keyword
MENU ▼
Read by QxMD icon Read
search

variant analytics

keyword
https://www.readbyqxmd.com/read/28550058/whole-genome-and-core-genome-multilocus-sequence-typing-and-single-nucleotide-polymorphism-analyses-of-listeria-monocytogenes-associated-with-an-outbreak-linked-to-cheese-united-states-2013
#1
Yi Chen, Yan Luo, Heather Carleton, Ruth Timme, David Melka, Tim Muruvanda, Charles Wang, George Kastanis, Lee S Katz, Lauren Turner, Angela Fritzinger, Terence Moore, Robert Stones, Joseph Blankenship, Monique Salter, Mickey Parish, Thomas S Hammack, Peter S Evans, Cheryl L Tarr, Marc W Allard, Errol A Strain, Eric W Brown
Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by Company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative isolates collected from Company A cheese and environmental samples during the investigation. The results strengthened the evidence for cheese as the vehicle. Surveillance sampling and WGS three months later revealed that the equipment purchased by Company B from Company A yielded an environmental isolate highly similar to all outbreak isolates...
May 26, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28549280/protocols-for-the-analytical-characterization-of-therapeutic-monoclonal-antibodies-i-non-denaturing-chromatographic-techniques
#2
Alexandre Goyon, Valentina D'Atri, Balazs Bobaly, Elsa Wagner-Rousset, Alain Beck, Szabolcs Fekete, Davy Guillarme
Size-, charge- and hydrophobicity-related variants of a biopharmaceutical product have to be deeply characterized for batch consistency and for the assessment of immunogenicity and safety effects. Size exclusion chromatography (SEC) and ion exchange chromatography (IEX) are considered as the gold standard for the analysis of high molecular weight species (HMWS) and charge-related variants, respectively. Hydrophobic interaction chromatography (HIC) has drawn renewed attention to monitor the small drug payload distribution in the cysteine-linked antibody-drug conjugates (ADC)...
May 11, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28544059/objective-assessment-of-the-evolutionary-action-equation-for-the-fitness-effect-of-missense-mutations-across-cagi-blinded-contests
#3
Panagiotis Katsonis, Olivier Lichtarge
A major challenge in genome interpretation is to estimate the fitness effect of coding variants of unknown significance (VUS). Labor, limited understanding of protein functions, and lack of assays generally limit direct experimental assessment of VUS, and make robust and accurate computational approaches a necessity. Often, however, algorithms that predict mutational effect disagree amongst themselves and with experimental data, slowing their adoption for clinical diagnostics. To objectively assess such methods, the Critical Assessment of Genome Interpretation (CAGI) community organizes contests to predict unpublished experimental data, available only to CAGI assessors...
May 23, 2017: Human Mutation
https://www.readbyqxmd.com/read/28543614/capillarys-2-flex-piercing-analytical-performance-assessment-according-to-clsi-protocols-for-hba1c-quantification
#4
Radhouene Doggui, Chaïma Abdelhafidh Sahli, Wassef Lotfi Aissa, Maroua Hammami, Maha Ben Sedrine, Rahma Mahjoub, Khemais Zouaoui, Rim Daboubi, Hajer Siala, Taieb Messaoud, Amina Bibi
HbA1c is used for monitoring diabetic balance. In this paper we report an assessment of the analytical performances of Capillarys 2 Flex Piercing (C2FP) for HbA1c measurement using CE (Capillary Electrophoresis). CLSI (Clinical and Laboratory Standard Institute) protocols are used for the evaluation of apparatus performances: precision, linearity, method comparison, truness and common interferences. HbA1c CVs average in intra-assay was 1.6% between run imprecision CV ranged from0.1 to 1.8%. The linearity was demonstrated between 4...
May 19, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28542587/seminal-plasma-induces-inflammation-and-enhances-hiv-1-replication-in-human-cervical-tissue-explants
#5
Andrea Introini, Stéphanie Boström, Frideborg Bradley, Anna Gibbs, Axel Glaessgen, Annelie Tjernlund, Kristina Broliden
The most immediate and evident effect of mucosal exposure to semen in vivo is a local release of proinflammatory mediators accompanied by an influx of leukocytes into the female genital mucosa (FGM). The implication of such response in HIV-1 transmission has never been addressed due to limitations of currently available experimental models. Using human tissue explants from the uterine cervix, we developed a system of mucosal exposure to seminal plasma (SP) that supports HIV-1 replication. Treatment of ectocervical explants with SP resulted in the upregulation of inflammatory and growth factors, including IL-6, TNF, CCL5, CCL20, CXCL1, and CXCL8, and IL1A, CSF2, IL7, PTGS2, as evaluated by measuring protein levels in explant conditioned medium (ECM) and gene expression in tissue...
