• ALU sequences
• LINE1 sequences
• breast cancer
• cfDI
• circulating cell-free DNA integrity
• liquid biopsy
• prostate cancer

• Humans
• Male
• Prostatic Neoplasms/genetics
• Prostatic Neoplasms/blood
• Prostatic Neoplasms/diagnosis
• Prostatic Neoplasms/therapy
• Prostatic Neoplasms/pathology
• Female
• Breast Neoplasms/genetics
• Breast Neoplasms/blood
• Breast Neoplasms/diagnosis
• Breast Neoplasms/therapy
• Breast Neoplasms/pathology
• Cell-Free Nucleic Acids/blood
• Cell-Free Nucleic Acids/genetics
• Biomarkers, Tumor/blood
• Biomarkers, Tumor/genetics
• Liquid Biopsy

• Cancer
• Diagnosis
• Prognosis
• Treatment
• ctDNA

• Humans
• Circulating Tumor DNA/blood
• Circulating Tumor DNA/genetics
• Neoplasms/blood
• Neoplasms/genetics
• Neoplasms/drug therapy
• Liquid Biopsy/methods
• Biomarkers, Tumor/blood
• Biomarkers, Tumor/genetics
• Precision Medicine/methods

• LINE1 element
• non-small-cell lung cancer
• plasma cfDNA
• quantitative real-time PCR

• Cell-free DNA
• Circulating tumor DNA
• Circulating tumor cells
• Gastric cancer
• Liquid biopsy
• Molecular

• Humans
• Stomach Neoplasms/diagnosis
• Stomach Neoplasms/therapy
• Neoplasm Recurrence, Local
• Liquid Biopsy
• Body Fluids
• Plasma

• CK19
• Dog
• Mammary gland tumor
• ddPCR

• Humans
• Dogs
• Animals
• Female
• Keratin-19/genetics
• Keratin-19/metabolism
• Mammary Neoplasms, Animal/diagnosis
• Mammary Neoplasms, Animal/genetics
• Mammary Neoplasms, Animal/metabolism
• Breast Neoplasms/diagnosis
• Breast Neoplasms/genetics
• Breast Neoplasms/pathology
• Breast Neoplasms/veterinary
• Polymerase Chain Reaction/veterinary
• Biomarkers, Tumor/genetics
• RNA, Messenger/genetics
• RNA, Messenger/metabolism
• Dog Diseases/diagnosis
• Dog Diseases/genetics
• Dog Diseases/metabolism

• cancer detection
• cell-free DNA
• generative language model

• Humans
• Carcinoma, Hepatocellular/diagnosis
• Carcinoma, Hepatocellular/genetics
• Area Under Curve
• Cell-Free Nucleic Acids/genetics
• Language
• Liver Neoplasms/diagnosis
• Liver Neoplasms/genetics

• 2021YFC2500400 National Key Research and Development Program of China
• 32270688 National Natural Science Foundation of China
• IRT_14R40 Program for Changjiang Scholars and Innovative Research Team in University in China
• TJYXZDXK-009A Tianjin Key Medical Discipline (Specialty) Construction Project

• Female
• Humans
• Breast Neoplasms/pathology
• Breast/pathology
• Prognosis
• Bone Neoplasms/pathology
• Biomarkers, Tumor
• Neoplasm Metastasis

• biotechnology
• cancer

• Humans
• Female
• Breast Neoplasms/diagnosis
• Breast Neoplasms/genetics
• Biomarkers, Tumor/genetics
• Cell-Free Nucleic Acids
• Chloroform
• Creatinine

• Biomarker
• Cell-free DNA
• Colorectal cancer
• DNA methylation
• Early detection

• 82103030 National Natural Science Foundation of China
• 62276084 National Natural Science Foundation of China
• GA19C003 Applied Technology Research and Development Plan of Heilongjiang Province

• RT-qPCR
• biomarker
• breast cancer
• cell-free DNA
• fluorometer
• spectrophotometer

