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Cell-free tumor dna

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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/29776633/molecular-diagnostics-in-colorectal-carcinoma-advances-and-applications-for-2018
#2
REVIEW
Amarpreet Bhalla, Muhammad Zulfiqar, Martin H Bluth
The molecular pathogenesis and classification of colorectal carcinoma are based on the traditional adenomaecarcinoma sequence, serrated polyp pathway, and microsatellite instability (MSI). The genetic basis for hereditary nonpolyposis colorectal cancer is the detection of mutations in the MLH1, MSH2, MSH6, PMS2, and EPCAM genes. Genetic testing for Lynch syndrome includes MSI testing, methylator phenotype testing, BRAF mutation testing, and molecular testing for germline mutations in MMR genes. Molecular makers with predictive and prognostic implications include quantitative multigene reverse transcriptase polymerase chain reaction assay and KRAS and BRAF mutation analysis...
June 2018: Clinics in Laboratory Medicine
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/29764589/-influence-of-different-therapies-on-egfr-mutants-by-circulating-cell-free-dna-of-lung-adenocarcinoma-and-prognosis
#4
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
#5
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/29761368/idh1-mutation-in-human-glioma-induces-chemical-alterations-that-are-amenable-to-optical-raman-spectroscopy
#6
Ortrud Uckermann, Wenmin Yao, Tareq A Juratli, Roberta Galli, Elke Leipnitz, Matthias Meinhardt, Edmund Koch, Gabriele Schackert, Gerald Steiner, Matthias Kirsch
INTRODUCTION: Mutations in the isocytrate dehydrogenase 1 (IDH1) gene are early genetic events in glioma pathogenesis and cause profound metabolic changes. Because this genotype is found in virtually every tumor cell, therapies targeting mutant IDH1 protein are being developed. The intraoperative administration of those therapies would require fast technologies for the determination of IDH1 genotype. As of today, there is no such diagnostic test available. Recently, infrared spectroscopy was shown to bridge this gap...
May 14, 2018: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29761074/the-clinical-utility-of-cell-free-dna-measurement-in-differentiated-thyroid-cancer-a-systematic-review
#7
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/29759151/circulating-tumour-dna-for-detecting-minimal-residual-disease-in-multiple-myeloma
#8
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/29755432/murine-endogenous-retroviruses-are-detectable-in-patient-derived-xenografts-but-not-in-patient-individual-cell-lines-of-human-colorectal-cancer
#9
Stephanie Bock, Christina S Mullins, Ernst Klar, Philippe Pérot, Claudia Maletzki, Michael Linnebacher
Endogenous retroviruses are remnants of retroviral infections. In contrast to their human counterparts, murine endogenous retroviruses (mERV) still can synthesize infectious particles and retrotranspose. Xenotransplanted human cells have occasionally been described to be mERV infected. With genetic engineered mice and patient-derived xenografts (PDXs) on the rise as eminent research tools, we here systematically investigated, if different tumor models harbor mERV infections. Relevant mERV candidates were first preselected by next generation sequencing (NGS) analysis of spontaneous lymphomas triggered by colorectal cancer (CRC) PDX tissue...
2018: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29754146/transcriptional-e2f1-2-5-8-as-potential-targets-and-transcriptional-e2f3-6-7-as-new-biomarkers-for-the-prognosis-of-human-lung-carcinoma
#10
Cheng-Cao Sun, Qun Zhou, Wei Hu, Shu-Jun Li, Feng Zhang, Zhen-Long Chen, Guang Li, Zhuo-Yue Bi, Yong-Yi Bi, Feng-Yun Gong, Tao Bo, Zhan-Peng Yuan, Wei-Dong Hu, Bo-Tao Zhan, Qian Zhang, Qi-Zhu Tang, De-Jia Li
E2F is a group of genes that encode a family of transcription factors (TFs) in higher eukaryotes and participate in cell cycle regulation and DNA synthesis in mammalian cells. Evidence from cell lines, mouse models, and human tissues indicates that TFs are implicated in lung cancer (LC) tumorigenesis. However, the diverse expression patterns and prognostic values of eight E2Fs have yet to be elucidated. In the current study, we examined the transcriptional and survival data of E2Fs in patients with LC from ONCOMINE, GEPIA, Kaplan-Meier Plotter, and cBioPortal databases...
