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Cell-Free Nucleic Acids

Cell-Free Nucleic Acids (CFNAs) refer to extracellular nucleic acids (DNA and RNA) that are present in bodily fluids, such as blood, urine, and cerebrospinal fluid, without being associated with intact cells.
These CFNAs originate from various sources, including apoptotic cells, necrotic cells, and actively secreted vesicles.
The analysis of CFNAs has emerged as a powerful tool for non-invasive diagnostics, disease monitoring, and therapeutic response assessment across a range of medical conditions, including cancer, prenatal screening, and neurodegenerative disorders.
The study of CFNAs provides a unique window into the molecular changes occurring within the body, offering the potential for early detection, personalized treatment, and improved patient outcomes.
Researchers and clinicians can leverage the power of PubCompare.ai's AI-powered platform to effortlessly locate the best protocols from literature, preprints, and patents, enabling seamless comparisons and optimization suggestions to revolutionize their work and find the ideal solutions to advance their CFNA-related studies.

Most cited protocols related to «Cell-Free Nucleic Acids»

1
Plasma Cell-Free DNA Sequencing
Eligible subjects were asked to participate in the study after receiving counseling about the invasive diagnostic test. Approximately 10 mL of whole blood was collected from each subject and placed in a Cell-Free DNA BCT™ tube (Streck, Omaha, NE, USA) before the invasive procedure. Within 6 hours of collection, the maternal blood samples were centrifuged first at 1,200×g for 15 min at 4°C. Plasma was transferred to microcentrifuge tubes, centrifuged again at 16,000×g for 10 min at 4°C to remove residual cells, transferred to fresh tubes, and stored at −80°C. For each sample, plasma cfDNA was extracted from 1 mL of plasma using the QIAamp Circulating Nucleic Acid Kit from Qiagen (Hilden, Germany). The resulting plasma cfDNA was used as input DNA to make a library for sequencing. End-repair of the plasma cfDNA was performed with T4 DNA polymerase, Klenow DNA polymerase, and T4 polynucleotide kinase. The adapter-ligated DNA libraries were analyzed with the Ion Proton™ System (Life Technologies, Grand Island, NY, USA) with an average 0.3×sequencing coverage per nucleotide. Ion PI™ Chip Kit version 2.0 (Life Technologies) was used for cfDNA sequencing and 10 cfDNA samples per chip were analyzed. Average total raw reads per sample was 6.5 million and mean rate of uniquely mapped reads was 59.0%.
Jeon Y.J., Zhou Y., Li Y., Guo Q., Chen J., Quan S., Zhang A., Zheng H., Zhu X., Lin J., Xu H., Wu A., Park S.G., Kim B.C., Joo H.J., Chen H, & Bhak J. (2014). The Feasibility Study of Non-Invasive Fetal Trisomy 18 and 21 Detection with Semiconductor Sequencing Platform. PLoS ONE, 9(10), e110240.
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Publication 2014
BLOOD Cell-Free DNA Cell-Free Nucleic Acids Cells DNA-Directed DNA Polymerase DNA Chips DNA Library Plasma Polynucleotide 5'-Hydroxyl-Kinase Protons Tests, Diagnostic
2
Plasma-Derived cfDNA Profiling for Cancer
344 plasma samples from 200 patients with multiple cancer types were collected along with plasma from 65 healthy controls. Among the patients, 172 individuals, and notably the OV04 samples, were recruited through prospective clinical studies at Addenbrooke’s Hospital, Cambridge, UK, approved by the local research ethics committee (REC reference numbers: 07/Q0106/63; and NRES Committee East of England - Cambridge Central 03/018). Written informed consent was obtained from all patients, and blood samples were collected before and after initiation of treatment with surgery or chemotherapeutic agents. DNA was extracted from 2 mL of plasma using the QIAamp circulating nucleic acid kit (Qiagen) or QIAsymphony (Qiagen) according to the manufacturer’s instructions. In addition, 28 patients were recruited as part of the Copenhagen Prospective Personalized Oncology (CoPPO) program (Ref: PMID: 25046202) at Rigshospitalet, Copenhagen, Denmark, approved by the local research ethics committee. Baseline tumor tissue biopsies were available from all 28 patients, together with re-biopsies collected at relapse from two patients, and matched plasma samples. Brain tumor patients were recruited at Addenbrooke’s Hospital, Cambridge, UK, as part of the BLING study (REC – 15/EE/0094). Bladder cancer patients were recruited at the Netherlands Cancer Institute, Amsterdam, The Netherlands, and approval according to national guidelines was obtained (N13KCM/CFMPB250) (47 ). 65 plasma samples were obtained from healthy control individuals using a similar collection protocol (Seralab). Plasma samples have not been freeze-thawed more than 2 times to reduce artifactual fragmentation of cfDNA. A flowchart of the study is presented in fig. S1.