• DNA integrity index
• LINE-1
• cell-free DNA
• dog
• liquid biopsy
• melanoma

• ALU
• EEF1A2
• LINE-1
• breast cancer
• cfDI
• cfDNA
• copy number ratio
• ddPCR
• liquid biopsy

• Humans
• Female
• Breast Neoplasms/diagnosis
• Breast Neoplasms/genetics
• Breast Neoplasms/pathology
• Case-Control Studies
• DNA Copy Number Variations
• Quality of Life
• Biomarkers, Tumor/genetics
• Cell-Free Nucleic Acids/genetics
• DNA, Neoplasm
• Polymerase Chain Reaction
• Peptide Elongation Factor 1/genetics

• research grant 2015 Lega Italiana per la Lotta ai Tumori
• BEN 2016/16 Beneficentia Stiftung

• Biomarker
• CtDNA
• Lung cancer
• Precision medicine
• Treatment

• Humans
• Carcinoma, Non-Small-Cell Lung/pathology
• Circulating Tumor DNA/genetics
• Circulating Tumor DNA/therapeutic use
• Lung Neoplasms/pathology
• Biomarkers, Tumor/genetics
• Small Cell Lung Carcinoma

• ALU 247
• breast cancer
• ctDNA
• disease progression
• liquid biopsy
• prognosis

• breast cancer
• tumour biomarkers
• cancer
• biomarkers
• molecular medicine
• biological techniques
• high-throughput screening
• isolation, separation and purification

• DNA integrity index
• chronic liver disease
• circulating free DNA
• circulating tumor DNA
• hepatocellular carcinoma
• liquid biopsy

• biomarkers
• breast cancer
• cell-free DNA
• cell-free DNA integrity
• fragmentomics
• liquid biopsy

• Humans
• Female
• Cell-Free Nucleic Acids/genetics
• Breast Neoplasms/diagnosis
• Breast Neoplasms/genetics
• Breast Neoplasms/pathology
• Biomarkers, Tumor/genetics
• Circulating Tumor DNA
• Liquid Biopsy

• cancers
• cancer‐derived exosomes
• liquid biopsies
• separation methods

• National Natural Science Foundation of China
• Ningbo Science and Technology Bureau
• Chinese Academy of Sciences

Liquid biopsy is a broad term that refers to the testing of body fluids for biomarkers that correlate with a pathological condition. While a variety of body-fluid components (e.g., circulating tumor cells, extracellular vesicles, RNA, proteins, and metabolites) are studied as potential liquid biopsy biomarkers, cell-free DNA (cfDNA) has attracted the most attention in recent years. The total cfDNA population in a typical biospecimen represents an immensely rich source of biological and pathological information and has demonstrated significant potential as a versatile biomarker in oncology, non-invasive prenatal testing, and transplant monitoring. As a significant portion of cfDNA is composed of repeat DNA sequences and some families (e.g., pericentric satellites) were recently shown to be overrepresented in cfDNA populations vs their genomic abundance, it holds great potential for developing liquid biopsy-based biomarkers for the early detection and management of patients with cancer. By outlining research that employed cell-free repeat DNA sequences, in particular the ALU and LINE-1 elements, we highlight the clinical potential of the repeat-element content of cfDNA as an underappreciated marker in the cancer liquid biopsy repertoire.

The study of plasma cell-free DNA integrity (cfDI) has shown potential for providing useful information in neoplastic patients. The aim of this study is to estimate the accuracy of an electrophoresis-based method for cfDI evaluation in the assessment of pathologic complete response (pCR) in patients with breast cancer (BC) undergoing neoadjuvant chemotherapy (NACT).

