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https://www.readbyqxmd.com/read/29776953/the-landscape-of-actionable-genomic-alterations-in-cell-free-circulating-tumor-dna-from-21-807-advanced-cancer-patients
#1
Oliver A Zill, Kimberly C Banks, Stephen R Fairclough, Stefanie Mortimer, James V Vowles, Reza Mokhtari, David R Gandara, Philip C Mack, Justin I Odegaard, Rebecca J Nagy, Arthur M Baca, Helmy Eltoukhy, Darya I Chudova, Richard B Lanman, AmirAli Talasaz
PURPOSE: Cell-free DNA (cfDNA) sequencing provides a non-invasive method for obtaining actionable genomic information to guide personalized cancer treatment, but the presence of multiple alterations in circulation related to treatment and tumor heterogeneity complicate the interpretation of the observed variants. Experimental Design: We describe the somatic mutation landscape of 70 cancer genes from cfDNA deep-sequencing analysis of 21,807 patients with treated, late-stage cancers across >50 cancer types...
May 18, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29776293/analysis-of-circulating-tumor-dna-the-next-paradigm-shift-in-detection-and-treatment-of-lung-cancer
#2
EDITORIAL
David S Schrump, Julie A Hong
No abstract text is available yet for this article.
June 2018: Journal of Thoracic and Cardiovascular Surgery
https://www.readbyqxmd.com/read/29775621/methylation-of-nbpf1-as-a-novel-marker-for-the-detection-of-plasma-cell-free-dna-of-breast-cancer-patients
#3
REVIEW
Dandan Li, Pengchang Li, Jie Yi, Yaling Dou, Xiuzhi Guo, Yicong Yin, Danchen Wang, Chaochao Ma, Jie Wu, Ling Qiu
BACKGROUND: Recent studies revealed that tumor-specific gene methylation can be detected in the circulating cell-free DNA (cfDNA) of cancer patients; therefore, methylated cfDNA is considered a promising biomarker. Human neuroblastoma breakpoint family member 1 (NBPF1) was originally identified in a neuroblastoma (NB) patient. The present study is the first to evaluate the presence of NBPF1 gene methylation in cell-free DNA (cfDNA) in plasma of breast cancer patients. METHODS: Differentially methylated cfDNA was screened using bisulfite sequencing with a next-generation sequencer (BS-seq) among 25 breast cancer patients, 25 patients with a benign breast disease and 25 healthy female volunteers...
May 15, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29775157/blood-based-biomarkers-in-breast-cancer-from-proteins-to-circulating-tumor-cells-to-circulating-tumor-dna
#4
Michael J Duffy, Enda W McDermott, John Crown
Biomarkers are the key to personalized treatment in patients with breast cancer. While tissue biomarkers are most useful in determining prognosis and upfront predicting response to therapy, circulating protein biomarkers such as CA 15-3 and carcinoembryonic antigen are mainly used in monitoring response to endocrine or chemotherapy in patients with advanced disease. Although several centers measure biomarkers in asymptomatic patients following curative surgery for primary breast cancer, the clinical utility of this practice is unclear...
May 2018: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/29774603/programmed-nanoparticle-loaded-nanoparticles-for-deep-penetrating-3d-cancer-therapy
#5
Jinhwan Kim, Changshin Jo, Won-Gwang Lim, Sungjin Jung, Yeong Mi Lee, Jun Lim, Haeshin Lee, Jinwoo Lee, Won Jong Kim
Tumors are 3D, composed of cellular agglomerations and blood vessels. Therapies involving nanoparticles utilize specific accumulations due to the leaky vascular structures. However, systemically injected nanoparticles are mostly uptaken by cells located on the surfaces of cancer tissues, lacking deep penetration into the core cancer regions. Herein, an unprecedented strategy, described as injecting "nanoparticle-loaded nanoparticles" to address the long-lasting problem is reported for effective surface-to-core drug delivery in entire 3D tumors...
May 18, 2018: Advanced Materials
https://www.readbyqxmd.com/read/29768879/a-novel-assay-coupling-dephosphorylation-and-blue-white-colony-screening-for-the-g-a-hotspot-mutation-at-codon-13-of-kras-gene
#6
Cuilan Zhou, Wangyang Pu, Yu-Fang Yin, Li Xiao, Dixian Luo, Fenjiao Wang, Cuiying Peng, Zifen Guo, Xuan Liu, Huifen Xu, Chungen Xing, Nongyue He, Wanping Sun, Weijun Cai, Duanfang Liao, Kai Li
Development of sensitive assay for detection of hotspot mutations of cancer driving gene is crucial for circulating tumor DNA analysis. This study tested the possibilities of applying restriction enzyme digestion and dephosphorylation coupled with blue/white screening technology for analyzing a hotspot point mutation in codon 13 of KRAS gene. The present study has documented that the combination of PCR with restriction digestion, dephosphorylation, blue/white screening and Sanger's sequencing can identify rare mutations with sensitivities at 0...
