Minimal residual disease (MRD) assessment using circulating nuclear DNA (cir-nDNA) testing has demonstrated strong prognostic value in patients with operable stage III colon cancer (CC). However, further clinical research is needed to optimize the use of adjuvant therapy in this context. Since the sensitivity of variant allele frequency (VAF)-based MRD detection depends on total cirDNA concentration, we investigated its variation in 67 stage III CC patients over 8 weeks following surgery. A majority of patients showed significantly higher post-surgical cir-nDNA levels compared to their pre-surgical baseline-71.1% during the first month and 51.4% during the second. Cir-nDNA levels tended to considerably vary (up to 18-fold), especially during the first 3 weeks after surgery. We also observed a strong correlation between cir-nDNA levels and neutrophil extracellular traps (NETs) markers throughout the 2-month post-operative period. While previous studies have generally assumed that cir-nDNA levels decrease significantly within 1 month post-surgery in MRD-negative stage III patients, our findings challenge this paradigm. NETs appear to be a substantial source of cir-nDNA and represent a major confounding factor in interpreting total cir-nDNA, given the high inter-individual variability in NETs production after surgery. Our data suggest that defining a single optimal time point for MRD testing may be misleading. Instead, we propose a sampling window between fourth and sixth week post-surgery. Additionally, our results call into question the reliance on VAF as a standalone metric for MRD detection. The most robust strategy would involve integrated monitoring of total cir-nDNA concentration, absolute mutant DNA levels, and NETs-associated inflammation.

The study of cell-free circulating DNA (cirDNA) fragments (fragmentomics) from liquid biopsies has received increasing attention to detect biomarkers. CirDNA found in blood plasma originates from cells in diverse tissues with a predominance for hematopoietic cells. CirDNA fragments are associated with nucleosomes which protect them against DNAse degradation. The genomic positions of CirDNA fragments originating from different cohorts of healthy individual and cancer patients were obtained from the public database FinaleDB. Various bioinformatic and statistical analyses were conducted on these fragments. By mapping a large ensemble of well-positioned nucleosomes (WPNs), we found that nucleosome occupancy was associated with histone-DNA affinity, as evidenced by codon usage bias and differences in cirDNA fragment sizes. Moreover, nucleosome occupancy was different in healthy and cancer samples, thus allowing developing a high-performance machine learning approach for cancer detection (specificity and sensitivity > 0.95 for seven cancer types). Cancer influenced nucleosome occupancy in a global manner, although distinct cancer types retained specific features. WPN occupancy at transcription factor binding sites revealed shared, pan-cancer regulation of transcriptional programs involved in hematopoietic cell differentiation and neutrophil biology, the main cirDNA sources. This work provides new fundamental insights into cirDNA and DNA sequence using cirDNA as a physical readout. It also bares translational significance by disclosing a new high-performance strategy for cancer detection from liquid biopsies.

This study evaluated circulating mRNAs (B2M, TIMP-1, CLU, SERPINE1, GAL3, and S100A9) as potential biomarkers for colorectal cancer (CRC). Plasma levels were measured in CRC patients (stages I-IV, n = 178) and healthy individuals (HIs, n = 171). B2M, TIMP-1, CLU, and S100A9 mRNA levels were significantly elevated in CRC patients vs. HIs. B2M differed only in stage IV, while TIMP-1, CLU, and S100A9 showed significance across all stages except I. A composite index, I-BTC, was developed using B2M, TIMP-1, and CLU via logistic regression. I-BTC improved discrimination between HIs and CRC patients, even at stage I (p = 0.001), with stronger significance in later stages (p ≤ 0.0001). These results validate analytical robustness of the method and highlight its diagnostic potential including for early-stage CRC through specific mRNAs combinations.

The persistence of vasculo-thrombotic complications has been put forward as a possible contributing factor in the Long COVID (LC) syndrome. Given the recently reported separate demonstration of the association of LC with elevated levels of heterogenous fibrin(ogen) amyloidogenic particles (microclots) and with those neutrophil extracellular traps (NETs), markers that are linked to thromboinflammation, this study considers the association of microclots with NETs. The results show that NETs markers (Myeloperoxydase, Neutrophil Elastase, and circulating DNA) are quantitatively and structurally associated with the size and number of microclots in patients with LC. These markers showed a strong diagnostic performance, both independently and when combined. Our study revealed that NETs may be a component of circulating microclots. We suggest that higher NETs formation might promote the stabilization of microclots in the circulation, potentially leading to deleterious effects which contribute causally to the LC syndrome.

