scholarly journals Rapid clinical diagnostic variant investigation of genomic patient sequencing data with iobio web tools

2017 ◽  
Vol 1 (6) ◽  
pp. 381-386 ◽  
Author(s):  
Alistair Ward ◽  
Mary A. Karren ◽  
Tonya Di Sera ◽  
Chase Miller ◽  
Matt Velinder ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Real Time ◽  
Computational Analysis ◽  
Disease Diagnosis ◽  
Epileptic Encephalopathy ◽  
Inherited Disease ◽  
Sequencing Data ◽  
Web Based ◽  
Web Tools ◽  
Clinical Diagnostic

IntroductionComputational analysis of genome or exome sequences may improve inherited disease diagnosis, but is costly and time-consuming.MethodsWe describe the use of iobio, a web-based tool suite for intuitive, real-time genome diagnostic analyses.ResultsWe used iobio to identify the disease-causing variant in a patient with early infantile epileptic encephalopathy with prior nondiagnostic genetic testing.ConclusionsIobio tools can be used by clinicians to rapidly identify disease-causing variants from genomic patient sequencing data.

scholarly journals 2278

2017 ◽  
Vol 1 (S1) ◽  
pp. 13-14
Author(s):  
Alistair N. Ward ◽  
Matt Velinder ◽  
Chase Miller ◽  
Tony Di Sera ◽  
Yi Qiao ◽  
...  
Keyword(s):  
Real Time ◽  
Protein Function ◽  
Variant Calling ◽  
Compound Heterozygote ◽  
Treacher Collins Syndrome ◽  
Whole Genome Sequencing Data ◽  
Missense Mutations ◽  
Sequencing Data ◽  
Web Based ◽  
Functional Studies

OBJECTIVES/SPECIFIC AIMS: The objective of the study was 2-fold; to identify potentially deleterious alleles in a child with Treacher Collins syndrome, and; to demonstrate the value of the iobio analysis platform for intuitively and rapidly analyzing genomic data. METHODS/STUDY POPULATION: We used the iobio suite of web-based applications to analyze quality metrics for the sequencing data and called variants for the proband and his parents. We then visually interrogated variants in genes potentially associated with the syndrome in real-time, using the intuitive gene.iobio application. We sought high impact variants that demonstrated a predicted impact on the protein function, and were simultaneously at low allele frequency in the general human population. Variants were also compared against the ClinVar database of known mutations to identify variants that have already been associated with this, or related syndromes in the literature or clinical studies. Finally, the gene.iobio tool allows users to interrogate the primary sequencing data to ensure that no variants had been missed by the primary variant calling pipeline. This analysis pipeline was performed using intuitive web-based apps in real time, and consequently represents a system that is available to users that traditionally are excluded from these analyses. RESULTS/ANTICIPATED RESULTS: The iobio suite was used to rapidly assess data quality and interrogate genetic variants for a child with Treacher Collins syndrome. A compound heterozygote consisting of 2 missense alleles in the TCOF1 gene was identified as a compelling pathogenic allele, necessitating further functional investigation. The study helped validate the use of the intuitive iobio tools in such analyses, strengthening the case for greater involvement of medical professionals in data analysis. DISCUSSION/SIGNIFICANCE OF IMPACT: The performed analyses demonstrated that the whole genome sequencing data for the family being studied was of a very high quality, although 1 gene demonstrated a local region of almost zero coverage. This ensured that study conclusions can be presented with confidence. A variant associated with Treacher Collins syndrome 1 in ClinVar was uncovered in the TCOF1 gene, however, given it’s benign rating, this variant was not considered further. The most interesting candidate was a compound heterozygote, consisting of 2 missense mutations, also in the TCOF1 gene. These mutations occurred with allele frequencies of 22% and 8% in the general population, and additional molecular and functional studies are currently being pursued.

scholarly journals Web-based design and analysis tools for CRISPR base editing

2018 ◽  
Author(s):  
Gue-Ho Hwang ◽  
Jeongbin Park ◽  
Kayeong Lim ◽  
Sunghyun Kim ◽  
Jihyeon Yu ◽  
...  
Keyword(s):  
High Efficiency ◽  
Target Sequence ◽  
Sequencing Data ◽  
Gene Correction ◽  
Web Based ◽  
Base Editing ◽  
Link Type ◽  
Web Tools ◽  
A Genome ◽  
Ngs Data

