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https://www.readbyqxmd.com/read/28936894/recent-advances-in-protein-engineering-and-biotechnological-applications-of-glutathione-transferases
#1
Fereniki Perperopoulou, Fotini Pouliou, Nikolaos E Labrou
Glutathione transferases (GSTs, EC 2.5.1.18) are a widespread family of enzymes that play a central role in the detoxification, metabolism, and transport or sequestration of endogenous or xenobiotic compounds. During the last two decades, delineation of the important structural and catalytic features of GSTs has laid the groundwork for engineering GSTs, involving both rational and random approaches, aiming to create new variants with new or altered properties. These approaches have expanded the usefulness of native GSTs, not only for understanding the fundamentals of molecular detoxification mechanisms, but also for the development medical, analytical, environmental, and agricultural applications...
September 22, 2017: Critical Reviews in Biotechnology
https://www.readbyqxmd.com/read/28934590/the-relationship-between-the-human-genome-and-microbiome-comes-into-view
#2
Julia K Goodrich, Emily R Davenport, Andrew G Clark, Ruth E Ley
The body's microbiome, composed of microbial cells that number in the trillions, is involved in human health and disease in ways that are just starting to emerge. The microbiome is assembled at birth, develops with its host, and is greatly influenced by environmental factors such as diet and other exposures. Recently, a role for human genetic variation has emerged as also influential in accounting for interpersonal differences in microbiomes. Thus, human genes may influence health directly or by promoting a beneficial microbiome...
September 20, 2017: Annual Review of Genetics
https://www.readbyqxmd.com/read/28930088/comparison-of-pcr-methods-for-the-detection-of-genetic-variants-of-carp-edema-virus
#3
Mikolaj Adamek, Marek Matras, Verena Jung-Schroers, Felix Teitge, Max Heling, Sven M Bergmann, Michal Reichert, Keith Way, David M Stone, Dieter Steinhagen
The infection of common carp and its ornamental variety, koi, with the carp edema virus (CEV) is often associated with the occurrence of a clinical disease called 'koi sleepy disease'. The disease may lead to high mortality in both koi and common carp populations. To prevent further spread of the infection and the disease, a reliable detection method for this virus is required. However, the high genetic variability of the CEV p4a gene used for PCR-based diagnostics could be a serious obstacle for successful and reliable detection of virus infection in field samples...
September 20, 2017: Diseases of Aquatic Organisms
https://www.readbyqxmd.com/read/28926605/assessment-of-common-somatic-mutations-of-egfr-kras-braf-nras-in-pulmonary-non-small-cell-carcinoma-using-iplex%C3%A2-hs-a-new-highly-sensitive-assay-for-the-massarray%C3%A2-system
#4
Bobbie C Sutton, Ryan T Birse, Kevin Maggert, Tammy Ray, Jessica Hobbs, Amobi Ezenekwe, Jason Kazmierczak, Michael Mosko, Joan Kish, Andrew Bullock, Zonggao Shi, M Sharon Stack, Darryl Irwin
Increased early detection and personalized therapy for lung cancer have coincided with greater use of minimally invasive sampling techniques such as endobronchial ultrasound-guided biopsy (EBUS), endoscopic ultrasound-guided biopsy (EUS), and navigational biopsy, as well as thin needle core biopsies. As many lung cancer patients have late stage disease and other comorbidities that make open surgical procedures hazardous, the least invasive biopsy technique with the highest potential specimen yield is now the preferred first diagnostic study...
2017: PloS One
https://www.readbyqxmd.com/read/28926139/the-synonymous-nucleotide-substitution-rhd-1056c-g-alters-mrna-splicing-associated-with-serologically-weak-d-phenotype
#5
Sejong Chun, Jae Won Yun, Geon Park, Duck Cho
BACKGROUND: D antigen is one of the most clinically significant blood group antigens. Variation of the RHD gene can cause weak D or partial D phenotypes. While most variations are missense substitutions with amino acid changes, those without are called "silent" or "synonymous" substitutions. Synonymous substitutions often have little effect on the protein, not altering the phenotype. However, effect on splicing can affect end-product protein. We report a new synonymous variation, RHD 1056C>G, that resulted in weak D phenotype, and predicted its effect with various in silico methods...
