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https://www.readbyqxmd.com/read/28225258/nanoparticle-based-discrimination-of-single-nucleotide-polymorphism-in-long-dna-sequences
#1
Maria Sanroman-Iglesias, Charles Lawrie, Luis M Liz-Marzán, Marek Grzelczak
Circulating DNA (ctDNA) and specifically the detection cancer-associated mutations in liquid biopsies promises to revolutionize cancer detection. The main difficulty however is that the length of typical ctDNA fragments (~150 bases) can form secondary structures potentially obscuring the mutated fragment from detection. We show that an assay based on gold nanoparticles (65 nm) stabilized with DNA (Au@DNA) can discriminate single nucleotide polymorphism in clinically-relevant DNA sequences (70-140 bases). The preincubation step was crucial to this process, allowing sequential bridging of Au@DNA, so that single base mutation can be discriminated, down to 100 pM concentration...
February 22, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28214514/detecting-circulating-tumor-dna-in-renal-cancer-an-open-challenge
#2
Claudia Corrò, Tomas Hejhal, Cédric Poyet, Tullio Sulser, Thomas Hermanns, Thomas Winder, Gerald Prager, Peter J Wild, Ian Frew, Holger Moch, Markus Rechsteiner
BACKGROUND: Detection of circulating tumor DNA (ctDNA) in blood of cancer patients is regarded as an important step towards personalized medicine and treatment monitoring. In the present study, we investigated the clinical applicability of ctDNA as liquid biopsy in renal cancer. METHODS: ctDNA in serum and plasma samples derived from ccRCC and colon cancer patients as well as ctDNA isolated from RCC xenografts with known VHL mutation status was investigated using next generation sequencing (NGS)...
February 15, 2017: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/28206954/rassf1a-promoter-methylation-in-high-grade-serous-ovarian-cancer-a-direct-comparison-study-in-primary-tumors-adjacent-morphologically-tumor-cell-free-tissues-and-paired-circulating-tumor-dna
#3
Lydia Giannopoulou, Issam Chebouti, Kitty Pavlakis, Sabine Kasimir-Bauer, Evi S Lianidou
The RASSF1A promoter is frequently methylated in high-grade serous ovarian cancer (HGSC). We examined RASSF1A promoter methylation in primary tumors, adjacent morphologically tumor cell-free tissues and corresponding circulating tumor DNA (ctDNA) samples of patients with HGSC, using a real-time methylation specific PCR (real-time MSP) and a methylation-sensitive high-resolution melting analysis (MS-HRMA) assay for the detection and semi-quantitative estimation of methylation, respectively. Two groups of primary HGSC tumor FFPE samples were recruited (Group A n=67 and Group B n=61), along with matched adjacent morphologically tumor cell-free tissues (n=58) and corresponding plasma samples (n=59) for group B...
February 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28205231/analysis-of-ctdna-to-predict-prognosis-and-monitor-treatment-responses-in-metastatic-pancreatic-cancer-patients
#4
He Cheng, Chen Liu, Jiahao Jiang, Guopei Luo, Yu Lu, Kaizhou Jin, Meng Guo, Zhenzhen Zhang, Jin Xu, Liang Liu, Quanxing Ni, Xianjun Yu
Cell-free circulating tumor DNA (ctDNA) in plasma has been used as a potential noninvasive biomarker for various tumors. The current study was performed to evaluate the clinical implications of ctDNA detection in patients with metastatic pancreatic cancer. Firstly, we attempted to prospectively screen a panel of 60 genes in cell-free DNA (cfDNA) from ten metastatic pancreatic cancer patients via exome sequencing. Secondly, droplet digital PCR (ddPCR) was used to identify potential mutations in a cohort of 188 patients with metastatic pancreatic cancer...
February 16, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28187169/prognostic-value-of-circulating-tumor-dna-in-patients-with-colon-cancer-systematic-review
#5
Gaowei Fan, Kuo Zhang, Xin Yang, Jiansheng Ding, Zujian Wang, Jinming Li
The application of circulating tumor DNA(ctDNA) represents a non-invasive method for tumor detection. Its prognostic significance in patients with colorectal cancer is controversial. We performed a systematic review of data from published studies to assess the prognostic values of ctDNA in patients with colorectal cancer. We searched Medline, Embase, Web of Science, the Cochrane Library, and Scopus databases to identify eligible studies reporting disease-free survival (DFS) and overall survival (OS) stratified by ctDNA prior to December 6, 2016...
