How To’s & Advanced Workflows

Review of VarSeq Export Options

Mar 10, 2022

Although best known for its auto-generation of custom reports, VarSeq comes with a slew of options for exporting your data. In this blog, we will review some of the lesser-known methods for exporting your data into usable formats. These four export options can all be found under the Export tab…

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Integrating Custom Gene Panels for Variant Annotations Q&A Follow Up

Feb 16, 2022

Thanks to all those who attended the recent webcast by Dr. Rana Smalling, “Integrating Custom Gene Panels for Variant Annotations”. If you were unable to attend or would like to recap, here is a link to watch the broadcast. We covered a lot of content regarding virtual gene panels, and…

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How to Create Your Own CNV Frequency Catalog

Jan 20, 2022

Global population frequency catalogs like 1kG Phase 3, gnomAD, DGV, and others are excellent resources for identifying rare variants in your copy number variant (CNV) analysis. However, they are not exhaustive, and the reality is a lot of variants that are missing from global population frequency catalogs are still common…

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VS-CNV Command-Line CNV Tool

Dec 9, 2021

If you stay current on the developments of Golden Helix features, you are aware of the substantial evolution of our copy number detection and evaluation capabilities in VarSeq. The process of CNV detection and evaluation is typically handled through the VarSeq graphic user interface. However, in some cases, users benefit…

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Top FAS Tricks You Wish You Knew When Getting Started with VSClinical

Nov 18, 2021

As a newer member of the Golden Helix FAS Team I, like many of our customers, went through a phase of learning the ins, outs, and shortcuts of clicking around the program. In an effort to expedite new users coming up to speed, or to teach some tricks to experienced…

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Validating Your CNV Workflow

Nov 16, 2021

The VarSeq CNV calling algorithm, VS-CNV, is a powerful tool for calling CNVs from the NGS coverage data stored in your BAM files. However, before this algorithm can be deployed in a clinical setting, it must be tuned and validated using data that is representative of your lab’s NGS workflow.…

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Efficient Gene Panel Utilization in VarSeq

Aug 24, 2021

Clinical diagnostic efforts in next-generation sequencing are commonly defined at a gene panels level. The validation process of adding new genes to any diagnostic panel is ongoing, but labs typically construct and validate their clinical workflows for the current status of verified genes. This is not limited to primary finding…

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Manage gene lists across projects with VarSeq and VSClinical

Aug 18, 2021

Clinical labs often maintain gene panels, which are lists of genes with evidence of disease association. These panels are used to prioritize variants and limit interpretations to a predefined set of test-specific genes. In general, gene panels should be stored independently of any specific project or interpretation, as it is…

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Easily Edit Algorithms in VarSeq Projects with a Quick Right-Click

May 20, 2021

Thanks for checking out this blog on how to to get more out of your VarSeq projects! The best way to show off one of my favorite new features that have been incorporated into the latest VarSeq 2.2.3 release is with a scenario: You work in a lab that processes…

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Webcast Recap: High Precision Exome CNV Detection with VS-CNV

May 7, 2021

Thank you to those who attended the recent webcast, “High Precision Exome CNV Detection with VS-CNV”. For those who could not attend but wish to watch, here is a link to the recording. This webcast delved into the complex world of CNV calling for whole-exome samples, which presents unique challenges that…

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VarSeq NGS Workflow Design: Clinical vs. Research

Apr 22, 2021

In many cases, VarSeq users design their next-gen sequencing workflows for a clinical application. One of the major values of using VarSeq is the standardization of sample analysis via project templates for filtering down to rare variants and isolate any clinically relevant variant. However, VarSeq also doubles as a robust…

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VarSeq Update: Support for the Interpretation of Non-coding and Splice Site Variants

Apr 15, 2021

While VarSeq has always had excellent support for variant interpretation and analysis, we continue to find new edge cases in the clinical literature that improve our interpretation capabilities. In this blog, we will be covering some of the new improvements in VarSeq to support the interpretation of non-coding and splice…

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Orphanet Annotations in VarSeq

Mar 18, 2021

Orphanet is a public database available in VarSeq that aims to improve the current understanding and treatment options for patients affected by rare diseases. This resource was established in France in 1997 and has gradually grown to cover a consortium of over 40 countries in Europe. The primary goal of…

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Customizing New VSClinical Report Templates

Mar 9, 2021

Clinical testing labs produce reports as the end product of the NGS variant detection and interpretation workflow, and purpose-built clinical genomics software is essential to that process. Necessarily, the content, detail, and presentation of the report needs to be specialized to each clinical lab, and potentially each offered test. Our…

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Implementation of ClinGen Dosage Sensitivity in VSClinical

Mar 4, 2021

The collaboration between the Clinical Genome Resource (ClinGen) consortium and the American College of Medical Genetics (ACMG) recently developed published guidelines for the interpretation of CNVs called on next-generation sequencing data. These new guidelines are the first to provide a robust set of rules for the interpretation of small intragenic…

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New Mendel Error Algorithm in VarSeq

Mar 2, 2021

In many cases, VarSeq users typically run single trio projects or perhaps an extended family project. Not only are all the inheritance model algorithms available in the VarSeq software to capture de novo, dominant, or recessively inherited variants but there are a number of quality control fields to help ensure…

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New VSClinical ACMG Word Report Templates

Feb 18, 2021

The recent release of VarSeq 2.2.2 brings our Word report template system, previously featured in VSClinical AMP, to the VSClinical ACMG workflow. This blog post will describe how to use the Word template system using one of our shipped templates as well as how to start customizing your own templates.…

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Applying the Probability Segregation Algorithm for CNV Analysis

Feb 4, 2021

VarSeq 2.2.2 has incorporated a multitude of interesting new features. In this blog, I want to continue discussing these features and how each can be incorporated into your workflow. I will also discuss the application of the Probability Segregation algorithm for copy number variation (CNV) analysis. The Probability Segregation algorithm…

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Updates on Splice Site Analysis

Feb 2, 2021

Our latest VarSeq release is one of the largest we’ve ever had, boasting an extensive list of new features and improvements. As part of this release, we have dramatically expanded our support for splice site analysis. This includes improvements to our novel splice site algorithm and support for splice site…

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VSClinical: Defining Sample Phenotypes

Jan 20, 2021

Our recent release of VarSeq 2.2.2 comes with a long list of upgrades and new features. In this blog post, we will demonstrate how defining sample phenotypes are available in VSClinical. One noticeable change is the ACMG guideline variant evaluation in VSClinical. Not only has this interface added CNV guideline…

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