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circulating tumor dna

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https://www.readbyqxmd.com/read/28814544/direct-detection-of-early-stage-cancers-using-circulating-tumor-dna
#1
Jillian Phallen, Mark Sausen, Vilmos Adleff, Alessandro Leal, Carolyn Hruban, James White, Valsamo Anagnostou, Jacob Fiksel, Stephen Cristiano, Eniko Papp, Savannah Speir, Thomas Reinert, Mai-Britt Worm Orntoft, Brian D Woodward, Derek Murphy, Sonya Parpart-Li, David Riley, Monica Nesselbush, Naomi Sengamalay, Andrew Georgiadis, Qing Kay Li, Mogens Rørbæk Madsen, Frank Viborg Mortensen, Joost Huiskens, Cornelis Punt, Nicole van Grieken, Remond Fijneman, Gerrit Meijer, Hatim Husain, Robert B Scharpf, Luis A Diaz, Siân Jones, Sam Angiuoli, Torben Ørntoft, Hans Jørgen Nielsen, Claus Lindbjerg Andersen, Victor E Velculescu
Early detection and intervention are likely to be the most effective means for reducing morbidity and mortality of human cancer. However, development of methods for noninvasive detection of early-stage tumors has remained a challenge. We have developed an approach called targeted error correction sequencing (TEC-Seq) that allows ultrasensitive direct evaluation of sequence changes in circulating cell-free DNA using massively parallel sequencing. We have used this approach to examine 58 cancer-related genes encompassing 81 kb...
August 16, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/28812303/circulating-tumor-dna-as-a-liquid-biopsy-current-clinical-applications-and-future-directions
#2
REVIEW
Kimberly M Komatsubara, Adrian G Sacher
Tumor genomic sequencing has become part of routine oncology practice in many tumor types, in order to identify potentially targetable mutations and to personalize cancer care. Plasma genotyping via circulating tumor DNA analysis is a noninvasive and rapid alternative method of detecting and monitoring genomic alterations throughout the course of disease. Multiple assays have been developed to date, each with different test characteristics and degrees of clinical validation. Here we review the clinical data supporting these different plasma genotyping methodologies, and present a practical approach to the interpretation of the results of these tests...
August 15, 2017: Oncology (Williston Park, NY)
https://www.readbyqxmd.com/read/28811315/quantitative-whole-genome-sequencing-of-circulating-tumor-cells-enables-personalized-combination-therapy-of-metastatic-cancer
#3
Natali Gulbahce, Mark Jesus M Magbanua, Robert Chin, Misha R Agarwal, Xuhao Luo, Jia Liu, Daniel M Hayden, Qing Mao, Serban Ciotlos, Zhenyu Li, Yanxiang Chen, Xingpeng Chen, Yuxiang Li, Rebecca Yu Zhang, Katharine Lee, Rick Tearle, Emily Park, Snezana Drmanac, Hope S Rugo, John W Park, Radoje Drmanac, Brock A Peters
Much effort has been dedicated to developing circulating tumor cells (CTC) as a noninvasive cancer biopsy, but with limited success as yet. In this study, we combine a method for isolation of highly pure CTCs using immunomagnetic enrichment/fluorescence-activated cell sorting with advanced whole genome sequencing (WGS), based on long fragment read technology, to illustrate the utility of an accurate, comprehensive, phased, and quantitative genomic analysis platform for CTCs. Whole genomes of 34 CTCs from a patient with metastatic breast cancer were analyzed as 3,072 barcoded subgenomic compartments of long DNA...
August 15, 2017: Cancer Research
https://www.readbyqxmd.com/read/28810735/accurate-electrochemistry-analysis-of-circulating-methylated-dna-from-clinical-plasma-based-on-paired-end-tagging-and-amplifications
#4
Feng Chen, Xuyao Wang, Xiaowen Cao, Yongxi Zhao
Circulating methylated DNA has been a new kind of cancer biomarker, yet its small fraction of trace total DNA from clinical samples impairs the accurate analysis. Though fluorescence methods based on quantitative methylation specific PCR (qMSP) have been adopted routinely, yet alternative electrochemistry assay of such DNA from clinical samples remains a great challenge. Herein, we report accurate electrochemistry analysis of circulating methylated DNA from clinical plasma samples based on a paired-end tagging and amplifications strategy...
August 16, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28807979/single-stranded-dna-library-preparation-does-not-preferentially-enrich-circulating-tumor-dna
#5
Tina Moser, Peter Ulz, Qing Zhou, Samantha Perakis, Jochen B Geigl, Michael R Speicher, Ellen Heitzer
No abstract text is available yet for this article.
