Tumor circulating DNA analysis by next generation sequencing on cancer pediatric patients

Pediatric cancer evolution may be compromised by the presence of low represented mutations. Thus, bad evolution or relapse could be associated to the increase of minority clones with pathological mutations. Next generation sequencing (NGS) of tumor circulating DNA (ctDNA) may be an interesting alternative for genotypic evaluation of the tumor before treatment. This approach may permit the detection of low prevalence mutations that could be monitored during the patients’ treatment. The aim of this work was to detect low prevalence mutations on ctDNA of cancer pediatric patients by NGS before treatment and its monitoring by digital PCR (dPCR) during the follow up.

Methods: 15 cancer pediatric patients were included in the study. Serum cfDNA before treatment was sequenced by Agilent Technologies for Illumina. Serum ctDNA specific mutations of the patients were analyzed by dPCR assay using the QX200 Droplet DPCR System before treatment and at 2, 4 and 6 months.

Results: Most patients showed a good evolution during the first months of treatment. In spite of this, 2 neuroblastoma patients died, one due to a relapse and the other one under a septic shock. Besides, one patient suffering a rhabdomyosarcoma showed a temporary relapse. All patients included in the study presented a variable landscape of low prevalence mutations associated with pediatric cancer before treatment. During the follow up of patients with good evolution, the analysis of specific mutations by dPCR showed a clear disappearance of the mutations detected by NGS after the treatment. Opposite to that presence of mutations during follow up were observed when patients presented a bad response to the treatment.

Conclusions: NGS analysis of pediatric cancer associated mutations may be an interesting approach in order to stratify the patients before treatment. Thus it would be a useful tool for therapeutic decisions and would allow personalizing cancer therapy.