AbstractBackgroundAs a result of its simplicity and high efficiency, the CRISPR-Cas system has been widely used as a genome editing tool. Recently, CRISPR base editors, which consist of deactivated Cas9 (dCas9) or Cas9 nickase (nCas9) linked with a cytidine or a guanine deaminase, have been developed. Base editing tools will be very useful for gene correction because they can produce highly specific DNA substitutions without the introduction of any donor DNA, but dedicated web-based tools to facilitate the use of such tools have not yet been developed.ResultsWe present two web tools for base editors, named BE-Designer and BE-Analyzer. BE-Designer provides all possible base editor target sequences in a given input DNA sequence with useful information including potential off-target sites. BE-Analyzer, a tool for assessing base editing outcomes from next generation sequencing (NGS) data, provides information about mutations in a table and interactive graphs. Furthermore, because the tool runs client-side, large amounts of targeted deep sequencing data (>100MB) do not need to be uploaded to a server, substantially reducing running time and increasing data security. BE-Designer and BE-Analyzer can be freely accessed at http://www.rgenome.net/bedesigner/ and http://www.rgenome.net/be-analyzer/respectivelyConclusionWe develop two useful web tools to design target sequence (BE-Designer) and to analyze NGS data from experimental results (BE-Analyzer) for CRISPR base editors.

scholarly journals High-precision and cost-efficient sequencing for real-time COVID-19 surveillance

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sung Yong Park ◽  
Gina Faraci ◽  
Pamela M. Ward ◽  
Jane F. Emerson ◽  
Ha Youn Lee
Keyword(s):  
Los Angeles ◽  
Whole Genome Sequencing ◽  
Real Time ◽  
Genome Sequencing ◽  
High Precision ◽  
High Throughput Sequencing ◽  
Whole Genome ◽  
Sequencing Data ◽  
Public Health Response ◽  
Cost Efficient

AbstractCOVID-19 global cases have climbed to more than 33 million, with over a million total deaths, as of September, 2020. Real-time massive SARS-CoV-2 whole genome sequencing is key to tracking chains of transmission and estimating the origin of disease outbreaks. Yet no methods have simultaneously achieved high precision, simple workflow, and low cost. We developed a high-precision, cost-efficient SARS-CoV-2 whole genome sequencing platform for COVID-19 genomic surveillance, CorvGenSurv (Coronavirus Genomic Surveillance). CorvGenSurv directly amplified viral RNA from COVID-19 patients’ Nasopharyngeal/Oropharyngeal (NP/OP) swab specimens and sequenced the SARS-CoV-2 whole genome in three segments by long-read, high-throughput sequencing. Sequencing of the whole genome in three segments significantly reduced sequencing data waste, thereby preventing dropouts in genome coverage. We validated the precision of our pipeline by both control genomic RNA sequencing and Sanger sequencing. We produced near full-length whole genome sequences from individuals who were COVID-19 test positive during April to June 2020 in Los Angeles County, California, USA. These sequences were highly diverse in the G clade with nine novel amino acid mutations including NSP12-M755I and ORF8-V117F. With its readily adaptable design, CorvGenSurv grants wide access to genomic surveillance, permitting immediate public health response to sudden threats.

scholarly journals Deep-Framework: A Distributed, Scalable, and Edge-Oriented Framework for Real-Time Analysis of Video Streams

Sensors ◽  
2021 ◽  
Vol 21 (12) ◽  
pp. 4045
Author(s):  
Alessandro Sassu ◽  
Jose Francisco Saenz-Cogollo ◽  
Maurizio Agelli
Keyword(s):  
Deep Learning ◽  
Real Time ◽  
Video Data ◽  
Video Analytics ◽  
Web Based ◽  
Real Time Analysis ◽  
Open Source Framework ◽  
Cluster Configuration ◽  
Time Requirements ◽  
High Level

Edge computing is the best approach for meeting the exponential demand and the real-time requirements of many video analytics applications. Since most of the recent advances regarding the extraction of information from images and video rely on computation heavy deep learning algorithms, there is a growing need for solutions that allow the deployment and use of new models on scalable and flexible edge architectures. In this work, we present Deep-Framework, a novel open source framework for developing edge-oriented real-time video analytics applications based on deep learning. Deep-Framework has a scalable multi-stream architecture based on Docker and abstracts away from the user the complexity of cluster configuration, orchestration of services, and GPU resources allocation. It provides Python interfaces for integrating deep learning models developed with the most popular frameworks and also provides high-level APIs based on standard HTTP and WebRTC interfaces for consuming the extracted video data on clients running on browsers or any other web-based platform.

