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Welcome to the TEAM wiki!
TEAM (Targeted Enrichment Analysis and Management) is an open web-based tool for the design and management of panels of genes for targeted enrichment and massive sequencing for diagnostic applications.
TEAM allows users to define their own panels of genes. The definition is based on disease terms obtained from different databases (HGMD-public, HUMSAVAR, ClinVar and COSMIC). Each disease term has the corresponding disease genes associated. The panels so defined are configurable, and new genes can be added or undesired genes removed. Thus, when a VCF file is uploaded in the systems, TEAM searches for known diagnostic mutation(s). Looking for known diagnostic variants in the known disease genes optimize the resources in a clinic context while drastically reduces the risk of unsolicited findings.
TEAM is a web application based on HTML5 and javascript. The tool is developed in javascript with the Ext JS framework. The Front-end has been developed using the Bootstrap framework. The entire application runs locally. The system uses HTML5 local storage and no data is sent to the server. Only the information on the panels, genes and disease variants are obtained from the web services of CellBase .
TEAM represents a new philosophy in which remote highly efficient database query systems move the information to the local genomic data rather than the opposite as many other programs do.
TEAM has been designed with these goals in mind:
- This tool is written in Javascript using the new HTML5 standards and runs in modern web browsers.
- The genomic data (in standard VCF format) are analysed locally in the user’s computer that request relevant information on disease-related mutations and variant potential pathogenicity to the remote database CellBase (published previously in NAR). It is important noticing that by keeping patient’s genomic data local TEAM avoids any type of privacy or confidentiality issue.
Despite the increasing use of panels of genes for diagnostic purposes the analysis of results must be carried out with general purpose programs distributed with the instruments. To our knowledge there are no open bioinformatic tools specifically designed for this purpose available.
TEAM offers an intuitive and easy-to-use environment for the definition of gene panels and the processing and analysis of targeted enrichment sequencing data.
In the Tutorial you will learn how to use TEAM web application. Tutorial covers main functionalities such as:
- User interface functionality.
- TEAM inputs and outputs.
- Management gene panels.
To report an error or suggestion, please contact us at: babelomics@cipf.es