2017: PloS One
https://www.readbyqxmd.com/read/28185687/circulating-tumor-cells-and-circulating-tumor-dna-what-surgical-oncologists-need-to-know
#6
REVIEW
L Cabel, C Proudhon, P Mariani, D Tzanis, G Beinse, I Bieche, J-Y Pierga, F-C Bidard
As a result of recent progress in detection techniques, circulating tumor DNA (ctDNA) and circulating tumor cells (CTC) can now be accurately detected in the blood of most cancer patients. While these new biomarkers can provide a better understanding of key biological mechanisms underlying cancer growth and dissemination, they also open up a wide range of possible clinical applications in medical oncology, radiation oncology and surgical oncology. In this review, we summarize the results obtained with ctDNA and CTC together with their potential future clinical applications in the field of surgical oncology, with particular focus on the perioperative setting of various types of cancer...
January 29, 2017: European Journal of Surgical Oncology
https://www.readbyqxmd.com/read/28164427/application-of-circulating-tumor-dna-in-prospective-clinical-oncology-trials-standardization-of-pre-analytical-conditions
#7
Lisanne F van Dessel, Nick Beije, Jean C A Helmijr, Silvia R Vitale, Jaco Kraan, Maxime P Look, Ronald de Wit, Stefan Sleijfer, Maurice P H M Jansen, John W M Martens, Martijn P J K Lolkema
Circulating tumor DNA (ctDNA) has emerged as a potential new biomarker with diagnostic, predictive and prognostic applications for various solid tumor types. Before beginning large prospective clinical trials to prove the added value of utilizing ctDNA in clinical practice, it is essential to investigate the effects of various pre-analytical conditions on the quality of cell-free DNA (cfDNA) in general and of ctDNA in particular in order to optimize and standardize these conditions. Whole blood samples were collected from patients with metastatic cancer bearing a known somatic variant...
February 6, 2017: Molecular Oncology
https://www.readbyqxmd.com/read/28164088/effective-implementation-of-novel-met-pharmacodynamic-assays-in-translational-studies
#8
REVIEW
Apurva K Srivastava, Tony Navas, William G Herrick, Melinda G Hollingshead, Donald P Bottaro, James H Doroshow, Ralph E Parchment
MET tyrosine kinase (TK) dysregulation is significantly implicated in many types of cancer. Despite over 20 years of drug development to target MET in cancers, a pure anti-MET therapeutic has not yet received market approval. The failure of two recently concluded phase III trials point to a major weakness in biomarker strategies to identify patients who will benefit most from MET therapies. The capability to interrogate oncogenic mutations in MET via circulating tumor DNA (ctDNA) provides an important advancement in identification and stratification of patients for MET therapy...
January 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28162206/-hot-topics-of-circulating-tumor-dna-testing-in-breast-cancer
#9
Y H Liu, B Zhou, L Xu, L Xin
The progress of gene detection technologies represented by next generation sequencing (NGS) and digital PCR laid a foundation for studies of circulating tumor DNA (ctDNA) in breast cancer. In 2014, the NGS workgroup organized by the College of American Pathologists (CAP) published the College of American Pathologists' Laboratory Standards for Next-Generation Sequencing Clinical Tests, which provides a blueprint for the standardization of gene testing. In 2015, the Guidelines for Diagnostic Next-generation Sequencing published by the European Society of Human Genetics claimed that NGS is unacceptable in clinical practice before studies guided by guidelines are approved...
February 1, 2017: Zhonghua Wai Ke za Zhi [Chinese Journal of Surgery]
https://www.readbyqxmd.com/read/28149760/comparison-of-methods-for-circulating-cell-free-dna-isolation-using-blood-from-cancer-patients-impact-on-biomarker-testing
#10
Clara Pérez-Barrios, Irene Nieto-Alcolado, María Torrente, Carolina Jiménez-Sánchez, Virginia Calvo, Lourdes Gutierrez-Sanz, Magda Palka, Encarnación Donoso-Navarro, Mariano Provencio, Atocha Romero
BACKGROUND: The implementation of liquid biopsy for biomarker testing and response to treatment monitoring in cancer patients would presumable increase laboratory throughput, requiring the development of automated methods for circulating free DNA (cfDNA) isolation. METHODS: The present study compares the MagNA Pure Compact (MPC) Nucleic Acid Isolation Kit I and Maxwell(®) RSC (MR) ccfDNA Plasma Kit and the later with QIAamp Circulating Nucleid Acid (QCNA) Kit using 57 plasma samples from cancer patients...
