Biospecimen Science of Blood for cfDNA Genetic Analyses

Ammerlaan, Wim; Betsou, Fay

doi:10.1007/s40139-019-00193-7

Cited by 8 publications

(11 citation statements)

References 58 publications

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“…As generally seen for liquid biopsy samples [ 50 – 52 ], the amount of total cfDNA extracted per millilitre (ml) of plasma was low ( Fig 6 ). For cohort I, the median amount of DNA extracted per ml of plasma was 11.30 ng [2.33ng/ml;86.28ng/ml].…”

Section: Resultssupporting

confidence: 55%

A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies

Jensen

Epistolio

Madsen³

et al. 2021

PLoS ONE

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Background A major perspective for the use of circulating tumor DNA (ctDNA) in the clinical setting of non-small cell lung cancer (NSCLC) is expected as predictive factor for resistance and response to EGFR TKI therapy and, especially, as a non-invasive alternative to tissue biopsy. However, ctDNA is both highly fragmented and mostly low concentrated in plasma and serum. On this basis, it is important to use a platform characterized by high sensitivity and linear performance in the low concentration range. This motivated us to evaluate the newly developed and commercially available SensiScreen® EGFR Liquid assay platform (PentaBase) with regard to sensitivity, linearity, repeatability and accuracy and finally to compare it to our already implemented methods. The validation was made in three independent European laboratories using two cohorts on a total of 68 unique liquid biopsies. Results Using artificial samples containing 1600 copies of WT DNA spiked with 50% - 0.1% of mutant copies across a seven—log dilution scale, we assessed the sensitivity, linearity, repeatability and accuracy for the p.T790M, p.L858R and exon 19 deletion assays of the SensiScreen® EGFR Liquid assay platform. The lowest value detectable ranged from 0.5% to 0.1% with R2≥0,97 indicating good linearity. High PCR efficiency was shown for all three assays. In 102 single PCRs each containing theoretical one copy of the mutant at initiating, assays showed repeatable positivity in 75.5% - 80.4% of reactions. At low ctDNA levels, as in plasma, the SensiScreen® EGFR Liquid assay platform showed better sensitivity than the Therascreen® EGFR platform (Qiagen) and equal performance to the ctEGFR Mutation Detection Kit (EntroGen) and the IOT® Oncomine cell-free nucleic acids assay (Thermo Fisher Scientific) with 100% concordance at the sequence level. Conclusion For profiling clinical plasma samples, characterized by low ctDNA abundance, the SensiScreen® EGFR Liquid assay is able to identify down to 1 copy of mutant alleles and with its high sensitivity, linearity and accuracy it may be a competitive platform of choice.

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Section: Resultssupporting

confidence: 55%

A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies

Jensen

Epistolio

Madsen³

et al. 2021

PLoS ONE

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“…The isolation of cfDNA from plasma samples instead of serum is also preferable, given that it avoids the release of cellular DNA from lysing cells during the clotting process. In addition, due to low concentrations, extraction methods must guarantee high yields of cfDNA [92]. The low quantities and small fraction of ctDNA in circulation require the use of highly sensitive detection techniques, such as droplet digital Polymerase Chain Reaction (ddPCR), Next Generation Sequencing (NGS) [41] or BEAMing (beads, emulsion, amplification and magnetics) [12].…”

Section: Advantages and Disadvantages Of Liquid Biopsiesmentioning

confidence: 99%

Liquid Biopsies: Applications for Cancer Diagnosis and Monitoring

Martins

Ribeiro

Jorge

et al. 2021

Genes

131

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The minimally—or non-invasive detection of circulating tumor-derived components in biofluids, such as blood, liquid biopsy is a revolutionary approach with significant potential for the management of cancer. Genomic and transcriptomic alterations can be accurately detected through liquid biopsies, which provide a more comprehensive characterization of the heterogeneous tumor profile than tissue biopsies alone. Liquid biopsies could assist diagnosis, prognosis, and treatment selection, and hold great potential to complement current surveilling strategies to monitor disease evolution and treatment response in real-time. In particular, these are able to detect minimal residual disease, to predict progression, and to identify mechanisms of resistance, allowing to re-orient treatment strategies in a timelier manner. In this review we gathered current knowledge regarding the role and potential of liquid biopsies for the diagnosis and follow-up of cancer patients. The presented findings emphasize the strengths of liquid biopsies, revealing their chance of improving the diagnosis and monitoring of several tumor types in the near future. However, despite growing evidence supporting their value as a management tool in oncology, some limitations still need to be overcome for their implementation in the routine clinical setting.

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“…By ‘lifestyle factor’, we refer to all external variables that involve individual choice, such as exercise, alcohol consumption, occupation and smoking. We have chosen to include only studies conducted on plasma and exclude all studies on serum as serum has been shown to be the less preferred substrate due to its propensity for leukocyte DNA contamination and dependence on processing time ( Ammerlaan and Betsou, 2019 ; Trigg et al, 2018 ; Warton et al, 2014 ). The use of serum was the only exclusion criterion that we imposed.…”

Section: Introductionmentioning

confidence: 99%

The influence of biological and lifestyle factors on circulating cell-free DNA in blood plasma

Yuwono

Warton

Ford

2021

eLife

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Research and clinical use of circulating cell-free DNA (cirDNA) is expanding rapidly; however, there remain large gaps in our understanding of the influence of lifestyle and biological factors on the amount of cirDNA present in blood. Here, we review 66 individual studies of cirDNA levels and lifestyle and biological factors, including exercise (acute and chronic), alcohol consumption, occupational hazard exposure, smoking, body mass index, menstruation, hypertension, circadian rhythm, stress, biological sex and age. Despite technical and methodological inconsistences across studies, we identify acute exercise as a significant influence on cirDNA levels. Given the large increase in cirDNA induced by acute exercise, we recommend that controlling for physical activity prior to blood collection is routinely incorporated into study design when total cirDNA levels are of interest. We also highlight appropriate selection and complete reporting of laboratory protocols as important for improving the reproducibility cirDNA studies and ability to critically evaluate the results.

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Biospecimen Science of Blood for cfDNA Genetic Analyses

Cited by 8 publications

References 58 publications

A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies

A new sensitive and fast assay for the detection of EGFR mutations in liquid biopsies

Liquid Biopsies: Applications for Cancer Diagnosis and Monitoring

The influence of biological and lifestyle factors on circulating cell-free DNA in blood plasma

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