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https://www.readbyqxmd.com/read/28094373/conformational-dynamics-and-self-association-of-intrinsically-disordered-huntingtin-exon-1-in-cells
#1
Steffen Büning, Abhishek Sharma, Shivang Vachharajani, Estella Newcombe, Angelique Ormsby, Mimi Gao, David Gnutt, Tobias Vöpel, Danny M Hatters, Simon Ebbinghaus
Huntington's disease is caused by a CAG trinucleotide expansion mutation in the Huntingtin gene that leads to an artificially long polyglutamine sequence in the Huntingtin protein. A key feature of the disease is the intracellular aggregation of the Huntingtin exon 1 protein (Httex1) into micrometer sized inclusion bodies. The aggregation process of Httex1 has been extensively studied in vitro, however, the crucial early events of nucleation and aggregation in the cell remain elusive. Here, we studied the conformational dynamics and self-association of Httex1 by in-cell experiments using laser-induced temperature jumps and analytical ultracentrifugation...
January 17, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28090285/pulmonary-vascular-and-ventricular-dysfunction-in-the-susceptible-patient-2015-grover-conference-series
#2
REVIEW
Bradley A Maron, Roberto F Machado, Larissa Shimoda
Pulmonary blood vessel structure and tone are maintained by a complex interplay between endogenous vasoactive factors and oxygen-sensing intermediaries. Under physiological conditions, these signaling networks function as an adaptive interface between the pulmonary circulation and environmental or acquired perturbations to preserve oxygenation and maintain systemic delivery of oxygen-rich hemoglobin. Chronic exposure to hypoxia, however, triggers a range of pathogenetic mechanisms that include hypoxia-inducible factor 1α (HIF-1α)-dependent upregulation of the vasoconstrictor peptide endothelin 1 in pulmonary endothelial cells...
December 2016: Pulmonary Circulation
https://www.readbyqxmd.com/read/28087462/impact-of-disease-linked-mutations-targeting-the-oligomerization-interfaces-of-aldehyde-dehydrogenase-7a1
#3
David A Korasick, John J Tanner, Michael T Henzl
Aldehyde dehydrogenase 7A1 (ALDH7A1) is involved in lysine catabolism, catalyzing the oxidation of α-aminoadipate semialdehyde to α-aminoadipate. Certain mutations in the ALDH7A1 gene, which are presumed to reduce catalytic activity, cause an autosomal recessive seizure disorder known as pyridoxine-dependent epilepsy (PDE). Although the genetic association between ALDH7A1 and PDE is well established, little is known about the impact of PDE-mutations on the structure and catalytic function of the enzyme. Herein we report the first study of the molecular consequences of PDE mutations using purified ALDH7A1 variants...
January 10, 2017: Chemico-biological Interactions
https://www.readbyqxmd.com/read/28076869/computational-prediction-of-the-global-functional-genomic-landscape-applications-methods-and-challenges
#4
Weiqiang Zhou, Ben Sherwood, Hongkai Ji
Technological advances have led to an explosive growth of high-throughput functional genomic data. Exploiting the correlation among different data types, it is possible to predict one functional genomic data type from other data types. Prediction tools are valuable in understanding the relationship among different functional genomic signals. They also provide a cost-efficient solution to inferring the unknown functional genomic profiles when experimental data are unavailable due to resource or technological constraints...
2016: Human Heredity
https://www.readbyqxmd.com/read/28074108/cellulolytic-robolector-towards-an-automated-high-throughput-screening-platform-for-recombinant-cellulase-expression
#5
Martina Mühlmann, Martin Kunze, Joaquim Ribeiro, Bertram Geinitz, Christian Lehmann, Ulrich Schwaneberg, Ulrich Commandeur, Jochen Büchs
BACKGROUND: Cellulases are key player in the hydrolyzation of cellulose. Unfortunately, this reaction is slow and a bottleneck in the process chain from biomass to intermediates and biofuels due to low activities of the enzymes. To overcome this draw back, a lot of effort is put into the area of protein engineering, to modify these enzymes by directed evolution or rational design. Huge clone libraries are constructed and have to be screened for improved variants. High-throughput screening is the method of choice to tackle this experimental effort, but up to now only a few process steps are adapted to automated platforms and little attention has been turned to the reproducibility of clone rankings...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28063150/mutants-of-ca-2-regulated-photoprotein-obelin-for-site-specific-conjugation
#6
Vasilisa V Krasitskaya, Ludmila P Burakova, Anastasia A Komarova, Eugenia E Bashmakova, Ludmila A Frank
Color variants of Ca(2+) -regulated photoprotein obelin were shown to be an important tool for dual-analyte binding assay. To provide site-directed conjugation with biospecific molecules, several obelin color mutants carrying unique cysteine residues were obtained and characterized for their novel properties. A pair of obelins Y138F,A5C and W92F,H22E,D12C was found to be most suitable (in terms of high bioluminescent activity and stability) as reporters in simultaneous assay of two targets in a sample. Availability of SH-groups, accessible for chemical modification essentially simplifies the synthesis of biospecific conjugates, increases their yield and conserves obelins' bioluminescence activity...
