July 9, 2025 | Molecular testing for minimal residual disease (MRD) is increasingly being used to detect cancer recurrence, and to that end many companies are actively developing assays. The tumor-informed approach based on the genetic mutations of patients has been particularly popular and often employs cell-free DNA (cfDNA) and more specifically circulating tumor DNA (ctDNA) analysis.
Delfi Diagnostics, one of the MRD test providers that will be showcasing their technology at the upcoming Next Generation Dx Summit, goes at the task an entirely different way with its cfDNA assay for monitoring treatment response and disease progression in a tumor- and mutation-independent fashion. DELFI-tumor fraction (DELFI-TF), as it is known, launched as a research service about 18 months ago and uses low-coverage whole genome sequencing to calculate the relative proportion of tumor-derived DNA (ctDNA) in a blood sample.
Delfi’s fragmentation approach, originally aimed at preventive screening for lung cancer, expanded about two years ago to “the other side of the coin”—the monitoring of patients in oncology clinical trials to provide early evidence of their response to therapy and a prognostic evaluation of their disease progression, according to Nicholas Dracopoli, Ph.D., chief scientific officer and cofounder of the company who will be presenting at the conference.
DELFI-TF “uses essentially the same wet lab procedure that we use for the screening test,” he says. The only difference is the algorithm interpreting the data to generate a score representing the genome-wide abnormalities of a patient. Typically, treatment response and disease progression are tracked using an allele fractions score measuring the change in individual bases within the genome.
Among the advantages of Delfi’s method is that it provides a more representative profile of cancer’s genetic abnormalities and can be done much less expensively, Dracopoli says. Importantly, particularly in early clinical trials, the assay can be done using a small amount of plasma—only about 800 microliters, compared to mutation testing, which often requires between 2 and 4 milliliters.
“In phase 1a and 1b clinical trials, a huge amount of blood is already required for pharmacokinetic analyses, so adding additional [blood-based] tests is always problematic,” he notes. “I lived this for many years in my time in pharma, at BMS and Janssen, where getting additional samples for pharmacodynamic measurements was very difficult because of the demand for blood to measure the amount of circulating antibodies or small molecules.”
The fragmentation approach on which Delfi Diagnostics was founded came out of the lab of Victor Velculescu, M.D., Ph.D., at Johns Hopkins, who served as the company’s CEO of the company for many years (succeeded by Susan Tousi last year) and currently serves as board director. The technology was licensed to the company in 2019.
Fragmentation is a well-established biological concept whereby very short fragments of DNA, averaging around 200 base pairs, get released into circulation from intact cells with chromosome-length DNA molecules, explains Dracopoli. Enzymes known as endonucleases cleave DNA as part of this process.
The genius of scientists in the Velculescu lab was the observation that this is not a random process, he adds. Rather, “the DNA is organized in the genome in a way to control and regulate the gene expression.” It is bound to the underlying nucleosomes, allowing access to the messenger RNA complex that is crucial to a cell’s identity.
In other words, says Dracopoli, “by deconvoluting the cfDNA fragmentation profile that we see in the blood... we can infer from whence they came. We can identify and differentiate DNA that’s derived from the epithelial cancer cells from what is coming from the much more common DNA in circulation... [derived] from white blood cells.” The reasoning was accomplished by reverse-engineering the low-coverage sequence data of the DNA from plasma using machine learning and artificial intelligence.
Delfi’s fragmentomics technology was initially envisioned as a screening tool because of its ability to “very sensitively” measure somatic genomic abnormalities that occur in cancer cells and find the evidence in blood, says Dracopoli. It could therefore be an affordable, minimally invasive test that could be applied to high-risk and, ultimately, population-based groups to check for cancer.
“The key issue with screening for cancer in otherwise asymptomatic individuals is the cost of finding any one particular cancer, so a screening test to be acceptable for broad use, even in high-risk groups, has to be very inexpensive,” he continues. Among the high-risk group as defined by the U.S. Preventive Services Task Force—aged 50 to 80 with a 20 pack-year smoking history and are current smokers or quit within the last 15 years—Delfi’s FirstLook Lung test is only expected to find about one cancer for every 140 people screened.
Screening tests are therefore “extremely cost-sensitive” when the aim is to apply them across large populations, says Dracopoli. For perspective, 15 million people in the U.S. are eligible for annual lung cancer screening via low-dose CT, the prevailing screening method for high-risk individuals.
