scholarly journals P2T2: Protein Panoramic annoTation Tool for the interpretation of protein coding genetic variants

JAMIA Open ◽  
2021 ◽  
Vol 4 (3) ◽  
Author(s):  
Elias DeVoe ◽  
Gavin R Oliver ◽  
Roman Zenka ◽  
Patrick R Blackburn ◽  
Margot A Cousin ◽  
...  
Keyword(s):  
Genomic Variation ◽  
Multiple Sources ◽  
Protein Coding ◽  
Web Based ◽  
Rest Api ◽  
Diverse Data ◽  
Sequence Domain ◽  
Related Proteins ◽  
Coding Variants ◽  
Structural Levels

Abstract Motivation Genomic data are prevalent, leading to frequent encounters with uninterpreted variants or mutations with unknown mechanisms of effect. Researchers must manually aggregate data from multiple sources and across related proteins, mentally translating effects between the genome and proteome, to attempt to understand mechanisms. Materials and methods P2T2 presents diverse data and annotation types in a unified protein-centric view, facilitating the interpretation of coding variants and hypothesis generation. Information from primary sequence, domain, motif, and structural levels are presented and also organized into the first Paralog Annotation Analysis across the human proteome. Results Our tool assists research efforts to interpret genomic variation by aggregating diverse, relevant, and proteome-wide information into a unified interactive web-based interface. Additionally, we provide a REST API enabling automated data queries, or repurposing data for other studies. Conclusion The unified protein-centric interface presented in P2T2 will help researchers interpret novel variants identified through next-generation sequencing. Code and server link available at github.com/GenomicInterpretation/p2t2.

scholarly journals RegulationSpotter: annotation and interpretation of extratranscriptic DNA variants

2019 ◽  
Vol 47 (W1) ◽  
pp. W106-W113 ◽  
Author(s):  
Jana Marie Schwarz ◽  
Daniela Hombach ◽  
Sebastian Köhler ◽  
David N Cooper ◽  
Markus Schuelke ◽  
...  
Keyword(s):  
Disease Genes ◽  
Phenotypic Data ◽  
Protein Coding ◽  
Web Based ◽  
Genome Wide ◽  
Dna Variants ◽  
Regulatory Effects ◽  
Key Aspects ◽  
User Friendly ◽  
Coding Variants

Abstract RegulationSpotter is a web-based tool for the user-friendly annotation and interpretation of DNA variants located outside of protein-coding transcripts (extratranscriptic variants). It is designed for clinicians and researchers who wish to assess the potential impact of the considerable number of non-coding variants found in Whole Genome Sequencing runs. It annotates individual variants with underlying regulatory features in an intuitive way by assessing over 100 genome-wide annotations. Additionally, it calculates a score, which reflects the regulatory potential of the variant region. Its dichotomous classifications, ‘functional’ or ‘non-functional’, and a human-readable presentation of the underlying evidence allow a biologically meaningful interpretation of the score. The output shows key aspects of every variant and allows rapid access to more detailed information about its possible role in gene regulation. RegulationSpotter can either analyse single variants or complete VCF files. Variants located within protein-coding transcripts are automatically assessed by MutationTaster as well as by RegulationSpotter to account for possible intragenic regulatory effects. RegulationSpotter offers the possibility of using phenotypic data to focus on known disease genes or genomic elements interacting with them. RegulationSpotter is freely available at https://www.regulationspotter.org.

scholarly journals SMAP: A pipeline for sample matching in proteogenomics

2021 ◽  
Author(s):  
Ling Li ◽  
Mingming Niu ◽  
Alyssa Erickson ◽  
Jie Luo ◽  
Kincaid Rowbotham ◽  
...  
Keyword(s):  
Large Scale ◽  
Ribosome Profiling ◽  
Sequencing Data ◽  
Protein Coding ◽  
Web Based ◽  
Link Type ◽  
Genomics And Proteomics ◽  
Sample Data ◽  
Dependent Protein ◽  
Coding Variants

AbstractIntegration of genomics and proteomics (proteogenomics) offers unprecedented promise for in-depth understanding of human diseases. However, sample mix-up is a pervasive, recurring problem, due to complex sample processing in proteogenomics. Here we present a pipeline for Sample Matching in Proteogenomics (SMAP) for verifying sample identity to ensure data integrity. SMAP infers sample-dependent protein-coding variants from quantitative mass spectrometry (MS), and aligns the MS-based proteomic samples with genomic samples by two discriminant scores. Theoretical analysis with simulation data indicates that SMAP is capable of uniquely match proteomic and genomic samples, when ≥20% genotypes of individual samples are available. When SMAP was applied to a large-scale proteomics dataset from 288 biological samples generated by the PsychENCODE BrainGVEX project, we identified and corrected 18.8% (54/288) mismatched samples. The correction was further confirmed by ribosome profiling and assay for transposase-accessible chromatin sequencing data from the same set of samples. Thus our results demonstrate that SMAP is an effective tool for sample verification in a large-scale MS-based proteogenomics study. The source code, manual, and sample data of the SMAP are publicly available at https://github.com/UND-Wanglab/SMAP, and a web-based SMAP can be accessed at https://smap.shinyapps.io/smap/.

