The Use of Cell-free DNA in Clinical Practice: Work in Progress

A recent review outlines the use of circulating tumor DNA (ctDNA) in clinical practice and the requirements necessary to extend the use of this technology for health impact.

Cell-free DNA (cfDNA) is extracellular strands of DNA present in body fluids. Circulating tumor DNA (ctDNA) is a specific type of cfDNA that originates from a primary tumor, circulating tumor cells or metastasized cells. ctDNA is currently the most common form of liquid biopsy, a term used to refer to utilizing circulating cancer cells, DNA and other omic markers from blood or fluid sample.

Research efforts on the analytic validity, clinical validity and utility of cfDNA as a diagnostic and therapeutic biomarker have expanded in the past decade, yet very few applications fall into CDC Tier 1 classified guidelines (genomic applications with a level of evidence established for use in practice. A 2022 blog by our office highlighted publications that meet criteria for Tier 1 genomic applications.

In this blog, we briefly outline existing cfDNA Tier 1 and 2 genomic applications and discuss the current status of cfDNA research and its potential for health impact.

The Landscape of Current cfDNA Tier 1 and 2 Applications

Non-small cell lung cancer and other cancers

Current National Comprehensive Cancer Network (NCCN) 2022 guidelines specific to NSCLC (V5.2022) advise plasma cell-free/circulating tumor DNA testing should not be used in lieu of histologic tissue diagnosis, although it can be considered in specific clinical circumstances (i.e., if a patient is not suitable for invasive tissue sampling, if insufficient material following pathologic confirmation or incomplete assessment of all recommended biomarkers in the initial diagnostic setting). NCCN reports ctDNA testing studies have shown high specificity but compromised sensitivity for detecting molecular biomarkers that guide therapeutic interventions, therefore data supports complementary testing to reduce turnaround time and increase yield of targetable alteration detection.

One clinical guideline (published in three different journals) endorsed by multiple national professional organizations, focuses on the role of testing circulating cfDNA in lung cancer management. The recommendations based on a systematic review determined that there was insufficient evidence to inform the use of cfDNA or ctDNA for diagnosis of primary lung adenocarcinoma or identification of mutations at the time of EGFR TKI resistance. In some clinical settings in which tissue is limited and/or insufficient for molecular testing, physicians may use a cfDNA assay to identify EGFR mutations. A consensus report concurred with the published guidelines above.

CMS coverage has been approved under specific clinical scenarios for liquid biopsy for patients with lung cancer, as well NSCLC, colorectal, breast, and other solid tumors. Another CMS coverage determination has been approved for liquid biopsy as a follow up to a sample taken from baseline tumor diagnostic material as part of minimal residual disease testing for cancer. All CMS approved testing meet criteria for Tier 1 guidelines.

An FDA companion diagnostic device received premarket approval, which includes indications for NSCLC and prostate cancer, and was updated to also include ovarian and breast cancer genetic testing using cfDNA. Another FDA premarket approval includes indications for only NSCLC genetic testing using cfDNA. All FDA approved companion diagnostic device meet criteria for Tier 1 guidelines.

A Canadian clinical guideline publication recommends liquid biopsy being performed first for the detection of EGFR T790M mutation in patients with EGFR sensitizing mutation-positive NSCLC who progress on first- or second-generation EGFR TKI therapy, followed up with tissue biopsy if the liquid biopsy is negative for T790M.

Prenatal fetal aneuploidy

Three clinical guideline publications address use of cfDNA for screening prenatal fetal aneuploidy, also referred to as noninvasive prenatal screening (NIPS). A 2015 updated American College of Obstetrics and Gynecology (ACOG) Committee Opinion (Tier 2) recommended conventional screening methods as the most appropriate choice for first-line screening for most women in the general obstetric population since cell-free DNA screening has limitations in performance and limited data on cost-effectiveness in the low-risk obstetric population. An American College of Medical Genetics and Genomics (ACMG) 2016 updated position statement (Tier 2) recommended all pregnant women be informed that NIPS using cell-free DNA is the most sensitive screening option for traditionally screened aneuploidies (trisomies 13, 18 and 21). In 2017, consensus recommendations (Tier 2) were developed through relevant stakeholder groups, including ACMG and ACOG, to create clear and consistent guidelines for prenatal genetic tests. Their recommendations include MSAFP with ultrasound nuchal translucency to increase detection for a broader range of conditions compared to cfDNA when the risk for common trisomies exit. A 2022 ACMG Systematic Evidence Review concludes NIPS is a highly accurate screening method for trisomies 13, 18 and 21 in both singleton and twin pregnancies and requires diagnostic confirmation of positive findings.

Allograft rejection

CMS coverage determination has been approved for cell-free testing for kidney and heart allografts and another for non-specific solid organ allograft rejection. These tests are used in patients who have undergone transplant with suspicion of, or evaluation of transplant rejection, and can guide management decisions regarding immunosuppression.

Going Forward:  Potential Health Impact of cfDNA

Since its discovery in 1948, the utility of cfDNA has been studied extensively in screening, diagnosis, prognosis, therapy and monitoring disease progression. Although effort has focused on cancer, and mostly in NSCLC, other areas of research are ongoing, including autoimmune disease, metabolic disorders, Alzheimer’s disease, and other neurologic conditions, COVID-19, myocarditis and dilated cardiomyopathy, and refractory epilepsy.

In addition to circulating cfDNA, potential clinical applications exist for other omics, including epigenetics and exosomal miRNAs, as well as use of cfDNA in other body fluids (e.g. urine).

The future potential for cfDNA- with its clear advantage of non-invasive sample ascertainment and potential for early diagnosis, will depend on improvements in standardizing techniques such as clinical practice guidelines for pre-analytic procedures, development of best practice guidelines, analytical and clinical validity in various contexts, and an increase in clinical trial research.

Please submit your input and comments about the promise and limitations of cfDNA here.