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https://www.readbyqxmd.com/read/28344774/the-dockstore-enabling-modular-community-focused-sharing-of-docker-based-genomics-tools-and-workflows
#1
Brian D O'Connor, Denis Yuen, Vincent Chung, Andrew G Duncan, Xiang Kun Liu, Janice Patricia, Benedict Paten, Lincoln Stein, Vincent Ferretti
As genomic datasets continue to grow, the feasibility of downloading data to a local organization and running analysis on a traditional compute environment is becoming increasingly problematic. Current large-scale projects, such as the ICGC PanCancer Analysis of Whole Genomes (PCAWG), the Data Platform for the U.S. Precision Medicine Initiative, and the NIH Big Data to Knowledge Center for Translational Genomics, are using cloud-based infrastructure to both host and perform analysis across large data sets. In PCAWG, over 5,800 whole human genomes were aligned and variant called across 14 cloud and HPC environments; the processed data was then made available on the cloud for further analysis and sharing...
2017: F1000Research
https://www.readbyqxmd.com/read/28344655/interactions-among-cox-2-gpiiia-and-p2y1-variants-are-associated-with-aspirin-responsiveness-and-adverse-events-in-patients-with-ischemic-stroke
#2
Xingyang Yi, Zhao Han, Qiang Zhou, Jing Lin, Chun Wang
BACKGROUND: The effect of gene variants and their interactions on response to aspirin and clinical adverse outcomes after an acute ischemic stroke (IS) is not fully understood. The aim of this study was to investigate the association of aspirin-relevant gene variants and their interactions with clinical adverse outcomes in IS patients taking aspirin. METHODS: A total of 14 variants from six genes encoding COX enzymes (COX-1, COX-2), platelet membrane receptors (TXAS1, P2Y1, P2Y12) and glycoprotein receptor (GPIIIa) were examined in 850 acute IS patients...
March 2017: Therapeutic Advances in Neurological Disorders
https://www.readbyqxmd.com/read/28344127/replicated-association-between-the-european-gwas-locus-rs10503253-at-csmd1-and-schizophrenia-in-asian-population
#3
Weiqing Liu, Fang Liu, Xiufeng Xu, Yan Bai
Schizophrenia is one of the most severe mental disorders with significant heritability. Recent genetic association studies including genome-wide association studies (GWAS) have identified multiple common variants conferring risk of schizophrenia. An intronic SNP within CSMD1, rs10503253, is one of the top risk SNPs for schizophrenia in Europeans discovered through large GWAS. However, whether rs10503253 is also a risk SNP for schizophrenia in other populations, such as Asians, is still unknown. To answer this question, we examined the association of rs10503253 with schizophrenia in a total of 7,514 schizophrenia patients, 9,058 healthy controls and 1,115 nuclear families originated from Asia using a meta-analytic approach...
March 23, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28341590/guidelines-for-validation-of-next-generation-sequencing-based-oncology-panels-a-joint-consensus-recommendation-of-the-association-for-molecular-pathology-and-college-of-american-pathologists
#4
REVIEW
Lawrence J Jennings, Maria E Arcila, Christopher Corless, Suzanne Kamel-Reid, Ira M Lubin, John Pfeifer, Robyn L Temple-Smolkin, Karl V Voelkerding, Marina N Nikiforova
Next-generation sequencing (NGS) methods for cancer testing have been rapidly adopted by clinical laboratories. To establish analytical validation best practice guidelines for NGS gene panel testing of somatic variants, a working group was convened by the Association of Molecular Pathology with liaison representation from the College of American Pathologists. These joint consensus recommendations address NGS test development, optimization, and validation, including recommendations on panel content selection and rationale for optimization and familiarization phase conducted before test validation; utilization of reference cell lines and reference materials for evaluation of assay performance; determining of positive percentage agreement and positive predictive value for each variant type; and requirements for minimal depth of coverage and minimum number of samples that should be used to establish test performance characteristics...