scholarly journals MichelaNglo: sculpting protein views on web pages without coding

2020 ◽  
Vol 36 (10) ◽  
pp. 3268-3270 ◽  
Author(s):  
Matteo P Ferla ◽  
Alistair T Pagnamenta ◽  
David Damerell ◽  
Jenny C Taylor ◽  
Brian D Marsden
Keyword(s):  
Digital Media ◽  
Structural Information ◽  
Web Pages ◽  
Protein Coding ◽  
Web Based ◽  
Functional Consequences ◽  
Static Images ◽  
Interactive 3D ◽  
Coding Variants ◽  
Do So

Abstract Motivation The sharing of macromolecular structural information online by scientists is predominantly performed via 2D static images, since the embedding of interactive 3D structures in webpages is non-trivial. Whilst the technologies to do so exist, they are often only implementable with significant web coding experience. Results Michelaɴɢʟo is an accessible and open-source web-based application that supports the generation, customization and sharing of interactive 3D macromolecular visualizations for digital media without requiring programming skills. A PyMOL file, PDB file, PDB identifier code or protein/gene name can be provided to form the basis of visualizations using the NGL JavaScript library. Hyperlinks that control the view can be added to text within the page. Protein-coding variants can be highlighted to support interpretation of their potential functional consequences. The resulting visualizations and text can be customized and shared, as well as embedded within existing websites by following instructions and using a self-contained download. Michelaɴɢʟo allows researchers to move away from static images and instead engage, describe and explain their protein to a wider audience in a more interactive fashion. Availability and implementation Michelaɴɢʟo is hosted at michelanglo.sgc.ox.ac.uk. The Python code is freely available at https://github.com/thesgc/MichelaNGLo, along with documentations about its implementation.

As-RaD System as a Design Model of the Network Automation Configuration System Based on the REST-API and Django Framework

2020 ◽  
pp. 291-298
Author(s):  
Adian Fatchur Rochim ◽  
Abda Rafi ◽  
Adnan Fauzi ◽  
Kurniawan Teguh Martono
Keyword(s):  
Information Technology ◽  
Application Programming Interface ◽  
Design Model ◽  
Automation System ◽  
Network Configuration ◽  
Web Based ◽  
Representational State Transfer ◽  
Application Programming ◽  
Rest Api ◽  
Python Programming

The use of information technology these days are very high. From business through education activities tend to use this technology most of the time. Information technology uses computer networks for integration and management data. To avoid business problems, the number of network devices installed requires a manageable network configuration for easier maintenance. Traditionally, each of network devices has to be manually configured by network administrators. This process takes time and inefficient. Network automation methods exist to overcome the repetitive process. Design model uses a web-based application for maintenance and automates networking tasks. In this research, the network automation system implemented and built a controller application that used REST API (Representational State Transfer Application Programming Interface) architecture and built by Django framework with Python programming language. The design modeled namely As-RaD System. The network devices used in this research are Cisco CSR1000V because it supports REST API communication to manage its network configuration and could be placed on the server either. The As-RaD System provides 75% faster performance than Paramiko and 92% than NAPALM.

scholarly journals Process evaluation of the ACTION programme: a strategy for implementing person‐centred communication in home care

BMC Nursing ◽  
2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Tanja Gustafsson ◽  
Annelie J Sundler ◽  
Elisabeth Lindberg ◽  
Pernilla Karlsson ◽  
Hanna Maurin Söderholm
Keyword(s):  
Home Care ◽  
Process Evaluation ◽  
Organizational Support ◽  
Qualitative Data ◽  
Education Programme ◽  
Multiple Sources ◽  
Web Based ◽  
Action Programme ◽  
Web Based Education ◽  
The Web

