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mermegar edited this page Oct 11, 2016 · 160 revisions

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

This section explains how to use main tasks for TEAM:

TEAM

  • On the right top of home page, there are two buttons Login and Sign up, and a help option that contains: documentation and tutorial.

team_login

  • After logging in, other options can be visualized on the top of main page.

team_home

  • To create a new account in TEAM, you only have to click sign in. It will appear a new window where you can select new account and fill in some fields. It is free. Once your account is created you can log in into a private session. All the jobs you run and all the panels you create will be saved there and will appear in the next session.
  • We'll see the different functionalities of the tool.

A. Loading Samples

From My Data or from My Samples you can:

  • Create a Project
  • Create a Study
  • Upload Files: The input is a VCF file: individual VCF file for only one sample or multisample VCF file for several samples (families or group of cases /controls).

team_upload

You must click in Upload button and a new window will open. You can choose a VCF file and wait to finish the validation. If there is no errors in your file,then you can click in Upload and the VCF will load and begin automatic indexing. If there are one or more errors can not load the file, you must correct the errors shown in errors tab. If there is more than hundred errors, validation is stopped automatically. There is also a stop button and a revalidate button.

team_indexing

When the file is in READY status, you can Add a suspected diagnosis. This is mandatory and you can't use a sample for a job without a suspected diagnosis.

team_suspected

B. Creating Panels

After upload VCF file, you can create a New Panel from Panels or from Run Diagnosis (step2).

team_newpanel

You can add diseases, genes and mutations in the panel. A panel with genes can diagnose variants categorized in Secondary Findings and a panel with mutations can diagnose Diagnostic variants. You can include genes and mutations in the same panel for obtain both categories of variants.

  • Add Diseases: You can select one or more diseases using the table on the left, searching by name or by database and click in Add button. When a disease is added, genes and mutations associated to selected disease are added too to the panel.

team_newpanel_diseases

  • Select Genes: you can see the associated genes with the selected disease in the previous step. Also, you can add more genes using the options in left.

team_newpanel_genes

  • Select Mutations: you can see the associated mutations with the selected disease in the first step. Also, you can add more mutations using the options in left.

team_newpanel_mutations

  • Save the Panel.

team_newpanel_save

Now, you can see the panel in Panels window: in this option you can edit the panel, archive the panel, view the panel content in Panel Preview or create an other New Panel.

team_panels

C. Run Diagnosis

After the VCF file previously uploaded is in READY status and has a suspicious diagnosis, and after create a Panel, is the moment to Run a Diagnosis following the next steps:

  • Choose one or more Samples in Ready status and with a suspicious diagnosis added.

team_run_samples

  • Choose a Panel.

team_run_panel

  • Job information and Run.

team_run_run

D. View result

From Diagnostic you can view the list of the launched jobs.

team_diagnostics

TEAM searches first for known diagnostic mutation(s). If a hit is found, a diagnostic variant is reported in Diagnostic. In Secondary findings, TEAM reports all the variants of uncertain effect, with a possible deleterious or pathologic effects found in the genes of the panel.

There are diferents tabs with diferent information about the selected job: (You can select the Job clicking it)

  • Overview: You can view interesting graphs and download diagnostic and secondary findings files in CSV format.

team_result_overview

team_result_overview

  • Diagnostic: In this tab you can find the Diagnostic Variants. These are the variants in our sample that are within the regions and appear in the list of mutations of our panel.

team_result_diagnostic

  • Secondary Findings: In this tab you can find the Secondary Variants. These are the variants that are within the regions of our panel, but not in the list of mutations.

team_result_secondary

team_result_secondary

The tool has two types of filters for priorization of secondary variants: Static filters and Custom filters

Static filters are predefined. They include differents params (sift, polyphen,phastcons,pylop and cadd) for categorize Secondary findings variants in four levels: Most likely pathogenic, Potentially pathogenic, Unkown significance and Likely benign.

team_static_filters

Custom filters. There are several filters to define the best strategy of variant selection. It is possible to choose one or several filtering options at the same time and use Search button to filter variants. For more information about filters view [Filters] (wiki/Filters).

team_custom_filters

Also, you can choose a filter used previously, selecting it in the Filters History.

team_filters_history

  • Report: In this tab you can choose the information that you want to show in your Team report using the left menu. TEAM report can be sent to a HTML report by clicking Export to PDF/print button with selected information. Before that, you must include the Patient data information and Editable conslusions and click in Save Report for consult the saved data again. The following data are mandatory:

    • Patient ID
    • Instrument
    • Analyzed by
    • Sample Origin: Only if it is known.
    • Patient Diagnosis: selecting this disease from a list of phenotypes that will be loading as you type.

team_result_report

Contact

To report an error or suggestion, please contact us at: babelomics@cipf.es

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