scholarly journals Concentration and Methylation of Cell-Free DNA from Blood Plasma as Diagnostic Markers of Renal Cancer

2016 ◽  
Vol 2016 ◽  
pp. 1-10 ◽  
Author(s):  
Inessa Skrypkina ◽  
Liudmyla Tsyba ◽  
Kateryna Onyshchenko ◽  
Dmytro Morderer ◽  
Olena Kashparova ◽  
...  
Keyword(s):  
Blood Plasma ◽  
Cancer Patients ◽  
Renal Cancer ◽  
Cpg Islands ◽  
Tumor Development ◽  
Diagnostic Markers ◽  
Cell Free Dna ◽  
Free Dna ◽  
Healthy Donors ◽  
Fluorescence Test

The critical point for successful treatment of cancer is diagnosis at early stages of tumor development. Cancer cell-specific methylated DNA has been found in the blood of cancer patients, indicating that cell-free DNA (cfDNA) circulating in the blood is a convenient tumor-associated DNA marker. Therefore methylated cfDNA can be used as a minimally invasive diagnostic marker. We analysed the concentration of plasma cfDNA and methylation of six tumor suppressor genes in samples of 27 patients with renal cancer and 15 healthy donors as controls. The cfDNA concentrations in samples from cancer patients and healthy donors was measured using two different methods, the SYBR Green I fluorescence test and quantitative real-time PCR. Both methods revealed a statistically significant increase of cfDNA concentrations in cancer patients. Hypermethylation on cfDNA was detected for theLRRC3B(74.1%),APC(51.9%),FHIT(55.6%), andRASSF1(62.9%) genes in patients with renal cancer. Promoter methylation ofVHLandITGA9genes was not found on cfDNA. Our results confirmed that the cfDNA level and methylation of CpG islands ofRASSF1A,FHIT, andAPCgenes in blood plasma can be used as noninvasive diagnostic markers of cancer.

scholarly journals Comparison of quantification algorithms for circulating cell-free DNA methylation biomarkers in blood plasma from cancer patients

2017 ◽  
Vol 9 (1) ◽  
Author(s):  
Luka de Vos ◽  
Heidrun Gevensleben ◽  
Andreas Schröck ◽  
Alina Franzen ◽  
Glen Kristiansen ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Blood Plasma ◽  
Cancer Patients ◽  
Cell Free Dna ◽  
Free Dna ◽  
In Blood Plasma ◽  
Circulating Cell Free Dna

Detection of Cell-Free DNA in Blood Plasma Samples of Cancer Patients

10.3791/61449 ◽  
2020 ◽  
Author(s):  
Vikrant Palande ◽  
Dorith Raviv Shay ◽  
MILANA Frenkel-Morgenstern
Keyword(s):  
Blood Plasma ◽  
Cancer Patients ◽  
Plasma Samples ◽  
Cell Free Dna ◽  
Free Dna ◽  
In Blood Plasma

scholarly journals Cancer Detection and Classification by CpG Island Hypermethylation Signatures in Plasma Cell-Free DNA

Cancers ◽  
2021 ◽  
Vol 13 (22) ◽  
pp. 5611
Author(s):  
Jinyong Huang ◽  
Alex C. Soupir ◽  
Brian D. Schlick ◽  
Mingxiang Teng ◽  
Ibrahim H. Sahin ◽  
...  
Keyword(s):  
Cancer Patients ◽  
Cancer Detection ◽  
Cpg Island ◽  
Cpg Islands ◽  
Response Monitoring ◽  
Aberrant Methylation ◽  
Tumor Type ◽  
Multiple Cancer ◽  
Cell Free Dna ◽  
Free Dna