January 1, 2018: Journal of Nanoscience and Nanotechnology
https://www.readbyqxmd.com/read/29764589/-influence-of-different-therapies-on-egfr-mutants-by-circulating-cell-free-dna-of-lung-adenocarcinoma-and-prognosis
#7
Fei Su, Ke Zheng, Yiyun Fu, Qian Wu, Yuan Tang, Weiya Wang, Lili Jiang
BACKGROUND: Epidermal growth factor receptor (EGFR) gene mutation is closely related to the EGFR-TKI target treatment and prognosis of lung adenocarcinoma patients. The mutation status of EGFR is limited by tissue detection. The purpose of this study was to investigate the difference of EGFR mutants in plasmacirculating cell-free DNA (cfDNA) obtained from patients with non-small cell lung cancer (NSCLC) in three groups: pre-therapy, after traditional chemotherapy and targeted therapy...
May 20, 2018: Zhongguo Fei Ai za Zhi, Chinese Journal of Lung Cancer
https://www.readbyqxmd.com/read/29762619/isolation-and-genome-sequencing-of-individual-circulating-tumor-cells-using-hydrogel-encapsulation-and-laser-capture-microdissection
#8
Emily S Park, Justin P Yan, Richard A Ang, Jeong Hyun Lee, Xiaoyan Deng, Simon P Duffy, Kevin Beja, Matti Annala, Peter C Black, Kim N Chi, Alexander W Wyatt, Hongshen Ma
Circulating tumor cells (CTCs) are malignant cells released into the bloodstream with the potential to form metastases in secondary sites. These cells, acquired non-invasively, represent a sample of highly relevant tumor tissue that is an alternative to difficult and low-yield tumor biopsies. In recent years, there has been growing interest in genomic profiling of CTCs to enable longitudinal monitoring of the tumor's adaptive response to therapy. However, due to their extreme rarity, genotyping CTCs has proved challenging...
May 15, 2018: Lab on a Chip
https://www.readbyqxmd.com/read/29761074/the-clinical-utility-of-cell-free-dna-measurement-in-differentiated-thyroid-cancer-a-systematic-review
#9
Jonathan M Fussey, Jennifer L Bryant, Nikolaos Batis, Rachael J Spruce, Andrew Hartley, James S Good, Christopher J McCabe, Kristien Boelaert, Neil Sharma, Hisham Mehanna
Background: Cell-free DNA (cfDNA) can be detected in the circulation of healthy individuals, but is found in higher concentrations in cancer patients. Furthermore, mutations in tumor cells can be identified in circulating DNA fragments. This has been the subject of significant interest in the field of cancer research, but little has been published in thyroid cancer. Objectives: To assess all available evidence on the use of circulating cfDNA in the diagnosis, management and surveillance of patients with differentiated thyroid cancer, and collate it into a systematic review to guide future research...
2018: Frontiers in Oncology
https://www.readbyqxmd.com/read/29760807/quality-control-of-next-generation-sequencing-based-in-vitro-diagnostic-test-for-onco-relevant-mutations-using-multiplex-reference-materials-in-plasma
#10
Donglai Liu, Haiwei Zhou, Dawei Shi, Shu Shen, Yabin Tian, Lin Wang, Jiatao Lou, Rong Cong, Juan Lu, Henghui Zhang, Meiru Zhao, Shida Zhu, Zhisheng Cao, Ruilin Jin, Yin Wang, Xiaoni Zhang, Guohua Yang, Youchun Wang, Chuntao Zhang
Background: Widespread clinical implementation of next-generation sequencing (NGS)-based cancer in vitro diagnostic tests (IVDs) highlighted the urgency to establish reference materials which could provide full control of the process from nucleic acid extraction to test report generation. The formalin-fixed, paraffin-embedded (FFPE) tissue and blood plasma containing circulating tumor deoxyribonucleic acid (ctDNA) were mostly used for clinically detecting onco-relevant mutations. Methods: We respectively developed multiplex FFPE and plasma reference materials covering three clinically onco-relevant mutations within the epidermal growth factor receptor ( EGFR ) gene at serial allelic frequencies...