INTRODUCTION:Patient-derived tumor organoids (PDTOs) have histological, molecular and clinical (drug sensitivity) characteristics comparable to those of their originating tumors. However, little is known about their ability to replicate the release of tumor-derived DNA. METHODS:Supernatants from 21 colorectal cancer PDTO cultures, established from 13 patients, were prospectively collected. The presence, structure, and mutational landscape of nuclear (cf-nDNA) and mitochondrial (cf-mtDNA) cell-free DNA as well as extracellular mitochondria (ex-Mito) were analyzed using qPCR, fragmentomics and shallow whole-genome sequencing. Mutation profiling was performed via IntPlex qPCR and whole-exome sequencing (WES). RESULTS:Cf-nDNA was detected in 95 % of PDTO supernatants with concentrations ranging from 0.009 to 209 ng/mL. Cf-nDNA fragment size analysis revealed patterns consistent with circulating DNA, including mononucleosome-associated profile. Cf-mtDNA was present in all samples (0.27-89.2 pg/mL) and extracellular mitochondria was also detected (0.009-17.4 pg/mL). A strong concordance (>85 %) was observed between oncogenic mutations in cfDNA and the molecular alterations detected in PDTOs and patient tumors. CONCLUSION:PDTOs release both nuclear and mitochondrial cfDNA into their culture medium displaying high similarity with patient-derived circulating DNA (cirDNA), including fragmentation patterns and oncogenic mutations. This study strengthens the relevance of the PDTOs as patient tumors models and highlights the potential of analyzing PDTO-derived cfDNA as a non-invasive approach to investigate tumor evolution and as a valuable tool to support functional precision oncology.

In early detection of cancer, the use of circulating cell-free DNA (cirDNA) obtained from blood samples is notable for its minimally invasive nature. We have developed an algorithm designed to discriminate cancer patients and healthy individuals based on cirDNA fragment end motif analysis assisted by machine learning, using data obtained from shallow whole genome sequencing (a method we call EMA). We applied EMA to cirDNA from the plasma of patients with stage II-III breast cancer, stage I-III non-small cell lung cancer, and metastatic colorectal cancer (mCRC). CirDNA from 158 individuals was prepared following the conventional double-stranded DNA library preparation (DSP). Using 3 bp end motifs, each tumor type was detected with a sensitivity of 0.87-1.00, a specificity of 0.95, and an AUC above 0.96. The three selected cancer types could be differentiated with an accuracy (ACC) above 0.94. Multi-cancer detection by pooling samples from the three cancer types showed ACC, AUC and sensitivity of 0.98, 0.99 and 0.98, respectively. Comparisons with 4 and 2 bp end motifs were conducted, and our main observations were confirmed using an external public dataset (N=366). We also performed a single-stranded DNA library preparation (SSP) using mCRC patients and healthy control cirDNA, which allowed us to make the first ever end motif analysis in the literature which compares the use of DSP and SSP. As compared to EMAD (use of DSP), EMAS (use of SSP) produced a very significant difference in end motif frequency and an improved cancer detection performance (ACC, AUC and sensitivity of 0.97, 1.00 and 0.99, respectively). Furthermore, optimal performance was produced when the full-size range was used for EMAS, whereas when the dataset was restricted to fragments of 115 - 220 bp for EMAD. EMAS strong performance, coupled with its compatibility with cost-effective shallow cirDNA sequencing, positions this methodology as a potentially transformative tool in early cancer screening. ### Competing Interest Statement The authors have declared no competing interest.

Objectives: Elevated circulating DNA (cirDNA) concentrations were found to be associated with trauma or tissue damage which suggests involvement of inflammation or cell death in post-operative cirDNA release. We carried out the first prospective, multicenter study of the dynamics of cirDNA and neutrophil extracellular trap (NETs) markers during the perioperative period from 24 h before surgery up to 72 h after curative surgery in cancer patients. Methods: We examined the plasma levels of two NETs protein markers [myeloperoxidase (MPO) and neutrophil elastase (NE)], as well as levels of cirDNA of nuclear (cir-nDNA) and mitochondrial (cir-mtDNA) origin in 29 colon, prostate, and breast cancer patients and in 114 healthy individuals (HI). Results: The synergistic analytical information provided by these markers revealed that: (i) NETs formation contributes to post-surgery conditions; (ii) post-surgery cir-nDNA levels were highly associated with NE and MPO in colon cancer [r = 0.60 (P < 0.001) and r = 0.53 (P < 0.01), respectively], but not in prostate and breast cancer; (iii) each tumor type shows a specific pattern of cir-nDNA and NETs marker dynamics, but overall the pre- and post-surgery median values of cir-nDNA, NE, and MPO were significantly higher in cancer patients than in HI. Conclusion: Taken as a whole, our work reveals the association of NETs formation with the elevated cir-nDNA release during a cancer patient's perioperative period, depending on surgical procedure or cancer type. By contrast, cir-mtDNA is poorly associated with NETs formation in the studied perioperative period, which would appear to indicate a different mechanism of release or suggest mitochondrial dysfunction.