March 21, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28341588/targeted-next-generation-sequencing-of-51-genes-involved-in-primary-electrical-disease
#5
Dorien Proost, Johan Saenen, Geert Vandeweyer, Annelies Rotthier, Maaike Alaerts, Emeline M Van Craenenbroeck, Joachim Van Crombruggen, Geert Mortier, Wim Wuyts, Christiaan Vrints, Jurgen Del Favero, Bart Loeys, Lut Van Laer
Primary electrical disease (PED) is characterized by cardiac arrhythmias, which can lead to sudden cardiac death in the absence of detectable structural heart disease. PED encompasses a diversity of inherited syndromes, predominantly Brugada syndrome, early repolarization syndrome, long QT syndrome, short QT syndrome, arrhythmogenic right ventricular cardiomyopathy, and catecholaminergic polymorphic ventricular tachycardia. To overcome the diagnostic challenges imposed by the clinical and genetic heterogeneity of PED, we developed a targeted gene panel for next-generation sequencing of 51 PED genes...
March 21, 2017: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/28338761/influence-of-polynucleosome-preparation-methods-on-sedimentation-velocity-analysis-of-chromatin
#6
Tomoya Kujirai, Shinichi Machida, Akihisa Osakabe, Hitoshi Kurumizaka
Chromatin dynamics and higher order structures play essential roles in genomic DNA functions. Histone variants and histone post-translational modifications are involved in the regulation of chromatin structure and dynamics, cooperatively with DNA methylation and chromatin binding proteins. Therefore, studies of higher-order chromatin conformations have become important to reveal how genomic DNA is regulated during DNA transcription, replication, recombination and repair. The sedimentation velocity analysis by analytical ultracentrifugation has been commonly used to evaluate the higher-order conformation of in vitro reconstituted polynucleosomes, as model chromatin...
December 22, 2016: Journal of Biochemistry
https://www.readbyqxmd.com/read/28334342/tagging-snp-set-selection-with-maximum-information-based-on-linkage-disequilibrium-structure-in-genome-wide-association-studies
#7
Shudong Wang, Sicheng He, Fayou Yuan, Xinjie Zhu
Motivation: Effective tagging single-nucleotide polymorphism (SNP)-set selection is crucial to SNP-set analysis in genome-wide association studies (GWAS). Most of the existing tagging SNP-set selection methods cannot make full use of the information hidden in common or rare variants associated diseases. It is noticed that some SNPs have overlapping genetic information owing to linkage disequilibrium (LD) structure between SNPs. Therefore, when testing the association between SNPs and disease susceptibility, it is sufficient to elect the representative SNPs (called tag SNP-set or tagSNP-set) with maximum information...
March 16, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28327206/lessons-learned-from-additional-research-analyses-of-unsolved-clinical-exome-cases
#8
Mohammad K Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R Lalani, Christian P Schaaf, Michael F Wangler, Carlos A Bacino, Richard Alan Lewis, Lorraine Potocki, Brett H Graham, John W Belmont, Fernando Scaglia, Jordan S Orange, Shalini N Jhangiani, Theodore Chiang, Harsha Doddapaneni, Jianhong Hu, Donna M Muzny, Fan Xia, Arthur L Beaudet, Eric Boerwinkle, Christine M Eng, Sharon E Plon, V Reid Sutton, Richard A Gibbs, Jennifer E Posey, Yaping Yang, James R Lupski
BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease...
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28326591/arbitrarily-applicable-spatial-relational-responding
#9
Richard J May, Ian Stewart, Luisa Baez, Gary Freegard, Simon Dymond
Spatial reasoning, where novel spatial relationships are inferred based on trained relationships, can be conceptualized as arbitrarily applicable spatial relational responding. Here, we conducted two experiments to develop and validate, for the first time, a laboratory procedure to establish arbitrarily applicable spatial relational responding in adult humans. In Experiment 1, participants were trained on nonarbitrary spatial relational tasks designed to establish contextual cues for left of, right of, above, and below...
March 2017: Journal of the Experimental Analysis of Behavior
https://www.readbyqxmd.com/read/28322313/the-epidemic-dynamics-of-hepatitis-c-virus-subtypes-4a-and-4d-in-saudi-arabia
#10
Ahmed A Al-Qahtani, Guy Baele, Nisreen Khalaf, Marc A Suchard, Mashael R Al-Anazi, Ayman A Abdo, Faisal M Sanai, Hamad I Al-Ashgar, Mohammed Q Khan, Mohammed N Al-Ahdal, Philippe Lemey, Bram Vrancken
The relatedness between viral variants sampled at different locations through time can provide information pertinent to public health that cannot readily be obtained through standard surveillance methods. Here, we use virus genetic data to identify the transmission dynamics that drive the hepatitis C virus subtypes 4a (HCV4a) and 4d (HCV4d) epidemics in Saudi Arabia. We use a comprehensive dataset of newly generated and publicly available sequence data to infer the HCV4a and HCV4d evolutionary histories in a Bayesian statistical framework...
