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Cell-free tumor dna

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https://www.readbyqxmd.com/read/28096270/mutation-enrichment-next-generation-sequencing-for-quantitative-detection-of-kras-mutations-in-urine-cell-free-dna-from-patients-with-advanced-cancers
#1
Takeo Fuji, Afsaneh Barzi, Andrea Sartore-Bianchi, Andrea Cassingena, Giulia Siravegna, Daniel Karp, Sarina Piha-Paul, Vivek Subbiah, Apostolia M Tsimberidou, Helen Huang, Sillvio Veronese, Federica Di Nicolantonio, Sandeep C Pingle, Cecile Rose T Vibat, Saege Hancock, David Berz, Vladislava O Melnikova, Mark G Erlander, Rajyalakshmi Luthra, Scott Kopetz, Funda Meric-Bernstam, Salvatore Siena, Heinz-Josef Lenz, Alberto Bardelli, Filip Janku
PURPOSE: Tumor-derived cell-free DNA (cfDNA) from urine of patients with cancer offers non-invasive biologic material for detection of cancer-related molecular abnormalities such as mutations in Exon 2 of KRAS. EXPERIMENTAL DESIGN: A quantitative, mutation-enrichment next-generation sequencing test for detecting KRASG12/G13 mutations in urine cfDNA was developed and results were compared to clinical testing of archival tumor tissue and plasma cfDNA from patients with advanced cancer...
January 17, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28096087/diffuse-large-b-cell-lymphoma-genotyping-on-the-liquid-biopsy
#2
Davide Rossi, Fary Diop, Elisa Spaccarotella, Sara Monti, Manuela Zanni, Silvia Rasi, Clara Deambrogi, Valeria Spina, Alessio Bruscaggin, Chiara Favini, Roberto Serra, Antonio Ramponi, Renzo Boldorini, Robin Foa', Gianluca Gaidano
Accessible and real-time genotyping for diagnostic, prognostic or treatment purposes is increasingly impelling in diffuse large B-cell lymphoma (DLBCL). Cell-free DNA (cfDNA) is shed into the blood by tumor cells undergoing apoptosis and can be used as source of tumor DNA for the identification of DLBCL mutations, clonal evolution, and genetic mechanisms of resistance. Here we aimed at tracking the basal DLBCL genetic profile and its modification upon treatment using plasma cfDNA. Ultra-deep targeted next generation sequencing of pre-treatment plasma cfDNA from DLBCL patients correctly discovered DLBCL-associated mutations that were represented in >20% of the alleles of the tumor biopsy with a >90% sensitivity and a ~100% specificity...
January 17, 2017: Blood
https://www.readbyqxmd.com/read/28093244/novel-mutations-on-egfr-leu792-potentially-correlate-to-acquired-resistance-to-osimertinib-in-advanced-nsclc
#3
Kai Chen, Fei Zhou, Wenxiang Shen, Tao Jiang, Xue Wu, Xiaoling Tong, Yang W Shao, Songbing Qin, Caicun Zhou
Osimertinib is an irreversible third generation EGFR tyrosine kinase inhibitor (TKI) and has shown outstanding performances in treating EGFR T790M-positive advanced non-small cell lung cancer (NSCLC) patients, but acquired resistance is inevitable. EGFR C797S is the most notable resistance mechanism to this drug, but other EGFR mutations may also exist. In three lung adenocarcinoma patients resistant to osimertinib, we identified recurrent novel mutations at EGFR Leu792 codon by targeted next generation sequencing (NGS) of cell free DNA (cfDNA) from plasma or pleural effusion...
