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Plasma dna

Nicholas B Larson, Chen Wang, Jie Na, Ross A Rowsey, William Edward Highsmith, Nicole L Hoppman, Jean-Pierre Kocher, Eric W Klee
The recent advances in next-generation sequencing (NGS) technologies have enabled the development of effective high-throughput noninvasive prenatal screening (NIPS) assays for fetal genetic abnormalities using maternal circulating cell-free DNA (ccfDNA). An important NIPS quality assurance is quantifying the fetal proportion of the sampled ccfDNA. For methods using allelic read count ratios from targeted sequencing of single-nucleotide polymorphisms (SNPs), systematic biases and errors may reduce accuracy and diminish assay performance...
June 22, 2018: Journal of Computational Biology: a Journal of Computational Molecular Cell Biology
D Sculier, T Doco-Lecompte, S Yerly, K J Metzner, L A Decosterd, A Calmy
OBJECTIVES: Dolutegravir (DTG) is a highly effective integrase inhibitor with a strong genetic resistance barrier and a potential role in simplified HIV maintenance treatment. We assessed the feasibility of DTG maintenance monotherapy and measured HIV reservoirs on DTG monotherapy. METHODS: An interventional, open-label, single-arm study including eight virologically suppressed HIV-1-infected patients switched to DTG 50 mg once daily for 24 weeks was performed...
June 22, 2018: HIV Medicine
Z Yang, H M Yang, D Q Gong, S P Rose, V Pirgozliev, X S Chen, Z Y Wang
Dietary methionine (Met) restriction produces a coordinated series of transcriptional responses in the liver that limits growth performance and amino acid metabolism. Methyl donor supplementation with betaine (Bet) may protect against this disturbance and affect the molecular basis of gene regulation. However, a lack of genetic information remains an obstacle to understand the mechanisms underlying the relationship between Met and Bet supplementation and its effects on genetic mechanisms. The goal of this study was to identify the effects of dietary supplementation of Met and Bet on growth performance, transcriptomic gene expression, and epigenetic mechanisms in geese on a Met-deficient diet...
June 20, 2018: Poultry Science
G Le Conte, A Letourneau, J Jani, P Kleinfinger, L Lohmann, J-M Costa, A Benachi
OBJECTIVES: To evaluate the performance of noninvasive prenatal testing by cell-free circulating fetal DNA in maternal blood (cfDNA) in screening for trisomies 21 in twin pregnancies. METHODS: CfDNA was performed in 492 patients with twin pregnancies without ultrasound anomalies in the first trimester as a first-line screening test or after serum screening. Data were collected prospectively and a retrospective analysis was done. CfDNA was executed by massive parallel technique...
June 18, 2018: Gynecologie, Obstetrique, Fertilite & Senologie
Oliver J Harrison, Felino Cagampang, Sunil K Ohri, Christopher Torrens, Kareem Salhiyyah, Amit Modi, Narain Moorjani, Anthony D Whetton, Paul A Townsend
BACKGROUND: Bicuspid aortic valve (BAV) disease is the most common congenital cardiac abnormality affecting 1-2% of the population and is associated with a significantly increased risk of ascending aortic aneurysm. However, predicting which patients will develop aneurysms remains a challenge. This pilot study aimed to identify candidate plasma biomarkers for monitoring ascending aortic diameter and predicting risk of future aneurysm in BAV patients. METHODS: Plasma samples were collected pre-operatively from BAV patients undergoing aortic valve surgery...
June 22, 2018: Journal of Cardiothoracic Surgery
Maite Mendioroz, Leyre Martínez-Merino, Idoia Blanco-Luquin, Amaya Urdánoz, Miren Roldán, Ivonne Jericó
Noninvasive tests to diagnose and monitor the progression of neurodegenerative disorders have been a challenge for decades. The aim of this study was to explore the feasibility of applying liquid biopsy procedures to patients with a neurodegenerative disease such as amyotrophic lateral sclerosis (ALS). We isolated plasma cell-free DNA (cfDNA) in 20 ALS patients and 20 controls and used cfDNA to identify a novel differentially methylated mark in RHBDF2 gene in ALS patients compared to controls. Our findings support the notion that liquid biopsy may be applied to living patients as a source of potential epigenetic biomarkers for neurodegenerative disorders...