The FirstLook Lung test looks for individuals who are transitioning from a normal to an abnormal fragmentation profile as the cancer cells start to go through apoptosis and necrosis and release their contents into circulation, he explains. “In the monitoring setting, we are doing the reverse... measuring the change from advanced somatic abnormalities in cancer patients” as they respond to therapy and the fragmentation profile of the cfDNA in their plasma begins to normalize.
Currently, six health systems have adopted the FirstLook Lung test, a laboratory developed test (LDT) that can be ordered from a Clinical Laboratory Improvement Amendments (CLIS) laboratory in Palo Alto, California.
As with the FirstLook Lung test, DELFI-TF is also inexpensive and highly sensitive, says Dracopoli. More importantly, it is not confounded by clonal hematopoiesis—a condition where a group of blood cells with a common genetic mutation grows exponentially and increases the downstream risk of hematologic cancer and other diseases.
One of the perennial issues with mutation testing is to determine if an alteration is tumor-related or a “background mutation in the white blood cells [clonal hematopoiesis],” he says. It’s a “very common feature,” especially with aging.
Where a mutation occurs “obviously has very different clinical implications,” Dracopoli continues. In an earlier published study, Delfi scientists sequenced both the plasma and buffy coat of recovered cancer patients at high risk of a subsequent malignancy to find that half of the identified mutations in the p53 tumor suppressor gene were occurring in the white blood cells and had not yet changed the fragmentation profile (Nature Communications, DOI: 10.1038/s41467-020-14310-3). That is, DELFI-TF results were highly correlated with the mutant allele frequency, the measure often used to evaluate treatment response and resistance to immunotherapies in advanced cancer cases.
This research-grade assay is the basis of partnerships with numerous global pharmaceutical companies as well as several small ones, he says, particularly to aid development of immunotherapies where there are currently no ideal markers of treatment response. Delfi last year publicly announced one of its initial collaborations with Immunocore, which is exploring the use of the DELFI-TF test as an early predictor of benefit from treatment with a novel class of bispecific T cell receptor immunotherapies against cancer. Other approaches of its collaborators include targeted immunotherapy, checkpoint inhibitors, and CAR-T therapy.
As Dracopoli well knows, one of the challenging issues faced by big pharma companies is which compounds coming in from their discovery and licensing groups to take forward. Anywhere between 10 and 20 new molecular entities are in the mix every year, which translates to “an enormously complex mix of studies in different indications with different existing therapies and add-on study designs.”
Since not everything can advance to clinical trials, “early evidence of molecular response in early drug development is gold,” he says. “It’s a level of information that helps you risk-adjust how you develop these compounds.”
Industry partners have indicated that they want to do more treatment response monitoring in blood, but mutation-based assays are cost-prohibitive to deploy across all patients and studies, says Dracopoli, getting back to the appeal of DELFI-TF. At a much lower cost, the assay can provide companies with the same information about genome-wide effects based on an evaluation of changes in circulating tumor burden—and, as needed for dose escalation studies, deliver those results back within two weeks.
Since none of the data gets returned to patients or their oncologist, it can be used as a clinical research tool today, he says. The plan is to eventually turn the research-grade assay into an LDT, subject to regulation by the Centers for Medicare and Medicaid Services through CLIA.
In a paper published last fall, the DELFI-TF test was validated in two independent cohorts of patients with colorectal or lung cancer (Nature Communications, DOI: 10.1038/s41467-024-53017-7). Dracopoli says he will present data on a more diverse set of cancers as well as applications in immunotherapy at the 2025 Next Generation Dx Summit.
The biggest longstanding problem in both chemotherapy and targeted therapy development is that drugs that work in vitro or in animal models for some reason don’t work when brought into human clinical setting, he says. “The biggest risk of failure is lack of efficacy and monitoring tests [like DELFI-TF] basically give us an early look at [that]” based on evidence that a drug is “hitting its target and having some effect on the cell and downstream pathway of the target that we can measure.”
Evidence of molecular response may well manifest three months or more before the effects can be seen clinically, particularly when assessments are being made based on the changing size of a tumor, Dracopoli notes. “But we do know that changes in the circulating tumor burden within weeks after a therapy can be indicative of whether the drug is actively working... even at very low doses.”