March 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28302680/genomic-and-epigenomic-heterogeneity-of-hepatocellular-carcinoma
#11
De-Chen Lin, Anand Mayakonda, Huy Q Dinh, Pinbo Huang, Lehang Lin, Xiaoping Liu, Ling-Wen Ding, Jie Wang, Benjamin Berman, Erwei Song, Dong Yin, H Phillip Koeffler
Understanding the intratumoral heterogeneity of hepatocellular carcinoma (HCC) is instructive for developing personalized therapy and identifying molecular biomarkers. Here we applied whole-exome sequencing to 69 samples from 11 patients to resolve the genetic architecture of subclonal diversification. Spatial genomic diversity was found in all 11 HCC cases, with 29% of driver mutations being heterogeneous, including TERT, ARID1A, NOTCH2, and STAG2. Similar with other cancer types, TP53 mutations were always shared between all tumor regions i...
February 20, 2017: Cancer Research
https://www.readbyqxmd.com/read/28297603/improving-the-efficiency-of-non-equilibrium-sampling-in-the-aqueous-environment-via-implicit-solvent-simulations
#12
Hui Liu, Fu Chen, Huiyong Sun, Dan Li, Tingjun Hou
By means of estimators based on non-equilibrium work, equilibrium free energy differences or potentials of mean force (PMFs) of a system of interest can be computed from biased molecular dynamics (MD) simulations. The approach, however, is often plagued by slow conformational sampling and poor convergence, especially when the solvent effects are taken into account. Here, as a possible way to alleviate the problem, several widely used implicit-solvent models, which are derived from the analytic generalized Born (GB) equation and implemented in the AMBER suite of programs, were employed in free energy calculations based on non-equilibrium work and evaluated for their abilities to emulate explicit water...
March 23, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28291242/mining-outcome-relevant-brain-imaging-genetic-associations-via-three-way-sparse-canonical-correlation-analysis-in-alzheimer-s-disease
#13
Xiaoke Hao, Chanxiu Li, Lei Du, Xiaohui Yao, Jingwen Yan, Shannon L Risacher, Andrew J Saykin, Li Shen, Daoqiang Zhang
Neuroimaging genetics is an emerging field that aims to identify the associations between genetic variants (e.g., single nucleotide polymorphisms (SNPs)) and quantitative traits (QTs) such as brain imaging phenotypes. In recent studies, in order to detect complex multi-SNP-multi-QT associations, bi-multivariate techniques such as various structured sparse canonical correlation analysis (SCCA) algorithms have been proposed and used in imaging genetics studies. However, associations between genetic markers and imaging QTs identified by existing bi-multivariate methods may not be all disease specific...
March 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28287753/parental-educational-attainment-and-adult-offspring-personality-an-intergenerational-life-span-approach-to-the-origin-of-adult-personality-traits
#14
Angelina R Sutin, Martina Luchetti, Yannick Stephan, Richard W Robins, Antonio Terracciano
Why do some individuals have more self-control or are more vulnerable to stress than others? Where do these basic personality traits come from? Although a fundamental question in personality, more is known about how traits are related to important life outcomes than their developmental origins. The present research took an intergenerational life span approach to address whether a significant aspect of the childhood environment-parental educational attainment-was associated with offspring personality traits in adulthood...
March 13, 2017: Journal of Personality and Social Psychology
https://www.readbyqxmd.com/read/28284623/prevalence-and-molecular-epidemiology-of-canine-parvovirus-2-in-diarrheic-dogs-in-colombia-south-america-a-possible-new-cpv-2a-is-emerging
#15
Yeison Duque-García, Manuela Echeverri-Zuluaga, Juanita Trejos-Suarez, Julian Ruiz-Saenz
Since its identification in 1978, Canine parvovirus type 2 (CPV-2) has been considered a pathogen of great importance in the canine population because it causes severe enteritis with high mortality rates in pups. CPV-2 is a virus belonging to the family Parvoviridae. Currently, there are three described antigenic variants (CPV-2a, CPV-2b, and CPV-2c). CPV-2c is an emerging virus that is seen as a global health hazard. The objective of this work was to confirm the presence of CPV-2 in dogs with acute gastroenteritis compatible with parvovirus and to molecularly characterize the antigenic variants circulating in two regions of Colombia...
