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https://www.readbyqxmd.com/read/28928368/detection-of-clinically-relevant-copy-number-alterations-in-oral-cancer-progression-using-multiplexed-droplet-digital-pcr
#1
Curtis B Hughesman, X J David Lu, Kelly Y P Liu, Yuqi Zhu, Rebecca M Towle, Charles Haynes, Catherine F Poh
Copy number alterations (CNAs), a common genomic event during carcinogenesis, are known to affect a large fraction of the genome. Common recurrent gains or losses of specific chromosomal regions occur at frequencies that they may be considered distinctive features of tumoral cells. Here we introduce a novel multiplexed droplet digital PCR (ddPCR) assay capable of detecting recurrent CNAs that drive tumorigenesis of oral squamous cell carcinoma. Applied to DNA extracted from oral cell lines and clinical samples of various disease stages, we found good agreement between CNAs detected by our ddPCR assay with those previously reported using comparative genomic hybridization or single nucleotide polymorphism arrays...
September 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28923315/development-of-a-digital-droplet-pcr-assay-to-measure-hbv-dna-in-patients-receiving-long-term-tdf-treatment
#2
Yang Liu, Andrea L Cathcart, William E Delaney, Kathryn M Kitrinos
The COBAS TaqMan assay has a lower limit of quantification (LLOQ) of 169 HBV copies/mL and a lower limit of detection (LLOD) of 58 copies/mL. HBV DNA below the TaqMan LLOQ is classified as target not detected (TND) (<58 copies/mL) or target detected (TD) (between 58 to 169 copies/mL). Here we have developed a more sensitive digital droplet PCR (ddPCR) assay to evaluate the impact of long-term tenofovir disoproxil fumarate (TDF) treatment in patients that did or did not achieve HBsAg seroconversion. A ddPCR assay was developed to detect HBV DNA to 8 copies/mL...
September 15, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28921124/droplet-volume-variability-as-a-critical-factor-for-accuracy-of-absolute-quantification-using-droplet-digital-pcr
#3
Alexandra Bogožalec Košir, Carla Divieto, Jernej Pavšič, Stefano Pavarelli, David Dobnik, Tanja Dreo, Roberto Bellotti, Maria Paola Sassi, Jana Žel
Accurate and precise nucleic-acid quantification is crucial for clinical and diagnostic decisions, as overestimation or underestimation can lead to misguided treatment of a disease or incorrect labelling of the products. Digital PCR is one of the best tools for absolute nucleic-acid copy-number determination. However, digital PCR needs to be well characterised in terms of accuracy and sources of uncertainty. With droplet digital PCR, discrepancies between the droplet volume assigned by the manufacturer and measured by independent laboratories have already been shown in previous studies...
September 18, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28920396/-inhibition-of-chitin-oligosaccharide-on-dyslipidemia-and-the-potential-molecular-mechanism-exploration
#4
Fanqi Yi, Junping Zheng, Qiongyu Li, Siming Jiao, Yuguang Du, Yun Ye, Hongtao Liu
The inhibitory effect of NACOS on dyslipidemia and potential molecular mechanisms by in vitro and in vivo experiments were investigated. For in vitro study, four experimental groups were designed by using HepG2 cells, including the control group, palmitic acid (PA) treatment alone group, NACOS treatment alone group and NACOS + PA treatment group. For in vivo study, male C57BL/6 mice were divided into four groups (n=5) at random including the normal control group (NCD), high fat diet (HFD) group, NACOS treatment alone group, NACOS+HFD group, which were treated for 20 weeks...
April 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28915237/dna-replication-stress-restricts-ribosomal-dna-copy-number
#5
Devika Salim, William D Bradford, Amy Freeland, Gillian Cady, Jianmin Wang, Steven C Pruitt, Jennifer L Gerton
Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen the yeast conditional temperature-sensitive mutant collection of essential genes...
September 15, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28913408/hepatocyte-specific-deletion-of-mouse-lamin-a-c-leads-to-male-selective-steatohepatitis
#6
Raymond Kwan, Graham F Brady, Maria Brzozowski, Sujith V Weerasinghe, Hope Martin, Min-Jung Park, Makayla J Brunt, Ram K Menon, Xin Tong, Lei Yin, Colin L Stewart, M Bishr Omary
BACKGROUND & AIMS: Lamins are nuclear intermediate filament proteins that comprise the major components of the nuclear lamina. Mutations in LMNA, which encodes lamins A/C, cause laminopathies, including lipodystrophy, cardiomyopathy, and premature aging syndromes. However, the role of lamins in the liver is unknown, and it is unclear whether laminopathy-associated liver disease is caused by primary hepatocyte defects or systemic alterations. METHODS: To address these questions, we generated mice carrying a hepatocyte-specific deletion of Lmna (knockout [KO] mice) and characterized the KO liver and primary hepatocyte phenotypes by immunoblotting, immunohistochemistry, microarray analysis, quantitative real-time polymerase chain reaction, and Oil Red O and Picrosirius red staining...