Fifty-one patients with BC undergoing anthracycline-/taxane-based NACT were recruited. Plasma samples were collected from each patient at diagnosis (t0), after anthracycline administration (t1), and after NACT completion (t2). The concentration of differently sized cell-free DNA fragments was assessed by automated electrophoresis. cfDI, expressed as cfDI index, was calculated as the ratio of 321-1,000 bp sized fragment concentration to 150-220 bp sized fragment concentration assessed at t2. cfDI index was then used to build an exploratory classifier for BC response to NACT, directly comparing its sensitivity and specificity with magnetic resonance imaging (MRI), through bootstrapped logistic regression.

cfDI index was assessed on 38 plasma samples collected from as many patients at t2, maintaining a 30/70 ratio between pCR and non-pCR patients. cfDI index showed an area under the receiver operating characteristic curve in predicting the achievement of pCR of 81.6, with a cutoff above 2.71 showing sensitivity = 81.8 and specificity = 81.5. The combination of cfDI index and MRI showed, in case of concordance, an area under the receiver operating characteristic curve of 92.6 with a predictive value of complete response of 87.5 and a predictive value of absence of complete response of 94.7.

cfDI index measured after NACT completion shows great potential in the assessment of pCR in patients with BC. The evaluation of its use in combination with MRI is strongly warranted in prospective studies.

Plasma DNA fragmentation assessment predicts response to neoadjuvant chemotherapy in breast cancer.

Cell-free DNA (cfDNA) has attracted considerable attention in precision medicine. However, few data are available regarding to the prognostic value of cfDNA variables in CA15-3 normal breast cancer (BC) patients. Here, we aimed at investigating the prognostic value of cfDNA variables including gene mutations in CA15-3 normal BC patients.

A total of 68 BC patients with normal CA15-3 levels were enrolled. cfDNA concentration and integrity were assessed based on qPCR. cfDNA gene mutations were conducted by using next gene sequencing (NGS). The association between cfDNA variables and the prognosis of patients was analyzed.

cfDNA concentration was related to tumor stage (P = 0.002), metastases (P = 0.001), and distant metastases (P < 0.001). The elevated copy number variants (CNV) were found in distant metastasis patients compared with patients without distant metastases (P = 0.008). Nineteen mutant genes were validated in enrolled CA15-3 normal BC patients. Thirty-two patients (47.0%) had single nucleotide variants (SNV), and 13 (19.1%) patients had TP53 mutations (TP53^mut). SNV (P = 0.033) was related to tumor stage, and TP53^mut was related to metastases (P = 0.016) and distant metastases (P = 0.006). In multivariate logistic analysis, cfDNA concentration was associated with metastases (OR = 3.404, 95% CI: 1.074-10.788, P = 0.037) and distant metastases (OR = 13.750, 95% CI: 1.473-128.358, P = 0.021). Cases with high cfDNA levels (>15.6 ng/ml), SNV, and TP53^mut showed worse DFS compared with patients with low cfDNA levels (P < 0.001), without SNV (P = 0.002) and with TP53 wildtype (P < 0.001), respectively. In the multivariate Cox proportional hazard model, cfDNA concentration was an independent predictor of poor survival (HR = 5.786, 95% CI: 1.101-30.407, P = 0.038).

Assessment of cfDNA concentration, CNV, SNV, and TP53^mut could be useful in predicting prognosis for CA15-3 normal BC patients. The cfDNA concentration was an independent predictor prognostic factor in CA15-3 normal BC patients.

Cancer is a major health issue worldwide. cfDNA integrity has been reported as a potential diagnostic molecular marker for different types of cancer, identifying the importance of liquid biopsy. The aim of this review was to evaluate the prognostic and diagnostic performance of Arthrobacter luteus (ALU) repeat in tumor. Following a thorough review of the literature published from January, 2000 to September 2021, 36 studies were included. All of the study descriptions were analyzed. According to several studies, there were increased concentrations of ALU repetitive elements in cancer patients, while these concentrations were decreased in control, benign, different cancer stage, and other diseases. The total ALU (115 and 247) sequence levels are potential biomarkers for the purpose of investigations and cancer prognosis.

