Analysis Screen

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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