BACKGROUND: Malignant lymphomas represent a highly heterogeneous group of tumors with varied clinical behavior - from indolent to very aggressive forms with survival in the order of months. From the very beginning, these diseases are considered systemic, often occurring in several anatomical locations simultaneously. However, diagnosis and exact classification are usually inferred from a bio-psy of a single pathological lymph node or infiltrate, even though clinical experience shows that the bio-logical behavior of lymphoma is not necessarily identical across anatomical locations. In an effort to address this issue as well as the problem of bio-psy of not easily accessible compartments, circulating free DNA (cfDNA), which contains circulating tumor DNA (ctDNA) released from dead tumor cells, has been extensively studied in recent years. This DNA is easily accessible from liquid bio-psies such as blood or other patient's bodily fluids. PURPOSE: This article summarizes current scientific knowledge on cfDNA and ctDNA, particularly in the context of malignant lymphoma, and foreshadows its potential future uses. CONCLUSION: Detection and analysis of cfDNA represents a new approach that can lead to future improvements in all phases of lymphoma treatment from diagnostics to minimal residual disease monitoring.

• Klíčová slova
• Circulating tumor DNA, circulating free DNA, circulating tumor DNA, disease monitoring, liquid bio­psy, malignant lymphoma, minimal residual disease,
• MeSH
• cirkulující nádorová DNA * MeSH
• DNA MeSH
• lidé MeSH
• lymfatické uzliny MeSH
• lymfom * diagnóza   genetika   terapie   MeSH
• volné cirkulující nukleové kyseliny * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• cirkulující nádorová DNA * MeSH
• DNA MeSH
• volné cirkulující nukleové kyseliny * MeSH

As the number of cancer patients globally increases, a need for reliable biomarkers including circulating tumour DNA from liquid biopsy for diagnosis, prognosis and monitoring of the disease is rising. Currently, mainly tissue samples from biopsy are used, but there are certain limitations: firstly, it is an invasive technique, and secondly, in some cases it is almost impossible to obtain an acceptable tissue sample. This could be changed by using circulating cell-free DNA from liquid biopsy, which also gives the possibility of repeated examination. Here, we focus on the options of isolating circulating cell-free DNA from plasma samples using two isolation techniques: precision manual QIAamp Circulating Nucleic Acid Kit and automatic MagNA Pure Compact (MPC) using Nucleic Acid Isolation Kit I. Manual extraction gave significantly better yields of circulating tumour DNA (P < 0.05). This DNA also had less contaminants (organic compounds or proteins). DNA obtained by both tested methods of isolation is suitable for subsequent molecular genetic methods.

• MeSH
• cirkulující nádorová DNA * MeSH
• lidé MeSH
• nádory * MeSH
• tekutá biopsie MeSH
• volné cirkulující nukleové kyseliny * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• cirkulující nádorová DNA * MeSH
• volné cirkulující nukleové kyseliny * MeSH

BACKGROUND: Testicular germ cell tumors (TGCT) are unique malignancies of young adult men; their biology is, however, underexplored and there has not been much progress in their treatment for decades. Circulating free tumor DNA (cfDNA) analysis represents a promising way of discovering novel diagnostic and treatment options. OBJECTIVE: The study evaluates the clinical value of cfDNA detection in TGCT patients. DESIGN AND METHODS: Total cfDNA concentration and ratio of its 2 main fragments (180 and 360 bp) were evaluated by spectrophotometry, capillary electrophoresis and qPCR in peripheral blood plasma of 96 TGCT patients (173 samples) and 31 normal controls. Non-parametric tests were used for statistical analyses. RESULTS: The total cfDNA concentration was significantly higher in TGCT than in controls (P < 0.0001), with the highest levels at disease progression, but with no clear threshold between malignant and normal samples. Patients with positive tumor markers had higher cfDNA concentrations than those with negative markers (P = 0.01). Longer 360 bp cfDNA fragments were found in 58% of TGCT patients including almost all samples from relapse or disease progression but no normal controls (P < 0.0001). CONCLUSION: Total cfDNA levels are significantly increased in TGCT patients but without a clear threshold separating normal and tumor samples, thus total cfDNA amount itself is not a sensitive enough marker to identify or monitor TGCT. Longer cfDNA fragments have been found exclusively in a proportion of tumors and predominantly at disease progression, representing a novel potential marker for TGCT monitoring that would deserve further exploration.

