2. Introduction to the VarSeq Suite

The VarSeq is a set of diagnostic analysis software used as a component of in vitro laboratory developed testing. The software automates analysis of variants found in gene panels, exomes and whole genomes NGS assays. This analysis allows the identification and classification of causal variants to aid in making informed decisions, diagnoses and targeted therapy applications in hereditary disorders and cancer.

To meet the diverse needs of the clinical testing market, a workflow engine for the analysis of this data must be able to support multiple guidelines and levels of laboratory-specific customizations within the same solution. The VarSeq Suite provides a flexible automated workflow that applies the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) guidelines for interpreting NGS results to alleviate the complexities of manual interpretation. The result is a standardized and repeatable approach for variant interpretation in a clinical context that is customized to the practices of individual laboratories.

The basic VarSeq Suite workflow is described below and can be enhanced with additional components including Copy Number Analysis, vsclinical_amp, vsclinical_acmg, vswarehouse and VarSeq Pipeline Runner to fit your specific needs.

To gain experience using VarSeq try the VarSeq Tutorials.

The basic VarSeq workflow from importing VCF files to generating patient reports

2.1. Create a Project

After secondary analysis of NGS data, including sequence alignment and variant calling, the first step in using VarSeq is creating a project. In VarSeq, a project is a mechanism for analyzing a set of data from one or more samples using the same workflow from filtering and annotation to classification and reporting. To create a new project, go to the VarSeq Welcome screen and click Create New Project in the left side of the screen.

The VarSeq Welcome Screen

The New Project dialog will open where you can specify the genome assembly used to align your data, choose a template, if available, name your project and browse for a storage location. Creating a project is described in more detail in section 3.1.4.`https://doc.goldenhelix.com/VarSeq/latest/vsmanual/orientation.html`Create a New Project and Creating a New Project in the Golden Helix Learning Hub.

The New Project dialog

2.2. Import Data

Once your project is created, you can use the Import Variants… button at the center of the open tab to access the Import Variants Wizard.

The Import Variants… button.

The Importing Variants Wizard allows you to import files of variant calls like VCF, alignment files and sample information and is described in detail in section 4.4 importing_variants.

The Import Variants Wizard

2.3. Add Annotations

After you import your variant files, tabs containing Variants, CNVs and Breakends will be displayed on the right side of the |vsName|| screen. Instructions for navigating this screen and descriptions of each component can be found in section 3.3. Navigating VarSeq. To add annotations, click on the Add button on the main toolbar and select Variant Annotations….

Adding Variant Annotations

In the Select Data Source dialog, your current Data Source Library is displayed. For more information on navigating this dialog see data_source_library. Select one or more data sources to annotate and filter the variants in your samples.

Select Data Source to Annotate Variants

These Annotations will be displayed to the right of your imported variant information in the Variants tab table.

New Annotations are added on the right side of the variants table.

2.4. Filter Variants

You can filter the large number of variants typically found in a sample based on selected criteria using VarSeq’s Filter Chain function. A filter is added by right clicking on an annotation column header and selecting Add to Filter. This adds a filter to the left side of the screen where you can specify conditions to filter the variants in your sample. For more information see Filter View.

Adding an annotation to a Filter Chain

2.5. Visualize in GenomeBrowse

Add a tab displaying the GenomeBrowse visualization tool by clicking the + at the top of the Variants table and selecting GenomeBrowse.

Adding a GenomeBrowse Tab

This will open a schematic view of a selected variant in the context of the genome, chromosome, gene, and protein as well as additional data such as variant frequencies. The Console on the right of the screen gives the details of any selected feature in the graphic. For more information see genomebrowseview.

GenomeBrowse loaded with the selection in the Variants tab

2.6. Interpret Results

After viewing the Annotations for each variant and its’ genomic context, specify the variants you wish to report for a sample using the Create Variant Set function at the top of the tab.

Creating a set of variants to report.

Then, add a tab for interpreting the results by clicking the + at the top of the Variants table selecting Report. The Report tab allows you to enter the overall Patient Result and interpretations for Primary Findings and Incidental Findings.

2.7. Patient Report

To generate a Patient Report, click the Refresh button at the top of the tab. The Report will appear in a new tab along with the location where it is saved. Use the button at the top left of the new tab to open an external link to save and view the Patient Report.

Signing off on a patient report after review

To gain experience using VarSeq try Introduction to VarSeq Tutorial