January 13, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28081183/circulating-cell-free-dna-in-dogs-with-mammary-tumors-short-and-long-fragments-and-integrity-index
#4
Giorgia Beffagna, Alessandro Sammarco, Chiara Bedin, Chiara Romualdi, Marta Mainenti, Antonio Mollo, Laura Cavicchioli, Silvia Ferro, Davide Trez, Raffaella De Maria, Donato Nitti, Andrea Saccani, Michelangelo Campanella, Marco Agostini, Valentina Zappulli
Circulating cell-free DNA (cfDNA) has been considered an interesting diagnostic/prognostic plasma biomarker in tumor-bearing subjects. In cancer patients, cfDNA can hypothetically derive from tumor necrosis/apoptosis, lysed circulating cells, and some yet unrevealed mechanisms of active release. This study aimed to preliminarily analyze cfDNA in dogs with canine mammary tumors (CMTs). Forty-four neoplastic, 17 non-neoplastic disease-bearing, and 15 healthy dogs were recruited. Necrosis and apoptosis were also assessed as potential source of cfDNA on 78 CMTs diagnosed from the 44 dogs...
2017: PloS One
https://www.readbyqxmd.com/read/28069440/inter-and-intra-cellular-mechanism-of-nf-kb-dependent-survival-advantage-and-clonal-expansion-of-radio-resistant-cancer-cells
#5
Hui Yu, Natarajan Aravindan, Ji Xu, Mohan Natarajan
Understanding the underlying mechanism by which cancer cells acquire resistance to radiation and favorably selected for its clonal expansion will provide molecular insight into tumor recurrence at the treatment site. In the present study, we investigated the molecular mechanisms prompted in MCF-7 breast cancer cells in response to clinical radiation and the associated coordination of intra- and inter-cellular signaling that orchestrate radio-resistance and tumor relapse/recurrence. Our findings showed that 2 or 10Gy of (137)Cs γ-rays at a dose rate of 1...
January 6, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/28063009/dna-methylation-signatures-in-circulating-cell-free-dna-as-biomarkers-for-the-early-detection-of-cancer
#6
REVIEW
Junyun Wang, Xiao Han, Yingli Sun
Detecting cell-free DNA (cfDNA) or circulating tumor DNA (ctDNA) in plasma or serum could serve as a "liquid biopsy", which would be useful for numerous diagnostic applications. cfDNA methylation detection is one of the most promising approaches for cancer risk assessment. Here, we reviewed the literature related to the use of serum or plasma circulating cell-free DNA for cancer diagnosis in the early stage and their power as future biomarkers.
January 5, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28061461/estimation-of-cell-free-circulating-egfr-mutation-concentration-predicts-outcomes-in-nsclc-patients-treated-with-egfr-tkis
#7
Yan-Juan Zhu, Hai-Bo Zhang, Yi-Hong Liu, Fu-Li Zhang, Ya-Zhen Zhu, Yong Li, Jian-Ping Bai, Li-Rong Liu, Yan-Chun Qu, Xin Qu, Xian Chen, Yan Li, Guang-Juan Zheng
Detection of circulating tumor DNA using droplet digital polymerase chain reaction (ddPCR) is a highly-sensitive, minimally invasive alternative to serial biopsies for assessment and management of cancer. We used ddPCR to assess the utility of measuring plasma concentrations of common epidermal growth factor receptor (EGFR) mutations (L858R, exon 19 deletion, and T790M) in 57 non-small cell lung cancer (NSCLC) patients treated with EGFR tyrosine kinase inhibitors (EGFR-TKIs). High baseline plasma EGFR mutation (pEGFRmut) concentrations were associated with shorter progression-free survival (8...
January 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28061446/%C3%AE-40p53-is-involved-in-the-inactivation-of-autophagy-and-contributes-to-inhibition-of-cell-death-in-hct116-%C3%AE-40p53-cells
#8
Yunjin Zang, Ying Shi, Kai Liu, Luxin Qiao, Xianghua Guo, Dexi Chen
Δ40p53 is an isoform of wild-type p53 (wtp53). Here, we assessed whether Δ40p53 has the same functions as wild-type p53 in the regulation of cell death and autophagy. First, we used HCT116 (p53+/+) and H1299 (p53-free) cells to produce two cell lines (HCT116-Δ40p53 and H1299-Δ40p53) that express exogenous Δ40p53 but not wtp53. By using these cell lines, we determined that Δ40p53 inhibited starvation-induced autophagy, as does wtp53. This inhibition arises from both Δ40p53 and wtp53 having 3'-5' exonuclease activity, which reduces the levels of double-stranded RNA (dsRNA) and then inhibits PKR/eIF2α-induced autophagy in cells exposed to starvation...