Mouliere F., Chandrananda D., Piskorz A.M., Moore E.K., Morris J., Ahlborn L.B., Mair R., Goranova T., Marass F., Heider K., Wan J.C., Supernat A., Hudecova I., Gounaris I., Ros S., Jimenez-Linan M., Garcia-Corbacho J., Patel K., Østrup O., Murphy S., Eldridge M.D., Gale D., Stewart G.D., Burge J., Cooper W.N., van der Heijden M.S., Massie C.E., Watts C., Corrie P., Pacey S., Brindle K., Baird R.D., Mau-Sørensen M., Parkinson C.A., Smith C.G., Brenton J.D, & Rosenfeld N. (2018). Enhanced detection of circulating tumor DNA by fragment size analysis. Science translational medicine, 10(466), eaat4921.
Publication 2018
Antineoplastic Agents Biopsy BLOOD Brain Neoplasms Cancer of Bladder Cell-Free DNA Cell-Free Nucleic Acids Ethics Committees, Research Freezing Malignant Neoplasms Neoplasms Operative Surgical Procedures Patients Plasma Relapse Tissues
3
Plasma DNA Extraction Protocol
Whole blood (9 ml) was collected in routine ethylenediamine tetraacetic acid (EDTA) Vacutainer tubes (BD Biosciences, Heidelberg, Germany). To stabilize cell membranes and to impede cell lysis, 0.225 ml of a 10% neutral buffered solution containing formaldehyde (4% weight per volume) (Sigma-Aldrich, Vienna, Austria) was added immediately after blood withdrawal. Blood samples were gently inverted, stored at room temperature and further processed within 2 hr. Plasma was prepared according to Ref.22 (link). In brief, tubes were centrifuged at 200g for 10 min with the brake and acceleration powers set to zero, followed by a subsequent centrifugation step at 1600g for 10 min. The supernatant was collected, transferred to a new 15 ml tube and spun at 1600g for 10 min. The plasma was carefully aliquoted into new 2 ml Eppendorf tubes and stored at −80°C.
DNA was isolated from plasma samples using the QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany) or the Qiagen Circulating Nucleic Acids Kit (CNA) (Qiagen, Hilden, Germany) according to the manufacturer's instructions. DNA was eluted in 30 μl of distilled water for Mini Kit extractions and in 100 µl for CNA Kit, respectively.
Heitzer E., Auer M., Hoffmann E.M., Pichler M., Gasch C., Ulz P., Lax S., Waldispuehl-Geigl J., Mauermann O., Mohan S., Pristauz G., Lackner C., Höfler G., Eisner F., Petru E., Sill H., Samonigg H., Pantel K., Riethdorf S., Bauernhofer T., Geigl J.B, & Speicher M.R. (2013). Establishment of tumor-specific copy number alterations from plasma DNA of patients with cancer. International Journal of Cancer. Journal International du Cancer, 133(2), 346-356.
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Publication 2013
Acceleration BLOOD Cell-Free Nucleic Acids Cells Centrifugation Edetic Acid Formalin Plasma Plasma Membrane
4
Comprehensive Genomic Profiling of ctDNA
Genetic analysis was conducted as previously described (25 (link), 26 (link)). Briefly, ctDNA was isolated from 4 to 5 mL of plasma using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Valencia, CA). Serial sections from formalin-fixed paraffin-embedded tumor tissues were used for genomic tumor DNA extraction using the QIAamp DNA mini kit (Qiagen, Valencia, CA). DNA from leukocytes was extracted using the DNeasy Blood Kit (Qiagen, Valencia, CA). Sequencing libraries were prepared from ctDNA using KAPA DNA Library Preparation Kits (Kapa Biosystems, Wilmington, MA, USA), and genomic DNA sequencing libraries were prepared with Illumina TruSeq DNA Library Preparation Kits (Illumina, San Diego, CA). Libraries were hybridized to custom-designed biotinylated oligonucleotide probes (Roche NimbleGen, Madison, WI, USA) targeting 1,021 genes (Supplementary Table S1), including MLH1, MSH2, MSH6, and PMS2. Prepared libraries were sequenced on a NextSeq CN 500 (Illumina, San Diego, CA).
Sun S., Liu Y., Eisfeld A.K., Zhen F., Jin S., Gao W., Yu T., Chen L., Wang W., Chen W., Yuan M., Chen R., He K, & Guo R. (2019). Identification of Germline Mismatch Repair Gene Mutations in Lung Cancer Patients With Paired Tumor-Normal Next Generation Sequencing: A Retrospective Study. Frontiers in Oncology, 9, 550.
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Publication 2019
Birth BLOOD Cell-Free Nucleic Acids DNA, Neoplasm DNA Library Formalin Genes Genome Genomic Library Leukocytes MLH1 protein, human MSH6 protein, human Neoplasms Oligonucleotide Probes Paraffin Embedding Plasma PMS2 protein, human
5
Quantifying Donor-Derived Cell-Free DNA

