User Guide

Dashboard

The TGex dashboard provides access to all the analyses and samples in your account, and allows you to start a new analysis using our Analsis wizard.

Start new analysis

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.

Analyses

The Analyses section contains two main areas:

  • Analyses list (on the right)- A table listing all your analyses. For each, it displays:
    • Modify Date - The last modification date for this analysis
    • Analysis - The name of the analysis, including its identifier. Clicking on this will take you to the summary information about the analysis.
    • # Samples - The number of samples used in this analysis
    • Subject - The name of the subject
    • View/Analyze Button - Depending on the status of the analysis, you will see the "Analyze" button, for analyses that have not yet been analyzed (no report has been generated), or the "View" button (for analyses that have been analyzed and have a report generated for them). Clicking on "Analyze" will take you to the Analysis screen, whereas clicking on "View" will take  you to the summary page for this analysis.
  • Summary graph (on the left) - The graph on the left provides a quick summary for your workflow, showing the number of analyses that are still pending analysis, or those that are missing samples (can't yet be analyzed).

You can also use the Search area to search for a specific analysis.

Samples

The Samples section contains two main areas:

  • Samples list (on the right) - A table listing all your samples. For each, it displays:
    • Modify Date - The last modification date for this sample
    • Sample - The name of the sample. Clicking on this will take you to the Sample's information page.
    • Subject - The name of the subject. Clicking on this will take you to the Subject's information page.
    • Version Set - The version set used to annotate this sample
    • Status - The status of the sample (Ready, In Annotation, Failed)
    • Notes - Notes about the status of the sample
    • "New Analysis" button - Clicking on this button allows you to start a new analysis using this sample
  • Summary graph (on the left) - The graph on the left provides a quick summary of the status of samples that are not associated with an analysis. This includes samples that are New, In Annotation or Failed to be annotated.

You can also use the Search area to search for a specific sample.

New Analysis Wizard

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. 

Protocol

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:

  • Germline - Single Sample - This case is commonly used to analyze germline samples when you only have access to the affected sample.
  • Germline - Trio - This case is commonly used to analyze a rare genetics case when you have access to samples for the parents and the affected.
  • Tumor Biopsy - Single Sample - This case is commonly used to analyze somatic samples when you have no access to the germline sample.
  • Tumor Biopsy - with Germline - This case is commonly used to analyze somatic samples together with their germline counterparts.

NOTE: Premium accounts include the option of creating their own protocols to optimize their workflow. 

Subject

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:

  • Subject ID (required) - A unique identifier for your subject. Commonly it would be the patient identifier in your EMR or LIMS system, but it can be any identifier you choose.
  • Name (optional) - The name of your subject
  • Date of birth (optional) - The date of birth of your subject
  • Gender (optional) - Male / Female. Leave blank for unknown / unspecified
  • Consanguinity (optional) - Commonly used to specify parental consanguinity in cases of rare disease analysis
  • Population type (optional) - Population, people or ethnic groups

Samples

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.

Clinical Info

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:

  • Serial Number (required) - Specify a unique identifier for this analysis. A default value is automatically generated but can be replaced with your own identifier (for example, ID of the case in your system)
  • Name (optional) - The name of this analysis, which default to 
  • Owner (optional) - The name of the referring clinician
  • Description (optional) - Free text to describe the clinical aspects of the case
  • Disease frequency (required) - Expected frequency of this disease occuring in the population. This number will populate a default filter which will not display any variants that appear more commonly during the analysis stage 
  • Genetic models (required) - By default, each protocol has a set of genetic models that can be used to analyze the case. For rare genetics, these would be "Recessive Homozygote", "Recessive Compound Heterozygote" and "Dominant Heterozygote". You can elect to remove irrelevant models from this list for the analysis stage
  • Phenotype terms for VarElect (optional) - Any biological term (phenotype) that will be used by VarElect to score and rank the candidate variants. You can read more about VarElect HERE.
  • Gene list (optional) - Entering a list of comma-separated genes here will automatically apply a filter on the list of variants, displaying only those occuring within the list of genes 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.

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.

Analysis Screen

The main analysis screen is designed to provide you with all the information you may need for the analysis.

Summary Information

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:

  • Under Subject you will see the general details about the subject
  • Under Clinical you can review the clinical details of the analysis and the keywords selected for scoring and ranking the genes
  • Under Samples you can see which samples were used in this analysis and their details

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'.

Main Analysis Area

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 and filtering.

You can reset all the column filters using the ‘Settings’ icon on the top right. 

Data Attributes

Genomic & Genetic Data

  • LOCATION - chromosome and genomic coordinate of the variant (link to the UCSC Genome Browser)
  • GENE - a popup will show a summary of ClinVar entries for the gene including the mode of inheritance when applicable
  • REF - the reference allele as presented in the genome reference
  • ALT - the alternative call for the main sample
  • AA - the amino acid change when applicable 
  • ZYGOSITY - the genotype call in the main sample

Associated Samples

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.

Variant Calling Q & R

This section includes attributes that can help in assessing the quality and reliability of the genotype call.

  • Q&R SCORE- classify calls by their quality (Low: Coverage<10x and GQ<15; Med: Coverage<20x and GQ<50; High: Coverage>=20x and GQ>=50)
  • DP4 - read counts (ref+, ref-, alt+, alt-)
  • % ALT - the percentage of reads showing the alternative allele

Evidence

  • VARELECT - the score for the association between the gene and the phenotype terms. Clicking on the score will present a summary of the supporting evidence for the association. More details on VarElect HERE
  • MATCHED PHENOTYPES - the number of matching terms and the relevant list of phenotypes terms associated with the gene
  • COSMIC - list and links to mathing COSMIC entries
  • CLINVAR - the clinical significance of matching ClinVar entries

Effect & Prediction

  • EFFECT - the effect of the variant on the protein level (including splicing effects)
  • SEVERITY - classify the effects into three levels:

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')

Frequency

  • MAX AF - the maximal allele frequency observed in the following control datasets:

1000 Genomes, ESV (~6500 Exomes), EXaC (~65,000 Exomes)

Filters and Tools

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.

Creating a Report

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. 

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