January 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28060757/line-1-hypomethylation-status-of-circulating-cell-free-dna-in-plasma-as-a-biomarker-for-colorectal-cancer
#9
Yuzo Nagai, Eiji Sunami, Yoko Yamamoto, Keisuke Hata, Satoshi Okada, Koji Murono, Koji Yasuda, Kensuke Otani, Takeshi Nishikawa, Toshiaki Tanaka, Tomomichi Kiyomatsu, Kazushige Kawai, Hiroaki Nozawa, Soichiro Ishihara, Dave S B Hoon, Toshiaki Watanabe
Colorectal cancer (CRC) is a serious public health problem and non-invasive biomarkers improving diagnosis or therapy are strongly required. Circulating cell-free DNA (cfDNA) has been a promising target for this purpose. In this study, we evaluated the potential of long interspersed nuclear element-1 (LINE-1) hypomethylation as a blood biomarker for CRC. LINE-1 hypomethylation level in plasma cfDNA in 114 CRC patients was retrospectively examined by absolute quantitative analysis of methylated alleles real-time PCR, and was expressed using LINE-1 hypomethylation index (LHI) [unmethylated copy number/ (methylated copy number + unmethylated copy number)]...
January 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28060130/intracardiac-low-grade-sarcoma-following-treatment-for-ewing-sarcoma
#10
Michael V Ortiz, Heather Magnan, Emily K Slotkin, Srikanth R Ambati, Alexander J Chou, Leonard H Wexler, Paul A Meyers, Michael F Walsh, Todd Heaton, Leonard N Girardi, Suzanne L Wolden, Anita P Price, Jennifer A Kennedy, Ahmet Zehir, Meera Hameed, Michael F Berger, Alex Kentsis, Neerav Shukla
A 16-year-old male was diagnosed with Ewing sarcoma of the ribcage with pulmonary metastases. Six months after completion of scheduled therapy, he was found to have a new intracardiac mass, presumed recurrent Ewing sarcoma. EWSR1 fusion was not detected by droplet digital polymerase chain reaction from blood plasma. After no improvement with salvage chemotherapy, he underwent surgical resection that identified a low-grade spindle cell sarcoma. Despite the near-synchronous presentation of 2 unrelated sarcomas, extensive genomic analyses did not reveal any unifying somatic or germline mutations nor any apparent cancer predisposition...
January 5, 2017: Journal of Pediatric Hematology/oncology
https://www.readbyqxmd.com/read/28057464/graphene-quantum-dots-for-cancer-targeted-drug-delivery
#11
Daniela Iannazzo, Alessandro Pistone, Marina Salamò, Signorino Galvagno, Roberto Romeo, Salvatore V Giofré, Caterina Branca, Giuseppa Visalli, Angela Di Pietro
A biocompatible and cell traceable drug delivery system Graphene Quantum Dots (GQD) based, for the targeted delivery of the DNA intercalating drug doxorubicin (DOX) to cancer cells, is here reported. Highly dispersible and water soluble GQD, synthesized by acidic oxidation and exfoliation of multi-walled carbon nanotubes (MWCNT), were covalently linked to the tumor targeting module biotin (BTN), able to efficiently recognize biotin receptors over-expressed on cancer cells and loaded with DOX. Biological test performed on A549 cells reported a very low toxicity of the synthesized carrier (GQD and GQD-BTN)...
January 2, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28056336/the-clinical-role-of-circulating-free-tumor-dna-in-gastrointestinal-malignancy
#12
REVIEW
Jessica A Howell, Shahid A Khan, Susanne Knapp, Mark R Thursz, Rohini Sharma
Circulating cell-free DNA (cfDNA) is DNA released from necrotic or apoptotic cells into the bloodstream. While both healthy cells and cancer cells release cfDNA, tumors are associated with higher levels of tumor-derived circulating cell-free DNA (ctDNA) detectable in blood. Absolute levels of ctDNA and its genetic mutations and epigenetic changes show promise as potentially useful biomarkers of tumor biology, progression, and response to therapy. Moreover, studies have demonstrated the discriminative accuracy of ctDNA levels for diagnosis of gastrointestinal cancer compared with benign inflammatory diseases...
