Adjustments to the preanalytical phase of quantitative cell-free DNA analysis.

Abel Jacobus Bronkhorst,Piet J Pretorius,Janine Aucamp

doi:10.1016/j.dib.2015.12.009

Abstract

Evaluating the kinetics of cell-free DNA (cfDNA) in the blood of cancer patients could be a strong auxiliary component to the molecular characterization of cfDNA, but its potential clinical significance is obscured by the absence of an analytical consensus. To utilize quantitative cfDNA assessment with confidence, it is crucial that the preanalytical phase is standardized. In a previous publication, several preanalytical variables that may affect quantitative measurements of cfDNA were identified, and the most confounding variables were assessed further using the growth medium of cultured cancer cells as a source of cfDNA (“Cell-free DNA: Preanalytical variables” [1]). The data accompanying this report relates to these experiments, which includes numerous changes to the sample handling and isolation protocols, and can be used for the interpretation of these results and other similar experiments by different researchers.

Highlights

Evaluating the kinetics of cell-free DNA in the blood of cancer patients could be a strong auxiliary component to the molecular characterization of cfDNA, but its potential clinical significance is obscured by the absence of an analytical consensus
To utilize quantitative cfDNA assessment with confidence, it is crucial that the preanalytical phase is standardized
The data accompanying this report relates to these experiments, which includes numerous changes to the sample handling and isolation protocols, and can be used for the interpretation of these results and other similar experiments by different researchers. & 2015 Published by Elsevier Inc

Summary

Data accessibility

Table PCR amplification of cell-free DNA was measured using a real-time quantitative assay for the β-globin gene. This data will be useful considerations when optimizing protocols and setting up a standard operating procedure, which should expedite the translation of cfDNA analyses to clinical practice. This data could be compared to other studies that investigated the effect of methodological variables on quantitative measurements of cfDNA. The data is presented in a supplementary file as a single table, which includes several quantitative measurements of cfDNA following modifications to the standard protocol followed.

Cell culturing

Extraction of cfDNA

Findings

Quantification of cell-free DNA