August 14, 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/28807936/genomic-alterations-in-circulating-tumor-dna-from-diverse-cancer-patients-identified-by-next-generation-sequencing
#6
Maria Schwaederle, Ranajoy Chattopadhyay, Shumei Kato, Paul T Fanta, Kimberly C Banks, In Sil Choi, David E Piccioni, Sadakatsu Ikeda, AmirAli Talasaz, Richard B Lanman, Lyudmila Bazhenova, Razelle Kurzrock
Non-invasive genomic profiling of tumors may be possible with next-generation sequencing (NGS) of blood-derived circulating tumor DNA (ctDNA), but proof of concept in a large cohort <p>of patients with diverse cancers has yet to be reported. Here we report the results of an analysis of plasma-derived ctDNA from 670 patients with diverse cancers.</p> The tumors represented in the patient cohort were mainly gastrointestinal (31.8%), brain (22.7%) or lung (20.7%). ctDNA obtained from most patients (N = 423 (63%)) displayed at least 1 alteration...
August 14, 2017: Cancer Research
https://www.readbyqxmd.com/read/28807240/role-of-exosomes-in-treatment-of-hepatocellular-carcinoma
#7
REVIEW
Demetrios Moris, Eliza W Beal, Jeffery Chakedis, Richard A Burkhart, Carl Schmidt, Mary Dillhoff, Xufeng Zhang, Stamatios Theocharis, Timothy M Pawlik
Exosomes are nanovesicles that may play a role in intercellular communication by acting as carriers of functional contents such as proteins, lipids, RNA molecules and circulating DNA from donor to recipient cells. In addition, exosomes may play a potential role in immunosurveillance and tumor pathogenesis and progression. Recently, research has increasingly focused on the role of exosomes in hepatocellular carcinoma (HCC), the most common primary liver malignancy. We herein review data on emerging experimental and clinical studies focused on the role of exosomes in the pathogenesis, diagnosis, progression and chemotherapy response of patients with HCC...
September 2017: Surgical Oncology
https://www.readbyqxmd.com/read/28801547/early-changes-in-plasma-dna-levels-of-mutant-kras-as-a-sensitive-marker-of-response-to-chemotherapy-in-pancreatic-cancer
#8
Marzia Del Re, Caterina Vivaldi, Eleonora Rofi, Enrico Vasile, Mario Miccoli, Chiara Caparello, Paolo Davide d'Arienzo, Lorenzo Fornaro, Alfredo Falcone, Romano Danesi
Pancreatic cancer (PDAC) is still lacking of reliable markers to monitor tumor response. CA 19-9 is the only biomarker approved, despite it has several limitations in sensitivity and specificity. Since mutations of KRAS occur in more than 90% of tumors, its detection in circulating free tumor DNA (cftDNA) could represent a biomarker to monitor chemotherapy response. Twenty-seven advanced PDAC patients given first-line 5-fluorouracil, irinotecan and oxaliplatin or gemcitabine and nab-paclitaxel were enrolled...
August 11, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28801248/clinical-value-of-ctdna-in-upper-gi-cancers-a-systematic-review-and-meta-analysis
#9
REVIEW
A Creemers, S Krausz, M Strijker, M J van der Wel, E C Soer, R J Reinten, M G Besselink, J W Wilmink, M J van de Vijver, C J M van Noesel, J Verheij, S L Meijer, F Dijk, M F Bijlsma, M G H van Oijen, H W M van Laarhoven
BACKGROUND: The recent expanding technical possibilities to detect tumor derived mutations in blood, so-called circulating tumor DNA (ctDNA), has rapidly increased the interest in liquid biopsies. This review and meta-analysis explores the clinical value of ctDNA in malignancies of the upper gastro-intestinal tract. METHODS: PubMed, Cochrane and Embase databases were searched to identify studies reporting the diagnostic, prognostic or predictive value of ctDNA in patients with esophageal, gastric and pancreatic cancer, until January 2017...
August 8, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28778025/comparison-of-esr1-mutations-in-tumor-tissue-and-matched-plasma-samples-from-metastatic-breast-cancer-patients
#10
Takashi Takeshita, Yutaka Yamamoto, Mutsuko Yamamoto-Ibusuki, Mai Tomiguchi, Aiko Sueta, Keiichi Murakami, Yoko Omoto, Hirotaka Iwase
BACKGROUND: ESR1 mutation in circulating cell-free DNA (cfDNA) is emerging as a noninvasive biomarker of acquired resistance to endocrine therapy, but there is a paucity of data comparing the status of ESR1 gene in cfDNA with that in its corresponding tumor tissue. The objective of this study is to validate the degree of concordance of ESR1 mutations between plasma and tumor tissue. METHODS: ESR1 ligand-binding domain mutations Y537S, Y537N, Y537C, and D538G were analyzed using droplet digital PCR in 35 patients with metastatic breast cancer (MBC) (35 tumor tissue samples and 67 plasma samples)...