May 19, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28535921/out-of-field-in-vivo-dosimetry-using-tld-in-sabr-for-primary-kidney-cancer-involving-mixed-photon-fields
#6
P Lonski, S Keehan, S Siva, D Pham, R D Franich, M L Taylor, T Kron
PURPOSE: To assess out-of-field dose using three different variants of LiF thermoluminescence dosimeters (TLD) for ten patients who underwent stereotactic ablative body radiotherapy (SABR) for primary renal cell carcinoma (RCC) and compare with treatment planning system (TPS) dose calculations. METHODS AND MATERIALS: Thermoluminescent dosimeter (TLD) measurements were conducted at 20, 30, 40 and 50cm from isocentre on ten patients undergoing SABR for primary RCC...
May 2017: Physica Medica: PM
https://www.readbyqxmd.com/read/28533135/enhanced-local-disorder-in-a-clinically-elusive-von-willebrand-factor-provokes-high-affinity-platelet-clumping
#7
Alexander Tischer, Venkata R Machha, Juan P Frontroth, Maria A Brehm, Tobias Obser, Reinhard Schneppenheim, Leland Mayne, S Walter Englander, Matthew Auton
Mutation of the cysteines forming the disulfide loop of the platelet GPIbα adhesive A1 domain of von Willebrand factor causes quantitative VWF deficiencies in the blood and von Willebrand disease. We report two cases of transient severe thrombocytopenia induced by DDAVP-treatment. Cys1272Trp and Cys1458Tyr mutations identified by genetic sequencing implicate an abnormal gain-of-function phenotype, evidenced by thrombocytopenia, that quickly relapses back to normal platelet counts and deficient plasma VWF. Using surface plasmon resonance, analytical rheology, and hydrogen-deuterium exchange mass spectrometry (HXMS), we decipher mechanisms of A1-GPIbα mediated platelet adhesion and resolve dynamic secondary structure elements that regulate the binding pathway...
May 19, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28502727/concordance-between-research-sequencing-and-clinical-pharmacogenetic-genotyping-in-the-emerge-pgx-study
#8
Laura J Rasmussen-Torvik, Berta Almoguera, Kimberly F Doheny, Robert R Freimuth, Adam S Gordon, Hakon Hakonarson, Jared B Hawkins, Ammar Husami, Lynn Ivacic, Iftikhar J Kullo, Michael D Linderman, Teri A Manolio, Aniwaa O Obeng, Renata Pellegrino, Cynthia A Prows, Marylyn D Ritchie, Maureen Smith, Sarah C Stallings, Wendy A Wolf, Kejian Zhang, Stuart A Scott
There has been extensive debate about both the necessity of orthogonal confirmation of next-generation sequencing (NGS) results in Clinical Laboratory Improvement Amendments-approved laboratories and return of research NGS results to participants enrolled in research studies. In eMERGE-PGx, subjects underwent research NGS using PGRNseq and orthogonal targeted genotyping in clinical laboratories, which prompted a comparison of genotyping results between platforms. Concordance (percentage agreement) was reported for 4077 samples tested across nine combinations of research and clinical laboratories...
May 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28502726/utility-of-nist-whole-genome-reference-materials-for-the-technical-validation-of-a-multigene-next-generation-sequencing-test
#9
Bennett O V Shum, Ilya Henner, Daniele Belluoccio, Marcus J Hinchcliffe
The sensitivity and specificity of next-generation sequencing laboratory developed tests (LDTs) are typically determined by an analyte-specific approach. Analyte-specific validations use disease-specific controls to assess an LDT's ability to detect known pathogenic variants. Alternatively, a methods-based approach can be used for LDT technical validations. Methods-focused validations do not use disease-specific controls but use benchmark reference DNA that contains known variants (benign, variants of unknown significance, and pathogenic) to assess variant calling accuracy of an NGS workflow...
May 11, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28501176/liquid-chromatography-high-resolution-mass-spectrometric-methods-for-the-surveillance-monitoring-of-cyanotoxins-in-freshwaters
#10
Sara Bogialli, Claudio Bortolini, Iole Maria Di Gangi, Federica Nigro Di Gregorio, Luca Lucentini, Gabriella Favaro, Paolo Pastore
A comprehensive risk management on human exposure to cyanotoxins, whose production is actually unpredictable, is limited by reliable analytical tools for monitoring as many toxic algal metabolites as possible. Two analytical approaches based on a LC-QTOF system for target analysis and suspect screening of cyanotoxins in freshwater were presented. A database with 369 compounds belonging to cyanobacterial metabolites was developed and used for a retrospective data analysis based on high resolution mass spectrometry (HRMS)...
