scholarly journals Interactive Web-Based Resource for Annotation of Genetic Variants Causing Hereditary Angioedema (HADA): Database Development, Implementation, and Validation (Preprint)

2020 ◽  
Author(s):  
Alejandro Mendoza-Alvarez ◽  
Adrián Muñoz-Barrera ◽  
Luis Alberto Rubio-Rodríguez ◽  
Itahisa Marcelino-Rodriguez ◽  
Almudena Corrales ◽  
...  
Keyword(s):  
Hereditary Angioedema ◽  
Genetic Condition ◽  
First Line ◽  
International Consensus ◽  
Web Based ◽  
Genetics And Genomics ◽  
User Friendly ◽  
Current Guidelines ◽  
Generation Sequencing ◽  
Esterase Inhibitor

BACKGROUND Hereditary angioedema is a rare genetic condition caused by C1 esterase inhibitor deficiency, dysfunction, or kinin cascade dysregulation, leading to an increased bradykinin plasma concentration. Hereditary angioedema is a poorly recognized clinical entity and is very often misdiagnosed as a histaminergic angioedema. Despite its genetic nature, first-line genetic screening is not integrated in routine diagnosis. Consequently, a delay in the diagnosis, and inaccurate or incomplete diagnosis and treatment of hereditary angioedema are common. OBJECTIVE In agreement with recent recommendations from the International Consensus on the Use of Genetics in the Management of Hereditary Angioedema, to facilitate the clinical diagnosis and adapt it to the paradigm of precision medicine and next-generation sequencing–based genetic tests, we aimed to develop a genetic annotation tool, termed Hereditary Angioedema Database Annotation (HADA). METHODS HADA is built on top of a database of known variants affecting function, including precomputed pathogenic assessment of each variant and a ranked classification according to the current guidelines from the American College of Medical Genetics and Genomics. RESULTS HADA is provided as a freely accessible, user-friendly web-based interface with versatility for the entry of genetic information. The underlying database can also be incorporated into automated command-line stand-alone annotation tools. CONCLUSIONS HADA can achieve the rapid detection of variants affecting function for different hereditary angioedema types, and further integrates useful information to reduce the diagnosis odyssey and improve its delay.

scholarly journals Interactive Web-Based Resource for Annotation of Genetic Variants Causing Hereditary Angioedema (HADA): Database Development, Implementation, and Validation

10.2196/19040 ◽  
2020 ◽  
Vol 22 (10) ◽  
pp. e19040
Author(s):  
Alejandro Mendoza-Alvarez ◽  
Adrián Muñoz-Barrera ◽  
Luis Alberto Rubio-Rodríguez ◽  
Itahisa Marcelino-Rodriguez ◽  
Almudena Corrales ◽  
...  
Keyword(s):  
Hereditary Angioedema ◽  
Genetic Condition ◽  
First Line ◽  
International Consensus ◽  
Web Based ◽  
Genetics And Genomics ◽  
User Friendly ◽  
Current Guidelines ◽  
Generation Sequencing ◽  
Esterase Inhibitor

Background Hereditary angioedema is a rare genetic condition caused by C1 esterase inhibitor deficiency, dysfunction, or kinin cascade dysregulation, leading to an increased bradykinin plasma concentration. Hereditary angioedema is a poorly recognized clinical entity and is very often misdiagnosed as a histaminergic angioedema. Despite its genetic nature, first-line genetic screening is not integrated in routine diagnosis. Consequently, a delay in the diagnosis, and inaccurate or incomplete diagnosis and treatment of hereditary angioedema are common. Objective In agreement with recent recommendations from the International Consensus on the Use of Genetics in the Management of Hereditary Angioedema, to facilitate the clinical diagnosis and adapt it to the paradigm of precision medicine and next-generation sequencing–based genetic tests, we aimed to develop a genetic annotation tool, termed Hereditary Angioedema Database Annotation (HADA). Methods HADA is built on top of a database of known variants affecting function, including precomputed pathogenic assessment of each variant and a ranked classification according to the current guidelines from the American College of Medical Genetics and Genomics. Results HADA is provided as a freely accessible, user-friendly web-based interface with versatility for the entry of genetic information. The underlying database can also be incorporated into automated command-line stand-alone annotation tools. Conclusions HADA can achieve the rapid detection of variants affecting function for different hereditary angioedema types, and further integrates useful information to reduce the diagnosis odyssey and improve its delay.