December 22, 2016: Translational Research: the Journal of Laboratory and Clinical Medicine
https://www.readbyqxmd.com/read/28055005/enhanced-expression-of-survivin-has-distinct-roles-in-adipocyte-homeostasis
#13
Liping Ju, Xiaoyan Zhang, Yujie Deng, Junfeng Han, Jian Yang, Shuqin Chen, Qichen Fang, Ying Yang, Weiping Jia
Although precisely controlled lipolysis is crucial for maintaining physiological levels of circulating free fatty acids in response to energetic stress, the underlying mechanisms by which this process is governed remain poorly understood. Survivin is a gene that has been found to be highly expressed in the most common human tumors, and it is considered to be associated with tumorigenesis. Survivin expression in normal tissue is developmentally downregulated and is undetectable in most terminally differentiated adult tissues...
January 5, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28052016/total-dna-input-is-a-crucial-determinant-of-the-sensitivity-of-plasma-cell-free-dna-egfr-mutation-detection-using-droplet-digital-pcr
#14
Yu Zhang, Yan Xu, Wei Zhong, Jing Zhao, Minjiang Chen, Li Zhang, Longyun Li, Mengzhao Wang
We evaluated the use of droplet digital PCR (ddPCR) to detect plasma cell-free DNA (cfDNA) epidermal growth factor receptor (EGFR) mutations in advanced non-small cell lung cancer (NSCLC) patients. Compared with tumor-tissue-based detection, the sensitivity of ddPCR for detecting plasma cfDNA tyrosine kinase inhibitor (TKI)-sensitizing EGFR mutations was 61.3%, the specificity was 96.7%, and the consistency rate was 81.4% (κ=0.605, 95% confidence interval: 0.501-0.706, p <0.0001). The sensitivity declined from 82...
December 30, 2016: Oncotarget
https://www.readbyqxmd.com/read/28051879/wnt5a-promoter-methylation-is-associated-with-better-responses-and-longer-progression-free-survival-in-colorectal-cancer-patients-treated-with-5-fluorouracil-based-chemotherapy
#15
Guozhong Jiang, Jiangxin Lin, Weiwei Wang, Miaomiao Sun, Kuisheng Chen, Feng Wang
BACKGROUND: Aberrant activation of the canonical WNT or WNT/β-catenin signaling pathway plays a pivotal role in multiple types of cancers. WNT5A, a nontransforming WNT protein suppressing the Wnt/β-catenin signaling pathway, is frequently detected to be hypermethylated in colorectal cancer (CRC). In this study, we investigated the prognostic value of WNT5A methylation in human patients and its potential underlying molecular mechanisms in cultured human CRC cells. METHODS: We measured WNT5A mRNA level using qRT-PCR and DNA methylation using methylation-specific PCR (MSP) in HCT116, HT29, SW620, HCT8, LoVo, SW480, and Rko CRC cells...
January 4, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28049139/a-randomized-phase-2-study-of-mk-2206-versus-everolimus-in-refractory-renal-cell-carcinoma
#16
E Jonasch, E Hasanov, P Corn, T Moss, K Shaw, S Stovall, V Marcott, B Gan, S Bird, X Wang, K Do, P Altamirano, A Zurita, L Doyle, P Lara, N M Tannir
BACKGROUND: Activation of the phosphoinisitide-3 kinase (PI3K) pathway through mutation and constitutive upregulation have been described in renal cell carcinoma (RCC), making it an attractive target for therapeutic intervention. We performed a randomized phase II study in vascular endothelial growth factor (VEGF) therapy refractory patients to determine whether MK-2206, an allosteric inhibitor of AKT, was more efficacious than the mammalian target of rapamycin inhibitor everolimus. PATIENTS AND METHODS: A total of 43 patients were randomized in a 2:1 distribution, with 29 patients assigned to the MK-2206 arm and 14 to the everolimus arm...