September 19, 2017: Journal of Clinical Laboratory Analysis
https://www.readbyqxmd.com/read/28921510/development-of-a-formaldehyde-biosensor-with-application-to-synthetic-methylotrophy
#6
Benjamin M Woolston, Timothy Roth, Ishwar Kohale, David Liu, Gregory Stephanopoulos
Formaldehyde is a prevalent environmental toxin and a key intermediate in single carbon metabolism. The ability to monitor formaldehyde concentration is therefore of interest for both environmental monitoring and for metabolic engineering of native and synthetic methylotrophs, but current methods suffer from low sensitivity, complex workflows, or require expensive analytical equipment. Here we develop a formaldehyde biosensor based on the FrmR repressor protein and cognate promoter of E. coli. Optimization of the native repressor binding site and regulatory architecture enabled detection at levels as low as 1 µM...
September 16, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28914264/comprehensive-use-of-extended-exome-analysis-improves-diagnostic-yield-in-rare-disease-a-retrospective-survey-in-1-059-cases
#7
Gaber Bergant, Ales Maver, Luca Lovrecic, Goran Čuturilo, Alenka Hodzic, Borut Peterlin
PurposeWe sought to determine the analytical sensitivity of several extended exome variation analysis approaches in terms of their contribution to diagnostic yield and their clinical feasibility.MethodsWe retrospectively analyzed the results of genetic testing in 1,059 distinct cases referred for exome sequencing to our institution. In these, we routinely employed extended exome analysis approaches in addition to basic variant analysis, including (i) copy-number variation (CNV) detection, (ii) nonconsensus splice defect detection, (ii) genomic breakpoint detection, (iv) homozygosity mapping, and (v) mitochondrial variant analysis...
September 14, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28903898/current-status-of-pathway-analysis-in-genome-wide-association-study
#8
Yu-Yan Wang, Zi-Xing Wang, Yao-da Hu, Lei Wang, Ning Li, Biao Zhang, Wei Han, Jing-Mei Jiang
Since the first publication in 2005, the genome-wide association study (GWAS) strategy has contributed significantly to the understanding of the mechanisms of human genetic diseases. Integrations of statistical methods and systematic biology are important means to explore the GWAS data. Pathway analysis establishes the importance of genetic variants from GWAS and provides insights into their biological significance. It is conducive in correlating the genetic variants, which have only small but interactive changes, to their importance in the biological pathways...
August 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28898266/translating-natural-genetic-variation-to-gene-expression-in-a-computational-model-of-the-drosophila-gap-gene-regulatory-network
#9
Vitaly V Gursky, Konstantin N Kozlov, Ivan V Kulakovskiy, Asif Zubair, Paul Marjoram, David S Lawrie, Sergey V Nuzhdin, Maria G Samsonova
Annotating the genotype-phenotype relationship, and developing a proper quantitative description of the relationship, requires understanding the impact of natural genomic variation on gene expression. We apply a sequence-level model of gap gene expression in the early development of Drosophila to analyze single nucleotide polymorphisms (SNPs) in a panel of natural sequenced D. melanogaster lines. Using a thermodynamic modeling framework, we provide both analytical and computational descriptions of how single-nucleotide variants affect gene expression...
2017: PloS One
https://www.readbyqxmd.com/read/28892063/interpreting-short-tandem-repeat-variations-in-humans-using-mutational-constraint
#10
Melissa Gymrek, Thomas Willems, David Reich, Yaniv Erlich
Identifying regions of the genome that are depleted of mutations can distinguish potentially deleterious variants. Short tandem repeats (STRs), also known as microsatellites, are among the largest contributors of de novo mutations in humans. However, per-locus studies of STR mutations have been limited to highly ascertained panels of several dozen loci. Here we harnessed bioinformatics tools and a novel analytical framework to estimate mutation parameters for each STR in the human genome by correlating STR genotypes with local sequence heterozygosity...