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Publication 2017
Base Pairing Cell-Free DNA Cell-Free Nucleic Acids DNA Library Genome, Human Plasma Tissue Donors

Most recents protocols related to «Cell-Free Nucleic Acids»

1
Extraction and Quantification of cfDNA

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Publication 2023
Biological Assay Biopsy BLOOD Blood Cells Cell-Free DNA Cell-Free Nucleic Acids Cells DNA, Double-Stranded Edetic Acid Freezing Genome Hypersensitivity Nitrogen Nucleic Acids Patients Plasma Surgery, Day Tissues Touch Veins
2
Plasma Isolation and Cell-free DNA Extraction
Blood was collected into acid-citrate dextrose (ACD) blood tubes and processed within four hours of collection using standard blood processing methods. Briefly, whole blood was centrifuged once at 1300 × g for 10 min in a swinging bucket centrifuge with the brakes turned off. The upper plasma was collected without disrupting the buffy coat layer, aliquoted (1 mL/aliquot) into prelabeled cryovials, and stored frozen at −80 °C. Cell-free DNA was isolated from 2 mL of ACD plasma using the QIAamp Circulating Nucleic Acid kit (Qiagen) following the manufacturer’s protocol for the vacuum manifold method and then sequenced.
Stecklein S.R., Kimler B.F., Yoder R., Schwensen K., Staley J.M., Khan Q.J., O’Dea A.P., Nye L.E., Elia M., Heldstab J., Home T., Hyter S., Isakova K., Pathak H.B., Godwin A.K, & Sharma P. (2023). ctDNA and residual cancer burden are prognostic in triple-negative breast cancer patients with residual disease. NPJ Breast Cancer, 9, 10.
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Publication 2023
acid citrate dextrose BLOOD Cell-Free DNA Cell-Free Nucleic Acids Freezing Plasma Vacuum
3
Targeted Sequencing of Tissue DNA and cfDNA
The tissue DNA was extracted using the QIAamp DNA FFPE Tissue Kit (Qiagen, Valencia, CA, USA) according to the manufacturer’s instructions. Circulating cfDNA was recovered from 4 to 5 mL plasma by using the QIAamp Circulating Nucleic Acid kit (Qiagen). The tissue DNA and cfDNA were profiled using a capture-based targeted sequencing panel that consisted of 520 or 168 cancer-related genes. The captured libraries were sequenced on Illumina NovaSeq 6000 with pair-end reads with 1000X for tissue DNA and 20,000 X for cfDNA, following the manufacturer instructions (Illumina, San Diego, CA, USA).
Sun H., Ren P., Chen Y., Lan L., Yan Z., Yang Y., Wang B., Wang C., Li Y., Li L., Zhang Y., Li Y., Wang Z., Pan Z, & Jiang Z. (2023). Optimal therapy for concomitant EGFR and TP53 mutated non-small cell lung cancer: a real-world study. BMC Cancer, 23, 198.
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Publication 2023
Cell-Free DNA Cell-Free Nucleic Acids Gene, Cancer Plasma Tissues
4
Targeted Bisulfite Sequencing of Genomic and Circulating DNA
One microgram of genomic DNA extracted from each of the 20 tissue samples were converted following the instruction of EpiTect Fast DNA Bisulfite Kit (QIAGEN). The converted DNA was amplified using the primers (Supplementary Table 1) before sequencing. The amplification was as follows: 0.4 μM primers, 1x Uc Buffer for Library Amplification, 0.2 mM each dNTP, 1U Phanta Uc Super-Fidelity DNA polymerase. The reactions were carried out on the ProFlex™ 3 ×32-well PCR System Applied Biosystems™ with the following program: initial denaturation at 95 °C for 3 min; 35 cycles of 94 °C for 30 s, 60 °C for 30 s, 72 °C for 60 s; then incubation at 72 °C for 7 min. The amplicons were analysed using gel electrophoresis, the band was cut and purified using QIAquick Gel Extraction Kit before the quantification with Qubit 4 Fluorometer. the PCR products were tested using Sanger sequencing. The inconsistent results were diluted 10,000 times and served as a template for nest methylated specific-PCR to generate the methylated specific-PCR product for a second round of sequencing. Sequencing data were analysed using Chromas (Technelcium Pty, v2.6.6).