We examined from a large exploratory study cohort of COVID-19 patients (N=549) a validated panel of neutrophil extracellular traps (NETs) markers in different categories of disease severity. Neutrophil elastase (NE), myeloperoxidase (MPO), and circulating nuclear DNA (cir-nDNA) levels in plasma were seen to gradually and significantly (P< 0.0001) increase with the disease severity: mild (3.7, 48.9, and 15.8 ng/mL, respectively); moderate (9.8, 77.5, and 27.7 ng/mL, respectively), severe (11.7, 99.5, and 29.0 ng/mL, respectively); and critical (13.1, 110.2 and 46.0 ng/mL, respectively); and are also statistically different with healthy individuals (N=140; P< 0.0001). All observations made in relation to the Delta variant infected patients are in line with omicron infected patients. We unexpectedly observed significantly higher levels of NETs in asymptomatic individuals as compared to healthy subjects (P <0.0001). Moreover, the balance of cir-nDNA and circulating mitochondrial DNA level was affected in COVID-19 infected patients attesting to mitochondrial dysfunction.

Background We studied the poorly-known dynamics of circulating DNA (cir-nDNA), as monitored prospectively over an extended post-surgery period, in patients with cancer. Methods On patients with stage III colon cancer (N = 120), using personalised molecular tags we carried out the prospective, multicenter, blinded cohort study of the post-surgery serial analysis of cir-nDNA concentration. 74 patients were included and 357 plasma samples tested. Findings During post-operative follow-up, the patients' median cir-nDNA concentration was greater (P < 0.0001 in the [43-364 days range]) than both the median value in healthy individuals and the pre-surgery value. These cir-nDNA levels were highly associated with NETs markers (P-value associating MPO and cir-nDNA, and NE and cir-nDNA are 6.6 x 10(-17), and 1.9 x 10(-7)), in accordance with previous reports which indicate that cir-nDNA are NETs by-products. Unexpectedly, in 34 out of 50 patients we found that NETs continued to be formed for an extended duration post-surgery, even in patients without disease progression. Given that this phenomenon was observed in patients without adjuvant CT, and in patients >18 months post-surgery, the data suggest that the persistence of NETs formation is not due to the adjuvant CT. Interpretation (1), Given the inter-patient heterogeneity, the post-surgery cir-nDNA level cannot be considered a reliable value, and caution must be exercised when determining mutation allele frequency or the mutation status; and (2), specific studies must be undertaken to investigate the possible clinical impact of the persistent, low-grade inflammation resulting from elevated NETs levels, such as observed in these post-surgery patients, given that such levels are known to potentially induce adverse cardiovascular or thrombotic events.

Chromosome stability is a key point in genome evolution, particularly that of the Y chromosome. The Y chromosome loss in blood and tumor cells is well established. Through processes that are common to other chromosomes too, the Y chromosome undergoes degradation and fragmentation in the blood stream before elimination. This process gives rise to circulating DNA (cirDNA) fragments, whose examination may provide potential insight into the role of DNA fragmentation in blood for the Y chromosome elimination. In this study, we employed shallow whole genome sequencing (sWGS) to comprehensively assess the total cirDNA and the individual chromosome fragment size profiles in the plasma of healthy male individuals. Here, we show that (i) the fragment size profiles of total circulating DNA (cirDNA) and DNA fragments originating from autosomes and the X chromosome in blood plasma are homogeneous, and have a remarkably low variability (mean CV = 7