scholarly journals Webinar : An Initial Experience with Web-based Real Time Interactive Clinical Seminars for Japanese Medical Students

2010 ◽  
Vol 11 (2) ◽  
pp. 87-90 ◽  
Author(s):  
Gerald H. Stein ◽  
Ayako Shibata ◽  
Miho Kojima Bautista ◽  
Yasuharu Tokuda
Keyword(s):  
Medical Students ◽  
Real Time ◽  
Initial Experience ◽  
Web Based

scholarly journals Multi-Parameter Vital Sign Telemedicine System Using Web Socket for COVID-19 Pandemics

Healthcare ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 285
Author(s):  
Chuchart Pintavirooj ◽  
Tanapon Keatsamarn ◽  
Treesukon Treebupachatsakul
Keyword(s):  
Real Time ◽  
Vital Sign ◽  
Vital Signs ◽  
Mobile Network ◽  
Cloud Platform ◽  
Telemedicine System ◽  
Web Based ◽  
The Real ◽  
Real Time Application ◽  
Commercial Platform

Telemedicine has become an increasingly important part of the modern healthcare infrastructure, especially in the present situation with the COVID-19 pandemics. Many cloud platforms have been used intensively for Telemedicine. The most popular ones include PubNub, Amazon Web Service, Google Cloud Platform and Microsoft Azure. One of the crucial challenges of telemedicine is the real-time application monitoring for the vital sign. The commercial platform is, by far, not suitable for real-time applications. The alternative is to design a web-based application exploiting Web Socket. This research paper concerns the real-time six-parameter vital-sign monitoring using a web-based application. The six vital-sign parameters are electrocardiogram, temperature, plethysmogram, percent saturation oxygen, blood pressure and heart rate. The six vital-sign parameters were encoded in a web server site and sent to a client site upon logging on. The encoded parameters were then decoded into six vital sign signals. Our proposed multi-parameter vital-sign telemedicine system using Web Socket has successfully remotely monitored the six-parameter vital signs on 4G mobile network with a latency of less than 5 milliseconds.

scholarly journals Deep Learning-Based Cattle Vocal Classification Model and Real-Time Livestock Monitoring System with Noise Filtering

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 357
Author(s):  
Dae-Hyun Jung ◽  
Na Yeon Kim ◽  
Sang Ho Moon ◽  
Changho Jhin ◽  
Hak-Jin Kim ◽  
...  
Keyword(s):  
Deep Learning ◽  
Real Time ◽  
Model Development ◽  
Classification Model ◽  
Intelligence Analysis ◽  
Noise Filtering ◽  
Meat Industry ◽  
Mel Frequency Cepstral Coefficients ◽  
Web Based ◽  
The Status

The priority placed on animal welfare in the meat industry is increasing the importance of understanding livestock behavior. In this study, we developed a web-based monitoring and recording system based on artificial intelligence analysis for the classification of cattle sounds. The deep learning classification model of the system is a convolutional neural network (CNN) model that takes voice information converted to Mel-frequency cepstral coefficients (MFCCs) as input. The CNN model first achieved an accuracy of 91.38% in recognizing cattle sounds. Further, short-time Fourier transform-based noise filtering was applied to remove background noise, improving the classification model accuracy to 94.18%. Categorized cattle voices were then classified into four classes, and a total of 897 classification records were acquired for the classification model development. A final accuracy of 81.96% was obtained for the model. Our proposed web-based platform that provides information obtained from a total of 12 sound sensors provides cattle vocalization monitoring in real time, enabling farm owners to determine the status of their cattle.

Preimplantation Genetic Testing for Rare Inherited Disease of MMA-CblC: an Unaffected Live Birth

2021 ◽  
Author(s):  
Cuiting Peng ◽  
Jun Ren ◽  
Yutong Li ◽  
Yuezhi Keqie ◽  
Fan Zhou ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Live Birth ◽  
Inherited Disease ◽  
Preimplantation Genetic Testing
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