June 2018: Annals of Clinical and Translational Neurology
Paolo Gamba, Luigina Rota, C Abeni, Alessandra Huscher, Gabriele Saldi, Alberto Soregaroli, Elena Padolecchia, Fausto Zorzi, Mario Bignardi, Alberto Zaniboni
Nasopharyngeal carcinoma (NPC) is an epithelial malignancy, with a high metastatic potential. Epstein-Barr virus (EBV) infection plays a fundamental role, even if it is not well understood. The diagnosis of the disease in its early stage is infrequent. Imaging studies, positron emission tomography scans in addition to clinical examination, endoscopic examination, and biopsy provide information on the extent of the disease. The application of neoadjuvant chemotherapy followed by concomitant chemoradiation can improve the control of NPC...
May 2018: Case Reports in Oncology
Yoshiteru Noda, Takema Kato, Asuka Kato, Haruki Nishizawa, Jun Miyazaki, Mayuko Ito, Sumire Terasawa, Takao Sekiya, Takuma Fujii, Hiroki Kurahashi
Examination of maternal plasma cell free DNA (cfDNA) for noninvasive prenatal testing for fetal trisomy is a highly effective method for pregnant women at high risk. This can be also applied to fetal gender determination in female carriers of severe X-linked disease. PCR analysis is a relatively simpler and less expensive method of detecting Y chromosome-specific repeats (Y-specific PCR; YSP), but is limited by the risk of false-negative results. To address this, we have developed a combined strategy incorporating YSP and an estimation of the fetal DNA fraction...
June 21, 2018: Congenital Anomalies
Eva Tvrdá, Francisca Arroyo, Jaime Gosálvez
AIM: The purpose of the study was to evaluate the impact of seminal plasma in human ejaculates on the sperm DNA quality and DNA longevity. METHODS: Semen samples for this study were obtained from 20 donors with a normal spermiogram. Following centrifugation, the sperm pellet was resuspended either in the seminal plasma proceeding from its respective donor, or in an equal amount of PBS, adjusting the concentration to 50 × 106 /ml. Each set of samples was incubated at 37 °C for 24 h and the sperm DNA damage was assessed using the chromatin-dispersion test following 0, 2, 6, and 24 h of incubation...
June 20, 2018: International Urology and Nephrology
Roni Lehmann-Werman, Judith Magenheim, Joshua Moss, Daniel Neiman, Ofri Abraham, Sheina Piyanzin, Hai Zemmour, Ilana Fox, Talya Dor, Markus Grompe, Giora Landesberg, Bao-Li Loza, Abraham Shaked, Kim Olthoff, Benjamin Glaser, Ruth Shemer, Yuval Dor
Liver damage is typically inferred from serum measurements of cytoplasmic liver enzymes. DNA molecules released from dying hepatocytes are an alternative biomarker, unexplored so far, potentially allowing for quantitative assessment of liver cell death. Here we describe a method for detecting acute hepatocyte death, based on quantification of circulating, cell-free DNA (cfDNA) fragments carrying hepatocyte-specific methylation patterns. We identified 3 genomic loci that are unmethylated specifically in hepatocytes, and used bisulfite conversion, PCR, and massively parallel sequencing to quantify the concentration of hepatocyte-derived DNA in mixed samples...
June 21, 2018: JCI Insight
Zhiqian Zhang, Changli Zhong, Taixian Yuan, Xiaoyan Zhou, Min Zhao, Husun Qian, Wei Cheng, Tingmei Chen
A hybridized chain reaction (HCR)-based biosensing method has been developed for the imaging detection of intracellular telomerase activity. The telomerase-targeting responder-transmitter DNA complex (HPT) consisting of telomerase primer sequence (HP) and a HCR initiator (trigger) is transfected into cell plasma. In the presence of telomerase, HPT can be recognized and extended, producing plenty of triggers which initiates HCR amplification reaction. Finally, a long nicked dsDNA with a lot of outstretched single chains was formed by hybridizing with Q of the reporter complex, generating an enhanced fluorescence signal...