December 2016: Translational Lung Cancer Research
https://www.readbyqxmd.com/read/28146051/circulating-cell-free-tumor-dna-detection-as-a-routine-tool-forlung-cancer-patient-management
#11
REVIEW
Julie A Vendrell, Frédéric Tran Mau-Them, Benoît Béganton, Sylvain Godreuil, Peter Coopman, Jérôme Solassol
Circulating tumoral DNA (ctDNA), commonly named "liquid biopsy", has emerged as a new promising noninvasive tool to detect biomarker in several cancers including lung cancer. Applications involving molecular analysis of ctDNA in lung cancer have increased and encompass diagnosis, response to treatment, acquired resistance and prognosis prediction, while bypassing the problem of tumor heterogeneity. ctDNA may then help perform dynamic genetic surveillance in the era of precision medicine through indirect tumoral genomic information determination...
January 29, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28126926/molecular-disease-monitoring-using-circulating-tumor-dna-in-myelodysplastic-syndromes
#12
Paul Yeh, Michael Dickinson, Sarah Ftouni, Tane Hunter, Devbarna Sinha, Stephen Q Wong, Rishu Agarwal, Ravikiran Vedururu, Kenneth Doig, Chun Yew Fong, Piers Blombery, David Westerman, Mark A Dawson, Sarah-Jane Dawson
The diagnosis and monitoring of myelodysplastic syndromes (MDS) are highly reliant on bone marrow morphology, which is associated with substantial inter-observer variability. Azacitidine is the mainstay of treatment in MDS, however only half of all patients respond. Therefore, there is an urgent need for improved modalities for the diagnosis and monitoring of MDS. The majority of MDS patients have either clonal somatic karyotypic abnormalities and/or gene mutations that aid in the diagnosis and can be used to monitor treatment response...
January 26, 2017: Blood
https://www.readbyqxmd.com/read/28126649/circulating-tumor-dna-as-an-early-detection-and-diagnostic-tool
#13
REVIEW
Timothy M Butler, Paul T Spellman, Joe Gray
The development of new circulating-tumor DNA (ctDNA) analysis techniques has led to an explosion of studies demonstrating exciting clinical applications. Non-invasive genotyping can characterize mutations of interest without the need for an invasive biopsy. Serial ctDNA monitoring can assess response to treatment, and potentially identify mechanisms of resistance. Perhaps most excitingly, sensitive ctDNA analysis methods allow for detection of minimally residual disease, predicting recurrence months before clinical presentation...
January 23, 2017: Current Opinion in Genetics & Development
https://www.readbyqxmd.com/read/28124376/the-feasibility-of-using-mutation-detection-in-ctdna-to-assess-tumor-dynamics
#14
REVIEW
Xin Yi, Jianhui Ma, Yanfang Guan, Rongrong Chen, Ling Yang, Xuefeng Xia
For many decades it has been known that tumor DNA is shed into the blood. As a consequence of technological limitations, researchers were unable to comprehensively characterize circulating DNA. The advent of ultrasensitive and highly specific molecular assays has provided a comprehensive profile of the molecular characteristics and dynamics of circulating DNA in healthy subjects and cancer patients. With these new tools in hand, significant interest has been provoked for an innovative type of tumor biopsy termed a "liquid biopsy"...
January 25, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28116811/deciphering-the-intercalative-binding-modes-of-benzoyl-peroxide-with-calf-thymus-dna
#15
Kaixin Xia, Guowen Zhang, Deming Gong
The binding of benzoyl peroxide (BPO), a flour brightener, with calf thymus DNA (ctDNA) was predicted by molecular simulation, and this were confirmed using multi-spectroscopic techniques and a chemometrics algorithm. The molecular docking result showed that BPO could insert into the base pairs of ctDNA, and the adenine bases were the preferential binding sites which were validated by the analysis of Fourier transform infrared spectra. The mode of binding of BPO with ctDNA was an intercalation as supported by the results from ctDNA melting and viscosity measurements, iodide quenching effects and competitive binding investigations...