scholarly journals SAVE: A secure cloud-based pipeline for CRISPR pooled screen deconvolution

2017 ◽  
Author(s):  
Hyun-Hwan Jeong ◽  
Seon Young Kim ◽  
Maxime WC Rosseaux ◽  
Huda Y Zoghbi ◽  
Zhandong Liu
Keyword(s):  
Next Generation Sequencing ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Sequencing Data ◽  
Analysis Pipeline ◽  
Web Based ◽  
Screening Experiments ◽  
Accelerate Development ◽  
User Friendly ◽  
Generation Sequencing

AbstractWe present a user-friendly, cloud-based, data analysis pipeline for the deconvolution of pooled screening data. This tool, termed SAVE for Screening Analysis Visual Explorer, serves a dual purpose of extracting, clustering and analyzing raw next generation sequencing files derived from pooled screening experiments while at the same time presenting them in a user-friendly way on a secure web-based platform. Moreover, SAVE serves as a useful web-based analysis pipeline for reanalysis of pooled CRISPR screening datasets. Taken together, the framework described in this study is expected to accelerate development of web-based bioinformatics tool for handling all studies which include next generation sequencing data. SAVE is available at http://save.nrihub.org.

Evol2Circos: A Web-Based Tool for Genome Synteny and Collinearity Analysis and its Visualization in Fishes

2020 ◽  
Vol 111 (5) ◽  
pp. 486-490
Author(s):  
Manmohan Pandey ◽  
Basdeo Kushwaha ◽  
Ravindra Kumar ◽  
Prachi Srivastava ◽  
Suman Saroj ◽  
...  
Keyword(s):  
Large Scale ◽  
Software Tool ◽  
Web Browser ◽  
Web Based ◽  
Specific Data ◽  
Sequencing Technologies ◽  
Assembly Algorithms ◽  
User Friendly ◽  
Research Domains ◽  
Generation Sequencing

Abstract The advent of high throughput next-generation sequencing technologies and improved assembly algorithms have resulted in the accumulation of voluminous genomic data in public domains. These technologies have opened up entries for large scale comparative genome studies, especially the identification of conserved syntenic blocks among species, facilitating studies of the evolutionary importance of the conservation and variation in genomic organization. Synteny construction and visualization require computational and bioinformatics skills to prepare input files for the synteny analysis pipeline. The syntenic information for fishes is still in a juvenile stage and is scattered among different research domains. Here, we present a web-based tool “Evol2Circos” to provide a user-friendly graphical user interface (GUI) to analyze user-specific data for synteny construction and visualization, and to facilitate the browsing of syntenic information of different fishes using the Circos, bar, dual, and dot plots. The information generated from the tool can also be used for further downstream analyses. Evol2Circos software tool is tested under Ubuntu Linux. The web-browser, source code, documentation, user manual, example dataset and scripts are available online at 203.190.147.148/evole2circos/

Anaphylaxis in Response to C1 Esterase Inhibitor in a Patient with Hereditary Angioedema

2007 ◽  
Vol 19 (4) ◽  
pp. 159-163 ◽  
Author(s):  
Marco Cicardi ◽  
Lorenza Zingale ◽  
Andrea Zanichelli ◽  
Daniela Lambertenghi Deliliers
Keyword(s):  
Hereditary Angioedema ◽  
C1 Esterase Inhibitor ◽  
Esterase Inhibitor

Kindler's Syndrome with Recurrent Neutropenia: Report of Two Cases from Saudi Arabia