July 31, 2017: Translational Oncology
https://www.readbyqxmd.com/read/28771008/dna-hydrogel-with-aptamer-toehold-based-recognition-cloaking-and-decloaking-of-circulating-tumor-cells-for-live-cell-analysis
#11
Ping Song, Dekai Ye, Xiaolei Zuo, Jiang Li, Jianbang Wang, Huajie Liu, Michael Taeyoung Hwang, Jie Chao, Shao Su, Lihua Wang, Jiye Shi, Lianhui Wang, Wei Huang, Ratnesh Lal, Chunhai Fan
Circulating tumor cells (CTCs) contain molecular information of the primary tumor and can be used for predictive cancer diagnostics. Capturing rare live CTCs and their quantification in whole blood remain technically challenging. Here we report an aptamer-trigger clamped hybridization chain reaction (atcHCR) method for in-situ identification and subsequent cloaking/de-cloaking of CTCs by porous DNA hydrogels. These de-cloaked CTCs were then used for live cell analysis. In our design, a DNA staple strand with aptamer-toehold bi-blocks specifically recognizes epithelial cell adhesion molecule (EpCAM) on the CTC surface that triggers subsequent atcHCR via toehold-initiated branch migration...
August 3, 2017: Nano Letters
https://www.readbyqxmd.com/read/28760909/-span-style-font-weight-400-circulating-tumor-dna-reveals-clinically-actionable-somatic-genome-of-metastatic-bladder-cancer-span
#12
Gillian R Vandekerkhove, Tilman Todenhöfer, Matti Annala, Werner J Struss, Amanda Wong, Kevin Beja, Elie Ritch, Sonal Brahmbhatt, Stas Volik, Jörg Hennenlotter, Matti Nykter, Kim N Chi, Scott North, Arnulf Stenzl, Colin C Collins, Bernhard J Eigl, Peter C Black, Alexander W Wyatt
Targeted agents and immunotherapies promise to transform the treatment of metastatic bladder cancer (BCa), but therapy selection will depend on practical tumor molecular stratification. Circulating tumor DNA (ctDNA) is established in several solid malignancies as a minimally-invasive tool to profile the tumor genome in real-time, but is critically under-explored in BCa. <p>Experimental Design: We applied a combination of whole exome sequencing and targeted sequencing across 50 BCa driver genes to plasma cell-free DNA (cfDNA) from 51 patients with aggressive BCa, including 37 with metastatic disease...
July 31, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28758104/liquid-biopsies-in-lung-cancer-time-to-implement-research-technologies-in-routine-care
#13
REVIEW
Linda Köhn, Mikael Johansson, Kjell Grankvist, Jonas Nilsson
Lung cancer is the leading cause of cancer mortality. A substantial progress in the understanding of lung cancer biology has resulted in several promising targeted therapies for advanced disease. Druggable targets today include point mutations such as EGFR, BRAF and re-arrangements in genes such as ALK and ROS1. Liquid biopsies collecting e.g., circulating tumor DNA (ctDNA) reflects overall tumor information and is not biased by analyzing of only a small fraction of the tumor and is always accessible in contrast to the lung cancer tissue...
July 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28754852/molecular-characterization-of-circulating-colorectal-tumor-cells-defines-genetic-signatures-for-individualized-cancer-care
#14
Say Li Kong, Xingliang Liu, Nur-Afidah Mohamed Suhaimi, Kenneth Jia Hao Koh, Min Hu, Daniel Yoke San Lee, Igor Cima, Wai Min Phyo, Esther Xing Wei Lee, Joyce A Tai, Yu Miin Foong, Jess Honganh Vo, Poh Koon Koh, Tong Zhang, Jackie Y Ying, Bing Lim, Min-Han Tan, Axel M Hillmer
Studies on circulating tumor cells (CTCs) have largely focused on platform development and CTC enumeration rather than on the genomic characterization of CTCs. To address this, we performed targeted sequencing of CTCs of colorectal cancer patients and compared the mutations with the matched primary tumors. We collected preoperative blood and matched primary tumor samples from 48 colorectal cancer patients. CTCs were isolated using a label-free microfiltration device on a silicon microsieve. Upon whole genome amplification, we performed amplicon-based targeted sequencing on a panel of 39 druggable and frequently mutated genes on both CTCs and fresh-frozen tumor samples...
July 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28753534/liquid-biopsy-in-ovarian-cancer-recent-advances-on-circulating-tumor-cells-and-circulating-tumor-dna
#15
Lydia Giannopoulou, Sabine Kasimir-Bauer, Evi S Lianidou
Ovarian cancer remains the most lethal disease among gynecological malignancies despite the plethora of research studies during the last decades. The majority of patients are diagnosed in an advanced stage and exhibit resistance to standard chemotherapy. Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) represent the main liquid biopsy approaches that offer a minimally invasive sample collection. Both have shown a diagnostic, prognostic and predictive value in many types of solid malignancies and recent studies attempted to shed light on their role in ovarian cancer...
