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 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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New Annotation: GnomAD – Gene Constraints

Feb 10, 2021

VarSeq recently received major upgrades in a wide range of areas, one of these areas includes adding annotations such as GnomAD. This includes new fundamental methods of CNV ACMG guideline processing but also a large number of small additions in annotations. One addition is the application of gnomADs – Gene…

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What You Need to Know About Staging Annotations

Jan 22, 2021

Annotating genomic variants is a very complex process but perhaps the most important part of next-generation sequencing variant analysis. Here at Golden Helix, we recognize the importance and value of having the most up-to-date sources available and curating new annotation sources as they become available for variant analysis. Golden Helix…

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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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Webcast Recap: VSClinical: A Complete Clinical Workflow Solution

Jan 15, 2021

Didn’t catch the webcast live? No worries! We cover ‘VSClinical: A Complete Clinical Workflow Solution’ Q&A’s in this blog post. The webcast, ‘VSClinical: A Complete Clinical Workflow Solution’ demonstrated how solutions provided by Golden Helix can be implemented to cover all requirements of a clinical workspace. Specifically, this webcast focused…

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Adding Population Catalogs to VSClinical

Dec 10, 2020

Our previous webcast demonstrated some of the new functionalities of VSClinical, including the ability to add ACMG frequency sources for the ACMG BA1, BS1, and PM2 criteria. This new feature was spurred by the feedback from our users, which requested supporting frequency tracks other than gnomAD Exomes and 1kG Phase3.…

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Webcast Recap: Evaluation of CNVs with VSClinical’s New ACMG Guideline Workflow

Nov 10, 2020

In the webcast, Evaluation of Copy Number Variants with VSClinical’s New ACMG Guideline Workflow, we discussed how VSClinical implements Section 4 of the ACMG guidelines. Specifically, we focused on integrating literature and publications to assess the pathogenicity of a CNV event when there was a lack of dosage sensitivity information.…

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Upcoming VS-CNV Update: CNV Event Reporting with ACMG Guidelines

Oct 22, 2020

Golden Helix is excited to release an upcoming VSClinical feature that allows users to analyze next-generation sequencing (NGS) CNV event reporting with ACMG guidelines. This feature will be the first in the NGS workspace to allow this capability and if you are curious about the functionalities you can get a…

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Webcast Recap: A User’s Perspective: ACMG Guidelines for CNVs in VSClinical

Oct 16, 2020

Our previous webcast from VP Gabe Rudy in September exposed us to some fundamentals of this years’ updated Technical standards for the interpretation and reporting of constitutional copy-number variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen). This…

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Variant Analysis of Bechet Disease Using VSClinical

Sep 15, 2020

VSClinical is a feature to evaluate clinically relevant variants according to the ACMG or AMP guidelines. This feature can also be used to identify if a variant has been observed previously or evaluate a manually inserted variant. Take, for example, the scenario where a colleague is interested to see if…

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Webcast Recap: VSClinical: First Commercial Product to Integrate the Updated ACMG Guidelines for CNVs

Sep 15, 2020

In our recent webcast announcing the upcoming release of VarSeq VSClinical and the implementation of the ACMG guidelines for NGS CNVs, we had a number of live questions we didn’t get a chance to cover at the end of the presentation. I will follow up on those questions in this blog post. But first,…

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Golden Helix gets full marks in ClinGen’s list of Genomic Analysis Software Platforms

Aug 26, 2020

The potential of genetic testing to impact a patient’s life has been greatly accelerated by the sharing of variant interpretations done by clinical labs in public repositories such as ClinVar. This is not an inevitable outcome, but the persistent work and advocacy of people like Dr. Heidi Rehm and organizations…

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Golden Helix’s NGS-Solutions for Clinical Variant Analysis: VSClinical’s Assessment Catalog

Aug 14, 2020

It doesn’t take much effort to find articles discussing the value of Next-Generation Sequencing (NGS). There is a consistent tone amongst authors that implementing NGS pipelines are critical for clinical efficiency in both hereditary disorders and somatic. However, NGS strategies do not come without their own challenges. Challenges include not…

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Building Gene Panels in VarSeq: Missense Variant in TP53

Aug 6, 2020

Golden Helix software provides huge analytic gain in handling large-scale genomic data. For example, a number of VarSeq users run cohort projects of whole genome level data processing hundreds of millions of variants at a time. However, many of our users are running gene panel level data for custom panels…

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Using the AMP Guidelines for Rhabdoid Tumor Analysis in VSClinical

Jul 15, 2020

Introduction: Malignant Rhabdoid tumors (MRT) are among the most aggressive and lethal forms of infant and child cancer (1). These tumors are characterized by an unusual combination of mixed cellular elements similar to but not typical of teratomas and can originate at any anatomic location. When MRTs are present in…

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Recent Webcast: Evaluating Oncogenicity in VSClinical

Jun 11, 2020

Abstract Before assessing the clinical significance of a somatic mutation, one must determine if the mutation is likely to be a driver mutation (i.e. a mutation that provides a selective growth advantage, thereby promoting cancer development). To aid clinicians in this process, VSClinical provides an oncogenicity scoring system, which uses…

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The New ACMG-Based Trio Tutorial

Apr 3, 2020

Our Support Team curates a variety of tutorials to help orient new users to the capabilities of VarSeq. We are happy to announce the team’s new release of the trio tutorial that places emphasis on using the ACMG guidelines. This tutorial gives insight into the proper setup of pedigree structure…

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Customizing Your VSClinical Workflow: Part II

Jan 27, 2020

In the first part of this series, we covered how VarSeq supports customizing ACMG guidelines in VSClinical to streamline the clinical analysis workflow. VSClinical’s various customization parameters within the ACMG Guidelines workflow includes the choice of how the internal knowledge base of previous variant interpretations are stored and what considerations…

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