Absolute measurement of the tissue origins of cell-free DNA in the healthy state and following paracetamol overdose

Laurent, Danny; Semple, Fiona; Lewis, Philip; Rose, Elaine; Black, Holly A.; Forbes, Stuart J.; Arends, Mark J.; Dear, James W.; Aitman, Timothy J.

doi:10.1101/715888

Cited by 4 publications

(5 citation statements)

References 45 publications

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“…14,39 Our study revealed an inverse correlation of cfDNA with ALC (r ¼ -0.683; P < 0.001); this was in line with Laurent et al, who stated that haematopoietic cells, including lymphoid and erythroid cells, are the major components of cfDNA. 40 There was a positive correlation of cfDNA with NLR (r ¼ 0.698; P < 0.001), which can be attributed to activation and migration of neutrophils to the bloodstream during COVID-19 and their release of large amounts of ROS which can induce cell DNA damage and release of circulating cfDNA. Likewise, associated lymphopenia due to lymphocyte apoptosis contributes to more release of cfDNA.…”

Section: Aucmentioning

confidence: 92%

Circulating cell-free DNA, peripheral lymphocyte subsets alterations and neutrophil lymphocyte ratio in assessment of COVID-19 severity

et al. 2021

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Cell destruction results in plasma accumulation of cell-free DNA (cfDNA). Dynamic changes in circulating lymphocytes are features of COVID-19. We aimed to investigate if cfDNA level can serve in stratification of COVID-19 patients, and if cfDNA level is associated with alterations in lymphocyte subsets and neutrophil-to-lymphocyte ratio (NLR). This cross-sectional comparative study enrolled 64 SARS-CoV-2-positive patients. Patients were subdivided to severe and non-severe groups. Plasma cfDNA concentration was determined by real-time quantitative PCR. Lymphocyte subsets were assessed by flow cytometry. There was significant increase in cfDNA among severe cases when compared with non-severe cases. cfDNA showed positive correlation with NLR and inverse correlation with T cell percentage. cfDNA positively correlated with ferritin and C-reactive protein. The output data of performed ROC curves to differentiate severe from non-severe cases revealed that cfDNA at cut-off ≥17.31 ng/µl and AUC of 0.96 yielded (93%) sensitivity and (73%) specificity. In summary, excessive release of cfDNA can serve as sensitive COVID-19 severity predictor. There is an association between cfDNA up-regulation and NLR up-regulation and T cell percentage down-regulation. cfDNA level can be used in stratification and personalized monitoring strategies in COVID-19 patients.

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Section: Aucmentioning

confidence: 92%

Circulating cell-free DNA, peripheral lymphocyte subsets alterations and neutrophil lymphocyte ratio in assessment of COVID-19 severity

et al. 2021

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“…Thus, the 1994 discovery of a KRAS p.G12D point mutation in ccfDNA derived from pancreatic cancer was a landmark occasion because the detection of tumour-derived ccfDNA (circulating tumour DNA [ctDNA]) provided incontrovertible molecular proof for the viability of the non-invasive detection of cancer [12]. Haematopoietic cells account for > 90% of the ccfDNA in healthy individuals [13][14][15][16]. The remaining portion of ccfDNA is principally derived from endothelial cells and hepatocytes [13,14,16].…”

Section: Why Is the Fragment Length Of Circulatingmentioning

confidence: 99%

“…Haematopoietic cells account for > 90% of the ccfDNA in healthy individuals [13][14][15][16]. The remaining portion of ccfDNA is principally derived from endothelial cells and hepatocytes [13,14,16]. In the presence of solid tumours, the proportion of ccfDNA composed of ctDNA is generally Advancing cell-free DNA diagnostics to early-stage and non-metastatic cancers has been limited by challenges associated with distinguishing the true signal of lowfrequency tumour-derived cell-free DNA from noise generated during next-generation sequencing.…”

Section: Why Is the Fragment Length Of Circulatingmentioning

confidence: 99%

Leveraging the Fragment Length of Circulating Tumour DNA to Improve Molecular Profiling of Solid Tumour Malignancies with Next-Generation Sequencing: A Pathway to Advanced Non-invasive Diagnostics in Precision Oncology?