• Klíčová slova
• Circulating free tumor DNA, Clinical application, Molecular aberrations, Testicular germ cell tumor,
• MeSH
• cirkulující nádorová DNA * MeSH
• germinální a embryonální nádory * MeSH
• lidé MeSH
• mladý dospělý MeSH
• nádorové biomarkery MeSH
• progrese nemoci MeSH
• testikulární nádory * MeSH
• volné cirkulující nukleové kyseliny * MeSH
• Check Tag
• lidé MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• cirkulující nádorová DNA * MeSH
• nádorové biomarkery MeSH
• volné cirkulující nukleové kyseliny * MeSH

There is a strong demand for the identification of new biomarkers in colorectal cancer (CRC) diagnosis. Among all liquid biopsy analysts, cell-free circulating DNA (cfDNA) is probably the most promising tool with respect to the identification of minimal residual diseases, assessment of treatment response and prognosis, and identification of resistance mechanisms. Circulating cell-free tumor DNA (ctDNA) maintains the same genomic signatures that are present in the matching tumor tissue allowing for the quantitative and qualitative evaluation of mutation burdens in body fluids. Thus, ctDNA-based research represents a non-invasive method for cancer detection. Among the numerous possible applications, the diagnostic, predictive, and/or prognostic utility of ctDNA in CRC has attracted intense research during the last few years. In the present review, we will describe the different aspects related to cfDNA research and evidence from studies supporting its potential use in CRC diagnoses and the improvement of therapy efficacy. We believe that ctDNA-based research should be considered as key towards the introduction of personalized medicine and patient benefits.

• Klíčová slova
• cell-free DNA, colorectal cancer, liquid biopsy,
• MeSH
• cirkulující nádorová DNA analýza   krev   genetika   MeSH
• kolon patologie   MeSH
• kolorektální nádory krev   diagnóza   genetika   patologie   MeSH
• lidé MeSH
• nádorové biomarkery analýza   krev   genetika   MeSH
• prognóza MeSH
• rektum patologie   MeSH
• tekutá biopsie metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• systematický přehled MeSH
• Názvy látek
• cirkulující nádorová DNA MeSH
• nádorové biomarkery MeSH

OBJECTIVE: In our review article we focused on the circulating HPV DNA and its potential role in the pathogenesis of cervical cancer and in the evaluation of patients´ prognosis with cervical cancer Design: The article is a systematic review study analyzing available scientific articles focused on the circulating HPV DNA. SETTING: Clinic of Obstetrics and Gynecology, Jesenius faculty of Medicine in Martin, Comenius University in Bratislava, Slovakia. METHODS: In our study we searched the medical database PubMed with the key words: circulating HPV DNA, cervical cancer, cervical precanceroses. The core of our work is focused on the scientific articles published in English language since year 1995. RESULTS: We identified 13 studies in PubMed database analyzing the circulating HPV DNA in the process of cervical carcinogenesis. It is clear from the results that circulating HPV DNA is a significant prognostic marker of cervical malignant diseases including the early stages. CONCLUSION: The results focused on circulating HPV DNA show the significance of molecular biology in assessing the prognosis of cervical cancer. This idea has to be supported by further relevant studies. The uniformity of studies and use of the most sophisticated methods could help to answer the question about the real role of circulating HPV DNA in the process of cervical carcinogenesis and disease progression.

• Klíčová slova
• HPV, cervical cancer, circulating HPV DNA,
• MeSH
• DNA MeSH
• dysplazie děložního hrdla * MeSH
• infekce papilomavirem * MeSH
• lidé MeSH
• nádory děložního čípku * MeSH
• Papillomaviridae * genetika   MeSH
• prekancerózy * MeSH
• volné cirkulující nukleové kyseliny * MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• systematický přehled MeSH
• Geografické názvy
• Slovenská republika MeSH
• Názvy látek
• DNA MeSH
• volné cirkulující nukleové kyseliny * MeSH

Psoriasis is a multifactorial chronic inflammatory disease. We aimed to examine blood levels of nucleosomes derived from apoptotic cells, nucleosomal cell-free DNA (cfDNA) and immune-inflammatory biomarkers tumor necrosis factor-α (TNF-α), C-reactive protein (CRP), and interleukin 6 (IL-6) in psoriatic subjects. The study included 28 patients with exacerbated psoriasis vulgaris and 22 controls. The clinical and laboratory investigations included the determination of PASI score, BMI, cfDNA (by real-time PCR), nucleosomes, TNF-α, CRP, and IL-6. The range of PASI score in psoriatic patients was 10-34 (median 19). In the patients, we found significantly elevated levels (p < 0.001) of cfDNA, nucleosomes, TNF-α, CRP, and IL-6. We did not find any significant relationship between the analyzed parameters in either group (i.e., experimental or control). Elevated levels of the biomarkers of inflammation (TNF-α, CRP, and IL-6) and the indicators of apoptosis (cfDNA, circulating nucleosomes) proved that exacerbated psoriasis vulgaris is associated with a high degree of systemic inflammatory responses and dysregulated apoptotic pathways.

