SAN FRANCISCO – A new assay based on methylation patterns in plasma cell-free DNA holds promise for improving detection of diverse gastrointestinal (GI) cancers when they are still curable, findings of the Circulating Cell-free Genome Atlas (CCGA) study suggest.
Among 447 patients with GI cancers of varied types and stages, the multicancer assay had sensitivity exceeding 80% for all stages (exceeding 70% for stages I to III) and specificity exceeding 99%, investigators reported at the 2020 GI Cancers Symposium. In addition, the assay correctly determined the tissue of origin about 90% of the time.
“To pursue early detection at a population scale while minimizing harm and cost, several features are important, including a low false-positive rate, a high detection rate, the ability to localize the site of origin of the malignancy, and limiting overdiagnosis,” noted lead investigator Brian M. Wolpin, MD, MPH, director of the Gastrointestinal Cancer Center and director of the Hale Family Center for Pancreatic Cancer Research at Dana-Farber Cancer Institute in Boston. “This multicancer early detection test evaluating cell-free DNA methylation may be a useful test to detect GI cancers and may guide further evaluation and workup.”
About three-quarters of all cancer patients in the study had symptoms that ultimately led to their diagnosis, Dr. Wolpin acknowledged. But the investigators are conducting two large additional studies among asymptomatic populations to better assess the assay’s screening potential: the STRIVE study, which has enrolled nearly 100,000 women undergoing screening mammography, and the SUMMIT study, which is enrolling 50,000 men and women without a known cancer diagnosis, with enrichment of the sample for smokers.
“The holy grail, of course, is to try to find any test – a blood test, a urine test, a breath test, a stool test – that will allow us to detect cancer at an earlier and more curable stage, and we have hints now that we are headed in the right direction,” session cochair George A. Fisher Jr., MD, PhD, said in an interview. “I don’t know that this is the technology that will do it, but I think it’s superior to the technology just looking at DNA mutations.”
It is a further merit that the assay also has good accuracy in ascertaining the cancer’s tissue of origin, as that should help streamline the diagnostic workup, he agreed.
The assay is already attractive for patients with suspicious lesions or symptoms, but further research will be needed to assess its performance in detecting asymptomatic cancer, and logistic issues would have to be addressed, according to Dr. Fisher of Stanford (Calif.) University.
“As an outright screening test, I don’t think we are there yet. We would have to identify the populations in whom to use the test and come up with some frequency of how often we use it,” he said. Consideration would need to be given to informed consent, especially as some patients may have a positive assay result but a cancer that can’t be found, generating psychological distress.
And cost will come into play. “The problem is, for most stage I cancers you can screen for, they are still very low in likelihood, so you have to screen a lot of people, which means a lot of expense,” he elaborated.
“It will be interesting in the research world to decide when such a test would become a reasonable standard of care, and how regulators will view that and how insurers will view that in terms of cost-efficacy analysis,” Dr. Fisher concluded.
The CCGA study has enrolled 15,254 participants with and without cancer at 142 U.S and Canadian sites. Participants provide blood samples (at diagnosis for those with cancer) and are followed up for 5 years.
To develop the assay, the investigators performed targeted methylation sequencing of cell-free DNA from plasma and trained an algorithm to use the methylation patterns to detect more than 20 cancer types and classify them based on the organ of origin.
Dr. Wolpin reported results for a CCGA substudy conducted among 2,185 patients with cancer and 2,131 individuals without cancer. About a fifth of the former group had cancers of the GI tract (colon or rectum in 174 patients, pancreas in 123, esophagus in 71, liver or bile duct in 40, stomach in 25, gallbladder in 14). The population was split into training and validation sets.
The assay had a specificity of 99.8% in the entire training set and 99.3% in the entire validation set, corresponding to false-positives in just 0.2% and 0.7% of the individuals without cancer, according to data reported at the symposium, which is sponsored by the American Gastroenterological Association, American Society of Clinical Oncology, the American Society for Radiation Oncology, and the Society of Surgical Oncology.
For GI cancers, assay sensitivity for stage I-IV disease was 82% in the training set and 81% in the validation set, and sensitivity for stage I-III disease was 73% and 71%, respectively. By specific nonmetastatic stage, sensitivity was about 50% for stage I disease, 75% for stage II disease, and 85% for stage III disease.
Fully 97% of the GI cancers having detectable cell-free DNA were assigned a tissue of origin by the assay. The predicted tissue of origin had an accuracy of 91% in the training set and 89% in the validation set, with similar values across GI cancer types.
Dr. Wolpin disclosed having a relationship with various pharmaceutical companies, including GRAIL, which funded the study. Dr. Fisher disclosed relationships with numerous pharmaceutical companies and that an immediate family member has stock in Seattle Genetics
SOURCE: Wolpin BM et al. 2020 GI Symposium, .