Abstract Background There is currently a strong emphasis on person-centred care (PCC) and communication; however, little research has been conducted on how to implement person-centred communication in home care settings. Therefore, the ACTION (A person-centred CommunicaTION) programme, which is a web-based education programme focusing on person-centred communication developed for nurse assistants (NAs) providing home care for older persons, was implemented. This paper reports on the process evaluation conducted with the aim to describe and evaluate the implementation of the ACTION programme. Methods A descriptive design with a mixed method approach was used. Twenty-seven NAs from two units in Sweden were recruited, and 23 of them were offered the educational intervention. Quantitative and qualitative data were collected from multiple sources before, during and after the implementation. Quantitative data were used to analyse demographics, attendance and participation, while qualitative data were used to evaluate experiences of the implementation and contextual factors influencing the implementation. Results The evaluation showed a high degree of NA participation in the first five education modules, and a decrease in the three remaining modules. Overall, the NAs perceived the web format to be easy to use and appreciated the flexibility and accessibility. The content was described as important. Challenges included time constraints; the heavy workload; and a lack of interaction, space and equipment to complete the programme. Conclusions The results suggest that web-based education seems to be an appropriate strategy in home care settings; however, areas for improvement were identified. Our findings show that participants appreciated the web-based learning format in terms of accessibility and flexibility, as well as the face-to-face group discussions. The critical importance of organizational support and available resources are highlighted, such as management involvement and local facilitation. In addition, the findings report on the implementation challenges specific to the dynamic home care context. Trial registration This intervention was implemented with nursing assistants, and the evaluation only involved nursing staff. Patients were not part of this study. According to the ICMJE, registration was not necessary ().

scholarly journals Assessing the contribution of rare-to-common protein-coding variants to circulating metabolic biomarker levels via 412,394 UK Biobank exome sequences

2021 ◽  
Author(s):  
Abhishek Nag ◽  
Lawrence Middleton ◽  
Ryan S Dhindsa ◽  
Dimitrios Vitsios ◽  
Eleanor M Wigmore ◽  
...  
Keyword(s):  
Gene Networks ◽  
Rare Variants ◽  
Association Studies ◽  
Low Frequency ◽  
Genome Wide Association Studies ◽  
Uk Biobank ◽  
Protein Coding ◽  
The Uk ◽  
Metabolic Biomarkers ◽  
Coding Variants

Genome-wide association studies have established the contribution of common and low frequency variants to metabolic biomarkers in the UK Biobank (UKB); however, the role of rare variants remains to be assessed systematically. We evaluated rare coding variants for 198 metabolic biomarkers, including metabolites assayed by Nightingale Health, using exome sequencing in participants from four genetically diverse ancestries in the UKB (N=412,394). Gene-level collapsing analysis, that evaluated a range of genetic architectures, identified a total of 1,303 significant relationships between genes and metabolic biomarkers (p<1x10-8), encompassing 207 distinct genes. These include associations between rare non-synonymous variants in GIGYF1 and glucose and lipid biomarkers, SYT7 and creatinine, and others, which may provide insights into novel disease biology. Comparing to a previous microarray-based genotyping study in the same cohort, we observed that 40% of gene-biomarker relationships identified in the collapsing analysis were novel. Finally, we applied Gene-SCOUT, a novel tool that utilises the gene-biomarker association statistics from the collapsing analysis to identify genes having similar biomarker fingerprints and thus expand our understanding of gene networks.

scholarly journals Awareness and Opinions of Research Professionals on India's New Drug and Clinical Trials Regulations: Protocol for a Cross-Sectional Web-Based Survey Study

10.2196/14744 ◽  
2020 ◽  
Vol 9 (1) ◽  
pp. e14744
Author(s):  
Vishal Vennu ◽  
Saurabh Dahiya
Keyword(s):  
Clinical Trial ◽  
Clinical Trials ◽  
New Drugs ◽  
Survey Study ◽  
Multiple Sources ◽  
Cross Sectional ◽  
Web Based ◽  
Google Docs ◽  
New Drug ◽  
Research Professionals

Background Although several studies have been conducted and several articles have been published on India's new clinical trial regulations, very few have examined the views of investigators and ethics board members regarding modifications to the previous regulations. Overall, they have neglected to find out the opinions of other relevant professionals, such as research assistants, coordinators, associates, and managers. To our knowledge, no study has yet investigated the awareness and opinions of Indian research professionals on the new 2019 regulations. Objective This study aims to describe the awareness and opinions of Indian research professionals on the new drug and clinical trial regulations. Methods In this cross-sectional, Web-based study, we will conduct an open survey for various Indian research professionals. These professionals will be selected randomly using multiple sources. The survey questionnaires, which have already been validated, were developed using the form function in Google docs. A Web link was generated for participants to take the survey. Descriptive statistics will be shown as means and standard deviations for constant variables, whereas certain variables will instead be shown as numbers and percentages. Results The survey was opened in July 2019. Enrollment has already started and will be completed in three months. The results calculations are expected to begin in October 2019. Conclusions The results of the survey are expected to represent the views of research professionals on the new regulations that will support the development of clinical research and the pharmaceutical industry in India. These regulations are expected to help advance clinical trials, help with the approval of new drugs, and enhance ethical norms in the country. International Registered Report Identifier (IRRID) PRR1-10.2196/14744

scholarly journals Identifying genetic variants associated with ritodrine-induced pulmonary edema