2018: Journal of Cancer
https://www.readbyqxmd.com/read/29760067/sequencing-based-counting-and-size-profiling-of-plasma-epstein-barr-virus-dna-enhance-population-screening-of-nasopharyngeal-carcinoma
#11
W K Jacky Lam, Peiyong Jiang, K C Allen Chan, Suk H Cheng, Haiqiang Zhang, Wenlei Peng, O Y Olivia Tse, Yu K Tong, Wanxia Gai, Benny C Y Zee, Brigette B Y Ma, Edwin P Hui, Anthony T C Chan, John K S Woo, Rossa W K Chiu, Y M Dennis Lo
Circulating tumor-derived DNA testing for cancer screening has recently been demonstrated in a prospective study on identification of nasopharyngeal carcinoma (NPC) among 20,174 asymptomatic individuals. Plasma EBV DNA, a marker for NPC, was detected using real-time PCR. While plasma EBV DNA was persistently detectable in 97.1% of the NPCs identified, ∼5% of the general population had transiently detectable plasma EBV DNA. We hypothesized that EBV DNA in plasma of subjects with or without NPC may have different molecular characteristics...
May 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29759151/circulating-tumour-dna-for-detecting-minimal-residual-disease-in-multiple-myeloma
#12
REVIEW
Trevor J Pugh
Circulating tumor DNA faithfully recapitulates somatic mutations detected in bone marrow aspirates from patients with newly diagnosed or relapsed or recurrent myeloma. Extending these methods to enable detection of minimal residual disease will require increased sensitivity and breadth of genomic assays to maximize information content from small quantities of cell-free DNA; as well as definition of a clinically meaningful ctDNA concentration in comparison with conventional bone marrow cell-count thresholds...
January 2018: Seminars in Hematology
https://www.readbyqxmd.com/read/29749584/droplet-digital-pcr-detects-high-rate-of-tp53-r249s-mutants-in-cell-free-dna-of-middle-african-patients-with-hepatocellular-carcinoma
#13
Agnès Marchio, Marie Amougou Atsama, Aubin Béré, Narcisse-Patrice Komas, Dominique Noah Noah, Paul Jean Adrien Atangana, Serge-Magloire Camengo-Police, Richard Njouom, Claudine Bekondi, Pascal Pineau
Hepatocellular carcinoma (HCC) is still a major killing malignancy in sub-Saharan Africa. Lifelong intoxication with aflatoxin B1 is considered as one of the primary causes of this situation. The role of aflatoxin in HCC from a given population is commonly estimated through the prevalence of R249S mutation of TP53, a hallmark for previous exposure to the mycotoxin. However, the role of AFB1 is barely known in large part of Africa. We conducted a survey on circulating cell-free DNA from 149 patients with HCC and 213 control subjects with and without liver diseases from Cameroon and Central African Republic using droplet digital PCR technique...
May 10, 2018: Clinical and Experimental Medicine
https://www.readbyqxmd.com/read/29747380/cancer-diagnosis-using-a-liquid-biopsy-challenges-and-expectations
#14
REVIEW
Francesc Castro-Giner, Sofia Gkountela, Cinzia Donato, Ilaria Alborelli, Luca Quagliata, Charlotte K Y Ng, Salvatore Piscuoglio, Nicola Aceto
The field of cancer diagnostics has recently been impacted by new and exciting developments in the area of liquid biopsy. A liquid biopsy is a minimally invasive alternative to surgical biopsies of solid tissues, typically achieved through the withdrawal of a blood sample or other body fluids, allowing the interrogation of tumor-derived material including circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) fragments that are present at a given time point. In this short review, we discuss a few studies that summarize the state-of-the-art in the liquid biopsy field from a diagnostic perspective, and speculate on current challenges and expectations of implementing liquid biopsy testing for cancer diagnosis and monitoring in the clinical setting...
May 9, 2018: Diagnostics
https://www.readbyqxmd.com/read/29740313/epigenome-wide-association-study-of-soluble-tumor-necrosis-factor-receptor-2-levels-in-the-framingham-heart-study
#15
Michael M Mendelson, Roby Johannes, Chunyu Liu, Tianxiao Huan, Chen Yao, Xiao Miao, Joanne M Murabito, Josée Dupuis, Daniel Levy, Emelia J Benjamin, Honghuang Lin
Background: Transmembrane tumor necrosis factor (TNF) receptors are involved in inflammatory, apoptotic, and proliferative processes. In the bloodstream, soluble TNF receptor II (sTNFR2) can modify the inflammatory response of immune cells and is predictive of cardiovascular disease risk. We hypothesize that sTNFR2 is associated with epigenetic modifications of circulating leukocytes, which may relate to the pathophysiology underlying atherogenic risk. Methods: We conducted an epigenome-wide association study of sTNFR2 levels in the Framingham Heart Study Offspring cohort (examination 8; 2005-2008)...