• Klíčová slova
• Apoptosis, Cell-free DNA, Inflammation, Nucleosomes, Psoriasis,
• MeSH
• apoptóza MeSH
• biologické markery krev   MeSH
• C-reaktivní protein analýza   MeSH
• dospělí MeSH
• interleukin-6 krev   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladý dospělý MeSH
• nukleozomy genetika   metabolismus   MeSH
• progrese nemoci MeSH
• psoriáza krev   patologie   MeSH
• senioři MeSH
• stupeň závažnosti nemoci MeSH
• TNF-alfa krev   MeSH
• volné cirkulující nukleové kyseliny krev   MeSH
• zánět MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• biologické markery MeSH
• C-reaktivní protein MeSH
• IL6 protein, human MeSH Prohlížeč
• interleukin-6 MeSH
• nukleozomy MeSH
• TNF-alfa MeSH
• volné cirkulující nukleové kyseliny MeSH

The development of minimally invasive and low-cost assay enabling early diagnosis, treatment response and prognosis in cancer patients may provide a promising alternative to tumor biopsy. Circulating cell-free DNA (cfDNA) is probably the most promising tool among all components of liquid biopsy. This review includes studies exploring cfDNA as the diagnostic, prognostic or predictive biomarker for all types of cancer. In this article, we systematically reviewed the relevant literature from PubMed about cfDNA. All articles presented higher cfDNA concentration in cancer patients when compared with patients with benign disease or healthy individuals. Most of the articles showed a connection between cfDNA and prognosis. The presence of high cfDNA level in serum or plasma was associated with worse overall patient's survival. This review supports the idea that the cfDNA analysis represents a promising research area and hopefully in the future, could be applied as a new biomarker for cancer detection, prognosis determination and prediction of the response to therapy.

• Klíčová slova
• Biomarker, Cancer, Cell-free DNA, Circulating-tumor DNA, Liquid biopsy,
• MeSH
• lidé MeSH
• nádorové biomarkery genetika   MeSH
• nádory diagnóza   genetika   patologie   MeSH
• prognóza MeSH
• tekutá biopsie metody   MeSH
• volné cirkulující nukleové kyseliny genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• systematický přehled MeSH
• Názvy látek
• nádorové biomarkery MeSH
• volné cirkulující nukleové kyseliny MeSH

BACKGROUND: Despite a myriad of attempts in the last three decades to diagnose ovarian cancer (OC) earlier, this clinical aim still remains a significant challenge. Aberrant methylation patterns of linked CpGs analyzed in DNA fragments shed by cancers into the bloodstream (i.e. cell-free DNA) can provide highly specific signals indicating cancer presence. METHODS: We analyzed 699 cancerous and non-cancerous tissues using a methylation array or reduced representation bisulfite sequencing to discover the most specific OC methylation patterns. A three-DNA-methylation-serum-marker panel was developed using targeted ultra-high coverage bisulfite sequencing in 151 women and validated in 250 women with various conditions, particularly in those associated with high CA125 levels (endometriosis and other benign pelvic masses), serial samples from 25 patients undergoing neoadjuvant chemotherapy, and a nested case control study of 172 UKCTOCS control arm participants which included serum samples up to two years before OC diagnosis. RESULTS: The cell-free DNA amount and average fragment size in the serum samples was up to ten times higher than average published values (based on samples that were immediately processed) due to leakage of DNA from white blood cells owing to delayed time to serum separation. Despite this, the marker panel discriminated high grade serous OC patients from healthy women or patients with a benign pelvic mass with specificity/sensitivity of 90.7% (95% confidence interval [CI] = 84.3-94.8%) and 41.4% (95% CI = 24.1-60.9%), respectively. Levels of all three markers plummeted after exposure to chemotherapy and correctly identified 78% and 86% responders and non-responders (Fisher's exact test, p = 0.04), respectively, which was superior to a CA125 cut-off of 35 IU/mL (20% and 75%). 57.9% (95% CI 34.0-78.9%) of women who developed OC within two years of sample collection were identified with a specificity of 88.1% (95% CI = 77.3-94.3%). Sensitivity and specificity improved further when specifically analyzing CA125 negative samples only (63.6% and 87.5%, respectively). CONCLUSIONS: Our data suggest that DNA methylation patterns in cell-free DNA have the potential to detect a proportion of OCs up to two years in advance of diagnosis and may potentially guide personalized treatment. The prospective use of novel collection vials, which stabilize blood cells and reduce background DNA contamination in serum/plasma samples, will facilitate clinical implementation of liquid biopsy analyses.

