Circulating tumor DNA sequencing of pediatric solid and brain tumor patients: An institutional feasibility study

Abstract

The potential of circulating tumor DNA (ctDNA) analysis to serve as a real-time “liquid biopsy” for children with central nervous system (CNS) and non-CNS solid tumors remains to be fully elucidated. We conducted a study to investigate the feasibility and potential clinical utility of ctDNA sequencing in pediatric patients enrolled on an institutional clinical genomics trial. A total of 240 patients had tumor DNA profiling performed during the study period. Plasma samples were collected at study enrollment from 217 patients and then longitudinally from a subset of patients. Successful cell-free DNA extraction and quantification occurred in 216 of 217 (99.5%) of these initial samples. Twenty-four patients were identified whose tumors harbored 30 unique variants that were potentially detectable on a commercially-available ctDNA panel. Twenty of these 30 mutations (67%) were successfully detected by next-generation sequencing in the ctDNA from at least one plasma sample. The rate of ctDNA mutation detection was higher in patients with non-CNS solid tumors (7/9, 78%) compared to those with CNS tumors (9/15, 60%). A higher ctDNA mutation detection rate was also observed in patients with metastatic disease (9/10, 90%) compared to non-metastatic disease (7/14, 50%), although tumor-specific variants were detected in a few patients in the absence of radiographic evidence of disease. This study illustrates the feasibility of incorporating longitudinal ctDNA analysis into the management of relapsed or refractory patients with childhood CNS or non-CNS solid tumors.

Keywords:

• cell-free DNA
• Central Nervous System Tumors
• circulating tumor DNA
• liquid biopsy
• precision oncology

Disclosure statement

J.R. owns stock in Invitae. S.L.P. is a member of an advisory board for Bayer Healthcare Pharmaceuticals, Inc. S.E.P. is a member (nonpaid) of the Scientific Advisory Panel of Baylor Genetics Laboratories.

Additional information

Funding

The Texas KidsCanSeq study is a Clinical Sequencing Evidence-Generating Research (CSER) consortium project supported by the NHGRI/NCI grant U01HG006485 (D.W.P and S.E.P). D.W.P. is the recipient of a St. Baldrick’s Innovation Award with additional support from the Chance for Hope Foundation (D.W.P. and F.Y.L.).