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circulating free DNA

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https://www.readbyqxmd.com/read/29230875/kinetics-of-plasma-cell-free-dna-and-creatine-kinase-in-a-canine-model-of-tissue-injury
#1
I J Wilson, R K Burchell, A J Worth, S E Burton, K R Gedye, K J Clark, K R Crosse, M Jack, T F Odom, S J De Grey, K M S McGlade, S C Tomlin, N Lopez-Villalobos, A Gal
BACKGROUND: Cell-free DNA (cfDNA) comprises short, double-stranded circulating DNA sequences released from damaged cells. In people, cfDNA concentrations correlate well with disease severity and tissue damage. No reports are available regarding cfDNA kinetics in dogs. OBJECTIVES/HYPOTHESIS: Cell-free DNA will have a short biological half-life and would be able to stratify mild, moderate, and severe tissue injury. Our study aims were to determine the kinetics and biological half-life of cfDNA and to contrast them with those of creatine kinase (CK)...
December 12, 2017: Journal of Veterinary Internal Medicine
https://www.readbyqxmd.com/read/29229500/diagnostic-value-of-circulating-cell-free-dna-levels-for-hepatocellular-carcinoma
#2
Linlin Yan, Yanhui Chen, Jiyuan Zhou, Hong Zhao, Henghui Zhang, Guiqiang Wang
OBJECTIVES: Circulating cell-free DNA (cfDNA) is a potential biomarker for tumor diagnosis. Hepatocyte damage is characteristic component of the pathobiology of hepatocellular carcinoma (HCC), which would be expected to result in substantial leakage of cfDNA into the circulation. However, the diagnostic value of cfDNA levels for HCC remains unclear. METHODS: Plasma samples were collected from 24 HCC patients and 62 HBV-related liver fibrosis patients. Plasma cfDNA levels was quantified by Qubit method...
December 8, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/29224828/cell-free-nucleic-acids-in-body-fluids-as-biomarkers-for-the-prediction-and-early-detection-of-recurrent-head-and-neck-cancer-a-systematic-review-of-the-literature
#3
REVIEW
Joost H van Ginkel, Fons J B Slieker, Remco de Bree, Robert J J van Es, Ellen M Van Cann, Stefan M Willems
Liquid biopsy is a minimally invasive detection method for molecular biomarkers in body fluids which may serve as a novel tool in management of head and neck cancer. The purpose of this systematic review is to outline the current status of liquid biopsy in head and neck squamous cell carcinoma (HNSCC) patients by systematically identifying and qualifying all published studies on the diagnostic or prognostic value of cell-free nucleic acids detection for posttreatment disease monitoring and/or disease outcome...
December 2017: Oral Oncology
https://www.readbyqxmd.com/read/29224167/dna-methylation-analysis-of-free-circulating-dna-in-body-fluids
#4
Maria Jung, Glen Kristiansen, Dimo Dietrich
Circulating cell-free DNA in body fluids is an analyte of great interest in basic and clinical research. The analyses of DNA methylation and hydroxymethylation patterns in body fluids might allow one to determine the certain state of a disease, in particular of cancer. DNA methylation biomarkers in liquid biopsies, i.e. blood plasma samples, may help optimizing personalized therapy for individual patients. DNA methylation analyses of specific loci usually require a bisulfite conversion of the DNA, which requires a sufficiently high amount of DNA at the appropriate concentration...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29224156/multiplexed-and-sensitive-dna-methylation-testing-using-methylation-sensitive-restriction-enzymes-msre-qpcr
#5
Gabriel Beikircher, Walter Pulverer, Manuela Hofner, Christa Noehammer, Andreas Weinhaeusel
DNA methylation is a chemically stable key-player in epigenetics. In the vertebrate genome the 5-methyl cytosine (5mC) has been found almost exclusively in the CpG dinucleotide context. CpG dinucleotides are enriched in CpG islands very frequently located within or close to gene promoters. Analyses of DNA methylation changes in human diagnostics have been conducted classically using methylation-sensitive restriction enzymes (MSRE). Since the discovery of bisulfite conversion-based sequencing and PCR assays, MSRE-based PCR assays have been less frequently used, although especially in the field of cancer epigenetics MSRE-based genome-wide discovery and targeted screening applications have been and are still performed successfully...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29218272/blood-based-biomarkers-in-lung-cancer-prognosis-and-treatment-decisions
#6
REVIEW
Meng Xu-Welliver, David P Carbone
Despite recent advances, non-small cell lung cancer (NSCLC) remains a devastating disease with overall poor prognosis. Major contributing factors include obstacles to diagnosing the disease early in its course during the asymptomatic stage as well as diversity and complexity of its biology underlying tumorigenesis and tumor progression. Advances in molecularly targeted therapies which drives the development of personalized cancer care require precise and comprehensive understanding of tumor biology, not only at the time of diagnosis but also during treatment course and surveillance...
