Abstract
ObjectivesLiquid biopsy technologies allow non-invasive tumor profiling for patients with solid tumor malignancies by sequencing circulating tumor DNA. These studies may be useful in risk-stratification, monitoring for relapse, and understanding tumor evolution. The quality of DNA obtained for these studies is improved when blood samples are collected in tubes that stabilizing white blood cells (WBC). However, ongoing germline research in pediatric oncology generally requires obtaining blood samples in EDTA tubes, which do not contain a WBC-stabilizing preservative. In this study, we explored whether blood samples collected in WBC-stabilizing tubes could be used for both liquid biopsy and germline studies simultaneously, minimizing blood collection volumes for pediatric patients.MethodsBlood was simultaneously collected from three patients in both EDTA and Streck Cell-Free DNA BCT® tubes. Germline DNA was extracted from all blood samples and subjected to whole-exome sequencing and microarray profiling.ResultsQuality control metrics of DNA quality, sequencing library preperation and whole-exome sequencing alignment were virtually identical regardless of the sample collection method. There was no discernable difference in patterns of variant calling for paired samples by either whole-exome sequencing or microarray analysis.ConclusionOur study demonstrates that high-quality genomic studies may be performed from germline DNA obtained in Streck tubes. Therefore, these tubes may be used to simultaneously obtain samples for both liquid biopsy and germline studies in pediatric patients when the volume of blood available for research studies may be limited.
Highlights
Strategies for applying liquid biopsy assays to the treatment of pediatric solid tumors is still in the early stages of development [1,2,3,4]
Our study demonstrates that high-quality genomic studies may be performed from germline DNA obtained in Streck tubes
The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
Summary
Strategies for applying liquid biopsy assays to the treatment of pediatric solid tumors is still in the early stages of development [1,2,3,4]. Efforts to determine the prognostic value of liquid biopsy assays in pediatric solid tumors will, necessitate coordinated efforts across multiple institutions. These studies will require samples to be collected at institutions that may not be capable of rapidly processing samples locally and, instead, samples will need to be shipped and processed uniformly at a central laboratory. For this reason, many collaborative trials are beginning to utilize specialized WBC-stabilizing blood collection tubes for liquid biopsy studies. Stabilizing the WBCs prior to sample processing prevents the release of large amounts of genomic DNA into the plasma that would otherwise dilute circulating tumor DNA (ctDNA) levels to undetectable proportions
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