January 7, 2017: Photochemistry and Photobiology
https://www.readbyqxmd.com/read/28061744/comprehensive-evaluation-of-extracellular-small-rna-isolation-methods-from-serum-in-high-throughput-sequencing
#7
Yan Guo, Kasey Vickers, Yanhua Xiong, Shilin Zhao, Quanhu Sheng, Pan Zhang, Wanding Zhou, Charles R Flynn
BACKGROUND: DNA and RNA fractions from whole blood, serum and plasma are increasingly popular analytes that are currently under investigation for their utility in the diagnosis and staging of disease. Small non-coding ribonucleic acids (sRNAs), specifically microRNAs (miRNAs) and their variant isoforms (isomiRs), and transfer RNA (tRNA)-derived small RNAs (tDRs) comprise a repertoire of molecules particularly promising in this regard. RESULTS: In this designed study, we compared the performance of various methods and kits for isolating circulating extracellular sRNAs (ex-sRNAs)...
January 7, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28059047/the-elusive-nature-of-apoe-%C3%AE%C2%B54-in-mid-adulthood-understanding-the-cognitive-profile
#8
Claire Lancaster, Naji Tabet, Jennifer Rusted
OBJECTIVES: The apolipoprotein E (APOE) ε4 allele is an established risk factor for dementia, yet this genetic variant is associated with a mixed cognitive profile across the lifespan. This study undertakes both a systematic and meta-analytic review of research investigating APOE-related differences in cognition in mid-adulthood, when detrimental effects of the allele may first be detectable. METHODS: Thirty-six papers investigating the behavioral effects of APOE ε4 in mid-adulthood (defined as a mean sample age between 35 and 60 years) were reviewed...
January 6, 2017: Journal of the International Neuropsychological Society: JINS
https://www.readbyqxmd.com/read/28052061/integrated-genomic-characterization-of-oesophageal-carcinoma
#9
(no author information available yet)
Oesophageal cancers are prominent worldwide; however, there are few targeted therapies and survival rates for these cancers remain dismal. Here we performed a comprehensive molecular analysis of 164 carcinomas of the oesophagus derived from Western and Eastern populations. Beyond known histopathological and epidemiologic distinctions, molecular features differentiated oesophageal squamous cell carcinomas from oesophageal adenocarcinomas. Oesophageal squamous cell carcinomas resembled squamous carcinomas of other organs more than they did oesophageal adenocarcinomas...
January 4, 2017: Nature
https://www.readbyqxmd.com/read/28049581/validation-of-a-next-generation-sequencing-panel-for-detection-of-hotspot-cancer-mutations-in-a-clinical-laboratory
#10
Reza Shahsiah, Jenefer DeKoning, Saeed Samie, Seyed Ziaeddin Latifzadeh, Zahra Mehdizadeh Kashi
Recent advances in sequencing technologies have enabled us to scrutinize the versatile underlying mechanisms of cancer more precisely. However, adopting these new sophisticated technologies is challenging for clinical labs as it involves complex workflows, and requires validation for diagnostic purposes. The aim of this work is towards the analytical validation of a next generation sequencing (NGS) panel for cancer hotspot mutation analysis. Characterized formalin-fixed paraffin-embedded (FFPE) samples including biopsy specimens and cell-lines were examined by NGS methods utilizing the Ion Torrent™ Oncomine™ Focus DNA Assay and the PGM™ platform...
December 16, 2016: Pathology, Research and Practice
https://www.readbyqxmd.com/read/28049435/detecting-very-low-allele-fraction-variants-using-targeted-dna-sequencing-and-a-novel-molecular-barcode-aware-variant-caller
#11
Chang Xu, Mohammad R Nezami Ranjbar, Zhong Wu, John DiCarlo, Yexun Wang
BACKGROUND: Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy...