March 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28283927/a-review-of-the-genetics-of-hypertension-with-a-focus-on-gene-environment-interactions
#16
REVIEW
R J Waken, Lisa de Las Fuentes, D C Rao
PURPOSE OF REVIEW: Here, we discuss the interpretation and modeling of gene-environment interactions in hypertension-related phenotypes, with a focus on the necessary assumptions and possible challenges. RECENT FINDINGS: Recently, small cohort studies have discovered several novel genetic variants associated with hypertension-related phenotypes through modeling gene-environment interactions. Several consortia-based meta-analytic efforts have uncovered many novel genetic variants in hypertension without modeling interaction terms, giving promise to future meta-analytic efforts that incorporate gene-environment interactions...
March 2017: Current Hypertension Reports
https://www.readbyqxmd.com/read/28264159/streamlined-synthesis-and-assembly-of-a-hybrid-sensing-architecture-with-solid-binding-proteins-and-click-chemistry
#17
Brian J F Swift, Jared A Shadish, Cole A DeForest, François Baneyx
Combining bioorthogonal chemistry with the use of proteins engineered with adhesive and morphogenetic solid-binding peptides is a promising route for synthesizing hybrid materials with the economy and efficiency of living systems. Using optical sensing of chloramphenicol as a proof of concept, we show here that a GFP variant engineered with zinc sulfide and silica-binding peptides on opposite sides of its β-barrel supports the fabrication of protein-capped ZnS:Mn nanocrystals that exhibit the combined emission signatures of organic and inorganic fluorophores...
March 13, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28259457/optimization-of-ion-exchange-sigmoidal-gradients-using-hybrid-models-implementation-of-quality-by-design-in-analytical-method-development
#18
Varsha S Joshi, Vijesh Kumar, Anurag S Rathore
Thorough product understanding is one of the basic tenets for successful implementation of Quality by Design (QbD). Complexity encountered in analytical characterization of biotech therapeutics such as monoclonal antibodies (mAbs) requires novel, simpler, and generic approaches towards product characterization. This paper presents a methodology for implementation of QbD for analytical method development. Optimization of an analytical cation exchange high performance liquid chromatography (CEX-HPLC) method utilizing a sigmoidal gradient has been performed using a hybrid mechanistic model that is based on Design of experiment (DOE) based studies...
March 31, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28259456/top-down-and-middle-down-approach-by-fraction-collection-enrichment-using-off-line-capillary-electrophoresis-mass-spectrometry-coupling-application-to-monoclonal-antibody-fc-2-charge-variants
#19
Michael Biacchi, Nassur Said, Alain Beck, Emmanuelle Leize-Wagner, Yannis-Nicolas François
The characterization of complex protein mixtures represents one of the biggest challenge in many research fields such as biological or biopharmaceutical sciences. Out of all categories, monoclonal antibodies (mAbs) and related products drawn the most interest due to their strong therapeutic potency and specificity. Because of their intrinsic complexity due to a large number of micro-heterogeneities, there is a crucial need for analytical methods to provide comprehensive in-depth characterization of these proteins...
February 27, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28257876/are-semantic-and-phonological-fluency-based-on-the-same-or-distinct-sets-of-cognitive-processes-insights-from-factor-analyses-in-healthy-adults-and-stroke-patients
#20
Charlotte S M Schmidt, Lena V Schumacher, Pia Römer, Rainer Leonhart, Lena Beume, Markus Martin, Andrea Dressing, Cornelius Weiller, Christoph P Kaller
Verbal fluency for semantic categories and phonological letters is frequently applied to studies of language and executive functions. Despite its popularity, it is still debated whether measures of semantic and phonological fluency reflect the same or distinct sets of cognitive processes. Word generation in the two task variants is believed to involve different types of search processes. Findings from the lesion and neuroimaging literature further suggest a stronger reliance of phonological and semantic fluency on frontal and temporal brain areas, respectively...
February 28, 2017: Neuropsychologia
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