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241215
Author(s):  
Seung Mi Lee ◽  
Yoomi Park ◽  
Young Ju Kim ◽  
Han-Sung Hwang ◽  
Heewon Seo ◽  
...  
Keyword(s):  
Pulmonary Edema ◽  
Pregnant Women ◽  
Genetic Variants ◽  
Cyclic Adenosine Monophosphate ◽  
Adenosine Monophosphate ◽  
Maternal Blood ◽  
Maternal Complications ◽  
Protein Coding ◽  
Whole Exome ◽  
Coding Variants

Introduction Ritodrine is one of the most commonly used tocolytics in preterm labor, acting as a ß2-adrenergic agonist that reduces intracellular calcium levels and prevents myometrial activation. Ritodrine infusion can result in serious maternal complications, and pulmonary edema is a particular concern among these. The cause of pulmonary edema following ritodrine treatment is multifactorial; however, the contributing genetic factors remain poorly understood. This study investigates the genetic variants associated with ritodrine-induced pulmonary edema. Methods In this case-control study, 16 patients who developed pulmonary edema during ritodrine infusion [case], and 16 pregnant women who were treated with ritodrine and did not develop pulmonary edema [control] were included. The control pregnant women were selected after matching for plurality and gestational age at the time of tocolytic use. Maternal blood was collected during admission for tocolytic treatment, and whole exome sequencing was performed with the stored blood samples. Results Gene-wise variant burden (GVB) analysis resulted in a total of 71 candidate genes by comparing the cumulative effects of multiple coding variants for 19729 protein-coding genes between the patients with pulmonary edema and the matched controls. Subsequent data analysis selected only the statistically significant and deleterious variants compatible with ritodrine-induced pulmonary edema. Two final candidate variants in CPT2 and ADRA1A were confirmed by Sanger sequencing. Conclusions We identified new potential variants in genes that play a role in cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) regulation, which supports their putative involvement in the predisposition to ritodrine-induced pulmonary edema in pregnant women.

scholarly journals Design-Based Research: Definition, Characteristics, Application and Challenges

2019 ◽  
Vol 5 (1) ◽  
pp. 26-35
Author(s):  
Hamed Vaezi ◽  
Hossein Karimi Moonaghi ◽  
Reyhaneh Golbaf
Keyword(s):  
Medical Education ◽  
Practical Knowledge ◽  
Educational Innovation ◽  
Sources Of Information ◽  
Multiple Sources ◽  
Short Term ◽  
Web Based ◽  
Design Based Research ◽  
Definition Of ◽  
New Research

In recent years medical education has developed dramatically, but lecturers often cite the existence of a gap between theoretical and practical knowledge. In the first decade of the present century, new research methodology named “design-based research (DBR)” was developed, which most experts and journals refer to as a fundamental way to make changes in the quality and applicability of studies and educational research as well as to enhance and improve the practice of instruction. The aim of the present study was introducing design-based research and its concepts, features, applications, and challenges. A narrative review was conducted in 2018. For this purpose, authorized English academic database including Web of Science, Science Direct, Google Scholar, international database and library in medical research filed with keywords including “design-based research, definition of DBR, DBR applications, medical education, and DBR challenges” without date limitation until 2018.11.21 were screened. Overall, 68 articles were selected and after careful reading, 21 article with related subjects were selected for material extraction. The conclusion was made that DBR that combines empirical research with design-based theories could be considered as an effective method for understanding quality, time and the cause of the phenomenon of educational innovation in practice. Usually DBR is formed by initial evaluation of a problem that occurs in a particular context, and this assessment continues throughout design and implementation. One of the characteristics of DBR is the guiding team, which includes researchers, professionals, designers, managers, teachers, trainers and others whose expertise and knowledge may in some way help. The application of DBR in web-based training programs is quite evident. The probability of non-returns in short-term projects is one of the main challenges of DBR. Medical education has developed dramatically in recent years, but it has made little progress in promoting innovative research methodologies. DBR can be used as a bridge between theories and practice and provide the basis for close communication between researchers, designers, and participants. By applying sophisticated methods and multiple sources of information, the success rate of an intervention in a particular environment is assessed, which ultimately leads to improved theories.

Sign in / Sign up

Export Citation Format

Share Document