August 1, 2017: Talanta
https://www.readbyqxmd.com/read/28493134/glycosylation-analysis-of-therapeutic-glycoproteins-produced-in-cho-cells
#11
Sara Carillo, Stefan Mittermayr, Amy Farrell, Simone Albrecht, Jonathan Bones
In the last decades, the number of approved therapeutic proteins drugs is increasing exponentially and a large number of new therapeutic entities are progressing through clinical trials, solidifying biologics as the most promising class of pharmaceuticals on the market. Several cell lines are available for biopharmaceutical processes but mammalian cells are preferred since they give fewer problems for immunogenicity as they produce human-like post-translational modifications (PTMs). Glycosylation is the most common and complex (for both bioprocess engineering and quality control) of these modifications...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28487120/surface-anchored-counterions-on-weak-chiral-anion-exchangers-accelerate-separations-and-improve-their-compatibility-for-mass-spectrometry-hyphenation
#12
Ulrich Woiwode, Adrian Sievers-Engler, Aleksandra Zimmermann, Wolfgang Lindner, Orlando L Sánchez-Muñoz, Michael Lämmerhofer
In the present work we propose new variants of chiral stationary phases (CSP) with tert-butylcarbamoylquinine (tBuCQN) as chiral selector molecule. Four tBuCQN-CSPs with distinct bonding chemistries are compared in terms of their pH-dependent surface charge by ζ-potential determinations, by achiral and chiral liquid chromatographic tests and LC-ESI-MS hyphenation. In one embodiment tBuCQN was immobilized on 3-mercaptopropylmethylsilyl-modified silica by thiol-ene click reaction (brush type CSP with selector coverage of 0...
April 28, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28473221/cyp2c19-activity-and-cardiovascular-risk-factors-in-patients-with-an-acute-coronary-syndrome
#13
Efrén Martínez-Quintana, Fayna Rodríguez-González, José María Medina-Gil, Paloma Garay-Sánchez, Antonio Tugores
INTRODUCTION: CYP2C19 is a major isoform of cytochrome P450 that metabolizes a number of drugs and is involved in the glucocorticoids synthesis. CYP2C19 polymorphisms have been associated with the genetic risk for type 2 diabetes. METHODS: Five hundred and three patients with an acute coronary event were studied to assess the association between the CYP2C19 activity (CYP2C19*2, CYP2C19*3 and CYP2C19*17 variants) and the type of acute coronary syndrome, cardiovascular risk factors (arterial systemic hypertension, diabetes mellitus, dyslipidemia and smoking), analytical parameters and the extent and severity of coronary atherosclerosis...
May 1, 2017: Medicina Clínica
https://www.readbyqxmd.com/read/28471661/analytical-derivative-coupling-for-multistate-caspt2-theory
#14
Jae Woo Park, Toru Shiozaki
The probability of nonradiative transitions in photochemical dynamics is determined by the derivative couplings, the couplings between different electronic states through the nuclear degrees of freedom. Efficient and accurate evaluation of the derivative couplings is, therefore, of central importance to realize reliable computer simulations of photochemical reactions. In this work, the derivative couplings for multistate multireference second-order perturbation theory (MS-CASPT2) and its "extended" variant (XMS-CASPT2) are studied, in which we present an algorithm for their analytical evaluation...
May 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28463571/accurate-identification-and-quantification-of-dna-species-by-next-generation-sequencing-in-adeno-associated-viral-vectors-produced-in-insect-cells
#15
Magalie Penaud-Budloo, Emilie Lecomte, Aurélien Guy-Duché, Sylvie Saleun, Alain Roulet, Céline Lopez-Roques, Benoît Tournaire, Benjamin Cogné, Adrien Léger, Veronique Blouin, Pierre Lindenbaum, Philippe Moullier, Eduard Ayuso
Recombinant adeno-associated viral vectors (rAAV) have proven excellent tools for the treatment of many genetic diseases and other complex diseases. However, the illegitimate encapsidation of DNA contaminants within viral particles constitutes a major safety concern for rAAV-based therapies. Moreover, the development of rAAV vectors for early-phase clinical trials has revealed the limited accuracy of the analytical tools used to characterize these new and complex drugs. While most published data concerning residual DNA in rAAV preparations have been generated by quantitative PCR, we recently developed a novel single-strand virus sequencing (SSV-Seq) method for quantification of DNA contaminants in AAV vectors produced in mammalian cells by next-generation sequencing (NGS)...