Introduction: The function, origin and structural features of circulating nuclear DNA (cir-nDNA) and mitochondrial DNA (cir-mtDNA) are poorly known, even though they have been investigated in numerous clinical studies, and are involved in a number of routine clinical applications. Based on our previous report disproving the conventional plasma isolation used for cirDNA analysis, this work enables a direct topological comparison of the circulating structures associated with nuclear DNA and mitochondrial cell-free DNA. Materials and methods: We used a Q-PCR and low-pass whole genome sequencing (LP-WGS) combination approach of cir-nDNA and cir-mtDNA, extracted using a procedure that eliminates platelet activation during the plasma isolation process to prevent mitochondria release in the extracellular milieu. Various physical procedures, such as filtration and differential centrifugation, were employed to infer their circulating structures. Results: DSP-S cir-mtDNA mean size profiles distributed on a slightly shorter range than SSP-S. SSP-S detected 40-fold more low-sized cir-mtDNA fragments (<90 bp/nt) and three-fold less long-sized fragments (>200 bp/nt) than DSP-S. The ratio of the fragment number below 90 bp over the fragment number above 200 bp was very homogenous among both DSP-S and SSP-S profiles, being 134-fold lower with DSP-S than with SSP-S. Cir-mtDNA and cir-nDNA DSP-S and SSP-S mean size profiles of healthy individuals ranged in different intervals with periodic sub-peaks only detectable with cir-nDNA. The very low amount of cir-mtDNA fragments of short size observed suggested that most of the cir-mtDNA is poorly fragmented and appearing longer than ∼1,000 bp, the readout limit of this LP-WGS method. Data suggested that cir-nDNA is, among DNA extracted in plasma, associated with ∼8.6% of large structures (apoptotic bodies, large extracellular vesicles (EVs), cell debris…), ∼27.7% in chromatin and small EVs and ∼63.7% mainly in oligo- and mono-nucleosomes. By contrast, cir-mtDNA appeared to be preponderantly (75.7%) associated with extracellular mitochondria, either in its free form or with large EVs; to a lesser extent, it was also associated with other structures: small EVs (∼18.4%), and exosomes or protein complexes (∼5.9%). Conclusion: This is the first study to directly compare the structural features of cir-nDNA and cir-mtDNA. The significant differences revealed between both are due to the DNA topological structure contained in the nucleus (chromatin) and in the mitochondria (plasmid) that determine their biological stability in blood. Although cir-nDNA and cir-mtDNA are principally associated with mono-nucleosomes and cell-free mitochondria, our study highlights the diversity of the circulating structures associated with cell-free DNA. They consequently have different pharmacokinetics as well as physiological functions. Thus, any accurate evaluation of their biological or diagnostic individual properties must relies on appropriate pre-analytics, and optimally on the isolation or enrichment of one category of their cirDNA associated structures.

In the early phase of the pandemic, we were among the first to postulate that neutrophil extracellular traps (NETs) play a key role in COVID‐19 pathogenesis. This exploratory prospective study based on 279 individuals showed that plasma levels of neutrophil elastase, myeloperoxidase and circulating DNA of nuclear and mitochondrial origins in nonsevere (NS), severe (S) and postacute phase (PAP) COVID‐19 patients were statistically different as compared to the levels in healthy individuals, and revealed the high diagnostic power of these NETs markers in respect to the disease severity. The diagnostic power of NE, MPO, and cir‐nDNA as determined by the Area Under Receiver Operating Curves (AUROC) was 0.95, 097, and 0.64; 0.99, 1.0, and 0.82; and 0.94, 1.0, and 0.93, in NS, S, and PAP patient subgroups, respectively. In addition, a significant fraction of NS, S as well as of PAP patients exhibited aCL IgM/IgG and anti‐B2GP IgM/IgG positivity. We first demonstrate persistence of these NETs markers in PAP patients and consequently of sustained innate immune response imbalance, and a prolonged low‐level pro‐thrombotic potential activity highlighting the need to monitor these markers in all COVID‐19 PAP individuals, to investigate postacute COVID‐19 pathogenesis following intensive care, and to better identify which medical resources will ensure complete patient recovery.

Summary: By shedding light on the cellular origins of circulating DNA (cirDNA), this research provides important insights into the mechanisms of cirDNA production in cancer. Contrary to expectations, the increased cirDNA in patients with cancer was not derived predominantly from neoplastic cells or surrounding nonneoplastic epithelial cells; rather, the excess cirDNA originated primarily from leukocytes, implying a systemic impact of cancer on cell turnover or DNA clearance. See related article by Mattox et al., p. 2166 (1).