December 2017: Translational Lung Cancer Research
https://www.readbyqxmd.com/read/29218253/clinical-applications-of-urinary-cell-free-dna-in-cancer-current-insights-and-promising-future
#7
REVIEW
Tian Lu, Jinming Li
Liquid biopsy is gaining significant attention as a tool for unveiling the molecular landscape of tumor and holds great promise for individualized medicine for cancer. Cell-free DNA serves as an extremely important component of liquid biopsy for cancer, and cell-free DNA in urine is even promising due to the remarkable advantage of urine as an ultra-noninvasive sample source over tissue and blood. Compared with the widely studied cell-free DNA in blood, less is known about the role of urinary cell-free DNA...
2017: American Journal of Cancer Research
https://www.readbyqxmd.com/read/29216356/improved-egfr-mutation-detection-using-combined-exosomal-rna-and-circulating-tumor-dna-in-nsclc-patient-plasma
#8
A K Krug, D Enderle, C Karlovich, T Priewasser, S Bentink, A Spiel, K Brinkmann, J Emenegger, D G Grimm, E Castellanos-Rizaldos, J W Goldman, L V Sequist, J-C Soria, D R Camidge, S M Gadgeel, H A Wakelee, M Raponi, M Noerholm, J Skog
Background: A major limitation of circulating tumor DNA (ctDNA) for somatic mutation detection has been the low level of ctDNA found in a subset of cancer patients. We investigated whether using a combined isolation of exosomal RNA (exoRNA) and cell-free DNA (cfDNA) could improve blood-based liquid biopsy for EGFR mutation detection in NSCLC patients. Patients and methods: Matched pretreatment tumor and plasma were collected from 84 patients enrolled in TIGER-X (NCT01526928), a Ph1/2 study of rociletinib in mutant EGFR NSCLC patients...
December 5, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29215645/cherchez-la-femme-maternal-incidental-findings-can-explain-discordant-prenatal-cell-free-dna-sequencing-results
#9
REVIEW
Diana W Bianchi
Circulating DNA fragments in a pregnant woman's plasma derive from three sources: placenta, maternal bone marrow, and fetus. Prenatal sequencing to noninvasively screen for fetal chromosome abnormalities is performed on this mixed sample; results can therefore reflect the maternal as well as the fetoplacental DNA. Although it is recommended that pretest counseling include the possibility of detecting maternal genomic imbalance, this seldom occurs. Maternal abnormalities that can affect a prenatal screening test result include disorders that affect the size and metabolism of DNA, such as B12 deficiency, autoimmune disease, and intrahepatic cholestasis of pregnancy...