May 2, 2017: Human Gene Therapy Methods
https://www.readbyqxmd.com/read/28463351/intrinsic-functional-and-architectonic-heterogeneity-of-tumor-targeted-protein-nanoparticles
#16
Mireia Pesarrodona, Eva Crosas, Rafael Cubarsi, Alejandro Sánchez-Chardi, Paolo Saccardo, Ugutz Unzueta, Fabian Rueda, Laura Sanchez-García, Naroa Serna, Ramón Mangues, Neus Ferrer-Miralles, Esther Vázquez, Antonio Villaverde
Self-assembling proteins are gaining attention as building blocks for application-tailored nanoscale materials. This is mostly due to the biocompatibility, biodegradability, and functional versatility of peptide chains. Such a potential for adaptability is particularly high in the case of recombinant proteins, which are produced in living cells and are suitable for genetic engineering. However, how the cell factory itself and the particular protein folding machinery influence the architecture and function of the final material is still poorly explored...
May 18, 2017: Nanoscale
https://www.readbyqxmd.com/read/28453252/polymer-inclusion-membranes-with-condensed-phase-membrane-introduction-mass-spectrometry-cp-mims-improved-analytical-response-time-and-sensitivity
#17
Gregory W Vandergrift, Erik T Krogh, Chris G Gill
Condensed phase membrane introduction mass spectrometry (CP-MIMS) is an online, in situ analysis technique for low volatility analytes. Analytes diffuse through a hollow fiber membrane, where they are then dissolved by a liquid (condensed) acceptor phase flowing through the membrane lumen. Permeating analytes are entrained to an atmospheric pressure ionization source for subsequent measurement by a mass spectrometer. Larger analytes, with inherently lower diffusivities, suffer from lengthy response times and lower sensitivity, limiting the use of CP-MIMS for their online, real-time measurement...
May 5, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28447902/reporting-results-of-molecular-tests-a-retrospective-examination-of-braf-mutation-reporting
#18
Amanda L Treece, Margaret L Gulley, Patricia Vasalos, Cherie Paquette, Neal I Lindeman, Lawrence J Jennings, Angela N Bartley
CONTEXT: - With enormous growth in the field of molecular pathology, the reporting of results gleaned from this testing is essential to guide patient care. OBJECTIVE: - To examine molecular reports from laboratories participating in proficiency testing for required elements to convey molecular laboratory test results to clinicians and patients. DESIGN: - Molecular laboratories participating in the College of American Pathologists (CAP) proficiency testing program for BRAF mutation analysis were solicited to submit examples of final reports from 2 separate proficiency testing reporting cycles...
May 2017: Archives of Pathology & Laboratory Medicine
https://www.readbyqxmd.com/read/28447426/next-generation-sequencing-as-a-tool-for-breakpoint-analysis-in-rearrangements-of-the-globin-gene-clusters
#19
REVIEW
B E Clark, C Shooter, F Smith, D Brawand, S L Thein
INTRODUCTION: Next-generation sequencing (NGS), now embedded within genomic laboratories, is well suited to the detection of small sequence changes but is less well adapt for detecting structural variants (SV), mainly due to the relatively short sequence reads. Of the available target enrichment methods, bait capture or whole-genome sequencing appears better suited to detecting SV as there is less PCR amplification and is therefore more representative of the genome being sequenced. MATERIAL AND METHODS: In 2015, we described the first inversion/deletion causing εγδβ- thalassemia using an NGS approach, with base-pair resolution...
May 2017: International Journal of Laboratory Hematology
https://www.readbyqxmd.com/read/28443838/charge-detection-mass-spectrometry-weighing-heavier-things
#20
REVIEW
David Z Keifer, Elizabeth E Pierson, Martin F Jarrold
Charge detection mass spectrometry (CDMS) is a single molecule method where the mass of each ion is directly determined from individual measurements of its mass-to-charge ratio and charge. CDMS is particularly valuable for the analysis of high mass and heterogeneous analytes, where conventional MS methods are often confounded. In the last few years, CDMS has received a renaissance. Technical developments have improved the resolution and dramatically increased the breadth of problems that can be addressed. These improvements have moved CDMS more into the mainstream as interest in the application of mass spectrometry to high molecular weight species has grown...
April 26, 2017: Analyst
keyword
keyword
96402
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"