BACKGROUND:Research on circulating mitochondrial DNA (cir-mtDNA) based diagnostic is insufficient, as to its function, origin, structural features, and particularly its standardization of isolation. To date, plasma preparation performed in previous studies do not take into consideration the potential bias resulting from the release of mitochondria by activated platelets.METHODS:To tackle this, we compared the mtDNA amount determined by a standard plasma preparation method or a method optimally avoiding platelet activation. MtDNA extracted from the plasma of seven healthy individuals was quantified by Q-PCR in the course of the process of both methods submitted to filtration, freezing or differential centrifugation.RESULTS:98.7 to 99.4% of plasma mtDNA corresponded to extracellular mitochondria, either free or into large extracellular vesicles. Without platelet activation, the proportion of both types of entities remained preponderant (76-80%), but the amount of detected mtDNA decreased 67-fold.CONCLUSION:We show the high capacity of platelets to release free mitochondria in "in vitro" conditions. This represents a potent confounding factor when extracting mtDNA for cir-mtDNA investigation. Platelet activation during pre-analytical conditions should therefore be avoided when studying cir-mtDNA. Our findings lead to a profound revision of the assumptions previously made by most works in this field. Overall, our data suggest the need to characterize or isolate mtDNA associated various structural forms, as well as to standardize plasma preparation, to better circumscribe cir-mtDNA's diagnostic capacity.

We postulate that a significant part of circulating DNA (cirDNA) originates in the degradation of neutrophil extracellular traps (NETs). In this study, we examined the plasma level of two markers of NETs (myeloperoxidase (MPO) and neutrophil elastase (NE)), as well as cirDNA levels in 219 patients with a metastatic colorectal cancer (mCRC), and in 114 healthy individuals (HI). We found that in patients with mCRC the content of these analytes was (i) highly correlated, and (ii) all statistically different (p < 0.0001) than in HI (N = 114). These three NETs markers may readily distinguish between patients with mCRC from HI, (0.88, 0.86, 0.84, and 0.95 AUC values for NE, MPO, cirDNA, and NE + MPO + cirDNA, respectively). Concomitant analysis of anti-phospholipid (anti-cardiolipin), NE, MPO, and cirDNA plasma concentrations in patients with mCRC might have value for thrombosis prevention, and suggested that NETosis may be a critical factor in the immunological response/phenomena linked to tumor progression.

Abstract Background As circulating DNA (cirDNA) is mainly detected as mononucleosome-associated circulating DNA (mono-N cirDNA) in blood, apoptosis has until now been considered as the main source of cirDNA. The mechanism of cirDNA release into the circulation, however, is still not fully understood. This work addresses that knowledge gap, working from the postulate that neutrophil extracellular traps (NET) may be a source of cirDNA, and by investigating whether NET may directly produce mono-N cirDNA. Methods We studied (1) the in vitro kinetics of cell derived genomic high molecular weight (gHMW) DNA degradation in serum; (2) the production of extracellular DNA and NET markers such as neutrophil elastase (NE) and myeloperoxidase (MPO) by ex vivo activated neutrophils; and (3) the in vitro NET degradation in serum; for this, we exploited the synergistic analytical information provided by specifically quantifying DNA by qPCR, and used shallow WGS and capillary electrophoresis to perform fragment size analysis. We also performed an in vivo study in knockout mice, and an in vitro study of gHMW DNA degradation, to elucidate the role of NE and MPO in effecting DNA degradation and fragmentation. We then compared the NET-associated markers and fragmentation size profiles of cirDNA in plasma obtained from patients with inflammatory diseases found to be associated with NET formation and high levels of cirDNA (COVID-19, N = 28; systemic lupus erythematosus, N = 10; metastatic colorectal cancer, N = 10; and from healthy individuals, N = 114). Results Our studies reveal that gHMW DNA degradation in serum results in the accumulation of mono-N DNA (81.3% of the remaining DNA following 24 h incubation in serum corresponded to mono-N DNA); “ex vivo” NET formation, as demonstrated by a concurrent 5-, 5-, and 35-fold increase of NE, MPO, and cell-free DNA (cfDNA) concentration in PMA-activated neutrophil culture supernatant, leads to the release of high molecular weight DNA that degrades down to mono-N in serum; NET mainly in the form of gHMW DNA generate mono-N cirDNA (2 and 41% of the remaining DNA after 2 h in serum corresponded to 1–10 kbp fragments and mono-N, respectively) independent of any cellular process when degraded in serum; NE and MPO may contribute synergistically to NET autocatabolism, resulting in a 25-fold decrease in total DNA concentration and a DNA fragment size profile similar to that observed from cirDNA following 8 h incubation with both NE and MPO; the cirDNA size profile of NE KO mice significantly differed from that of the WT, suggesting NE involvement in DNA degradation; and a significant increase in the levels of NE, MPO, and cirDNA was detected in plasma samples from lupus, COVID-19, and mCRC, showing a high correlation with these inflammatory diseases, while no correlation of NE and MPO with cirDNA was found in HI. Conclusions Our work describes the mechanisms by which NET and cirDNA are linked. In doing so, we demonstrate that NET are a major source of mono-N cirDNA independent of apoptosis and establish a new paradigm of the mechanisms of cirDNA release in normal and pathological conditions. We also demonstrate a link between immune response and cirDNA.

