Detection of Early-Stage Cancers With Circulating Tumor DNA
In a bid to detect cancers early and in a noninvasive way, scientists at the Johns Hopkins Kimmel Cancer Center, Baltimore, reported they have developed a test that spots tiny amounts of cancer-specific DNA in blood, and have used it to accurately identify more than half of 138 people with relatively early-stage colorectal, breast, lung, and ovarian cancers. The test, the scientists say, is novel in that it can distinguish between DNA shed from tumors and other altered DNA that can be mistaken for cancer biomarkers. A report on the research, performed on blood and tumor tissue samples from 200 people with all stages of cancer in the United States, Denmark, and the Netherlands, was published by Phallen et al in Science Translational Medicine.
“This study shows that identifying cancer early using DNA changes in the blood is feasible and that our high accuracy sequencing method is a promising approach to achieve this goal,” said Victor Velculescu, MD, PhD, Professor of Oncology at the Johns Hopkins Kimmel Cancer Center.
Blood Test Development
Blood tests for cancer are a growing part of clinical oncology, but they remain in the early stages of development. To find circulating tumor DNA (ctDNA) in the blood of patients with cancer, scientists have frequently relied on DNA alterations found in patients’ biopsied tumor samples as guideposts for the genetic mistakes they should be looking for among the masses of DNA circulating in those patients’ blood samples. To develop a cancer screening test that could be used to screen seemingly healthy people, scientists had to find novel ways to spot DNA alterations that could be lurking in a person’s blood but had not been previously identified.
“The challenge was to develop a blood test that could predict the probable presence of cancer without knowing the genetic mutations present in a person’s tumor,” said Dr. Velculescu.
The goal, added Jillian Phallen, a graduate student at the Johns Hopkins Kimmel Cancer Center who was involved in the research, was to develop a screening test that is highly specific for cancer and accurate enough to detect the cancer when present, while reducing the risk of false-positive results that often lead to unnecessary overtesting and overtreatments. The task is notably complicated, said Ms. Phallen, by the need to sort between true cancer-derived mutations and genetic alterations that occur in blood cells and as part of normal, inherited variations in DNA.
As blood cells divide, there is a chance these cells will acquire mistakes or mutations, explained Dr. Velculescu. In a small fraction of people, these changes will spur a blood cell to multiply faster than its neighboring cells, potentially leading to preleukemic conditions. However, most of the time, the blood-derived mutations are not cancer-initiating.
His team also ruled out so-called germline mutations, which are indeed alterations in DNA, but they occur as a result of normal variations between individuals and are not usually linked to particular cancers.
Detection Rate
To develop the new test, Dr. Velculescu, Ms. Phallen, and their colleagues obtained blood samples from 200 patients with breast, lung, ovarian, and colorectal cancer. The scientists’ blood test screened the patients’ blood samples for mutations within 58 genes widely linked to various cancers.
Overall, the scientists were able to detect 86 (62%) of 138 stage I and II cancers.
More specifically, among 42 people with colorectal cancer, the test correctly predicted cancer in half of the 8 patients with stage I disease, 8 of 9 (89%) with stage II disease, 9 of 10 (90%) with stage III, and 14 of 15 (93%) with stage IV disease.
Of 71 people with lung cancer, the scientists’ test identified cancer among 13 of 29 (45%) with stage I disease, 23 of 32 (72%) with stage II disease, 3 of 4 (75%) with stage III disease, and 5 of 6 (83%) with stage IV cancer.
For 42 patients with ovarian cancer, 16 of 24 (67%) with stage I disease were correctly identified, as well as 3 of 4 (75%) with stage II disease, 6 of 8 (75%) with stage III cancer, and 5 of 6 (83%) with stage IV disease.
Among 45 patients with breast cancer, the test spotted cancer-derived mutations in 2 of 3 (67%) patients with stage I disease, 17 of 29 (59%) with stage II disease, and 6 of 13 (46%) with stage III cancers.
They found none of the cancer-derived mutations among blood samples of 44 healthy individuals.
Dr. Velculescu and his team also performed independent genomic sequencing on available tumors removed from 100 of the 200 patients with cancer and found that 82 (82%) had mutations in their tumors that correlated with the genetic alterations found in the blood.
Deep Sequencing
The Johns Hopkins–developed blood test uses a type of genomic sequencing the researchers call “targeted error-correction sequencing.” The sequencing method is based on deep sequencing, which reads each chemical code in DNA 30,000 times. “We’re trying to find the needle in the haystack, so when we do find a DNA alteration, we want to make sure it is what we think it is,” said Dr. Velculescu.
Such deep sequencing, covering more than 80,000 base pairs of DNA, has the potential to be very costly, but Dr. Velculescu said sequencing technology is becoming less expensive, and his research team may eventually be able to reduce the number of DNA locations they screen while preserving the test’s accuracy.
He says the populations that could benefit most from such a DNA-based blood test include those at high risk for cancer, such as smokers—for whom standard computed tomography scans for identifying lung cancer often lead to false positives—and women with hereditary mutations for breast and ovarian cancer within the BRCA1 and BRCA2 genes.
The content in this post has not been reviewed by the American Society of Clinical Oncology, Inc. (ASCO®) and does not necessarily reflect the ideas and opinions of ASCO®.