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215049/str-profiling-and-copy-number-variation-analysis-on-single-preserved-cells-using-current-whole-genome-amplification-methods
#10
Ann-Sophie Vander Plaetsen, Lieselot Deleye, Senne Cornelis, Laurentijn Tilleman, Filip Van Nieuwerburgh, Dieter Deforce
The growing interest in liquid biopsies for cancer research and cell-based non-invasive prenatal testing (NIPT) invigorates the need for improved single cell analysis. In these applications, target cells are extremely rare and fragile in peripheral circulation, which makes the genetic analysis very challenging. To overcome these challenges, cell stabilization and unbiased whole genome amplification are required. This study investigates the performance of four WGA methods on single or a limited number of cells after 24 hour of Streck Cell-Free DNA BCT preservation...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29213339/comparison-of-quantification-algorithms-for-circulating-cell-free-dna-methylation-biomarkers-in-blood-plasma-from-cancer-patients
#11
Luka de Vos, Heidrun Gevensleben, Andreas Schröck, Alina Franzen, Glen Kristiansen, Friedrich Bootz, Dimo Dietrich
Background: SHOX2 and SEPT9 methylation in circulating cell-free DNA (ccfDNA) in blood are established powerful and clinically valuable biomarkers for diagnosis, staging, prognosis, and monitoring of cancer patients. The aim of the present study was to evaluate different quantification algorithms (relative quantification, absolute quantification, quasi-digital PCR) with regard to their clinical performance. Methods: Methylation analyses were performed in a training cohort (141 patients with head and neck squamous cell carcinoma [HNSCC], 170 control cases) and a testing cohort (137 HNSCC cases, 102 controls)...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/29213331/noninvasive-prenatal-diagnosis-of-fetal-aneuploidy-by-circulating-fetal-nucleated-red-blood-cells-and-extravillous-trophoblasts-using-silicon-based-nanostructured-microfluidics
#12
Chung-Er Huang, Gwo-Chin Ma, Hei-Jen Jou, Wen-Hsiang Lin, Dong-Jay Lee, Yi-Shing Lin, Norman A Ginsberg, Hsin-Fu Chen, Frank Mau-Chung Chang, Ming Chen
Background: Noninvasive prenatal testing (NIPT) based on cell-free DNA in maternal circulation has been accepted worldwide by the clinical community since 2011 but limitations, such as maternal malignancy and fetoplacental mosaicism, preclude its full replacement of invasive prenatal diagnosis. We present a novel silicon-based nanostructured microfluidics platform named as "Cell Reveal™" to demonstrate the feasibility of capturing circulating fetal nucleated red blood cells (fnRBC) and extravillous cytotrophoblasts (EVT) for cell-based noninvasive prenatal diagnosis (cbNIPD)...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/29212777/detection-and-monitoring-of-circulating-tumor-dna-in-adrenocortical-carcinoma
#13
Simon Garinet, Juliette Nectoux, Mario Neou, Eric Pasmant, Anne Jouinot, Mathilde Sibony, Lucie Orhant, Juliana Pipoli da Fonseca, Karine Hecale-Perlemoine, Leopoldine Bricaire, Lionel Groussin, Olivier Soubrane, Bertrand Dousset, Rossella Libé, Franck Letourneur, Jerome Bertherat, Guillaume Assié
Adrenocortical carcinomas (ACC) are aggressive tumors with limited prognostic and follow-up biomarkers. Circulating tumor DNA (ctDNA) is an emerging biomarker, now used for several cancer types. This study aimed to reliably detect and quantify ctDNA in ACC patients; to identify parameters impacting detection of ctDNA. A prospective monocentric study conducted in Cochin Hospital and Cochin Institute, Paris, France. Eleven ACC patients were included with either primary tumor or relapse or metastases from 2015 to 2016...
December 6, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/29212238/quantification-of-circulating-cell-free-dna-to-predict-patient-survival-in-non-small-cell-lung-cancer
#14
Myung Han Hyun, Jae Sook Sung, Eun Joo Kang, Yoon Ji Choi, Kyong Hwa Park, Sang Won Shin, Sung Yong Lee, Yeul Hong Kim
We used computed tomography (CT) to explore the prognostic value of cell-free (cf) DNA quantification and its predictive efficacy over time after chemotherapy in non-small-cell lung cancer (NSCLC) patients. In total, 177 NSCLC patients were enrolled in a prospective biomarker trial. Consecutive paired blood collection was performed to determine cfDNA concentrations at baseline CT and throughout serial follow-ups. The best cfDNA cut-off value to predict progression-free and overall survival was determined using X-tile analysis...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29206995/concordance-of-circulating-tumor-dna-and-matched-metastatic-tissue-biopsy-in-prostate-cancer
#15
Alexander W Wyatt, Matti Annala, Rahul Aggarwal, Kevin Beja, Felix Feng, Jack Youngren, Adam Foye, Paul Lloyd, Matti Nykter, Tomasz M Beer, Joshi J Alumkal, George V Thomas, Robert E Reiter, Matthew B Rettig, Christopher P Evans, Allen C Gao, Kim N Chi, Eric J Small, Martin E Gleave
Background: Real-time knowledge of the somatic genome can influence management of patients with metastatic castration-resistant prostate cancer (mCRPC). While routine metastatic tissue biopsy is challenging in mCRPC, plasma circulating tumor DNA (ctDNA) has emerged as a minimally invasive tool to sample the tumor genome. However, no systematic comparisons of matched "liquid" and "solid" biopsies have been performed that would enable ctDNA profiling to replace the need for direct tissue sampling...