Neuroendocrine neoplasias (NEN) are a heterogeneous group of frequent slow-progressing malignant tumors for which a reliable marker for tumor relapse and progression is still lacking. Previously, circulating cell-free DNA and its global methylation status and fragmentation rate have been proposed to be valuable prognostic tumor markers in a variety of malignancies. In the current study, we compared plasma cell-free DNA (cfDNA) properties of NEN patients with a healthy control group and a group of surgically cured patients. Our results revealed significantly higher plasma cfDNA concentrations with increased fragmentation and hypomethylation in patients with advanced metastatic NEN, which was strongly associated with tumor load and could help to differentiate between metastasized disease and presumably cured patients. This suggests that the combined analysis of plasma cfDNA characteristics is a potent and sensitive prognostic and therapeutic biomarker for tumor burden and disease progression in patients with neuroendocrine neoplasias.

Background: Neuroendocrine neoplasia (NEN) encompasses a diverse group of malignancies marked by histological heterogeneity and highly variable clinical outcomes. Apart from Chromogranin A, specific biomarkers predicting residual tumor disease, tumor burden, and disease progression in NEN are scant. Thus, there is a strong clinical need for new and minimally invasive biomarkers that allow for an evaluation of the prognosis, clinical course, and response to treatment of NEN patients, thereby helping implement individualized treatment decisions in this heterogeneous group of patients. In the current prospective study, we evaluated the role of plasma cell-free DNA concentration and its global hypomethylation and fragmentation as possible diagnostic and prognostic biomarkers in patients with neuroendocrine neoplasias. Methods: The plasma cfDNA concentration, cfDNA Alu hypomethylation, and LINE-1 cfDNA integrity were evaluated prospectively in 63 NEN patients with presumably cured or advanced metastatic disease. The cfDNA characteristics in NEN patients were compared to the results of a group of 29 healthy controls and correlated with clinical and histopathological data of the patients. Results: Patients with advanced NEN showed a significantly higher cfDNA concentration and percentage of Alu hypomethylation and a reduced LINE-1 cfDNA integrity as compared to the surgically cured NET patients and the healthy control group. The increased hypomethylation and concentration of cfDNA and the reduced cfDNA integrity in NEN patients were strongly associated with tumor burden and poor prognosis, while no correlation with tumor grading, differentiation, localization, or hormonal activity could be found. Multiparametric ROC analysis of plasma cfDNA characteristics was able to distinguish NEN patients with metastatic disease from the control group and the cured NEN patients with AUC values of 0.694 and 0.908, respectively. This was significant even for the group with only a low tumor burden. Conclusions: The present study, for the first time, demonstrates that the combination of plasma cfDNA concentration, global hypomethylation, and fragment length pattern has the potential to serve as a potent and sensitive prognostic and therapeutic “liquid biopsy” biomarker for tumor burden and disease progression in patients with neuroendocrine neoplasias.

• artificial intelligence
• liquid biopsy
• micrometastasis
• surface-enhanced Raman scattering
• tumor

• Humans
• Lymph Nodes/pathology
• Lymphatic Metastasis/pathology
• Neoplasm Micrometastasis/diagnosis
• Neoplasm Micrometastasis/pathology
• Neoplasm Staging
• Prognosis

• Zhejiang Provincial Natural Science Foundation of China for Distinguished Young Scholars
• Zhejiang province science and technology project of TCM
• National Natural Science Foundation of China

