Nanopore-Based Monitoring of Cell-Free DNA “Possible Biomarker in B-ALL”

Researchers at the University of Kentucky have demonstrated what they say is a simple, inexpensive method of isolating and detecting cell-free DNA (cfDNA) in the peripheral blood and central nervous system of patients with pediatric B-cell acute lymphoblastic leukemia (B-ALL). This method detected clones that were not present in the genomic DNA of bone-marrow biopsy samples, providing a more accurate assessment of B-ALL heterogeneity while using as little as 25 picograms of cfDNA per patient biofluid sample, the authors write.

The study, published in Frontiers in Oncology in December, “demonstrates the utility of a Nanopore sequencing workflow as a simple, rapid, and low-cost method” to visualize the clonal heterogeneity of unique patient-specific rearrangements of the immunoglobulin heavy chain (IGH) region of genomic and cfDNA and to track these clones throughout treatment, write senior author Jessica S. Blackburn, PhD, and colleagues.

Unlike next-generation sequencing platforms that “require specialized instruments, batch runs, long wait/turnaround times, and complex pipelines for data analysis,” their workflow based on Nanopore MinION sequencing of PCR-amplified variability, diversity, and joining rearrangements in cfDNA is inexpensive and uses freely available data analysis tools – features that “make the MinION sequencing for the detection of cfDNA a promising platform in the clinical setting,” the authors write.

The study used samples obtained from five patients with an initial diagnosis of B-ALL, one of whom was MRD-positive at the end of induction. Although this is a very small sample, “the observed data on IGHV sequencing of cfDNA and MRD status suggests a possible correlation,” the authors write. “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. Published 2022 Dec 14. doi:10.3389/fonc.2022.958673

Tags: MRD, study, B-cell, acute lymphoblastic leukemia, measurable residual disease

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