Open AccessBlood collection in cell-stabilizing tubes does not impact germline DNA quality for pediatric patients
Author(s) -
Bruce M. Wollison,
Edwin Thai,
Aimee McKinney,
Abigail Ward,
Andrea Clapp,
Catherine Clinton,
Anwesha Nag,
Aaron R. Thorner,
Julie M. GastierFoster,
Brian D. Crompton
Publication year - 2017
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0188835
Subject(s) - germline , exome sequencing , biopsy , cell free fetal dna , liquid biopsy , medicine , computational biology , biology , oncology , pathology , genetics , cancer , gene , mutation , prenatal diagnosis , fetus , pregnancy
Objectives Liquid 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. Methods Blood 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. Results Quality 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. Conclusion Our 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.