Plasma cfDNA was extracted by QIAamp® Circulating Nucleic Acid Kit (Qiagen, 55114) according to the manufacturer’s protocol. DNA was subjected to the bisulfite conversion step using EZ DNA Methylation-Lightning™ Kit (Zymo Research, D5030) according to the manufacturer’s protocol.
Targeted genome methylation analysis was conducted using the OPERA Mars® Universal Library Prep Kit (Apogenomics, APG-62001), OPERA® Index Adapter (Apogenomics, APG-23005A), and OPERA® Index Primer (Apogenomics, APG-23009A) according to the manufacturer’s protocol. Briefly, the procedures were divided into three main steps: (i) multi-cycle linear amplification using a single-primer panel, (ii) ligation between amplified ssDNA product and single strand UMI adapter, which contains index sequence, (iii) indexing PCR for amplifying the ligated product with Index Primer. These target-enriched libraries were further amplified with P5 and P7 primers and purified for sequencing on the NovaSeq 6000 System (Illumina Inc).
Targeted bisulfite conversion sequence data were first trimmed by cutadapt 1.18. The reads were mapped to targets around 600-700 bp reference sequence with bismark v0.19.1, and transferred to remove duplication reads with fgbio 1.0.0 following standard instructions. The deduplicated reads were mapped to reference and the co-methylated reads were counted by manual inspection in the integrative genomics viewer (IGV v2.8.9). Reads containing more than 4 methylated CpG site was classified as co-methylated.
Xu G., Yang H., Qiu J., Reboud J., Zhen L., Ren W., Xu H., Cooper J.M, & Gu H. (2023). Sequence terminus dependent PCR for site-specific mutation and modification detection. Nature Communications, 14, 1169.
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Publication 2023
Buffers Cell-Free DNA Cell-Free Nucleic Acids DNA, Single-Stranded DNA-Directed DNA Polymerase DNA Library DNA Methylation Electrophoresis Genome hydrogen sulfite Ligation Nested Polymerase Chain Reaction Oligonucleotide Primers Plasma Tissues
5
DNA Extraction and Quantification Protocol
The genomic DNA was extracted according to the instructions of the QIAamp Fast DNA Tissue Kit, and the purity and quantification of the obtained DNA were assessed by absorbance using a Nanodrop spectrophotometer (Thermo Fisher). Only extracted DNA with absorbance ratios of A260/A230 > 1.8 and A260/A280 > 1.8 was used. All extracted DNA was stored at −20 °C for less than 2 months before use.
Spin column-based cfDNA extraction (QIAamp Circulating Nucleic Acid Kit, lot No.55114) was performed according to the recommended protocol. The volume of human plasma varied from 1 to 2 mL. 60 μl of elution buffer was applied in the final elution step. The purity and quantification of extracted cfDNA was tested using Nanodrop. The fragmented size was evaluated using Qsep1.
The FFPE blocks were obtained from 2012/02/07–2012/10/25 with written informed patient consent and were stored in the dark at room temperature. The study was approved by the Ethics Committee of Renji Hospital.
Xu G., Yang H., Qiu J., Reboud J., Zhen L., Ren W., Xu H., Cooper J.M, & Gu H. (2023). Sequence terminus dependent PCR for site-specific mutation and modification detection. Nature Communications, 14, 1169.
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Publication 2023
Blood Plasma Volume Buffers Cell-Free DNA Cell-Free Nucleic Acids Ethics Committees, Clinical Genome Homo sapiens Patients Tissues

Top products related to «Cell-Free Nucleic Acids»