September 11, 2017: Nature Genetics
https://www.readbyqxmd.com/read/28881976/increasing-the-power-of-meta-analysis-of-genome-wide-association-studies-to-detect-heterogeneous-effects
#11
C H Lee, E Eskin, B Han
Motivation: Meta-analysis is essential to combine the results of genome-wide association studies (GWASs). Recent large-scale meta-analyses have combined studies of different ethnicities, environments and even studies of different related phenotypes. These differences between studies can manifest as effect size heterogeneity. We previously developed a modified random effects model (RE2) that can achieve higher power to detect heterogeneous effects than the commonly used fixed effects model (FE)...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28878566/elastic-deformation-of-twinned-microstructures
#12
Steffen Pfeiffer, Martin Franz-Xaver Wagner
Many crystalline materials exhibit twinned microstructures, where well-defined orientation relationships define the special symmetry between different, elastically anisotropic twin variants. When such twins are subjected to external loading, additional internal stresses necessarily occur at the twin boundaries in order to maintain compatibility. These compatibility stresses are constant inside each variant in repeating stacks of twins and considerably affect the local stress state. In this paper, we use anisotropic linear elasticity to derive general analytical solutions for compatibility stresses in a stack of twin variants in arbitrary materials, for arbitrary variant volume fractions and twin types, subjected to arbitrary applied stresses...
August 2017: Proceedings. Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28878002/combat-a-combined-association-test-for-genes-using-summary-statistics
#13
Minghui Wang, Jianfei Huang, Yiyuan Liu, Li Ma, James B Potash, Shizhong Han
Genome-wide association studies (GWAS) have been widely used for identifying common variants associated with complex diseases. Traditional analysis of GWAS typically examines one marker at a time, usually single nucleotide polymorphisms (SNPs), to identify individual variants associated with a disease. However, due to the small effect sizes of common variants, the power to detect individual risk variants is generally low. As a complementary approach to SNP-level analysis, a variety of gene-based association tests have been proposed...
September 6, 2017: Genetics
https://www.readbyqxmd.com/read/28877514/fast-gaussian-na%C3%A3-ve-bayes-for-searchlight-classification-analysis
#14
Marlis Ontivero-Ortega, Agustin Lage-Castellanos, Giancarlo Valente, Rainer Goebel, Mitchell Valdes-Sosa
The searchlight technique is a variant of multivariate pattern analysis (MVPA) that examines neural activity across large sets of small regions, exhaustively covering the whole brain. This usually involves application of classifier algorithms across all searchlights, which entails large computational costs especially when testing the statistical significance of the accuracies with permutation methods. In this article, a new implementation of the Gaussian Naive Bayes classifier is presented (henceforth massive-GNB)...
September 3, 2017: NeuroImage
https://www.readbyqxmd.com/read/28877219/a-new-approach-to-chromosome-wide-analysis-of-x-linked-markers-identifies-new-associations-in-asian-and-european-case-parent-triads-of-orofacial-clefts
#15
Øivind Skare, Håkon K Gjessing, Miriam Gjerdevik, Øystein A Haaland, Julia Romanowska, Rolv T Lie, Astanand Jugessur
BACKGROUND: GWAS discoveries on the X-chromosome are underrepresented in the literature primarily because the analytical tools that have been applied were originally designed for autosomal markers. Our objective here is to employ a new robust and flexible tool for chromosome-wide analysis of X-linked markers in complex traits. Orofacial clefts are good candidates for such analysis because of the consistently observed excess of females with cleft palate only (CPO) and excess of males with cleft lip with or without cleft palate (CL/P)...