May 11, 2018: Aging
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
#11
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/29749129/plasma-cell-free-dna-as-a-predictive-marker-after-radiotherapy-for-hepatocellular-carcinoma
#12
Sangjoon Park, Eun Jung Lee, Chai Hong Rim, Jinsil Seong
PURPOSE: Cell-free DNA (cfDNA) is gaining attention as a novel biomarker for oncologic outcomes. We investigated the clinical significance of cfDNA in hepatocellular carcinoma (HCC) patients treated with radiotherapy (RT). MATERIALS AND METHODS: Fifty-five patients with HCC who received RT were recruited from two prospective study cohorts: one cohort of 34 patients who underwent conventionally fractionated RT and a second of 21 patients treated with stereotactic body radiation therapy...
June 2018: Yonsei Medical Journal
https://www.readbyqxmd.com/read/29748181/clonal-hematopoiesis-a-new-layer-in-the-liquid-biopsy-story-in-lung-cancer
#13
Joshua Bauml, Benjamin Levy
Cell free DNA (cfDNA) is a unique biospecimen that contains multiple sources of DNA including tumor, germline, fetal, and others. Clonal hematopoiesis, a process that leads to expansion of mutations in peripheral blood cells, is an additional source of DNA that adds a layer of complexity when interpreting results.
May 10, 2018: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/29748005/genomic-alterations-of-plasma-cell-free-dnas-in-small-cell-lung-cancer-and-their-clinical-relevance
#14
Meijun Du, Jonathan Thompson, Hannah Fisher, Peng Zhang, Chiang-Ching Huang, Liang Wang
OBJECTIVES: To identify genomic variations in cell-free DNA (cfDNA) and evaluate their clinical utility in small cell lung cancer (SCLC). MATERIALS AND METHODS: We performed whole genome sequencing using plasma cfDNAs derived from 24 SCLC patients for copy number variation (CNV) analysis, and targeted sequencing using 17 pairs of plasma cfDNA and their matched gDNA for mutation analysis. We defined somatic mutations by comparing cfDNA to its matched gDNA with 5% variant alleles as the cutoff for mutation calls...
June 2018: Lung Cancer: Journal of the International Association for the Study of Lung Cancer
https://www.readbyqxmd.com/read/29747501/multi-proteomic-and-transcriptomic-analysis-of-oncogenic-%C3%AE-catenin-molecular-networks
#15
Rob M Ewing, Jing Song, Giridharan Gokulrangan, Sheldon Bai, Emily Bowler, Rachel Bolton, Paul Skipp, Yihua Wang, Zhenghe Wang
Dys-regulation of Wnt signalling is a frequent occurrence in many different cancers. Oncogenic mutations of CTNNB1/β-catenin, the key nuclear effector of canonical Wnt signalling, lead to accumulation and stabilization of β-catenin protein with diverse effects in cancer cells. Although the transcriptional response to Wnt/β-catenin signaling activation has been widely studied, an integrated understanding of the effects of oncogenic β-catenin on molecular networks is lacking. We used Affinity-Purification Mass-Spectrometry (AP-MS), label-free LC-MS/MS and RNA-Seq to compare protein-protein interactions, protein expression and gene-expression in colorectal cancer cells expressing mutant/oncogenic or wild-type β-catenin...
May 10, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29746588/aberrant-s100a16-expression-might-be-an-independent-prognostic-indicator-of-unfavorable-survival-in-non-small-cell-lung-adenocarcinoma
#16
De Chen, Linjie Luo, Chao Liang
S100A16 is a conserved member of the S100 protein family in mammals. Its upregulation was observed in many tumors and is related to malignant transformation. In this study, we explored the independent prognostic value of S100A16 in terms of overall survival (OS) and recurrence-free survival (RFS) by performing a retrospective study, using data in The Cancer Genome Atlas (TCGA)-lung adenocarcinoma (LUAD). Besides, by using deep sequencing data in TCGA-LUAD, we also explored the association between S100A16 expression and its DNA methylation and copy number alterations (CNAs)...