January 24, 2017: Luminescence: the Journal of Biological and Chemical Luminescence
https://www.readbyqxmd.com/read/28104619/osimertinib-benefit-in-egfr-mutant-nsclc-patients-with-t790m-mutation-detected-by-circulating-tumour-dna
#16
J Remon, C Caramella, C Jovelet, L Lacroix, A Lawson, S Smalley, K Howarth, D Gale, E Green, V Plagnol, N Rosenfeld, D Planchard, M V Bluthgen, A Gazzah, C Pannet, C Nicotra, E Auclin, J C Soria, B Besse
BACKGROUND: Approximately 50% of Epidermal growth factor receptor (EGFR) mutant non-small cell lung cancer (NSCLC) patients treated with EGFR tyrosine kinase inhibitors (TKIs) will acquire resistance by the T790M mutation. Osimertinib is the standard of care in this situation. The present study assesses the efficacy of osimertinib when T790M status is determined in circulating cell-free tumour DNA (ctDNA) from blood samples in progressing advanced EGFR-mutant NSCLC patients. MATERIAL AND METHODS: ctDNA T790M mutational status was assessed by Inivata InVision(TM) (eTAm-Seq(TM)) assay in 48 EGFR-mutant advanced NSCLC patients with acquired resistance to EGFR TKIs without a tissue biopsy between April 2015 and April 2016...
January 18, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28102343/individualised-multiplexed-circulating-tumour-dna-assays-for-monitoring-of-tumour-presence-in-patients-after-colorectal-cancer-surgery
#17
Sarah B Ng, Clarinda Chua, Matthew Ng, Anna Gan, Polly Sy Poon, Melissa Teo, Cherylin Fu, Wei Qiang Leow, Kiat Hon Lim, Alexander Chung, Si-Lin Koo, Su Pin Choo, Danliang Ho, Steve Rozen, Patrick Tan, Mark Wong, William F Burkholder, Iain Beehuat Tan
Circulating tumour DNA (ctDNA) has the potential to be a specific biomarker for the monitoring of tumours in patients with colorectal cancer (CRC). Here, our aim was to develop a personalised surveillance strategy to monitor the clinical course of CRC after surgery. We developed patient-specific ctDNA assays based on multiplexed detection of somatic mutations identified from patient primary tumours, and applied them to detect ctDNA in 44 CRC patients, analysing a total of 260 plasma samples. We found that ctDNA detection correlated with clinical events - it is detectable in pre-operative but not post-operative plasma, and also in patients with recurrent CRC...
January 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28073896/patient-specific-circulating-tumor-dna-detection-during-neoadjuvant-chemotherapy-in-triple-negative-breast-cancer
#18
Francesca Riva, Francois-Clement Bidard, Alexandre Houy, Adrien Saliou, Jordan Madic, Aurore Rampanou, Caroline Hego, Maud Milder, Paul Cottu, Marie-Paule Sablin, Anne Vincent-Salomon, Olivier Lantz, Marc-Henri Stern, Charlotte Proudhon, Jean-Yves Pierga
BACKGROUND: In nonmetastatic triple-negative breast cancer (TNBC) patients, we investigated whether circulating tumor DNA (ctDNA) detection can reflect the tumor response to neoadjuvant chemotherapy (NCT) and detect minimal residual disease after surgery. METHODS: Ten milliliters of plasma were collected at 4 time points: before NCT; after 1 cycle; before surgery; after surgery. Customized droplet digital PCR (ddPCR) assays were used to track tumor protein p53 (TP53) mutations previously characterized in tumor tissue by massively parallel sequencing...
January 10, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28073294/circulating-tumor-cells-and-dna-for-real-time-egfr-detection-and-monitoring-of-non-small-cell-lung-cancer
#19
Jinfeng He, Wei Tan, Jingping Ma
AIM: We investigate the suitability of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) in non-small-cell lung cancer management, which is challenging in conventional biopsies. MATERIALS & METHODS: We performed serial blood extraction from 120 patients of varying EGFR status. Molecular profiling was performed using droplet digital PCR and correlated to survival outcome. RESULTS: Overall, we observed 95% agreement using CTCs and ctDNA with conventional tissue biopsies, which indicated the disease's close correlation...
January 11, 2017: Future Oncology
https://www.readbyqxmd.com/read/28065930/rapid-changes-in-circulating-tumor-dna-in-serially-sampled-plasma-during-treatment-of-breast-cancer-a-case-report
#20
Hiroshi Nakagomi, Yosuke Hirotsu, Kenji Amemiya, Haruka Nakada, Masayuki Inoue, Hitoshi Mochizuki, Toshio Oyama, Masao Omata
BACKGROUND The analysis of circulating tumor DNA (ctDNA) is expected to be a modality to determine the status of cancer in real time. This case indicated utilities and issues in measuring the ctDNA in cancer patients. CASE REPORT A 45-year-old woman with metastatic breast cancer was treated with bevacizumab and paclitaxel. The lung metastases were decreased but the meningitis carcinoma developed rapidly and she died. During the treatment with bevacizumab and paclitaxel, blood samples were taken serially and ctDNA was analyzed using a next-generation sequencer...
January 9, 2017: American Journal of Case Reports
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