December 1, 2017: Journal of the National Cancer Institute
https://www.readbyqxmd.com/read/29206863/blood-collection-in-cell-stabilizing-tubes-does-not-impact-germline-dna-quality-for-pediatric-patients
#16
Bruce M Wollison, Edwin Thai, Aimee Mckinney, Abigail Ward, Andrea Clapp, Catherine Clinton, Anwesha Nag, Aaron R Thorner, Julie M Gastier-Foster, Brian D Crompton
OBJECTIVES: Liquid biopsy technologies allow non-invasive tumor profiling for patients with solid tumor malignancies by sequencing circulating tumor DNA. These studies may be useful in risk-stratification, monitoring for relapse, and understanding tumor evolution. The quality of DNA obtained for these studies is improved when blood samples are collected in tubes that stabilizing white blood cells (WBC). However, ongoing germline research in pediatric oncology generally requires obtaining blood samples in EDTA tubes, which do not contain a WBC-stabilizing preservative...
2017: PloS One
https://www.readbyqxmd.com/read/29205637/a-field-guide-for-cancer-diagnostics-using-cell-free-dna-from-principles-to-practice-and-clinical-applications
#17
REVIEW
Anna-Lena Volckmar, Holger Sültmann, Anja Riediger, Thoas Fioretos, Peter Schirmacher, Volker Endris, Albrecht Stenzinger, Steffen Dietz
Recently, many genome-wide profiling studies provided insights into the molecular background of major cancer types. The deeper understanding of the genetic alterations and their functional consequences leveraged the discovery of novel therapeutic opportunities, improving clinical management of cancer patients. While tissue-based molecular patient stratification is the gold standard for precision medicine, it has certain limitations: Tissue biopsies are risky invasive sampling procedures and may not represent the entire tumor due to genetic heterogeneity...
December 5, 2017: Genes, Chromosomes & Cancer
https://www.readbyqxmd.com/read/29198331/biomarkers-in-prostate-cancer-current-clinical-utility-and-future-perspectives
#18
REVIEW
Alexander Kretschmer, Derya Tilki
Current tendencies in the treatment course of prostate cancer patients increase the need for reliable biomarkers that help in decision-making in a challenging clinical setting. Within the last decade, several novel biomarkers have been introduced. In the following comprehensive review article, we focus on diagnostic (PHI®, 4K score, SelectMDx®, ConfirmMDx®, PCA3, MiPS, ExoDX®, mpMRI) and prognostic (OncotypeDX GPS®, Prolaris®, ProMark®, DNA-ploidy, Decipher®) biomarkers that are in widespread clinical use and are supported by evidence...
December 2017: Critical Reviews in Oncology/hematology
https://www.readbyqxmd.com/read/29197094/plasma-nt-probnp-and-cell-free-dna-concentrations-after-prolonged-strenuous-exercise-in-working-farm-dogs
#19
H Hunt, N Cave, J Bridges, K Gedye, K Hill
BACKGROUND: Plasma N-terminal pro-B-type natriuretic peptide (NT-proBNP) concentration is increased in dogs with myocardial dysfunction, and cell-free DNA (cfDNA) increases in numerous disease states. In humans, both of these biomarkers can be altered after endurance exercise. OBJECTIVE: To investigate the effect of prolonged strenuous exercise on circulating NT-proBNP and cfDNA concentrations in working farm dogs. ANIMALS: Six healthy, privately owned working farm dogs (4 Huntaways and 2 heading dogs) from the same hill country farm in New Zealand...
December 2, 2017: Journal of Veterinary Internal Medicine
https://www.readbyqxmd.com/read/29196748/cell-free-dna-kinetics-in-a-pre-clinical-model-of-head-and-neck-cancer
#20
Nidal Muhanna, Marco A Di Grappa, Harley H L Chan, Tahsin Khan, Cheng S Jin, Yangqiao Zheng, Jonathan C Irish, Scott V Bratman
In cancer patients, circulating tumour-derived DNA (ctDNA) levels imperfectly reflect disease burden apparent on medical imaging. Further evaluation of ctDNA levels over time is needed to better understand the correlation with tumour growth and therapeutic response. We describe ctDNA kinetics within an orthotopic, immunocompetent preclinical rabbit model of local-regionally advanced head and neck squamous cell carcinoma (HNSCC). Monitoring primary tumour and metastatic lymph node volume by computed tomography (CT), we observed a correlation between ctDNA levels and tumour burden...
December 1, 2017: Scientific Reports
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