January 3, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/28046008/cell-free-dna-provides-a-good-representation-of-the-tumor-genome-despite-its-biased-fragmentation-patterns
#17
Xiangyuan Ma, Liangjun Zhu, Xue Wu, Hua Bao, Xiaonan Wang, Zhili Chang, Yang W Shao, Zhenxin Wang
Cell-free DNA (cfDNA) is short, extracellular, fragmented double-stranded DNA found in plasma. Plasma of patients with solid tumor has been found to show significantly increased quantities of cfDNA. Although currently poorly understood, the mechanism of cfDNA generation is speculated to be a product of genomic DNA fragmentation during cellular apoptosis and necrosis. Sequencing of cfDNA with tumor origin has identified tumor biomarkers, elucidating molecular pathology and assisting in accurate diagnosis. In this study, we performed whole-genome sequencing ofcfDNA samples with matching tumor and whole blood samples from five patients diagnosed with stage IV gastric or lung cancer...
2017: PloS One
https://www.readbyqxmd.com/read/28039450/aberrant-promoter-methylation-of-hogg1-may-be-associated-with-increased-risk-of-non-small-cell-lung-cancer
#18
Hualong Qin, Jianjie Zhu, Yuanyuan Zeng, Wenwen Du, Dan Shen, Zhe Lei, Qian Qian, Jian-An Huang, Zeyi Liu
DNA methylation may epigenetically inactivate tumor suppressor genes in NSCLC. As the human 8-oxoguanine DNA glycosylase (hOGG1) gene promoter is frequently methylated in NSCLC, we evaluated whether genetic or epigenetic alterations of hOGG1 are associated with increased risk of non-small cell lung cancer. Three hOGG1 haplotype-tagging SNPs (htSNP) were genotyped in PCR-restriction fragment length polymorphism assays, and one htSNP was genotyped in a PCR-single-strand conformation polymorphism assay in case-control studies of 217 NSCLC patients and 226 healthy controls...
December 26, 2016: Oncotarget
https://www.readbyqxmd.com/read/28035516/circadian-rhythm-of-methylated-septin-9-cell-free-dna-amount-and-tumor-markers-in-colorectal-cancer-patients
#19
Kinga Tóth, Árpád V Patai, Alexandra Kalmár, Barbara Kinga Barták, Zsófia Brigitta Nagy, Orsolya Galamb, Barnabás Wichmann, Zsolt Tulassay, Béla Molnár
To determine the level of cell-free DNA (cfDNA), Septin 9 (SEPT9) and tumor markers (CEA, AFP, CA19-9, TPA, CA72-4). Plasma samples were collected four times a day (06:00, 12:00, 18:00, 24:00) from 9 patients with CRC (5 stage I-II, 4 stage III-IV), from one with colorectal adenoma and from one healthy control. CfDNA was isolated, quantified and bisulfite-converted. CfDNA and methylated SEPT9 were determined by RT-PCR. Plasma levels of conventional tumor markers were also measured. The lowest cfDNA concentrations were observed at 24:00 and 18:00 in stage I-III patients...
December 30, 2016: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/28035318/circulating-biomarkers-in-bladder-cancer
#20
REVIEW
Lakshminarayanan Nandagopal, Guru Sonpavde
Bladder cancer is a molecularly heterogeneous disease characterized by multiple unmet needs in the realm of diagnosis, clinical staging, monitoring and therapy. There is an urgent need to develop precision medicine for advanced urothelial carcinoma. Given the difficulty of serial analyses of metastatic tumor tissue to identify resistance and new therapeutic targets, development of non-invasive monitoring using circulating molecular biomarkers is critically important. Although the development of circulating biomarkers for the management of bladder cancer is in its infancy and may currently suffer from lower sensitivity of detection, they have inherent advantages owing to non-invasiveness...
October 27, 2016: Bladder Cancer
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