Background: The COVID-19 pandemic led to a significant reduction in the provision of screening, case identification and hospital referrals to cancer patients. To our knowledge, no study has yet correlated quantitatively the consequences of these limitations for cancer patient management. This study evaluates the implications of such reductions for patients newly diagnosed with metastatic colorectal cancer (mCRC) in both the pre- and post-lockdown periods. Methods: We examined 80 newly identified mCRC patients from 18 different clinical centers. These cases come from the screening procedure of a clinical trial which is using circulating DNA (cirDNA) analysis to determine their RAS and BRAF status. Results: The tumor burden as evaluated by the median total plasma cirDNA concentration showed a statistically higher level in patients diagnosed post-lockdown compared to those diagnosed pre-lockdown (119.2 versus 17.3 ng/mL; p<0.0001). In order to link tumor burden to survival, we compared the survival of these mCRC patients with previous studies in which cirDNA was examined in the same way (median survival, 16.2 months; median follow up, 48.7 months, N=135). Given the poor survival rate of mCRC patients with high cirDNA levels (14.7 vs 20.0 and 8.8 vs 19.3 months median survival when dichotomizing the cohort by the median cirDNA concentration 24.4 and 100 ng/mL, respectively), our study points to the potential deleterious consequences of the COVID-19 pandemic. Conclusions: Recognizing that our exploratory study offers a snapshot of an evolving situation, our observations nonetheless clearly highlight the need to determine actions which would minimize delays in diagnosis during the ongoing and future waves of COVID-19.

We postulate that a significant part of nuclear circulating cell-free DNA (cirDNA) originates in the degradation of neutrophil extracellular traps (NETs). In this study, we examined the plasma level of two markers of NETs formation (myeloperoxidase (MPO) and neutrophil elastase (NE)), as well as cirDNA levels in 219 patients with a metastatic colorectal cancer (mCRC) at initial diagnosis, and in 114 healthy individuals (HI). We found that in mCRC patients the plasma content of these three analytes was (i) highly correlated, and (ii) all statistically different (P<0.0001) than in HI (N=114). Data revealed that, in mCRC patients, a strong fraction of cirDNA derived from NETs. Receiver operating characteristic (ROC) analysis revealed the high potential of these NETs markers to distinguish between plasma from mCRC patients and from HI, given that it showed 0.88, 0.86, 0.84 and 0.95 AUC values for NE, MPO, cirDNA and NE+MPO+cirDNA, respectively. In addition, a high association of anti-phospholipid (anticardiolipin) levels with NE, MPO, and cirDNA plasma concentrations in mCRC patients suggested that NETosis might be a critical factor in the immunological response/phenomena linked to tumor progression.

To unequivocally address their unresolved intimate structures in blood, we scrutinized the size distribution of circulating cell-free DNA (cfDNA) using whole-genome sequencing (WGS) from both double- and single-strand DNA library preparations (DSP and SSP, n = 7) and using quantitative PCR (Q-PCR, n = 116). The size profile in healthy individuals was remarkably homogenous when using DSP sequencing or SSP sequencing. CfDNA size profile had a characteristic nucleosome fragmentation pattern. Overall, our data indicate that the proportion of cfDNA inserted in mono-nucleosomes, di-nucleosomes, and chromatin of higher molecular size (>1000 bp) can be estimated as 67.5% to 80%, 9.4% to 11.5%, and 8.5% to 21.0%, respectively. Although DNA on single chromatosomes or mono-nucleosomes is detectable, our data revealed that cfDNA is highly nicked (97%-98%) on those structures, which appear to be subjected to continuous nuclease activity in the bloodstream. Fragments analysis allows the distinction of cfDNA of different origins: first, cfDNA size profile analysis may be useful in cfDNA extract quality control; second, subtle but reliable differences between metastatic colorectal cancer patients and healthy individuals vary with the proportion of malignant cell-derived cfDNA in plasma extracts, pointing to a higher degree of cfDNA fragmentation and nuclease activity in samples with high malignant cell cfDNA content.