Circulating free DNA as non-invasive diagnostic biomarker for childhood solid tumors

PurposeOur aims are to determine circulating free DNA (cfDNA) in childhood solid tumor patients who underwent surgical intervention and to analyze any relationships with clinical parameters.MethodsFourty-four consenting children admitted with solid tumors between 2010 and 2014 were recruited. CfDNAs isolated from 0.5 mL plasma obtained before and 1-30 days after surgery were analyzed by next-generation sequencing (NGS: IonTorrent Cancer Hotspot panel) and by gene amplification analysis using a digital PCR (dPCR) platform.ResultsTotal amounts of cfDNA were 54-825 ng and were significantly associated with stage of disease. In cfDNA, 15 mutations or deletions (2 ALK, 2 TP53, 1 WT1, 3 CTNNB1, 1 APC, 1 KIT, 1 RET, 1 CDNK2AT, and 3 SMARCB1) were identified. In 10 neuroblastoma suspected cases, 2 showed high copy numbers of MYCN using dPCR. The positive rate in our cohort was 36%, and all of these aberrations were detected in the original tumors. None of the aberrations were detectable in cfDNA after surgery except for three cases whose tumors remained after surgery.ConclusionsThese data demonstrate the feasibility and potential utility of mutation/deletion/amplification screening in cfDNA using NGS and dPCR for the detection of tumor biomarkers in children with solid tumors. These markers also have the potential utility to evaluate complete resection after surgery.