Glioblastoma (GBM) is the most common type of glioma and is uniformly fatal. Currently, tumour heterogeneity and mutation acquisition are major impedances for tailoring personalized therapy. We collected blood and tumour tissue samples from 25 GBM patients and 25 blood samples from healthy controls. Cell‐free DNA (cfDNA) was extracted from the plasma of GBM patients and from healthy controls. Tumour DNA was extracted from fresh tumour samples. Extracted DNA was sequenced using a whole‐genome sequencing procedure. We also collected 180 tumour DNA datasets from GBM patients publicly available at the TCGA/PANCANCER project. These data were analysed for mutations and gene–gene fusions that could be potential druggable targets. We found that plasma cfDNA concentrations in GBM patients were significantly elevated (22.6 ± 5 ng·mL⁻¹), as compared to healthy controls (1.4 ± 0.4 ng·mL⁻¹) of the same average age. We identified unique mutations in the cfDNA and tumour DNA of each GBM patient, including some of the most frequently mutated genes in GBM according to the COSMIC database (TP53, 18.75%; EGFR, 37.5%; NF1, 12.5%; LRP1B, 25%; IRS4, 25%). Using our gene–gene fusion database, ChiTaRS 5.0, we identified gene–gene fusions in cfDNA and tumour DNA, such as KDR–PDGFRA and NCDN–PDGFRA, which correspond to previously reported alterations of PDGFRA in GBM (44% of all samples). Interestingly, the PDGFRA protein fusions can be targeted by tyrosine kinase inhibitors such as imatinib, sunitinib, and sorafenib. Moreover, we identified BCR–ABL1 (in 8% of patients), COL1A1–PDGFB (8%), NIN–PDGFRB (8%), and FGFR1–BCR (4%) in cfDNA of patients, which can be targeted by analogues of imatinib. ROS1 fusions (CEP85L–ROS1 and GOPC–ROS1), identified in 8% of patient cfDNA, might be targeted by crizotinib, entrectinib, or larotrectinib. Thus, our study suggests that integrated analysis of cfDNA plasma concentration, gene mutations, and gene–gene fusions can serve as a diagnostic modality for distinguishing GBM patients who may benefit from targeted therapy. These results open new avenues for precision medicine in GBM, using noninvasive liquid biopsy diagnostics to assess personalized patient profiles. Moreover, repeated detection of druggable targets over the course of the disease may provide real‐time information on the evolving molecular landscape of the tumour.

• Circulating cell-free DNA
• druggable
• gene mutation
• gene-gene fusion
• glioblastoma
• liquid biopsy

• cell-free DNA
• evcfDI
• extracellular vesicles
• maternal plasma
• non-invasive prenatal testing

• circulating tumor DNA (ctDNA)
• gene mutation
• liver cancer
• survival analysis
• tumor mutation burden (TMB)

A recent point of focus in breast cancer (BC) research has been the utilization of cell-free DNA and its concentration (cfDConc) and integrity (cfDI) as potential biomarkers. Though the association of cfDConc and BC survival is already recognized, studies on the prognostic value of cfDI have had contradictory results. The aim of this study was to investigate the prognostic potential of cfDConc and cfDI in Eastern Finnish BC cases with a non-metastatic disease. While the prognostic value of cfDConc remained non-significant in our analyses, high cfDI was an independent prognostic factor for poor overall survival (OS) and breast cancer-specific survival (BCSS). Inclusion of cfDI in the multivariate logistic regression model improved the predictive performance of the model, thus suggesting that the combined use of traditional tumor features and liquid biopsy could help to discriminate BC patients with poor OS and BCSS more accurately at the time of diagnosis.

Background: A recent point of focus in breast cancer (BC) research has been the utilization of cell-free DNA (cfDNA) and its concentration (cfDConc) and integrity (cfDI) as potential biomarkers. Though the association of cfDConc and poor survival is already recognized, studies on the prognostic value of cfDI have had contradictory results. Here, we provide further evidence to support the use of cfDI as a potential biomarker. Methods: We selected 204 Eastern Finnish BC cases with non-metastatic disease and isolated cfDNA from the serum collected at the time of diagnosis before any treatment was given. The cfDConc and cfDI were measured with a fluorometer and electrophoresis and analyzed with 25 years of survival data. Results: High cfDConc was not an independent prognostic factor in our analyses while high cfDI was found to be an independent prognostic factor for poor OS (p = 0.020, hazard ratio (HR) = 1.57, 95% confidence interval (CI) 1.07–2.29, Cox) and BCSS (p = 0.006, HR = 1.93, 95% CI 1.21–3.08)). Inclusion of cfDI in the multivariate logistic regression model improved the predictive performance. Conclusions: Our results show high cfDI is an independent prognostic factor for poor OS and BCSS and improves the predictive performance of logistic regression models, thus supporting its prognostic potential.