Cell-free DNA (cfDNA) methylation has emerged as a promising biomarker for early cancer detection, tumor type classification, and treatment response monitoring. Enrichment-based cfDNA methylation profiling methods such as cfMeDIP-seq have shown high accuracy in the classification of multiple cancer types. We have previously optimized another enrichment-based approach for ultra-low input cfDNA methylome profiling, termed cfMBD-seq. We reported that cfMBD-seq outperforms cfMeDIP-seq in the enrichment of high-CpG-density regions, such as CpG islands. However, the clinical feasibility of cfMBD-seq is unknown. In this study, we applied cfMBD-seq to profiling the cfDNA methylome using plasma samples from cancer patients and non-cancer controls. We identified 1759, 1783, and 1548 differentially hypermethylated CpG islands (DMCGIs) in lung, colorectal, and pancreatic cancer patients, respectively. Interestingly, the vast majority of DMCGIs were overlapped with aberrant methylation changes in corresponding tumor tissues, indicating that DMCGIs detected by cfMBD-seq were mainly driven by tumor-specific DNA methylation patterns. From the overlapping DMCGIs, we carried out machine learning analyses and identified a set of discriminating methylation signatures that had robust performance in cancer detection and classification. Overall, our study demonstrates that cfMBD-seq is a powerful tool for sensitive detection of tumor-derived epigenomic signals in cfDNA.

scholarly journals Enhanced specificity of clinical high-sensitivity tumor mutation profiling in cell-free DNA via paired normal sequencing using MSK-ACCESS

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
A. Rose Brannon ◽  
Gowtham Jayakumaran ◽  
Monica Diosdado ◽  
Juber Patel ◽  
Anna Razumova ◽  
...  
Keyword(s):  
Cancer Patients ◽  
De Novo ◽  
Low Frequency ◽  
High Sensitivity ◽  
Clinical Analysis ◽  
De Novo Mutation ◽  
Cell Free Dna ◽  
Free Dna ◽  
Somatic Alterations ◽  
Mutation Profiling

AbstractCirculating cell-free DNA from blood plasma of cancer patients can be used to non-invasively interrogate somatic tumor alterations. Here we develop MSK-ACCESS (Memorial Sloan Kettering - Analysis of Circulating cfDNA to Examine Somatic Status), an NGS assay for detection of very low frequency somatic alterations in 129 genes. Analytical validation demonstrated 92% sensitivity in de-novo mutation calling down to 0.5% allele frequency and 99% for a priori mutation profiling. To evaluate the performance of MSK-ACCESS, we report results from 681 prospective blood samples that underwent clinical analysis to guide patient management. Somatic alterations are detected in 73% of the samples, 56% of which have clinically actionable alterations. The utilization of matched normal sequencing allows retention of somatic alterations while removing over 10,000 germline and clonal hematopoiesis variants. Our experience illustrates the importance of analyzing matched normal samples when interpreting cfDNA results and highlights the importance of cfDNA as a genomic profiling source for cancer patients.

Potential clinical applications of circulating cell-free DNA in ovarian cancer patients

2018 ◽  
Vol 20 ◽  
Author(s):  
Ana Barbosa ◽  
Ana Peixoto ◽  
Pedro Pinto ◽  
Manuela Pinheiro ◽  
Manuel R. Teixeira
Keyword(s):  
Ovarian Cancer ◽  
Cancer Patients ◽  
Liquid Biopsy ◽  
Clinical Applications ◽  
Epigenetic Alterations ◽  
Cell Free Dna ◽  
Non Invasive ◽  
Free Dna ◽  
Potential Use ◽  
Circulating Cell Free Dna

AbstractCirculating cell-free DNA (cfDNA) consists of small fragments of DNA that circulate freely in the bloodstream. In cancer patients, a fraction of cfDNA is derived from tumour cells, therefore containing the same genetic and epigenetic alterations, and is termed circulating cell-free tumour DNA. The potential use of cfDNA, the so-called ‘liquid biopsy’, as a non-invasive cancer biomarker has recently received a lot of attention. The present review will focus on studies concerning the potential clinical applications of cfDNA in ovarian cancer patients.

Circulating cell-free DNA in plasma of colorectal cancer patients - A potential biomarker for tumor burden

2017 ◽  
Vol 26 (4) ◽  
pp. 395-401 ◽  
Author(s):  
Jagdeep Singh Bhangu ◽  
Hossein Taghizadeh ◽  
Tamara Braunschmid ◽  
Thomas Bachleitner-Hofmann ◽  
Christine Mannhalter
Keyword(s):  
Colorectal Cancer ◽  
Cancer Patients ◽  
Tumor Burden ◽  
Cell Free Dna ◽  
Free Dna ◽  
Potential Biomarker ◽  
Colorectal Cancer Patients ◽  
Circulating Cell Free Dna
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