2018: PloS One
https://www.readbyqxmd.com/read/29744610/walnut-phenolic-extract-inhibits-nuclear-factor-kappab-signaling-in-intestinal-epithelial-cells-and-ameliorates-experimental-colitis-and-colitis-associated-colon-cancer-in-mice
#17
Seong-Joon Koh, Youn-I Choi, Yuri Kim, Yoo-Sun Kim, Sang Woon Choi, Ji Won Kim, Byeong Gwan Kim, Kook Lae Lee
PURPOSE: Walnuts (Juglans regia) are known to have anti-cancer and immunomodulatory effects. However, little information is available on the effects of walnut phenolic extract (WPE) on intestinal inflammation and colitis-associated colon cancer. METHODS: COLO205 cells were pretreated with WPE and then stimulated with tumor necrosis factor (TNF)-α. In the acute colitis model, wild type mice (C57BL/6) were administered 4% dextran sulfate sodium (DSS) for 5 days. In the chronic colitis model, interleukin (IL)-10-/- mice were administered with either the vehicle or WPE (20 mg/kg) by oral gavage daily for 2 weeks...
May 9, 2018: European Journal of Nutrition
https://www.readbyqxmd.com/read/29743350/high-throughput-sequencing-of-the-t-cell-receptor-%C3%AE-gene-identifies-aggressive-early-stage-mycosis-fungoides
#18
Adele de Masson, John T O'Malley, Christopher P Elco, Sarah S Garcia, Sherrie J Divito, Elizabeth L Lowry, Marianne Tawa, David C Fisher, Phillip M Devlin, Jessica E Teague, Nicole R Leboeuf, Ilan R Kirsch, Harlan Robins, Rachael A Clark, Thomas S Kupper
Mycosis fungoides (MF), the most common cutaneous T cell lymphoma (CTCL) is a malignancy of skin-tropic memory T cells. Most MF cases present as early stage (stage I A/B, limited to the skin), and these patients typically have a chronic, indolent clinical course. However, a small subset of early-stage cases develop progressive and fatal disease. Because outcomes can be so different, early identification of this high-risk population is an urgent unmet clinical need. We evaluated the use of next-generation high-throughput DNA sequencing of the T cell receptor β gene ( TCRB ) in lesional skin biopsies to predict progression and survival in a discovery cohort of 208 patients with CTCL (177 with MF) from a 15-year longitudinal observational clinical study...
May 9, 2018: Science Translational Medicine
https://www.readbyqxmd.com/read/29739952/translational-study-identifies-xpf-and-mus81-as-predictive-biomarkers-for-oxaliplatin-based-peri-operative-chemotherapy-in-patients-with-esophageal-adenocarcinoma
#19
T P MacGregor, R Carter, R S Gillies, J M Findlay, C Kartsonaki, F Castro-Giner, N Sahgal, L M Wang, R Chetty, N D Maynard, J B Cazier, F Buffa, P J McHugh, I Tomlinson, M R Middleton, R A Sharma
Oxaliplatin-based chemotherapy is used to treat patients with esophageal adenocarcinoma (EAC), but no biomarkers are currently available for patient selection. We performed a prospective, clinical trial to identify potential biomarkers associated with clinical outcomes. Tumor tissue was obtained from 38 patients with resectable EAC before and after 2 cycles of oxaliplatin-fluorouracil chemotherapy. Pre-treatment mRNA expression of 280 DNA repair (DNAR) genes was tested for association with histopathological regression at surgery, disease-free survival (DFS) and overall survival (OS)...
May 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29738334/precision-medicine-and-lymphoma
#20
James A Heward, Emil A Kumar, Koorosh Korfi, Jessica Okosun, Jude Fitzgibbon
PURPOSE OF REVIEW: The treatment of the germinal center lymphomas, diffuse large B cell (DLBCL) and follicular lymphoma, has changed little beyond the introduction of immunochemotherapies. However, there exists a substantial group of patients within both diseases for which improvements in care will involve appropriate tailoring of treatment. RECENT FINDINGS: DLBCL consists of two major subtypes with striking differences in their clinical outcomes paralleling their underlying genetic heterogeneity...
May 5, 2018: Current Opinion in Hematology
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