2020 ◽  
Author(s):  
Yousef Binamer ◽  
Muzamil A. Chisti
Keyword(s):  
Autosomal Recessive ◽  
Common Mechanism ◽  
Sequencing Analysis ◽  
Loss Of Function ◽  
Skin Atrophy ◽  
Whole Exome ◽  
Infancy And Childhood ◽  
Genetics And Genomics ◽  
New Feature ◽  
Generation Sequencing

AbstractKindler syndrome (KS) is a rare photosensitivity disorder with autosomal recessive mode of inheritance. It is characterized by acral blistering in infancy and childhood, progressive poikiloderma, skin atrophy, abnormal photosensitivity, and gingival fragility. Besides these major features, many minor presentations have also been reported in the literature. We are reporting two cases with atypical features of the syndrome and a new feature of recurrent neutropenia. Whole exome sequencing analysis was done using next-generation sequencing which detected a homozygous loss-of-function (LOF) variant of FERMT1 in both patients. The variant is classified as a pathogenic variant as per the American College of Medical Genetics and Genomics guidelines. Homozygous LOF variants of FERMT1 are a common mechanism of KS and as such confirm the diagnosis of KS in our patients even though the presentation was atypical.

The Role of Web Based Accounting Online System 2.0 as the Company's Income and Expense Management

2017 ◽  
Vol 1 (1) ◽  
pp. 44-49
Author(s):  
Nur Azizah ◽  
Dedeh Supriyanti ◽  
Siti Fairuz Aminah Mustapha ◽  
Holly Yang
Keyword(s):  
Financial Management ◽  
Accounting System ◽  
Bank Account ◽  
Web Based ◽  
Online System ◽  
Version 2.0 ◽  
User Friendly ◽  
The Impact ◽  
A Company

In a company, the process of income and expense of money must have a profit-generating goal base. The success of financial management within the company, can be monitored from the ability of the financial management in managing the finances and utilize all the opportunities that exist with as much as possible with the aim to control the company's cash (cash flow) and the impact of generating profits in accordance with expectations. With a web-based online accounting system version 2.0, companies can be given the ease to manage money in and out of the company's cash. It has a user friendly system with navigation that makes it easy for the financial management to use it. Starting from the creation of a company's cash account used as a cash account and corporate bank account on the system, deletion or filing of cash accounts, up to the transfer invoice creation feature, receive and send money. Thus, this system is very effective and efficient in the management of income and corporate cash disbursements.   Keywords:​Accounting Online System, Financial Management, Cash and Bank

Web-Based Peer and Self-Assessment System Design and Development for Elementary School Students

2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Mehmet EMIN KORTAK
Keyword(s):  
Elementary School ◽  
Elementary School Students ◽  
Primary Schools ◽  
Peer Assessment ◽  
Assessment System ◽  
Assessment Process ◽  
School Students ◽  
Self Assessment ◽  
Web Based ◽  
User Friendly

This research aimed at designing and improving the web-based integrated peer and self- assessment. WesPASS (web-based peer-assessment system), developed in this research, allows students to assess their own or their peers’ performance and project assignments and to report about the result of these assessments so that they correct their assignments. This study employed design-based research. The participants included 102 fourth grade primary school students and their 4 teachers from 2 state and 2 private primary schools in Ankara, Kecioren (Turkey) who employed the system and were engaged in a questionnaire survey to assess its quality. The findings were analyzed through quantitative data analysis. The findings revealed that the system can be used by elementary school students for peer and self-assessment system. The participants stated that WesPASS is simple and user-friendly, and it accelerates the assessment process by employing information technology and allows to share opinions 

scholarly journals The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases

Metabolites ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 113
Author(s):  
Julia Koblitz ◽  
Sabine Will ◽  
S. Riemer ◽  
Thomas Ulas ◽  
Meina Neumann-Schaal ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Point Of View ◽  
Use Cases ◽  
Mathematical Methods ◽  
State Behavior ◽  
Web Based ◽  
Research Fields ◽  
Balance Analysis ◽  
Metabolic Models ◽  
User Friendly

Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes. Metano is a standalone, open-source toolbox for the analysis and refinement of metabolic models. While flux distributions in metabolic networks are predominantly analyzed from a reaction-centric point of view, the Metano methods of split-ratio analysis and metabolite flux minimization also allow a metabolite-centric view on flux distributions. In addition, we present MMTB (Metano Modeling Toolbox), a web-based toolbox for metabolic modeling including a user-friendly interface to Metano methods. MMTB assists during bottom-up construction of metabolic models by integrating reaction and enzymatic annotation data from different databases. Furthermore, MMTB is especially designed for non-experienced users by providing an intuitive interface to the most commonly used modeling methods and offering novel visualizations. Additionally, MMTB allows users to upload their models, which can in turn be explored and analyzed by the community. We introduce MMTB by two use cases, involving a published model of Corynebacterium glutamicum and a newly created model of Phaeobacter inhibens.

scholarly journals An Interactive Web Application for the Statistical Analysis of Continuous Glucose Monitoring Data in Epidemiological Studies

2021 ◽  
pp. 193229682098557
Author(s):  
Alysha M. De Livera ◽  
Jonathan E. Shaw ◽  
Neale Cohen ◽  
Anne Reutens ◽  
Agus Salim
Keyword(s):  
Continuous Glucose Monitoring ◽  
Web Application ◽  
Diabetes Management ◽  
Glucose Monitoring ◽  
Epidemiological Studies ◽  
Interactive Software ◽  
Web Based ◽  
Software Applications ◽  
Visualization Of Data ◽  
User Friendly

Motivation: Continuous glucose monitoring (CGM) systems are an essential part of novel technology in diabetes management and care. CGM studies have become increasingly popular among researchers, healthcare professionals, and people with diabetes due to the large amount of useful information that can be collected using CGM systems. The analysis of the data from these studies for research purposes, however, remains a challenge due to the characteristics and large volume of the data. Results: Currently, there are no publicly available interactive software applications that can perform statistical analyses and visualization of data from CGM studies. With the rapidly increasing popularity of CGM studies, such an application is becoming necessary for anyone who works with these large CGM datasets, in particular for those with little background in programming or statistics. CGMStatsAnalyser is a publicly available, user-friendly, web-based application, which can be used to interactively visualize, summarize, and statistically analyze voluminous and complex CGM datasets together with the subject characteristics with ease.

scholarly journals A Comprehensive Analysis of Hungarian MODY Patients—Part I: Gene Panel Sequencing Reveals Pathogenic Mutations in HNF1A, HNF1B, HNF4A, ABCC8 and INS Genes

Life ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 755
Author(s):  
Zsolt Gaál ◽  
Zsuzsanna Szűcs ◽  
Irén Kántor ◽  
Andrea Luczay ◽  
Péter Tóth-Heyn ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Low Dose ◽  
Comprehensive Analysis ◽  
First Line ◽  
Pathogenic Mutations ◽  
Appropriate Treatment ◽  
Causal Genes ◽  
Hnf1a Gene ◽  
Gene Panel Sequencing ◽  
Generation Sequencing

Maturity-onset diabetes of the young (MODY) has about a dozen known causal genes to date, the most common ones being HNF1A, HNF4A, HNF1B and GCK. The phenotype of this clinically and genetically heterogeneous form of diabetes depends on the gene in which the patient has the mutation. We have tested 450 Hungarian index patients with suspected MODY diagnosis with Sanger sequencing and next-generation sequencing and found a roughly 30% positivity rate. More than 70% of disease-causing mutations were found in the GCK gene, about 20% in the HNF1A gene and less than 10% in other MODY-causing genes. We found 8 pathogenic and 9 likely pathogenic mutations in the HNF1A gene in a total of 48 patients and family members. In the case of HNF1A-MODY, the recommended first-line treatment is low dose sulfonylurea but according to our data, the majority of our patients had been on unnecessary insulin therapy at the time of requesting their genetic testing. Our data highlights the importance of genetic testing in the diagnosis of MODY and the establishment of the MODY subtype in order to choose the most appropriate treatment.

Sign in / Sign up

Export Citation Format

Share Document