1
Qiaamp circulating nucleic acid kit by Qiagen
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The QIAamp Circulating Nucleic Acid Kit is a laboratory equipment product designed for the purification of cell-free circulating nucleic acids (e.g., DNA, RNA) from various biofluid samples such as plasma, serum, or urine. The kit utilizes a spin column-based technology to efficiently extract and concentrate the target nucleic acids for further analysis.
2
Qubit dsdna hs assay kit by Thermo Fisher Scientific
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The Qubit dsDNA HS Assay Kit is a fluorescence-based method for quantifying double-stranded DNA (dsDNA) in a sample. The kit provides a sensitive and accurate way to measure DNA concentration in a microplate or cuvette format.
3
Qiaamp dna ffpe tissue kit by Qiagen
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The QIAamp DNA FFPE Tissue Kit is a laboratory equipment designed for the purification of DNA from formalin-fixed, paraffin-embedded (FFPE) tissue samples. It is used to extract high-quality genomic DNA from FFPE samples for downstream applications such as PCR, sequencing, and other molecular biology techniques.
4
Qubit 2.0 fluorometer by Thermo Fisher Scientific
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The Qubit 2.0 Fluorometer is a compact and sensitive instrument designed for quantifying nucleic acids and proteins. It utilizes fluorescent dye-based detection technology to provide accurate and reproducible measurements of sample concentrations. The Qubit 2.0 Fluorometer is a self-contained unit that can be used for a variety of applications in research and clinical settings.
5
Qubit fluorometer by Thermo Fisher Scientific
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The Qubit fluorometer is a compact and sensitive instrument designed for precise quantification of nucleic acids and proteins. It utilizes fluorescent dye-based detection technology to provide accurate measurements of sample concentrations.
6
Qiamp circulating nucleic acid kit by Qiagen
Sourced in Germany, United States, France, Netherlands
The QIAamp Circulating Nucleic Acid Kit is a laboratory product designed for the purification of cell-free circulating nucleic acids from various liquid sample types, including plasma, serum, and cerebrospinal fluid. The kit utilizes a silica-based membrane technology to efficiently capture and purify these nucleic acids for downstream analysis.
7
Qiaamp dna mini kit by Qiagen
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The QIAamp DNA Mini Kit is a laboratory equipment product designed for the purification of genomic DNA from a variety of sample types. It utilizes a silica-membrane-based technology to efficiently capture and purify DNA, which can then be used for various downstream applications.
8
Agilent 2100 bioanalyzer by Agilent Technologies
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The Agilent 2100 Bioanalyzer is a lab instrument that provides automated analysis of DNA, RNA, and protein samples. It uses microfluidic technology to separate and detect these biomolecules with high sensitivity and resolution.
9
Circulating nucleic acid kit by Qiagen
Sourced in Germany, United States
The Circulating Nucleic Acid Kit is a laboratory product designed to extract and purify circulating nucleic acids, such as DNA and RNA, from various biological samples. The kit provides a standardized procedure for the isolation and concentration of these nucleic acids, which can be used for subsequent analysis or downstream applications.
10
Dneasy blood tissue kit by Qiagen
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The DNeasy Blood & Tissue Kit is a DNA extraction and purification kit designed for the efficient isolation of high-quality genomic DNA from a variety of sample types, including whole blood, tissue, and cultured cells. The kit utilizes a silica-based membrane technology to capture and purify DNA, providing a reliable and consistent method for DNA extraction.

More about "Cell-Free Nucleic Acids"

Cell-free nucleic acids (CFNAs) refer to extracellular DNA and RNA present in bodily fluids like blood, urine, and cerebrospinal fluid, without being associated with intact cells.
These CFNAs come from various sources, including apoptotic cells, necrotic cells, and secreted vesicles.
Analyzing CFNAs has emerged as a powerful non-invasive tool for disease diagnosis, monitoring, and treatment assessment across conditions like cancer, prenatal screening, and neurodegenerative disorders.
Researchers and clinicians can leverage platforms like PubCompare.ai to effortlessly locate the best protocols from literature, preprints, and patents, enabling seamless comparisons and optimization suggestions to advance CFNA-related studies.
The study of CFNAs provides a unique window into the molecular changes occurring within the body, offering the potential for early detection, personalized treatment, and improved patient outcomes.
Synonyms for cell-free nucleic acids include extracellular nucleic acids, circulating nucleic acids, and cell-free DNA/RNA.
Related terms include apoptosis, necrosis, exosomes, microvesicles, and liquid biopsy.
Abbreviations commonly used include cfDNA, cfRNA, ctDNA, and ctRNA.
Key subtopics in the CFNA field include sample collection and processing, extraction and purification methods (e.g., QIAamp Circulating Nucleic Acid Kit, QIAamp DNA FFPE Tissue Kit), quantification techniques (e.g., Qubit dsDNA HS Assay Kit, Qubit 2.0 Fluorometer), and downstream analyses (e.g., Agilent 2100 Bioanalyzer).
Researchers may also utilize kits like the QIAamp DNA Mini Kit and DNeasy Blood & Tissue Kit to isolate and analyze CFNA.
As the field of cell-free nucleic acids continues to evolve, the insights from this powerful non-invasive approach will undoubtedly contribute to advancements in personalized medicine and improved patient outcomes.