January 3, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28047435/mo-de-bra-06-3d-image-acquisition-and-reconstruction-explained-with-online-animations
#12
A Kesner
PURPOSE: Understanding the principles of 3D imaging and image reconstruction is fundamental to the field of medical imaging. Clinicians, technologists, physicists, patients, students, and inquisitive minds all stand to benefit from greater comprehension of the supporting technologies. To help explain the basic principles of 3D imaging, we developed multi-frame animations that convey the concepts of tomographic imaging. The series of free (gif) animations are accessible online, and provide a multimedia introduction to the main concepts of image reconstruction...
June 2016: Medical Physics
https://www.readbyqxmd.com/read/28045981/hpv-genotyping-of-modified-general-primer-amplicons-is-more-analytically-sensitive-and-specific-by-sequencing-than-by-hybridization
#13
Roger Meisal, Trine Ballestad Rounge, Irene Kraus Christiansen, Alexander Kirkeby Eieland, Merete Molton Worren, Tor Faksvaag Molden, Øyvind Kommedal, Eivind Hovig, Truls Michael Leegaard, Ole Herman Ambur
Sensitive and specific genotyping of human papillomaviruses (HPVs) is important for population-based surveillance of carcinogenic HPV types and for monitoring vaccine effectiveness. Here we compare HPV genotyping by Next Generation Sequencing (NGS) to an established DNA hybridization method. In DNA isolated from urine, the overall analytical sensitivity of NGS was found to be 22% higher than that of hybridization. NGS was also found to be the most specific method and expanded the detection repertoire beyond the 37 types of the DNA hybridization assay...
2017: PloS One
https://www.readbyqxmd.com/read/28026089/synonymous-somatic-variants-in-human-cancer-are-not-infamous-a-plea-for-full-disclosure-in-databases-and-publications
#14
Thierry Soussi, Peter E M Taschner, Yardena Samuels
Single Nucleotide Variants (SNVs) are the most frequent genetic changes found in human cancer. Most driver alterations are missense and nonsense variants localized in the coding region of cancer genes. Unbiased cancer genome sequencing shows that synonymous SNVs (sSNVs) can be found clustered in the coding regions of several cancer oncogenes or tumor suppressor genes suggesting purifying selection. sSNVs are currently underestimated, as they are usually discarded during analysis. Furthermore, several public databases do not display sSNVs, which can lead to analytical bias and the false assumption that this mutational event is uncommon...
December 27, 2016: Human Mutation
https://www.readbyqxmd.com/read/28025028/ifcc-approved-hplc-reference-measurement-procedure-for-the-alcohol-consumption-biomarker-carbohydrate-deficient-transferrin-cdt-its-validation-and-use
#15
François Schellenberg, Jos Wielders, Raymond Anton, Vincenza Bianchi, Jean Deenmamode, Cas Weykamp, John Whitfield, Jan-Olof Jeppsson, Anders Helander
Carbohydrate-deficient transferrin (CDT) is used as a biomarker of sustained high alcohol consumption. The currently available measurement procedures for CDT are based on various analytical techniques (HPLC, capillary electrophoresis, nephelometry), some differing in the definition of the analyte and using different reference intervals and cut-off values. The Working Group on Standardization of CDT (WG-CDT), initiated by the International Federation of Clinical Chemistry and Laboratory Medicine (IFCC), has validated an HPLC candidate reference measurement procedure (cRMP) for CDT (% disialotransferrin to total transferrin based on peak areas), demonstrating that it is suitable as a reference measurement procedure (RMP) for CDT...
December 23, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28017569/a-targeted-high-throughput-next-generation-sequencing-panel-for-clinical-screening-of-mutations-gene-amplifications-and-fusions-in-solid-tumors
#16
Rajyalakshmi Luthra, Keyur P Patel, Mark J Routbort, Russell R Broaddus, Jonathan Yau, Crystal Simien, Wei Chen, David Z Hatfield, L Jeffrey Medeiros, Rajesh R Singh
Clinical next-generation sequencing (NGS) assay choice requires careful consideration of panel size, inclusion of appropriate markers, ability to detect multiple genomic aberration types, compatibility with low quality and quantity of nucleic acids, and work flow feasibility. Herein, in a high-volume clinical molecular diagnostic laboratory, we have validated a targeted high-multiplex PCR-based NGS panel (OncoMine Comprehensive Assay) coupled with high-throughput sequencing using Ion Proton sequencer for routine screening of solid tumors...
