Category Archives: About Golden Helix

VSClinical: Defining Sample Phenotypes

         January 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 evaluation, simplified the reporting process with embedded Microsoft Word and… Read more »

Webcast Recap: VSClinical: A Complete Clinical Workflow Solution

         January 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 on a detailed workflow from a bioinformatician, geneticist, and lab… Read more »

Golden Helix Featured in Numerous Publications 2020

         January 12, 2021

Golden Helix continues to innovate and grow, and due to this, we have been garnering attention and praise. We are thrilled to share with you some of the accolades and interest from numerous publications from the last six months. Talking points ranged from diagnosing and tracking Covid-19 infections leveraging NGS to new workflows, interpreting and reporting on copy number variants… Read more »

ACGS Guidelines Now Available in VSClinical

         January 7, 2021
ACGS Guidelines Screen Shot

Golden Helix offers a market-leading bioinformatics solution that allows users to evaluate next-generation sequencing variants according to the ACMG and now ACGS guidelines. The ACMG guidelines were created in 2015 and are widely accepted as best practice for the interpretation of sequencing variants throughout the United States (Richard et al 2015).  Very similar are the ACGS guidelines that were developed… Read more »

Featured in The Journal of Precision Medicine: Golden Helix’s Recent Release for a New Workflow for Interpretating and Reporting Copy Number Variants in Concordance with the Recently Updated ACMG Guidelines: Introduction

         December 28, 2020

Have you seen us in The Journal of Precision Medicine? Last week, our team released VarSeq 2.2.2 loaded with a number of updates and VSClinical’s highly-anticipated ACMG-CNV Guideline workflow! We have spent the past several months sharing webcasts and blogs on this new capability. We are honored to also have this new solution recognized in The Journal of Precision Medicine… Read more »

Customer Publications Featuring VarSeq December 2020

         December 23, 2020

Reading scientific articles that our customers have recently published is one of my favorite things here at Golden Helix. It is fascinating to learn about the research and to see the various ways our software gets put to the test.Since we are rolling out our most extensive VarSeq update yet, I thought it would be a great time to look… Read more »

Updated Annotations: RefSeq with MANE Select Transcripts

         December 17, 2020

Our upcoming release of VarSeq is one of the largest we’ve ever had with our software! It comes with an extensive list of polishes and new features like our recently mentioned ACMG CNV classifier and a redesigned reporting interface with updated templates. Additionally, this new release is also paired with some major upgrades to our list of new and supported… Read more »

Need Coverage Statistics? VarSeq Has You Covered!

         December 15, 2020

Curious about how coverage statistics can be used in conjunction with VarSeq? Evaluating the coverage over target regions or whole genomes is essential whether you are working with variant or CNV analysis. VarSeq has had the capability to compute sample level coverage statistics for some time now, but in the 2.2.2 release of VarSeq, there are some new features that… Read more »

Adding Population Catalogs to VSClinical

         December 10, 2020
example population view

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. Now, users can implement population catalogs to VSClinical such as… Read more »

Webcast Recap: Exploring New Features and Clinical Reports in the ACMG Guideline Workflow

         December 3, 2020
In-demo image of rare variants

Webcast Recap In the recent webcast “Exploring New Features and Clinical Reports in the ACMG Guideline Workflow”, Gabe and I took viewers through an evaluation with CNVs and SNVs according to the ACMG Guidelines where we generated and customized a clinical report. Along the way, we highlighted many new features that will soon be available in the upcoming VarSeq release…. Read more »

Loss-of-Function Splice Variant in MTHFR

         November 26, 2020

In this blog post, I will be analyzing a loss-of-function splice variant in MTHFR using VarSeq. In the search for clinically relevant variants contributing to rare disorders, efficient filtering strategies are an important step in eliminating disinteresting variants. However, any applied filters must also ensure no interesting variants inadvertently get filtered out. Golden Helix provides the tools to complete this… Read more »

Webcast Follow-up: Evaluating CNVs with VSClinical’s New ACMG Guidelines

         November 19, 2020

In our previous webcast, Evaluating CNVs with VSClinical’s New ACMG Guidelines, we focused on a CNV deletion (12:27715515-29628122×1) in which the patient had a known disorder called Brachydactyly type E. The CNV was isolated using our VS-CNV caller and applied to the ACMG CNV guidelines using the intuitive steps of VSClinical. If you missed the webcast, you can watch the… Read more »

Golden Helix End-of-Year Bundles 2020

         November 17, 2020

Special pricing offers on our End-of-Year software bundles. It’s that time of year again! Golden Helix End-of-Year bundles have been released. We are currently offering our industry-leading products in special bundles for you to simplify and accelerate your current workflows. Whether analyzing and classifying variants, detecting large copy number variant events, or automating your workflow, our software bundles have options… Read more »

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

         November 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. One of the primary pieces of evidence for evaluating genes… Read more »

Golden Helix’s Virtual 2020 Conference Booth

         October 27, 2020

In lieu of conferences making the absolutely necessary decision to cancel this year’s conference, we created our Virtual 2020 Conference Booth! Even though it will never compare to the real deal, we hope you enjoy this blog post containing a few events we had planned this year. To start, let us paint the picture with some of our favorite conference… Read more »

Golden Helix’s NGS-Solutions for Clinical Variant Analysis: VSWarehouse

         August 27, 2020
VSWarehouse Updates

We have now reached the final blog of the NGS-Solutions for Clinical Variant Analysis series. Part I of this series explored the capture of variant classifications in the VSClinical environment when following the ACMG and AMP guidelines. Part II was similar in content but for the capture of clinically relevant copy number variants as well as using a CNV catalog… Read more »

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

         August 26, 2020
Clinical Genome Resource

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 like ClinGen. We recently participated in a survey and vetting… Read more »

WT1 Mutations: Side-by-Side Germline and Somatic Variant Evaluation in VSClinical

         July 28, 2020

It is common knowledge that variants can be germline or somatic depending on whether the variant was inherited or acquired after birth. A well-known example is cancer-causing mutations in the BRCA genes, wherein the mutation may or may not have been inherited. Understanding the origin of the cancer-causing mutation is important when assessing potential treatment options as well as identifying… Read more »

Featured in The Journal of Precision Medicine: Diagnosing and Tracking COVID-19 Infections Leveraging Next-Gen Sequencing

         July 8, 2020

It is an honor to be published in The Journal of Precision Medicine’s June/July 2020 issue in an article co-authored by Dr. Christiane Scherer and myself, “Diagnosing and Tracking COVID-19 Infections Leveraging Next-Gen Sequencing.” In this article, I detail: The key facts about COVID-19, reviewing the epidemiology, reservoir hosts, transmission routes, and clinical manifestation. Answering the question of how Next-Generation Sequencing can… Read more »

Coping Mechanisms in the COVID-19 World

         June 4, 2020
Working from home

Like many of you, I was supposed to attend the 2020 ACMG Meeting in San Antonio this March with a few colleagues. In addition to attending the conference, my first blog post for Golden Helix was going to be about our time at the conference. Thanks to the world-wide COVID-19 pandemic, none of us got to attend the conference. (We… Read more »