2017: PloS One
https://www.readbyqxmd.com/read/28870871/clinical-genomic-sequencing-as-a-routine-technology-for-case-finding-and-diagnosis-in-unselected-patient-populations-should-not-proceed-without-formal-comparative-evaluation-of-health-outcomes-and-system-impacts
#16
Brenda J Wilson, Fiona Alice Miller, François Rousseau
Next generation genomic sequencing (NGS) technologies - whole genome and whole exome sequencing - are now cheap enough to be within the grasp of many healthcare organizations. To many, NGS is symbolic of cutting edge healthcare, offering the promise of 'precision' and 'personalized' medicine. Historically, research and clinical application has been a two way street in clinical genetics: research often driven directly by the desire to understand and try to solve immediate clinical problems affecting real, identifiable patients and families, accompanied by a low threshold of willingness to apply research-driven interventions without resort to formal empirical evaluations...
September 1, 2017: Journal of Clinical Epidemiology
https://www.readbyqxmd.com/read/28867786/proposal-and-evaluation-of-ble-discovery-process-based-on-new-features-of-bluetooth-5-0
#17
Ángela Hernández-Solana, David Perez-Diaz-de-Cerio, Antonio Valdovinos, Jose Luis Valenzuela
The device discovery process is one of the most crucial aspects in real deployments of sensor networks. Recently, several works have analyzed the topic of Bluetooth Low Energy (BLE) device discovery through analytical or simulation models limited to version 4.x. Non-connectable and non-scannable undirected advertising has been shown to be a reliable alternative for discovering a high number of devices in a relatively short time period. However, new features of Bluetooth 5.0 allow us to define a variant on the device discovery process, based on BLE scannable undirected advertising events, which results in higher discovering capacities and also lower power consumption...
August 30, 2017: Sensors
https://www.readbyqxmd.com/read/28865156/gene-disease-associations-identify-a-connectome-with-shared-molecular-pathways-in-human-cholangiopathies
#18
Zhenhua Luo, Anil G Jegga, Jorge A Bezerra
Cholangiopathies are a diverse group of progressive diseases whose primary cell targets are cholangiocytes. To identify shared pathogenesis and molecular connectivity among the three main human cholangiopathies (biliary atresia [BA], primary biliary cholangitis [PBC] and primary sclerosing cholangitis [PSC]), we built a comprehensive platform of published data on gene variants, gene expression and functional studies, and applied network-based analytics in search for shared molecular circuits. Mining the data platform with largest connected component and interactome analyses, we validated previously reported associations and identified essential- and hub-genes...
September 2, 2017: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/28862393/microheterogeneity-of-recombinant-antibodies-analytics-and-functional-impact
#19
REVIEW
Beyer Beate, Schuster Manfred, Jungbauer Alois, Lingg Nico
Antibodies are typical examples of biopharmaceuticals which are composed of numerous, almost infinite numbers of potential molecular entities called variants or isoforms which constitutes the microheterogeneity of these molecules. These variants are generated during biosynthesis by so-called posttranslational modification, during purification or upon storage. The variants differ in biological properties such as pharmacodynamic properties, e.g. Antibody Dependent Cellular Cytotoxicity (ADCC), complement activation, pharmacokinetic properties, e...
September 1, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28846959/association-of-genetic-variations-in-the-serotonin-and-dopamine-systems-with-aggressive-behavior-in-the-chinese-adolescent-population-single-and-multiple-risk-genetic-variants
#20
Hongjuan Chang, Qiuge Yan, Lina Tang, Juan Huang, Yuqiao Ma, Xiaozhou Ye, Chunxia Wu, Linguo Wu, Yizhen Yu
BACKGROUND: Genetic predisposition is an important factor leading to aggressive behavior. However, the relationship between genetic polymorphisms and aggressive behavior has not been elucidated. METHODS: We identified candidate genes located in the dopaminergic and serotonin system (DRD3, DRD4, and FEV) that had been previously reported to be associated with aggressive behavior. We investigated 14 tag single-nucleotide polymorphisms (SNPs) using a multi-analytic strategy combining logistic regression (LR) and classification and regression tree (CART) to explore higher-order interactions between these SNPs and aggressive behavior in 318 patients and 558 controls...
August 22, 2017: Journal of Affective Disorders
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