Underhill

2021

Mol Diagn Ther

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Circulating cell-free DNA (ccfDNA) has emerged as a promising diagnostic tool in oncology. Identification of tumour-derived ccfDNA (i.e. circulating tumour DNA [ctDNA]) provides non-invasive access to a malignancy's molecular landscape to diagnose, inform therapeutic strategies, and monitor treatment efficacy. Current applications of ccfDNA to detect somatic mutations, however, have been largely constrained to tumour-informed searches and identification of common mutations because of the interaction between ctDNA signal and next-generation sequencing (NGS) noise. Specifically, the low allele frequency of ctDNA associated with non-metastatic and early-stage lesions may be indistinguishable from artifacts that accrue during sample preparation and NGS. Thus, using ccfDNA to achieve non-invasive and personalized molecular profiling to optimize individual patient care is a highly sought goal that remains limited in clinical practice. There is growing evidence, however, that further advances in the field of ccfDNA diagnostics may be achieved by improving detection of somatic mutations through leveraging the inherently shorter fragment lengths of ctDNA compared to non-neoplastic ccfDNA. Here, the origins and rationale for seeking to improve the mutation-based detection of ctDNA by using ccfDNA size profiling are reviewed. Subsequently, in vitro and in silico methods to enrich for a target ccfDNA fragment length are detailed to identify current practices and provide perspective into the potential of using ccfDNA size profiling to impact clinical applications in oncology.

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“…When a cell dies, DNA is released into the bloodstream in short fragments (approximately 160bp, the length of a nucleosome) [7]. All people are thought to have a low level of cfDNA in their blood [8] [9]. In healthy individuals, cfDNA in the blood likely arises from normal cell turnover.…”

Section: Introductionmentioning

confidence: 99%

Estimating the rate of cell type degeneration from epigenetic sequencing of cell-free DNA

Caggiano

Celona

Garton

et al. 2020

Preprint

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Circulating cell-free DNA (cfDNA) in the bloodstream originates from dying cells and is a promising non-invasive biomarker for cell death. Here, we develop a method to accurately estimate the relative abundances of cell types contributing to cfDNA. We leverage the distinct DNA methylation profile of each cell type throughout the body. Decomposing the cfDNA mixture is difficult, as fragments from relevant cell types may only be present in a small amount. We propose an algorithm, CelFiE, that estimates cell type proportion from both whole genome cfDNA input and reference data. CelFiE accommodates low coverage data, does not rely on CpG site curation, and estimates contributions from multiple unknown cell types that are not available in reference data. In simulations we show that CelFiE can accurately estimate known and unknown cell type of origin of cfDNA mixtures in low coverage and noisy data. Simulations also demonstrate that we can effectively estimate cfDNA originating from rare cell types composing less than 0.01% of the total cfDNA. To validate CelFiE, we use a positive control: cfDNA extracted from pregnant and non-pregnant women. CelFiE estimates a large placenta component specifically in pregnant women (p = 9.1 × 10 −5 ). Finally, we use CelFiE to decompose cfDNA from ALS patients and age matched controls. We find increased cfDNA concentrations in ALS patients (p = 3.0 × 10 −3 ). Specifically, CelFiE estimates increased skeletal muscle component in the cfDNA of ALS patients (p = 2.6 × 10 −3 ), which is consistent with muscle impairment characterizing ALS. Quantification of skeletal muscle death in ALS is novel, and overall suggests that CelFiE may be a useful tool for biomarker discovery and monitoring of disease progression.

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Absolute measurement of the tissue origins of cell-free DNA in the healthy state and following paracetamol overdose

Cited by 4 publications

References 45 publications

Circulating cell-free DNA, peripheral lymphocyte subsets alterations and neutrophil lymphocyte ratio in assessment of COVID-19 severity

Circulating cell-free DNA, peripheral lymphocyte subsets alterations and neutrophil lymphocyte ratio in assessment of COVID-19 severity

Leveraging the Fragment Length of Circulating Tumour DNA to Improve Molecular Profiling of Solid Tumour Malignancies with Next-Generation Sequencing: A Pathway to Advanced Non-invasive Diagnostics in Precision Oncology?

Estimating the rate of cell type degeneration from epigenetic sequencing of cell-free DNA

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