2018: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29739332/characterization-and-remediation-of-sample-index-swaps-by-non-redundant-dual-indexing-on-massively-parallel-sequencing-platforms
#16
Maura Costello, Mark Fleharty, Justin Abreu, Yossi Farjoun, Steven Ferriera, Laurie Holmes, Brian Granger, Lisa Green, Tom Howd, Tamara Mason, Gina Vicente, Michael Dasilva, Wendy Brodeur, Timothy DeSmet, Sheila Dodge, Niall J Lennon, Stacey Gabriel
BACKGROUND: Here we present an in-depth characterization of the mechanism of sequencer-induced sample contamination due to the phenomenon of index swapping that impacts Illumina sequencers employing patterned flow cells with Exclusion Amplification (ExAmp) chemistry (HiSeqX, HiSeq4000, and NovaSeq). We also present a remediation method that minimizes the impact of such swaps. RESULTS: Leveraging data collected over a two-year period, we demonstrate the widespread prevalence of index swapping in patterned flow cell data...
May 8, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29725452/assessment-of-basal-like-breast-cancer-by-circulating-tumor-dna-analysis
#17
Wei Wei, Xianyu Zhang, Shanshan Sun, Bingshu Xia, Xiaoshuan Liang, Yan Cui, Song Gao, Da Pang
Standardized methods for the detection and assessment of circulating tumor DNA (ctDNA) in breast cancer are not sufficient. In the present study, the method and the potential application of ctDNA in the diagnosis of breast cancer were explored. DNA was extracted from the tumor tissues, plasma and peripheral blood cells of 11 patients with early-stage invasive breast cancer. Primers were designed against the exons of phosphatidylinositol-4,5-biphosphate 3-kinase catalytic subunit α, p53, epidermal growth factor receptor, Akt and phosphatase and tensin homolog...
May 2018: Oncology Letters
https://www.readbyqxmd.com/read/29723618/adiponectin-gene-polymorphisms-and-obesity-increase-the-susceptibility-to-arsenic-related-renal-cell-carcinoma
#18
Yu-Mei Hsueh, Wei-Jen Chen, Ying-Chin Lin, Chao-Yuan Huang, Horng-Sheng Shiue, Shu-Mei Yang, Pui-Lam Ao, Yeong-Shiau Pu, Chien-Tien Su
Our recent study found that high urinary total arsenic levels were associated with renal cell carcinoma (RCC). Recent studies demonstrated that low circulating adiponectin was related to RCC. The aim of the present study was to explore the relationship between adiponectin gene (ADIPOQ) polymorphisms and RCC and investigate whether individuals with an ADIPOQ risk genotype, obesity, and high urinary total arsenic levels have a modified odds ratio (OR) of RCC. A total of 389 RCC patients and 389 age- and sex-matched controls were recruited between November 2006 and December 2012 in Taiwan...
April 30, 2018: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/29721388/circulating-tumor-dna-evaluated-by-next-generation-sequencing-is-predictive-of-tumor-response-and-prolonged-clinical-benefit-with-nivolumab-in-advanced-non-small-cell-lung-cancer
#19
Etienne Giroux Leprieur, Guillaume Herbretau, Coraline Dumenil, Catherine Julie, Violaine Giraud, Sylvie Labrune, Jennifer Dumoulin, Julie Tisserand, Jean-François Emile, Hélène Blons, Thierry Chinet
Nivolumab is an anti-PD1 antibody, given in second-line or later treatment in advanced non-small cell lung cancer (NSCLC). The objective of this study was to describe the predictive value of circulating tumor DNA (ctDNA) on the efficacy of nivolumab in advanced NSCLC. We prospectively included all consecutive patients with advanced NSCLC treated with nivolumab in our Department between June 2015 and October 2016. Plasma samples were obtained before the first injection of nivolumab and at the first tumor evaluation with nivolumab...
2018: Oncoimmunology
https://www.readbyqxmd.com/read/29720900/update-on-sporadic-colorectal-cancer-genetics
#20
REVIEW
Karin M Hardiman
Our understanding of the genetics of colorectal cancer has changed dramatically over recent years. Colorectal cancer can be classified in multiple different ways. Along with the advent of whole-exome sequencing, we have gained an understanding of the scale of the genetic changes found in sporadic colorectal cancer. We now know that there are multiple pathways that are commonly involved in the evolution of colorectal cancer including Wnt/β-catenin, RAS, EGFR, and PIK3 kinase. Another recent leap in our understanding of colorectal cancer genetics is the recognition that many, if not all tumors, are actually genetically heterogeneous within individual tumors and also between tumors...
May 2018: Clinics in Colon and Rectal Surgery
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