• Klíčová slova
• Cell-free DNA, DNA methylation, Early diagnosis, Ovarian cancer, Personalized treatment, Screening, Serum DNA,
• MeSH
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• metylace DNA * MeSH
• nádorové biomarkery krev   genetika   normy   MeSH
• nádory vaječníků krev   genetika   MeSH
• náhodné rozdělení MeSH
• sekvenční analýza DNA metody   normy   MeSH
• senioři MeSH
• volné cirkulující nukleové kyseliny genetika   MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• práce podpořená grantem MeSH
• Názvy látek
• nádorové biomarkery MeSH
• volné cirkulující nukleové kyseliny MeSH

In the clinical management of paediatric solid tumours, histological examination of tumour tissue obtained by a biopsy remains the gold standard to establish a conclusive pathological diagnosis. The DNA methylation pattern of a tumour is known to correlate with the histopathological diagnosis across cancer types and is showing promise in the diagnostic workup of tumour samples. This methylation pattern can be detected in the cell-free DNA. Here, we provide proof-of-concept of histopathologic classification of paediatric tumours using cell-free reduced representation bisulphite sequencing (cf-RRBS) from retrospectively collected plasma and cerebrospinal fluid samples. We determined the correct tumour type in 49 out of 60 (81.6%) samples starting from minute amounts (less than 10 ng) of cell-free DNA. We demonstrate that the majority of misclassifications were associated with sample quality and not with the extent of disease. Our approach has the potential to help tackle some of the remaining diagnostic challenges in paediatric oncology in a cost-effective and minimally invasive manner.

• Klíčová slova
• DNA methylation, biomarker, cell-free DNA, diagnosis, infinium, liquid biopsy, pediatric oncology, reduced representation bisulfite sequencing,
• MeSH
• dítě MeSH
• lidé MeSH
• metylace DNA MeSH
• nádory * MeSH
• retrospektivní studie MeSH
• sekvenční analýza DNA MeSH
• siřičitany MeSH
• volné cirkulující nukleové kyseliny * MeSH
• Check Tag
• dítě MeSH
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• hydrogen sulfite MeSH Prohlížeč
• siřičitany MeSH
• volné cirkulující nukleové kyseliny * MeSH

Hepatocellular carcinoma (HCC) is a severe neoplastic disease associated with high morbidity and mortality rates. HCC is often detected at advanced stages leading to ineffective curative treatments. Recently, liquid biopsy has emerged as a non-invasive method to identify highly specific HCC biomarkers in bodily fluids such as blood, serum, urine, and saliva. Circulating cell-free nucleic acids (cfNAs), particularly cell-free DNA (cfDNA) and cell-free RNA (cfRNA), have become promising candidates for biomarkers in liquid biopsy applications. While cfDNA presented significant challenges, researchers have turned their attention to cfRNA, which can be efficiently identified through various methods and is considered a potential biomarker for cancer diagnosis and prognosis. This review primarily focuses on studies related to detecting various cfRNA in body fluids as biomarkers. The aim is to provide a summary of available information to assist researchers in their investigations and the development of new diagnostic and prognostic tools.

• Klíčová slova
• Biomarker, Cell-free RNA, Diagnostic, Hepatocellular carcinoma, Liquid biopsy, Prognostic,
• MeSH
• hepatocelulární karcinom * diagnóza   krev   genetika   MeSH
• lidé MeSH
• nádorové biomarkery * krev   genetika   analýza   MeSH
• nádory jater * diagnóza   genetika   krev   MeSH
• prognóza MeSH
• tekutá biopsie metody   MeSH
• volné cirkulující nukleové kyseliny * krev   analýza   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• nádorové biomarkery * MeSH
• volné cirkulující nukleové kyseliny * MeSH