June 20, 2018: Methods and Applications in Fluorescence
Yu-Chen Wang, An-Sheng Lee, Long-Sheng Lu, Liang-Yin Ke, Wei-Yu Chen, Jian-Wen Dong, Jonathan Lu, Zhenping Chen, Chih-Sheng Chu, Hua-Chen Chan, Taha Y Kuzan, Ming-Hsien Tsai, Wen-Li Hsu, Richard A F Dixon, Tatsuya Sawamura, Kuan-Cheng Chang, Chu-Huang Chen
Dysregulation of plasma lipids is associated with age-related cardiovascular diseases. L5, the most electronegative subfraction of chromatographically resolved low-density lipoprotein (LDL), induces endothelial dysfunction, whereas the least electronegative subfraction, L1, does not. In this study, we examined the effects of L5 on endothelial senescence and its underlying mechanisms. C57B6/J mice were intravenously injected with L5 or L1 (2 mg kg-1  day-1 ) from human plasma. After 4 weeks, nuclear γH2AX deposition and senescence-associated β-galactosidase staining indicative of DNA damage and premature senescence, respectively, were increased in the aortic endothelium of L5-treated but not L1-treated mice...
June 19, 2018: Aging Cell
Irene Jiménez, Mathieu Chicard, Léo Colmet-Daage, Nathalie Clément, Adrien Danzon, Eve Lapouble, Gaelle Pierron, Mylène Bohec, Sylvain Baulande, Dominique Berrebi, Paul Fréneaux, Aurore Coulomb, Louise Galmiche-Rolland, Sabine Sarnacki, Georges Audry, Pascale Philippe-Chomette, Hervé J Brisse, François Doz, Jean Michon, Olivier Delattre, Gudrun Schleiermacher
Circulating tumor DNA (ctDNA) is a powerful tool for the molecular characterization of cancer. The most frequent pediatric kidney tumors (KT) are Wilms' tumors (WT), but other diagnoses may occur. According to the SIOP strategy, in most countries pediatric KT have a presumptive diagnosis of WT if they are clinically and radiologically compatible. The histologic confirmation is established after post-chemotherapy nephrectomy. Thus, there is a risk for a small fraction of patients to receive neoadjuvant chemotherapy that is not adapted to the disease...
June 19, 2018: International Journal of Cancer. Journal International du Cancer
Chang-Liang Luo, Zhi-Gao Xu, Hao Chen, Jia Ji, Yu-Hui Wang, Wei Hu, Kun Wang, Wu-Wen Zhang, Chun-Hui Yuan, Fu-Bing Wang
Background: Tissue biopsy-based cancer diagnosis has limitations because of the fact that tumor tissues are in constant evolution and extremely heterogeneous. The current study was aimed to examine whether tumor-educated blood platelets (TEPs) might be a potential all-in-one source for blood-based cancer diagnostics to overcome the limitations of conventional cancer biopsy. Methods: In the present study, we evaluated the expression pattern of MAGI2 antisense RNA 3 ( MAGI2-AS3 ) and ZNFX1 antisense RNA 1 ( ZFAS1 ) in both plasma and platelets of 101 non-small-cell lung cancer (NSCLC) patients...
2018: Cancer Management and Research
Keigo Kobayashi, Katsuhiko Naoki, Tadashi Manabe, Keita Masuzawa, Hanako Hasegawa, Hiroyuki Yasuda, Ichiro Kawada, Kenzo Soejima, Tomoko Betsuyaku
Background: Osimertinib, a third-generation epidermal growth factor receptor-tyrosine kinase inhibitor, exerts remarkable effects against EGFR T790M resistance mutation-positive non-small cell lung cancer. Identifying T790M mutation by re-biopsy is essential before prescribing osimertinib. Tissue biopsy is the golden standard for this purpose, but several factors limit its success rate. The liquid biopsy with blood, using circulating tumor DNA, has been an alternative method. However, the true biological meaning and equivalence of liquid biopsy and tumor biopsy are still under investigation...
