TY - JOUR
T1 - Interlaboratory evaluation of quality control methods for circulating cell-free DNA extraction
AU - Devonshire, Alison
AU - Jones, Gerwyn
AU - Gonzalez, Ana Fernandez
AU - Kofanova, Olga
AU - Trouet, Johanna
AU - Pinzani, Pamela
AU - Gelmini, Stefania
AU - Bonin, Serena
AU - Foy, Carole
N1 - Funding
This study was conducted under the SPIDIA4P project which received funding from the European Union ́s Horizon 2020 research and innovation programme under grant agreement no. 733112.
The work performed by the NML (LGC) was part-funded by the UK government Department for Science, Innovation and Technology (DSIT)
Copyright © 2023. Published by Elsevier B.V.
PY - 2023/9/18
Y1 - 2023/9/18
N2 - Analysis of circulating cell-free DNA (ccfDNA) isolated from liquid biopsies is rapidly being implemented into clinical practice. However, diagnostic accuracy is significantly impacted by sample quality and standardised approaches for assessing the quality of ccfDNA are not yet established. In this study we evaluated the application of nucleic acid "spike-in" control materials to aid quality control (QC) and standardisation of cfDNA isolation for use in in vitro diagnostic assays. We describe an approach for the design and characterisation of in-process QC materials, illustrating it with a spike-in material containing an exogenous Arabidopsis sequence and DNA fragments approximating to ccfDNA and genomic DNA lengths. Protocols for inclusion of the spike-in material in plasma ccfDNA extraction and quantification of its recovery by digital PCR (dPCR) were assessed for their suitability for process QC in an inter-laboratory study between five expert laboratories, using a range of blood collection devices and ccfDNA extraction methods. The results successfully demonstrated that spiking plasmid-derived material into plasma did not deleteriously interfere with endogenous ccfDNA recovery. The approach performed consistently across a range of commonly-used extraction protocols and was able to highlight differences in efficiency and variability between the methods, with the dPCR quantification assay performing with good repeatability (generally CV <5%). We conclude that initial findings demonstrate that this approach appears "fit for purpose" and spike-in recovery can be combined with other extraction QC metrics for monitoring the performance of a process over time, or in the context of external quality assessment. AVAILABILITY OF DATA AND MATERIALS: Processed data is available in Supplementary File 4. Raw data available upon request. Declaration of Competing Interest.
AB - Analysis of circulating cell-free DNA (ccfDNA) isolated from liquid biopsies is rapidly being implemented into clinical practice. However, diagnostic accuracy is significantly impacted by sample quality and standardised approaches for assessing the quality of ccfDNA are not yet established. In this study we evaluated the application of nucleic acid "spike-in" control materials to aid quality control (QC) and standardisation of cfDNA isolation for use in in vitro diagnostic assays. We describe an approach for the design and characterisation of in-process QC materials, illustrating it with a spike-in material containing an exogenous Arabidopsis sequence and DNA fragments approximating to ccfDNA and genomic DNA lengths. Protocols for inclusion of the spike-in material in plasma ccfDNA extraction and quantification of its recovery by digital PCR (dPCR) were assessed for their suitability for process QC in an inter-laboratory study between five expert laboratories, using a range of blood collection devices and ccfDNA extraction methods. The results successfully demonstrated that spiking plasmid-derived material into plasma did not deleteriously interfere with endogenous ccfDNA recovery. The approach performed consistently across a range of commonly-used extraction protocols and was able to highlight differences in efficiency and variability between the methods, with the dPCR quantification assay performing with good repeatability (generally CV <5%). We conclude that initial findings demonstrate that this approach appears "fit for purpose" and spike-in recovery can be combined with other extraction QC metrics for monitoring the performance of a process over time, or in the context of external quality assessment. AVAILABILITY OF DATA AND MATERIALS: Processed data is available in Supplementary File 4. Raw data available upon request. Declaration of Competing Interest.
UR - https://pubmed.ncbi.nlm.nih.gov/37730172
U2 - 10.1016/j.nbt.2023.09.005
DO - 10.1016/j.nbt.2023.09.005
M3 - Article
C2 - 37730172
SN - 1871-6784
VL - 78
SP - 13
EP - 21
JO - New Biotechnology
JF - New Biotechnology
ER -