• DNA fragmentation
• biomarker
• diagnostics
• liquid biopsy

• CcfDNA
• Circulating cell-free DNA
• Endometriosis
• Mitochondrial DNA
• Plasma
• Quantification

• Cell-free DNA
• Circulating tumour DNA
• Liquid biopsy
• Perioperative
• Surgery

• breast cancer
• chemotherapy
• circulating tumor DNA
• liquid biopsy
• recurrence

Circulating cell-free DNA (ccfDNA), released from normal and cancerous cells, is a promising biomarker for cancer detection as in neoplastic patients it is enriched in tumor-derived DNA (ctDNA). ctDNA contains cancer-specific mutations and epigenetic modifications, which can have diagnostic/prognostic value. However, in primary tumors, and in particular in localized prostate cancer (PCa), the fraction of ctDNA is very low and conventional strategies to study ccfDNA are unsuccessful. Here we demonstrate that prostate biopsy, by causing multiple injuries to the organ, leads to a significant increase in plasma concentration of ccfDNA (P<0.0024) in primary PCa patients. By calculating the minor allele fraction at patient-specific somatic mutations pre- and post-biopsy, we show that ctDNA is significantly enriched (from 3.9 to 164 fold) after biopsy, representing a transient “molecular window” to access and analyze ctDNA. Moreover, we show that newly released ccfDNA contains a larger fraction of di-, tri- and multi-nucleosome associated DNA fragments. This feature could be exploited to further enrich prostate-derived ccfDNA and to analyze epigenetic markers. Our data represent a proof-of-concept that liquid tumor profiling from peripheral blood performed just after the biopsy procedure can open a “valuable molecular metastatic window” giving access to the tumor genetic asset, thus providing an opportunity for early cancer detection and individual genomic profiling in the view of PCa precision medicine.

• biomarker
• biopsy
• circulating cell-free DNA
• circulating tumor DNA
• primary prostate cancer

• Alu DNA index
• Biomarker
• Cell-free DNA
• DNA methylation
• LINE-1

Lung cancer is the most common cancer and the leading cause of cancer mortality worldwide. To date, tissue biopsy has been the gold standard for the diagnosis and the identification of specific molecular mutations, to guide choice of therapy. However, this procedure has several limitations. Liquid biopsy could represent a solution to the intrinsic limits of traditional biopsy. It can detect cancer markers such as circulating tumor DNA or RNA (ctDNA, ctRNA), and circulating tumor cells, in plasma, serum or other biological fluids. This procedure is minimally invasive, reproducible and can be used repeatedly. The main clinical applications of liquid biopsy in non-small cell lung cancer (NSCLC) patients are the early diagnosis, stratification of the risk of relapse, identification of mutations to guide application of targeted therapy and the evaluation of the minimum residual disease. In this review, the current role of liquid biopsy and associated markers in the management of NSCLC patients was analyzed, with emphasis on ctDNA and CTCs, and radiotherapy.

Screening for early‐stage disease is vital for reducing colorectal cancer (CRC)‐related mortality. Methylation of circulating tumor DNA has been previously used for various types of cancer screening. A novel cell‐free DNA (cfDNA) methylation‐based model which can improve the early detection of CRC is warranted. For our study, we collected 313 tissue and 577 plasma samples from patients with CRC, advanced adenoma (AA), non‐AA and healthy controls. After quality control, 187 tissue DNA samples (91 non‐malignant tissue from CRC patients, 26 AA and 70 CRC) and 489 plasma cfDNA samples were selected for targeted DNA methylation sequencing. We further developed a cfDNA methylation model based on 11 methylation biomarkers for CRC detection in the training cohort (area under curve [AUC] = 0.90 (0.85–0.94]) and verified the model in the validation cohort (AUC = 0.92 [0.88–0.96]). The cfDNA methylation model robustly detected patients pre‐diagnosed with early‐stage CRC (AUC = 0.90 [0.86–0.95]) or AA (AUC = 0.85 [0.78–0.91]). Here we established and validated a non‐invasive cfDNA methylation model based on 11 DNA methylation biomarkers for the detection of early‐stage CRC and AA. The utilization of the model in clinical practice may contribute to the early diagnosis of CRC.