December 22, 2016: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28003950/toward-understanding-the-impacts-of-sediment-contamination-on-a-native-fish-species-transcriptional-effects-erod-activity-and-biliary-pah-metabolites
#17
Sven Koglin, Ulrike Kammann, Kathrin Eichbaum, Mathias Reininghaus, Bryanna Eisner, Steve Wiseman, Markus Hecker, Sebastian Buchinger, Georg Reifferscheid, Henner Hollert, Markus Brinkmann
BACKGROUND: Both frequency and intensity of flood events are expected to increase as a result of global climate change in the upcoming decades, potentially resulting in increased re-suspension of sediments in fluvial systems. Contamination of these re-suspended sediments with legacy contaminants, including dioxins and dioxin-like compounds (DLCs), as well as polycyclic aromatic hydrocarbons (PAHs) is of great ecotoxicological concern. DLCs, and to some extent also PAHs, exhibit their toxicity through activation of the aryl hydrocarbon receptor (AhR)...
2016: Environmental Sciences Europe
https://www.readbyqxmd.com/read/28003583/optimizing-an-ion-semiconductor-sequencing-data-analysis-method-to-identify-somatic-mutations-in-the-genomes-of-cancer-cells-in-clinical-tissue-samples
#18
Takeshi Nagashima, Yuji Shimoda, Tomoe Tanabe, Akane Naruoka, Junko Saito, Masakuni Serizawa, Keiichi Ohshima, Kenichi Urakami, Sumiko Ohnami, Shumpei Ohnami, Tohru Mochizuki, Masatoshi Kusuhara, Ken Yamaguchi
Identification of causal genomic alterations is an indispensable step in the implementation of personalized cancer medicine. Analytical methods play a central role in identifying such changes because of the vast amount of data produced by next generation sequencer. Most analytical techniques are designed for the Illumina platform and are therefore suboptimal for analyzing datasets generated by whole exome sequencing (WES) using the Ion Proton System. Accurate identification of somatic mutations requires the characterization of platform-dependent error profiles and genomic properties that affect the accuracy of sequence data as well as platform-oriented optimization of the pipeline...
2016: Biomedical Research
https://www.readbyqxmd.com/read/28003547/detection-of-prions-in-the-plasma-of-presymptomatic-and-symptomatic-patients-with-variant-creutzfeldt-jakob-disease
#19
Daisy Bougard, Jean-Philippe Brandel, Maxime Bélondrade, Vincent Béringue, Christiane Segarra, Hervé Fleury, Jean-Louis Laplanche, Charly Mayran, Simon Nicot, Alison Green, Arlette Welaratne, David Narbey, Chantal Fournier-Wirth, Richard Knight, Robert Will, Pierre Tiberghien, Stéphane Haïk, Joliette Coste
Variant Creutzfeldt-Jakob disease (vCJD) is a human prion disease resulting from the consumption of meat products contaminated by the agent causing bovine spongiform encephalopathy. Evidence supporting the presence of a population of silent carriers that can potentially transmit the disease through blood transfusion is increasing. The development of a blood-screening assay for both symptomatic vCJD patients and asymptomatic carriers is urgently required. We show that a diagnostic assay combining plasminogen-bead capture and protein misfolding cyclic amplification (PMCA) technologies consistently detected minute amounts of abnormal prion protein from French and British vCJD cases in the required femtomolar range...
December 21, 2016: Science Translational Medicine
https://www.readbyqxmd.com/read/28003022/the-variability-and-reproducibility-of-whole-genome-sequencing-technology-for-detecting-resistance-to-anti-tuberculous-drugs
#20
Jody Phelan, Denise M O'Sullivan, Diana Machado, Jorge Ramos, Alexandra S Whale, Justin O'Grady, Keertan Dheda, Susana Campino, Ruth McNerney, Miguel Viveiros, Jim F Huggett, Taane G Clark
BACKGROUND: The emergence of resistance to anti-tuberculosis drugs is a serious and growing threat to public health. Next-generation sequencing is rapidly gaining traction as a diagnostic tool for investigating drug resistance in Mycobacterium tuberculosis to aid treatment decisions. However, there are few little data regarding the precision of such sequencing for assigning resistance profiles. METHODS: We investigated two sequencing platforms (Illumina MiSeq, Ion Torrent PGM™) and two rapid analytic pipelines (TBProfiler, Mykrobe predictor) using a well characterised reference strain (H37Rv) and clinical isolates from patients with tuberculosis resistant to up to 13 drugs...
December 22, 2016: Genome Medicine
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