July 28, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/28748002/high-levels-of-circulating-folate-concentrations-are-associated-with-dna-methylation-of-tumor-suppressor-and-repair-genes-p16-mlh1-and-mgmt-in-elderly-chileans
#16
Hugo Sanchez, Mohammad B Hossain, Lydia Lera, Sandra Hirsch, Cecilia Albala, Ricardo Uauy, Karin Broberg, Ana M Ronco
BACKGROUND: Changes in DNA methylation, one of the most studied epigenetic mechanisms, are considered an initial marker for early cancer detection. We evaluated how availability of dietary factors (folates and vitamin B12) involved in one-carbon metabolism may contribute to DNA methylation changes of cancer-related genes in human subjects. METHODS: We studied, by pyrosequencing, the methylation of tumor suppressor gene p16, DNA repair genes MLH1 and MGMT, and the repetitive element LINE-1 (as a surrogate for global DNA methylation), in blood of elderly individuals (n = 249) who had been exposed to folic acid (FA) through FA-fortified wheat flour during the last 12 years...
2017: Clinical Epigenetics
https://www.readbyqxmd.com/read/28744793/application-of-liquid-biopsy-in-precision-medicine-opportunities-and-challenges
#17
REVIEW
Junyun Wang, Shuang Chang, Guochao Li, Yingli Sun
Precision medicine for cancer patients aims to adopt the most suitable treatment options during diagnosis and treatment of individuals. Detecting circulating tumor cell (CTC) or circulating tumor DNA (ctDNA) in plasma or serum could serve as liquid biopsy, which would be useful for numerous diagnostic applications. Liquid biopsies can help clinicians screen and detect cancer early, stratify patients to the most suitable treatment and real-time monitoring of treatment response and resistance mechanisms in the tumor, evaluate the risk for metastatic relapse, and estimate prognosis...
July 25, 2017: Frontiers of Medicine
https://www.readbyqxmd.com/read/28743887/tumor-derived-exosomes-induce-the-formation-of-neutrophil-extracellular-traps-implications-for-the-establishment-of-cancer-associated-thrombosis
#18
Ana C Leal, Daniella M Mizurini, Tainá Gomes, Natalia C Rochael, Elvira M Saraiva, Marcos S Dias, Claudio C Werneck, Micheli S Sielski, Cristina P Vicente, Robson Q Monteiro
Cancer patients are at an increased risk of developing thromboembolic complications. Several mechanisms have been proposed to explain cancer-associated thrombosis including the release of tumor-derived extracellular vesicles and the activation of host vascular cells. It was proposed that neutrophil extracellular traps (NETs) contribute to the prothrombotic phenotype in cancer. In this study, we evaluated the possible cooperation between tumor-derived exosomes and NETs in cancer-associated thrombosis. Female BALB/c mice were orthotopically injected with 4T1 breast cancer cells...
July 25, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28743309/efficient-treatment-of-a-metastatic-melanoma-patient-with-a-combination-of-braf-and-mek-inhibitors-based-on-circulating-tumor-dna-analysis-a-case-report
#19
Gaelle Quéreux, Guillaume Herbreteau, Anne-Chantal Knol, Audrey Vallée, Amir Khammari, Sandrine Théoleyre, Mélanie Saint-Jean, Brigitte Dréno, Marc G Denis
BACKGROUND: Fixed tissues are the standard samples used in routine practice for molecular testing. But sometimes tissues are lacking or difficult to obtain. In these cases, circulating tumor DNA released from tumor cells can be used as an alternative source of tumor DNA. CASE PRESENTATION: We present the case of a 63-year-old Caucasian woman with a metastatic melanoma and a very poor performance status. A plasma sample was tested and the BRAF p.V600E mutation was detected...
July 25, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28742791/correlation-between-circulating-tumor-dna-levels-and-response-to-tyrosine-kinase-inhibitors-tki-treatment-in-non-small-cell-lung-cancer
#20
Zhangjing Wei, Wenyue Wang, Zitan Shu, Xue Zhou, Yanfang Zhang
BACKGROUND Clinical monitoring of EGFR-positive NSCLC patients is important to gauge treatment response. The current study addresses the usage of circulating tumor DNA (ctDNA) as a prognostic marker during treatment of first-generation TKIs. MATERIAL AND METHODS Serial samplings of peripheral blood from 200 EGFR-positive NSCLC patients were taken. Baseline ctDNA quantification was conducted by digital droplet PCR before TKI treatment was administered and compared to primary biopsies. Thereafter blood sampling at different treatment cycles were measured and assessed for its prognostic and predictive value...
July 25, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
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