November 2017: Cellular and Molecular Gastroenterology and Hepatology
https://www.readbyqxmd.com/read/28911154/prognostic-significance-of-circulating-ret-m918t-mutated-tumor-dna-in-patients-with-advanced-medullary-thyroid-carcinoma
#7
Gilbert J Cote, Caitlin Evers, Mimi I Hu, Elizabeth G Grubbs, Michelle D Williams, Tao Hai, Dzifa Y Duose, Michal R Houston, Jacquelin H Bui, Meenakshi Mehrotra, Steven G Waguespack, Naifa L Busaidy, Maria E Cabanillas, Mouhammed Amir Habra, Rajyalakshmi Luthra, Steven I Sherman
Context: Interpretation of calcitonin measurement to predict the prognosis of medullary thyroid carcinoma (MTC) requires multiple measurements over an extended time period, making it an imperfect biomarker for evaluating prognosis or disease behavior. Single circulating cell-free DNA (cfDNA) values have been shown to be a valuable prognostic marker for several solid tumors. Objective: We tested the hypothesis that cfDNA containing the RET M918T mutation could be detected in the blood of patients with advanced MTC whose tumor harbored an M918T mutation and would be able to predict overall survival more reliably than calcitonin...
September 1, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28910375/application-of-droplet-digital-pcr-for-quantitative-detection-of-spiroplasma-citri-in-comparison-with-real-time-pcr
#8
Yogita Maheshwari, Vijayanandraj Selvaraj, Subhas Hajeri, Raymond Yokomi
Droplet digital polymerase chain reaction (ddPCR) is a method for performing digital PCR that is based on water-oil emulsion droplet technology. It is a unique approach to measure the absolute copy number of nucleic acid targets without the need of external standards. This study evaluated the applicability of ddPCR as a quantitative detection tool for the Spiroplasma citri, causal agent of citrus stubborn disease (CSD) in citrus. Two sets of primers, SP1, based on the spiral in housekeeping gene, and a multicopy prophage gene, SpV1 ORF1, were used to evaluate ddPCR in comparison with real time (quantitative) PCR (qPCR) for S...
2017: PloS One
https://www.readbyqxmd.com/read/28906277/effect-of-cytomegalovirus-and-epstein-barr-virus-replication-on-intestinal-mucosal-gene-expression-and-microbiome-composition-of-hiv-infected-and-uninfected-individuals
#9
Sara Gianella, Antoine Chaillon, Ece A Mutlu, Phillip A Engen, Robin M Voigt, Ali Keshavarzian, John Losurdo, Prachi Chakradeo, Steven M Lada, Masato Nakazawa, Alan L Landay
BACKGROUND: HIV-infection is associated with dramatic changes in the intestinal mucosa. The impact of other viral pathogens is unclear. METHODS: One hundred and eight (108) biopsies from left and right colon (n = 79) and terminal ileum (n = 29) were collected from 19 HIV-infected and 22 HIV-uninfected participants. Levels of cytomegalovirus (CMV) and Epstein-Barr virus (EBV) DNA were measured by droplet digital PCR. Mucosal gene expression was measured via multiplex-assay...
September 24, 2017: AIDS
https://www.readbyqxmd.com/read/28905136/highly-sensitive-detection-of-esr1-mutations-in-cell-free-dna-from-patients-with-metastatic-breast-cancer-using-molecular-barcode-sequencing
#10
Nanae Masunaga, Naofumi Kagara, Daisuke Motooka, Shota Nakamura, Tomohiro Miyake, Tomonori Tanei, Yasuto Naoi, Masafumi Shimoda, Kenzo Shimazu, Seung Jin Kim, Shinzaburo Noguchi
PURPOSE: We aimed to develop a highly sensitive method to detect ESR1 mutations in cell-free DNA (cfDNA) using next-generation sequencing with molecular barcode (MB-NGS) targeting the hotspot segment (c.1600-1713). METHODS: The sensitivity of MB-NGS was tested using serially diluted ESR1 mutant DNA and then cfDNA samples from 34 patients with metastatic breast cancer were analyzed with MB-NGS. The results of MB-NGS were validated in comparison with conventional NGS and droplet digital PCR (ddPCR)...
