Analysis Screen

The analysis screen will display all variant information provided by the VCF file as well as the annotations and genetics models that are populated based on the specified design protocol.

The Analysis screen displays all variant information

Summary Information #

Summary information regarding the sample is present in the upper right corner of the analysis page. The information that can be accessed includes:

  • Subject: Provides the general details about the subject.
  • Clinical: User can review the clinical details of the analysis and keywords selected

for scoring and ranking genes.

  • VCF Samples: Here the user can see which samples were used in the analysis, the total number of variants for those samples, and Identity by Descent.
    • Identity by Descent: Underlies genetically mediated similarities among individuals.
    • HET in both parents: reflects the total number (Count) of heterozygous mutations in both parents and the number of homozygous mutations in the proband (should be around 25% for a real trio).
    • HOM-ALT in Mother, HOM-Ref in Father reflects the alternate alleles that are potentially transmitted from the mother to the proband, missing in the father and called as heterozygous in the proband (should be around 100% for a real trio).
    •  HOM-ALT in Father, HOM-Ref in Mother reflects the alternate alleles that are potentially transmitted from the father to the proband, missing in the mother and called as heterozygous in the proband (should be around 100% for a real trio).
Identity by Descent is displayed under the VCF Sample tab

Variant Analysis #

The table interface is divided into tabs dedicated for each genetic model used for the analysis. Each tab is an interactive table where each row represents a variant and each column represents a certain attribute of the variant. In the Geneyx Analysis window, these attributes are divided into 5 categories, each can be collapsed or expanded using the ‘>’ icon to the right of each category title. Each column in the table can be customized to a specified width and through the settings icon, the default width can be restored.

Main Analysis window

By clicking on a column header, the variants can be sorted by ascending or descending order, or a filter can be applied by selecting the filter icon to the right of the individual column.

Filters can be applied to individual columns using the filter icon

Filters And Tools #

On the left you will find the Filters & Tools pane, summarizing the applied filters for the current tab. 

The filter logic can be viewed in the left side pane

Filters can be added to the Filters and Tools using the columns in the table or they can be removed using the delete option next to each filter. Each filter that is added will be displayed in this dialog and will be documented in the Methods section in the final report.

With this interface users can further filter using predefined Gene Panels, Gene Lists, and Variant Maps.  

The filter logic can be viewed in the left side pane

To add these additional filters, go to the Settings icon on the left side of the window.

The Settings option is located on the left side pane

Once the Settings icon is selected, the new window will give you options to create Gene Panels and Variant Maps that can be used in the filtering logic. Once created, these will be stored internally and can be applied to all analysis cases.

Genetic Models #

Fast Track: This applies filters that are designated to match the most relevant variants(s) to the clinical phenotype, if available, or to the pathogenicity.

FastTrack inheritance model

Recessive HOM: Displays the clinically relevant variants associated with recessive inheritance for which the proband is homozygous.

Recessive homozygous inheritance model

Recessive Compound HET: Displays the clinically relevant variants associated with recessive inheritance model for which the proband is heterozygous.

Recessive compound heterozygous inheritance model

Dominant HET: Displays the clinically relevant variants associated with dominant inheritance model for which the proband is heterozygous.

Dominant heterozygous inheritance model

Mitochondrial: Displays clinically relevant variants associated with mitochondrial DNA variants.

Mitochondrial inheritance model

CNV: Displays clinically relevant copy number variants.

Copy number variant analysis window

Incidental findings: Displays variants associated with ACMG incidental findings genes.

Incidental findings analysis window


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