cfDNA May Help Risk-Stratify Patients With ALL

The study authors said the method also has the advantages of having a quick turnaround and a relatively low cost.

Investigators say they have uncovered a potential new biomarker that could help physicians better assess the risk of relapse in patients treated for acute lymphoblastic leukemia (ALL). This new method relies on the analysis of cell-free DNA (cfDNA) to detect the presence of ALL in patients, which investigators say could help flag patients even if blasts are not readily apparent. The report was published in Frontiers in Oncology.

The study authors noted that ALL is the most common pediatric malignancy, but in a majority of cases (90%) is curable. Those who face the steepest odds are patients who experience relapse following treatment and those whose disease spreads to the central nervous system (CNS).

“The prevalence of CNS disease in ALL is high enough that every ALL patient receives prophylactic treatment involving multiple doses of intrathecal chemotherapy, which can have adverse and long-term side effects in pediatric patients,” the investigators noted.

Thus, they said, there is a need for more precise tools to risk stratify patients.

The current best practice of measuring response to treatment is looking at the presence or absence of minimal residual disease (MRD) by analyzing patient samples using flow cytometry or microscopy.

“Developing more sensitive assays that depend on the molecular detection of leukemic blasts via next-generation sequencing has proven difficult since ALL has one of the lowest mutational burdens of any cancer,” they wrote.

In their new paper, the investigators proposed looking at cfDNA, which are DNA fragments released by cancer cells and detectable in patient biofluids.

“Tumor-specific cfDNA increases as tumors grow,” they noted. “The half-life of cfDNA is only 15 to 120 minutes, making it a valuable and proven biomarker for detecting cancer development in healthy individuals and monitoring tumor response to treatment in cancer patients.”

The investigators decided to develop a workflow using Nanopore MinION sequencing of PCR-amplified B-cell–specific rearrangement of the IGH locus in the cfDNA of patients with B-cell ALL. They then tested the method on samples from 5 pediatric patients.

The results were compelling. The investigators said their method allowed them to assess patient response throughout the treatment process at a level superior to that of MRD.

“cfDNA was detected in patient biofluids with clinical diagnoses of MRD and CNS disease, and leukemic clones could be detected even when diagnostic cell-count thresholds for MRD were not met,” they wrote.

Moreover, they said their method has several other advantages, including a quick turnaround time and low cost. They added that the method could also be useful on a larger scale.

“The workflow could be scaled up for quickly and efficiently assessing the dynamics of B-ALL clones in response to treatment in large patient datasets, particularly in consortia studying B-ALL,” they wrote.

The authors conceded that their study was based on a small sample size of just 5 patients. However, they said the results suggest the workflow could be a useful tool. They said a future study with 20 to 30 patients “will be sufficient for proof of concept to show that cfDNA assays may be useful in detecting the presence of ALL in patients when blasts are not in the biofluid sample.”


Sampathi S, Chernyavskaya Y, Haney MG, et al. Nanopore sequencing of clonal IGH rearrangements in cell-free DNA as a biomarker for acute lymphoblastic leukemia. Front Oncol. 2022;12:958673. doi:10.3389/fonc.2022.958673

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