September 13, 2017: Breast Cancer Research and Treatment
https://www.readbyqxmd.com/read/28901323/human-epidermal-growth-factor-receptor-2-amplification-detection-by-droplet-digital-polymerase-chain-reaction-in-formalin-fixed-paraffin-embedded-breast-and-gastric-cancer-samples
#11
Xingwen Wang, Yunyan Wu, Xueling Song, Chengtao Sun, Changshun Wu, Hong Feng
OBJECTIVE: Human epidermal growth factor receptor 2 (HER2) is an important biomarker for the precise individualized treatment including trastuzumab of HER2-positive breast and gastric cancer. Immunohistochemistry (IHC) and fluorescence in situ hybridization (FISH) are the routine analyses for formalin-fixed paraffin-embedded (FFPE) samples. However, IHC is variable and depends on the evaluator, and FISH is a labor intensive and expensive method. We evaluated the feasibility of droplet digital polymerase chain reaction (ddPCR) as a precise and quantitative method for HER2 amplification test...
2017: Journal of Cancer Research and Therapeutics
https://www.readbyqxmd.com/read/28900844/a-pilot-study-on-the-use-of-cerebrospinal-fluid-cell-free-dna-in-intramedullary-spinal-ependymoma
#12
Ian David Connolly, Yingmei Li, Wenying Pan, Eli Johnson, Linya You, Hannes Vogel, John Ratliff, Melanie Hayden Gephart
Cerebrospinal fluid (CSF) represents a promising source of cell-free DNA (cfDNA) for tumors of the central nervous system. A CSF-based liquid biopsy may obviate the need for riskier tissue biopsies and serve as a means for monitoring tumor recurrence or response to therapy. Spinal ependymomas most commonly occur in adults, and aggressive resection must be delicately balanced with the risk of injury to adjacent normal tissue. In patients with subtotal resection, recurrence commonly occurs. A CSF-based liquid biopsy matched to the patient's spinal ependymoma mutation profile has potential to be more sensitive then surveillance MRI, but the utility has not been well characterized for tumors of the spinal cord...
September 12, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/28899979/clinical-performance-evaluation-of-the-idylla-nras-braf-mutation-test-on-retrospectively-collected-formalin-fixed-paraffin-embedded-colorectal-cancer-tissue
#13
Louise Johnston, Michael Power, Philip Sloan, Anna Long, Angela Silmon, Ben Chaffey, Andrea Jane Lisgo, Liam Little, Ellen Vercauteren, Torben Steiniche, Tine Meyer, John Simpson
AIMS: Understanding the molecular mechanisms of underlying disease has led to a movement away from the one-drug-fits-all paradigm towards treatment tailored to the genetic profile of the patient. The Biocartis Idylla platform is a novel fully automated, real-time PCR-based in vitro diagnostic system. The Idylla NRAS-BRAF mutation test has been developed for the qualitative detection of mutations in NRAS and BRAF oncogenes, facilitating genetic profiling of patients with cancer. The aim of this study was to carry out a formal clinical performance evaluation...
September 12, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28899967/circulating-cell-free-dna-for-metastatic-cervical-cancer-detection-genotyping-and-monitoring
#14
Zhigang Kang, Sanja Stevanović, Christian S Hinrichs, Liang Cao
PURPOSE: Circulating cell-free (ccf) human papillomavirus (HPV) DNA may serve as a unique tumor marker for HPV-associated malignancies, including cervical cancer. We developed a method to genotype and quantify circulating HPV DNA in patients with HPV16- or HPV18-positive metastatic cervical cancer for potential disease monitoring and treatment-related decision making. PATIENTS AND METHODS: In this retrospective study, HPV ccfDNA was measured in serum samples from 19 metastatic cervical cancer patients by duplex digital droplet (dd) PCR...
September 12, 2017: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
https://www.readbyqxmd.com/read/28898240/prevalence-of-signs-of-trachoma-ocular-chlamydia-trachomatis-infection-and-antibodies-to-pgp3-in-residents-of-kiritimati-island-kiribati
#15
Anaseini Cama, Andreas Müller, Raebwebwe Taoaba, Robert M R Butcher, Iakoba Itibita, Stephanie J Migchelsen, Tokoriri Kiauea, Harry Pickering, Rebecca Willis, Chrissy H Roberts, Ana Bakhtiari, Richard T Le Mesurier, Neal D E Alexander, Diana L Martin, Rabebe Tekeraoi, Anthony W Solomon
OBJECTIVE: In some Pacific Island countries, such as Solomon Islands and Fiji, active trachoma is common, but ocular Chlamydia trachomatis (Ct) infection and trachomatous trichiasis (TT) are rare. On Tarawa, the most populous Kiribati island, both the active trachoma sign "trachomatous inflammation-follicular" (TF) and TT are present at prevalences warranting intervention. We sought to estimate prevalences of TF, TT, ocular Ct infection, and anti-Ct antibodies on Kiritimati Island, Kiribati, to assess local relationships between these parameters, and to help determine the need for interventions against trachoma on Kiribati islands other than Tarawa...
