A blood sample could one day be enough to diagnose many types of solid cancers, or to monitor the amount of cancer in a patient’s body and responses to treatment. A new method recently reported in the journal Nature Medicine (2014; doi:10.1038/nm.3519) was able to accurately identify about 50% of people in the study with stage 1 lung cancer and all patients whose cancers were more advanced.
Previous versions of the approach, which relies on monitoring levels of tumor DNA circulating in the blood, have required cumbersome and time-consuming steps to customize it to each patient or have not been sufficiently sensitive.”We set out to develop a method that overcomes two major hurdles in the circulating tumor DNA field,” said Maximilian Diehn, MD, PhD, of Stanford University School of Medicine in California. “First, the technique needs to be very sensitive to detect the very small amounts of tumor DNA present in the blood. Second, to be clinically useful it’s necessary to have a test that works off the shelf for the majority of patients with a given cancer.”
“We’re trying to develop a general method to detect and measure disease burden,” said coauthor Ash Alizadeh, MD, PhD, also of Stanford. “Blood cancers like leukemias can be easier to monitor than solid tumors through ease of access to the blood. By developing a general method for monitoring circulating tumor DNA, we are, in effect, trying to transform solid tumors into liquid tumors that can be detected and tracked more easily.”
Even in the absence of treatment, cancer cells are continuously dividing and dying. As they die, they release DNA into the bloodstream, like tiny genetic messages in a bottle. Learning to read these messages—and to pick out the one in 1,000 or 10,000 that comes from a cancer cell—can allow clinicians to quickly and noninvasively monitor the volume of tumor, a patient’s response to therapy, and even how the tumor mutations evolve over time in the face of treatment or other selective pressures.
“The vast majority of circulating DNA is from normal, noncancerous cells, even in patients with advanced cancer,” Bratman said. “We needed a comprehensive strategy for isolating the circulating DNA from blood and detecting the rare, cancer-associated mutations. To boost the sensitivity of the technique, we optimized methods for extracting, processing, and analyzing the DNA.”
The researchers’ technique, which they have dubbed CAPP-Seq, for Cancer Personalized Profiling by deep Sequencing, is sensitive enough to detect just one molecule of tumor DNA in a sea of 10,000 healthy DNA molecules in the blood.
The group began by using a bioinformatics approach to collect information from the Cancer Genome Atlas on 407 patients with non-small cell lung cancer, looking for regions in the genome enriched for cancer-associated mutations.
“By sequencing only those regions of the genome that are highly enriched for cancer mutations, we’re able to keep costs down and identify multiple mutations per patient,” Diehn said.