The TGex dashboard provides access to all the analyses and samples in your account, and allows you to start a new analysis using our Analysis wizard.
You can initiate a new analysis by clicking on the "Start New Analysis" button, which will guide you through the the process using a straightforward wizard in which new samples can be uploaded (VCF format) and clinical details of the case can be entered together with general details regarding the subject of the analysis.
The Analyses section contains two main areas:
You can also use the Search area to search for a specific analysis.
The Samples section contains two main areas:
You can also use the Search area to search for a specific sample.
The New Analysis Wizard guides you through creating a new analysis in TGex. The process is separated into 4 stages, and information collected is summarized on the right side of the screen.
In the first stage of the analysis, you will be required to select the protocol for this analysis. A protocol is a template for analysis which includes predefined filters, the list of required and associated samples and the report template. Each new account includes four (4) default protocols representing the most common cases of NGS analysis. These include:
NOTE: Premium accounts include the option of creating their own protocols to optimize their workflow.
TGex was designed as a subject-centric platform. As such, each analysis contains a single main sample with the option to be accompanied by several associated samples (for example: the parents in a trio case or the matched germline in a tumor biopsy case).
In this section of the wizard you can enter general details regarding the subject of the analysis. These details will be available during the analysis process for reference, and automatically included in the analysis report.
You can also select an existing subject if one has already been created.
For new subjects, the following information can be entered:
In this section you can either upload a new sample or select an existing pre-loaded sample for the analysis by clicking on the "Select Sample" button next to the relevant sample. When a new VCF is uploaded into the system, TGex will automatically annotate it with the required data for analysis using its proprietary annotation pipeline (this may take a few minutes).
In the case of multiple samples, you will be required to associate or upload a sample for each associated sample, as well.
In this section you may include any clinical information about the analysis and its subject, decide which genetic models to analyze for the subject, and set phenotype terms that will be used to score and rank candidate variants during the analysis stage. Information entered here will be available during the analysis stage for reference.
The following information can be entered:
Clicking on ‘Save’ in the last section of the wizard will enter this new analysis to your account and will redirect you to the Analysis Summary Page.
Here you can examine all the details of the analysis and the progress of the sample annotation.
You can use the edit button on the top right to enter or modify the information or click on ‘Analyze’ just beside it to go to the Analysis Screen where you will actually browse variants and apply filters.
The main analysis screen is designed to provide you with all the information you may need for the analysis.
On the top you will find the breadcrumb on the left, the summary information in the middle and the ‘Report Preview’ button to the right.
Clicking on the 'Subject' or 'Analysis' in the breadcrumb will open a new tab with the Subject Summary Page or the Analysis Summary page, respectively.
You can easily review the summary of these before you actually start the analysis through the Info section on the right:
Clicking on ‘Report Preview’ will generate a visual summary of all the findings in addition to the general info. This is a feature that enables the review of the current results while analyzing the case and is discussed in details under 'Creating a Report'.
The main area is divided to tabs dedicated for each genetic model used for the analysis. Each tab is actually an interactive table where each row represents a variant and each column depicts a certain attribute of the variant. In TGex, these dozens of attributes are divided to 5 categories, each can be collapsed (by default) showing only the most relevant attributes or expanded using the ‘>’ icon to the right of each category title.
You can also reset the column view using the ‘Settings’ icon on the top right.
Each column has two interactive functionalities – sorting (by a click on the header) and filtering (clicking on the filter icon to the right).
You can reset all the column filters using the ‘Settings’ icon on the top right.
When applicable, a column per associated sample will present an icon depicting the genotype called for the specific variant in the relevant sample (single icon - HET; double icon - HOM).
Clicking on the icon, a table summarizing the variant calling attributes for all the samples in the analysis will be presented.
This section includes attributes that can help in assessing the quality and reliability of the genotype call.
High: Nonsense, Frameshift, Splicing Sites, Missense (when all prediction tools score as 'Damaging')
Med: Codon indels, Missense (at least one prediction tool scores as 'Damaging')
Low: Synonymous, Splice Site Region, Missense (none of the prediction tools score as 'Damaging')
Expanding this section will present all the prediction tools (GERP, LRT_Pred, PolyPhen2 and SIFT).
1000 Genomes, ESV (~6500 Exomes), ExAC (including GnomAD - ~120,000 Exomes)
On the left you will find the ‘Filters & Tools’ pane, summarizing all the applied filters for the current tab.
Through this pane or alternatively through each of the column titles in the grid you can easily add, edit or remove filters while reviewing the variants. Each filter that you add through the column title will also be displayed in this pane on the left and will be documented in the Methods section in the final report.
Under this pane you can also use predefined gene panels or manually entered gene lists. You can also edit the VarElect terms used for the ranking and the Disease frequency used for the Allele Frequency filter.
This pane can be minimized in order to allow more screen area for the table when not in use.
To the left of each variant row there are three annotation types that can be defined per candidate variant. Clicking on this section will present the Annotation & Interpretation popup where you can define the relevance (High, Med or Low) and the pathogenicity of the variant on the top. Below, you can add a note regarding the variant in free text after reviewing all the information (clinical and VarElect) and selecting the relevant disorder from OMIM when applicable.
Once the browsing of candidate variants in the various genetic models is done and several candidate variants were selected with their relevance score and related notes, you are ready to preview the current findings by clicking on the ‘Report Preview’ button on the top right.
This will generate a visual summary of all the findings in addition to the general info. Here you can also choose which of the evidence sections presented will enter the final report (Premium users only).
From the Report Preview you can either go back to the analysis to edit or add more candidates or proceed to ‘Generate Report’ where 2 files will be generated automatically – the full report in a pdf format with all the information and supporting evidence including publications and more, and an Excel file displaying the full variant tables that were analyzed.