September 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28891364/an-update-on-pcr-use-for-minimal-residual-disease-monitoring-in-acute-lymphoblastic-leukemia
#16
Vittorio Nunes, Gianni Cazzaniga, A Biondi
Acute lymphoblastic leukemia (ALL) is the first neoplasm where the assessment of early response to therapy by minimal residual disease (MRD) monitoring has proven to be a fundamental tool for guiding therapeutic choices. In recent years, thanks to real-time quantitative PCR (qPCR), MRD monitoring has further achieved higher levels of sensitivity and standardization. However, some outstanding issues still remain to be addressed and emerging technologies hold the promise of improving MRD detection in ALL patients...
September 11, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28881720/analysis-of-esr1-and-pik3ca-mutations-in-plasma-cell-free-dna-from-er-positive-breast-cancer-patients
#17
Takashi Takeshita, Yutaka Yamamoto, Mutsuko Yamamoto-Ibusuki, Mai Tomiguchi, Aiko Sueta, Keiichi Murakami, Yoko Omoto, Hirotaka Iwase
BACKGROUND: The measurement of ESR1 and PIK3CA mutations in plasma cell-free DNA (cfDNA) has been studied as a non-invasive method to quickly assess and monitor endocrine therapy (ET) resistant metastatic breast cancer (MBC) patients. METHODS: The subjects of this retrospective study were a total of 185 plasma samples from 86 estrogen receptor-positive BC patients, of which 151 plasma samples were from 69 MBC patients and 34 plasma samples were from 17 primary BC (PBC) patients...
August 8, 2017: Oncotarget
https://www.readbyqxmd.com/read/28881596/a-prediction-model-for-distinguishing-lung-squamous-cell-carcinoma-from-adenocarcinoma
#18
Hui Li, Zhengran Jiang, Qixin Leng, Fan Bai, Juan Wang, Xiaosong Ding, Yuehong Li, Xianghong Zhang, HongBin Fang, Harris G Yfantis, Lingxiao Xing, Feng Jiang
Accurate classification of squamous cell carcinoma (SCC) from adenocarcinoma (AC) of non-small cell lung cancer (NSCLC) can lead to personalized treatments of lung cancer. We aimed to develop a miRNA-based prediction model for differentiating SCC from AC in surgical resected tissues and bronchoalveolar lavage (BAL) samples. Expression levels of seven histological subtype-associated miRNAs were determined in 128 snap-frozen surgical lung tumor specimens by using reverse transcription-polymerase chain reaction (RT-PCR) to develop an optimal panel of miRNAs for acutely distinguishing SCC from AC...
August 1, 2017: Oncotarget
https://www.readbyqxmd.com/read/28872132/aqueous-droplets-used-as-enzymatic-microreactors-and-their-electromagnetic-actuation
#19
Huschyar Al-Kaidy, Kai Kuthan, Thomas Hering, Nils Tippkötter
For the successful implementation of microfluidic reaction systems, such as PCR and electrophoresis, the movement of small liquid volumes is essential. In conventional lab-on-a-chip-platforms, solvents and samples are passed through defined microfluidic channels with complex flow control installations. The droplet actuation platform presented here is a promising alternative. With it, it is possible to move a liquid drop (microreactor) on a planar surface of a reaction platform (lab-in-a-drop). The actuation of microreactors on the hydrophobic surface of the platform is based on the use of magnetic forces acting on the outer shell of the liquid drops which is made of a thin layer of superhydrophobic magnetite particles...
August 28, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28869259/anti-hyperlipidemic-effect-of-rice-bran-polysaccharide-and-its-potential-mechanism-in-high-fat-diet-mice
#20
Ying Nie, Feijun Luo, Long Wang, Tao Yang, Limin Shi, Xinhua Li, Junjun Shen, Wei Xu, Ting Guo, Qinlu Lin
Hyperlipidemia occurs very often in modern society along with a high calorie intake and is regarded as one of the greatest risk factors for the prevalence of cardiac vascular disease (CVD). In this study, we investigated the anti-hyperlipidemic effect of the rice bran polysaccharides (RBP) and its mechanism in a high fat diet animal model. 60 ICR mice were randomly divided into 3 groups, which included Control, HFD (high fat diet) and HFD + RBP, and each group included 20 mice. The control group was fed with a standard diet while the other two groups were fed with HFD...
September 4, 2017: Food & Function
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