• advanced adenoma
• cell-free DNA
• colorectal cancer
• early detection
• methylation
• sequencing

Circulating tumor DNA (ctDNA) detected before surgery disappears after complete surgical resection of the cancer. Residual ctDNA indicates minimal residual disease (MRD), which is a cause of recurrence. The presence of long‐fragment circulating cell‐free DNA (cfDNA) or methylated cfDNA also implies the presence of cancer. In this study, we evaluated the prognostic value of cfDNA methylation and long‐fragment cfDNA concentration in gastric cancer patients undergoing curative surgery

Ninety‐nine gastric cancer patients were included. Peripheral blood samples were collected before and 1 month after surgery. In patients administered chemotherapy, samples were collected before starting chemotherapy. qPCR was performed to detect long‐ and short‐fragment LINE‐1. A plasma HELP (HpaII tiny fragment Enrichment by Ligation‐mediated PCR) assay to determine the concentration of HpaII small fragments was performed using ligation‐mediated PCR and HpaII was quantified as the HpaII:MspI ratio to detect methylation levels of cfDNA.

Overall survival (OS) of patients with low methylation levels before starting treatment was significantly worse than that of patients with high methylation levels (P = 0.006). In the 90 patients who underwent curative surgery, recurrence‐free survival (RFS) and OS of patients with low methylation levels before surgery were worse than those with high methylation levels (P=0.08 and P = 0.11, respectively). RFS and OS of patients with high concentrations of long‐fragment LINE‐1 after surgery were significantly worse than those with low concentrations of long‐fragment LINE‐1 (P = 0.009, P = 0.04).

Pre‐surgical low methylation levels of LINE‐1 are a negative prognostic factor. Post‐surgical high concentrations of long‐fragment LINE‐1 indicate MRD and a high risk of recurrence.

• LINE-1
• biomarker
• circulating cell-free DNA
• gastric cancer
• repeated DNA sequences

• Breast cancer
• Circulating cell-free DNA (cfDNA)
• Circulating tumor cells (CTCs)
• EMT
• Stat3

Our research focuses in the elucidation of the nature of circulating cell-free DNA (ccfDNA) as a biological entity and its exploitation as a liquid biopsy biomaterial. Working on breast cancer, it became clear that although a promising biosource, its clinical exploitation is burdened mainly by gaps in knowledge about its biology and specific characteristics. The current review covers multiple aspects of ccfDNA in breast cancer. We cover key issues such as quantity, integrity, releasing structures, methylation specific changes, release mechanisms, biological role. Machine learning approaches for analyzing ccfDNA-generated data to produce classifiers for clinical use are also discussed.

Breast cancer (BC) is a leading cause of death between women. Mortality is significantly raised due to drug resistance and metastasis, while personalized treatment options are obstructed by the limitations of conventional biopsy follow-up. Lately, research is focusing on circulating biomarkers as minimally invasive choices for diagnosis, prognosis and treatment monitoring. Circulating cell-free DNA (ccfDNA) is a promising liquid biopsy biomaterial of great potential as it is thought to mirror the tumor’s lifespan; however, its clinical exploitation is burdened mainly by gaps in knowledge of its biology and specific characteristics. The current review aims to gather latest findings about the nature of ccfDNA and its multiple molecular and biological characteristics in breast cancer, covering basic and translational research and giving insights about its validity in a clinical setting.

• biomarker
• breast cancer
• circulating cell-free DNA
• liquid biopsy
• monitoring
• prognosis

• BRCA1BRCA2 mutations
• cancer risk
• cfDNA levels
• early detection