<< Back to MOTIFvations Blog Home Page

PeCan-Seq: A New Method for Cell-free DNA Analysis in Pediatric Cancer

By Stuart P. Atkinson, Ph.D.

July 1, 2025

Tweet

Introduction: Plasma DNA Analysis for Cancer Management – Adults Only?

The analysis of circulating tumor DNA (ctDNA) from liquid biopsies of various patient sample types (e.g., blood, urine, and saliva) represents an exciting non-invasive means of detecting cancer and monitoring progress and therapeutic responses in adult patients; however, this hugely encouraging strategy remains underutilized in pediatric cancer cases. Ongoing advances in high-throughput genomic sequencing have enabled the extensive profiling of pediatric cancer genomes (Ma et al.); however, the elevated level of genomic heterogeneity and the relatively low prevalence of recurrent oncogenic drivers in pediatric cancer cases represent significant challenges to ctDNA analysis (Sweet-Cordero & Biegel).

In their recent Leukemia study, researchers headed by Jeffery M. Klco, Ruth G. Tatevossian, and Charles G. Mullighan (St. Jude Children’s Research Hospital) reported on “pediatric cancer profiling by deep sequencing” or PeCan-Seq as a potential means of solving problems related to the detection and monitoring of pediatric cancer via cell-free DNA (of which ctDNA represents a component) in liquid biopsies (Lei et al.). The PeCan-Seq workflow employs 1 ml of blood serum and a DNA capture panel for the robust de novo detection of diverse genomic aberrations in over 300 childhood cancer-associated genes. The authors applied this cost-effective, highly sensitive, and minimally invasive deep sequencing method to compare somatic genomic variants discovered in plasma cfDNA with those in tumor DNA in over 200 pediatric cancer cases and, as such, describe the potential utility of PeCan-Seq in the diagnosis and monitoring of pediatric disease.

Active Motif is here to support your liquid biopsy-based studies, as highlighted by the recent release of RapCap (Rapid Capture) magnetic beads for the isolation of cfDNA. RapCap beads have revolutionized cfDNA isolation from blood plasma and saliva thanks to a simplified, column‐free workflow. Unlike traditional spin-column methods that rely on multiple centrifugation and binding steps, RapCap beads employ a surface engineered for high affinity to cfDNA, allowing rapid and efficient capture directly from plasma, saliva, or other patient samples isolated via liquid biopsies.

 Back to Table of Contents

PeCan-Seq Brings Plasma Cell-free DNA Analysis to Pediatric Cancer Patients

The study cohort of children (median age of 7) comprised 177 cases of hematologic malignancies, 38 solid tumors, and 18 brain tumors; importantly, the hematologic malignancies provided significantly higher plasma cfDNA yields and sequencing depths.

The study detected somatic variants in plasma cfDNA sampled at diagnosis in all hematologic malignancy cases, with a median ctDNA fraction in cfDNA of 0.77. PeCan-Seq analysis revealed a 97% overall detection rate for expected tumor variants, demonstrating that the plasma cfDNA mutational profiles created display high concordance with tumor DNA sequencing. In addition, PeCan-Seq detected plasma cfDNA-specific variants not detected by tumor DNA sequencing, which may arise from spatial tumor heterogeneity and sampling bias, different sequencing depths, and/or the different prevalence of tumor cells with these variants in bone marrow and peripheral blood.

PeCan-Seq also identified genomic aberrations in 19 of 38 plasma cfDNA samples from solid tumor cases, with varying ctDNA fraction levels observed. This analysis revealed significantly higher cfDNA yields in ctDNA-positive patients than in ctDNA-negative patients and again reported the detection of cfDNA-only variants. Of the 18 cases of brain tumors, PeCan-Seq analysis of cfDNA samples identified ctDNA for one case of pineoblastoma.

The subsequent part of the study aimed to explore the ability of PeCan-Seq analysis of plasma cfDNA to monitor minimal residual disease (MDR; the small number of cancer cells remaining after treatment, even after clinical remission) in B-cell acute lymphoblastic leukemia (B-ALL) cases during and after chemotherapeutic treatment. Overall, plasma cfDNA analysis successfully detected somatic mutations in all B-ALL patients with an MDR over 1%, one of three patients with MDR between 0.1-0.01%, and one of four patients with undetectable MDR. Finally, the team applied PeCan-Seq analysis of plasma cfDNA to detect multiple tumors in a single sample from one patient suffering from B-ALL, neuroblastoma, and then relapsed neuroblastoma with distinct genomic variants. Analysis of cfDNA collected three days before primary diagnosis revealed the presence of ctDNA derived from three distinct tumor entities, with 54% of total plasma cfDNA derived from B-ALL, 8% from neuroblastoma at diagnosis, and 23% from the relapse-fated subclone of neuroblastoma present at diagnosis.

 Back to Table of Contents

PeCan-Seq Analysis of cfDNA: The Future of Pediatric Cancer Patient Management?

Overall, these data support the ability of PeCan-seq to identify cfDNA/ctDNA alterations in liquid biopsies from patients with childhood hematologic malignancies and a subset of solid tumors and position this approach as a highly-sensitive, cost-effective, and non-invasive approach to cancer detection and disease monitoring. The limitations that must first be surpassed before PeCan-seq analysis of plasma cfDNA can truly flourish include expanding the coverage of childhood cancer variants (already partially addressed by the authors), solving problems related to the low sample volumes available for cfDNA studies in pediatric patients (mainly from solid tumors and with cerebrospinal fluid), and improving the range of the tumor types assessed. Will we see the application of PeCan-Seq to cfDNA samples for minimally invasive disease diagnosis, monitoring response to therapy, and potential surveillance testing for patients with cancer predisposition syndromes? Stay tuned to the Active Motif blog to find out!

For more on how PeCan-Seq brings the analysis of cell-free DNA from liquid biopsies to pediatric cancer cases, see Leukemia, November 2024.

 Back to Table of Contents

About the author

Stuart P. Atkinson, Ph.D.

Stuart was born and grew up in the idyllic town of Lanark (Scotland). He later studied biochemistry at the University of Strathclyde in Glasgow (Scotland) before gaining his Ph.D. in medical oncology; his thesis described the epigenetic regulation of the telomerase gene promoters in cancer cells. Following Post-doctoral stays in Newcastle (England) and Valencia (Spain) where his varied research aims included the exploration of epigenetics in embryonic and induced pluripotent stem cells, Stuart moved into project management and scientific writing/editing where his current interests include polymer chemistry, cancer research, regenerative medicine, and epigenetics. While not glued to his laptop, Stuart enjoys exploring the Spanish mountains and coastlines (and everywhere in between) and the food and drink that it provides!

Contact Stuart on X with any questions

Related Articles

<< Back to MOTIFvations Blog Home Page