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Detection and Monitoring of Tumor Associated Circulating DNA in Patient Biofluids
Published on: June 8, 2019
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Targeted locus amplification to develop robust patient-specific assays for liquid biopsies in pediatric solid tumors
Lieke M J van Zogchel1,2, Nathalie S M Lak1,2, Nina U Gelineau1,2
1Princess Máxima Center for Pediatric Oncology Research, Utrecht, Netherlands.
Frontiers in Oncology
|May 8, 2023
Summary
This study shows that patient-specific DNA markers can detect cancer DNA in children's blood. This liquid biopsy approach successfully tracked tumor burden in pediatric solid tumors, offering a promising new diagnostic tool.
Area of Science:
- Oncology
- Genetics
- Molecular Diagnostics
Background:
- Pediatric cancers often feature copy number alterations (CNAs) and fusion genes, unlike adult cancers which are mutation-driven.
- Tumor-specific DNA breakpoint sequences within these alterations are key targets for detection.
- Liquid biopsies offer a minimally invasive method for detecting residual disease in pediatric solid tumors.
Purpose of the Study:
- To investigate the feasibility of using tumor-specific DNA breakpoints to design patient-specific markers.
- To detect tumor-derived cell-free DNA (cfDNA) in plasma from pediatric solid tumor patients.
- To assess the utility of these markers in monitoring treatment response and disease recurrence.
Main Methods:
- Regions of interest (CNAs, fusion genes) were identified using standard diagnostic methods (SNP array, FISH, RT-qPCR).
- Targeted Locus Amplification (TLA) or Targeted Locus Capture (TLC) was used to design patient-specific primers and probes.
- Droplet digital PCR (ddPCR) assays were developed to analyze cfDNA in patient plasma samples collected at diagnosis and during therapy.
Main Results:
- Patient-specific ddPCR assays were successfully designed for all pediatric solid tumor patients studied.
- Tumor-specific markers were detected in cfDNA from diagnostic plasma samples.
- In neuroblastoma patients, cfDNA marker levels correlated with tumor burden, decreasing with treatment, disappearing at remission, and reappearing upon relapse. Rhabdomyosarcoma and Ewing sarcoma samples became negative post-therapy.
Conclusions:
- The study demonstrates the feasibility of using TLA/TLC to identify tumor-specific breakpoints in pediatric solid tumors for cfDNA analysis.
- This approach shows significant promise for monitoring pediatric cancers, given the prevalence of CNAs and fusion genes.
- Further research in larger cohorts with standardized protocols is warranted to fully realize the potential of this liquid biopsy method.
