay—a rapid, noninvasive way of screening a cancer for common genetic fingerprints—while avoiding the challenges of traditional invasive biopsies,” says Geoffrey Oxnard, MD, thoracic oncologist and lung cancer researcher at DF/BWCC and senior author of the study. “Our study was the first to demonstrate prospectively that a liquid biopsy technique can be a practical tool for making treatment decisions in cancer patients. The trial was such a success that we are transitioning the assay into a clinical test for lung cancer patients at DF/BWCC.”
The study involved 180 patients with NSCLC, 120 of whom were newly diagnosed, and 60 of whom had become resistant to a previous treatment, allowing the disease to recur. Participants’ cell-free DNA was tested for mutations in the EGFR and KRAS genes, and for a separate mutation in EGFR that allows tumor cells to become resistant to front-line targeted drugs. The test was performed with a technique known as droplet digital polymerase chain reaction (ddPCR), which counts the individual letters of the genetic code in cell-free DNA to determine whether specific mutations are present. Each participant also underwent a conventional tissue biopsy to test for the same mutations. The results of the liquid biopsies were then compared to those of the tissue biopsies.
The data showed that liquid biopsies returned results much more quickly. The median turnaround time for liquid biopsies was 3 days, compared to 12 days for tissue biopsies in newly diagnosed patients and 27 days in drug-resistant patients.
Liquid biopsy was also found to be highly accurate. In newly diagnosed patients, the predictive value of plasma ddPCR was 100% for the primary EGFR mutation and the KRAS mutation. For patients with the EGFR resistance mutation, the predictive value of the ddPCR test was 79%, suggesting the blood test was able to find additional cases with the mutation that were missed using standard biopsies.
“In some patients with the EGFR resistance mutation, ddPCR detected mutations missed by standard tissue biopsy,” Oxnard says. “A resistant tumor is inherently made up of multiple subsets of cells, some of which carry different patterns of genetic mutations. A single biopsy is only analyzing a single part of the tumor, and may miss a mutation present elsewhere in the body. A liquid biopsy, in contrast, may better reflect the distribution of mutations in the tumor as a whole.”
When ddPCR failed to detect these mutations, the cause was less clear-cut, Oxnard says. It could indicate that the tumor cells don’t carry the mutations or, alternatively, that the tumor isn’t shedding its DNA into the bloodstream. This discrepancy between the test results and the presence of mutations was less common in patients whose cancer had metastasized to multiple sites in the body, researchers found.
The ddPCR-based test was piloted and optimized for patients at the translational research lab of the Belfer Center for Applied Cancer Science at Dana-Farber. It was then validated for clinical use at Dana-Farber’s Lowe Center for Thoracic Oncology.
An advantage of this form of liquid biopsy is that it can help doctors quickly determine whether a patient is responding to therapy. Fifty participants in the study had repeat testing done after starting treatment for their cancer. “Those whose blood tests showed a disappearance of the mutations within 2 weeks were more likely to stay on the treatment than patients who didn’t see such a reduction,” says Adrian Sacher, MD, of Dana-Farber and Brigham and Women’s Hospital and lead author.
Because tumors are constantly evolving and acquiring additional mutations, repeated liquid biopsies can provide early detection of a new mutation—such as the EGFR resistance mutation—that can potentially be treated with targeted agents.
“The study data are compelling,” says Lynette Sholl, MD, pathologist at DF/BWCC. “We validated the authors’ findings by cross-comparing results from liquid and tissue biopsies in 34 NSCLC patients. To work as a real-world clinical test, liquid biopsy needs to provide reliable, accurate data and be logistically practical. That’s what we’ve seen with the ddPCR-based blood test.
“The test has great utility both for patients newly diagnosed with NSCLC and for those with a recurrence of the disease,” Sholl continues. “It’s fast, it’s quantitative—it indicates the amount of mutant DNA in a sample—and it can be readily employed at a cancer treatment center.”
For more information, visit Dana-Farber Cancer Institute.
- Sacher AG, Paweletz C, Dahlberg SE, et al. Prospective validation of rapid plasma genotyping for the detection of EGFR and KRAS mutations in advanced lung cancer. JAMA Oncol. Published online in advance, April 7, 2016; doi: 10.1001/jamaoncol.2016.0173.
- Lung cancer (non-small cell) [online]. Atlanta: American Cancer Society, 2016. Available at: http://www.cancer.org/cancer/lungcancer-non-smallcell/detailedguide/non-small-cell-lung-cancer-key-statistics.