2018: OncoTargets and Therapy
Sadia Naz, Muhammad Umair, Sajid Iqbal
Our objectives were to ascertain the comparison of Tris egg yolk-based, Triladyl® and Optixell® extender on postthaw quality, CASA parameters and in vivo fertility of Nili Ravi buffalo (Bubalus bubalis) bull spermatozoa. Semen samples (n = 35) from five bulls were diluted in Tris egg yolk-based, Triladyl® , Optixell® extender and frozen in 0.50 ml French straws. Postthaw sperm CASA motility (%) was higher (p < 0.05) in Optixell extender as compared to Triladyl and Tris egg yolk-based extender. Although sperm progressive motility (%), morphology (%), average path velocity (μm/s), straight line velocity (μm/s), curvilinear velocity (μm/s), amplitude of lateral head displacement (μm), beat cross-frequency (Hz), straightness (%), length of curvilinear path (μm), length of average path (μm), intact plasma and acrosome membrane (%), and DNA integrity (%) were higher (p < 0...
June 19, 2018: Andrologia
Anne Grosen, Jacob Nersting, Mona Bungum, Lisbet Ambrosius Christensen, Kjeld Schmiegelow, Marcello Spanò, Mette Julsgaard, Eugenia Cordelli, Giorgio Leter, Peter Braad Larsen, Christian Lodberg Hvas, Jens Kelsen
Background & Aims: Sperm DNA integrity, concentration and motility are suspected to be altered by thiopurines (azathioprine (AZA) and 6-mercaptopurine (6-MP)). We investigated the impact of thiopurines on semen quality in men with inflammatory bowel disease (IBD) by a comprehensive panel of semen analyses. Methods: Semen from 40 men with IBD in remission on AZA/6-MP therapy was prospectively collected and compared with samples from 40 healthy volunteers. Paired samples (off and on AZA/6-MP) were obtained from a subset of IBD patients, and blood and semen were collected to determine 6-MP transmission to the ejaculate...
June 16, 2018: Journal of Crohn's & Colitis
Li Guo, Ruobing Xu, Lu Gou, Zhichao Liu, Yiming Zhao, Dingxin Liu, Lei Zhang, Hailan Chen, Michael G Kong
Viruses are serious pathogenic contamination that severely affect the environment and human health. Cold atmospheric-pressure plasma efficiently inactivates pathogenic bacteria, however, the mechanism of virus inactivation by plasma is not fully understood. In this study, surface plasma in argon mixed with 1% air and plasma-activated water were used to treat water containing bacteriophages. Both agents efficiently inactivated bacteriophages T4, Φ174, and MS2 in a time-dependent manner. Prolonged storage had marginal effects on the anti-viral activity of plasma-activated water...
June 18, 2018: Applied and Environmental Microbiology
M Cabanero, M S Tsao
The advent of targeted therapy in non-small-cell lung cancer (nsclc) has made the routine molecular diagnosis of EGFR mutations crucial for optimal patient management. Obtaining tumour tissue for biomarker testing, especially in the setting of re-biopsy, can present many challenges. A potential alternative source of tumour dna is circulating cell-free tumour-derived dna (ctdna). Although ctdna is present in low quantities in plasma, the convenience of sample acquisition and the increasing reliability of detection methods make this approach a promising one...
June 2018: Current Oncology
Jyotirmaya Behera, Akash K George, Michael J Voor, Suresh C Tyagi, Neetu Tyagi
Hydrogen sulfide (H2 S) is a novel gasotransmitter produced endogenously in mammalian cells, which works by mediating diverse physiological functions. An imbalance in H2 S metabolism is associated with defective bone homeostasis. However, it is unknown whether H2 S plays any epigenetic role in bone loss induced by hyperhomocysteinemia (HHcy). We demonstrate that diet-induced HHcy, a mouse model of metabolite induced osteoporosis, alters homocysteine metabolism by decreasing plasma levels of H2 S. Treatment with NaHS (H2 S donor), normalizes the plasma level of H2 S and further alleviates HHcy induced trabecular bone loss and mechanical strength...
June 13, 2018: Bone
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