Lock in Annotation Source Versions to Increase Workflow Consistency

         February 25, 2021
Annoation Sources

Next-generation sequencing generates an immense amount of data which is then subject to a multi-step process to establish a validated bioinformatic pipeline. From processing raw sequence data to the detection of genetic mutations, establishing a validated and consistent bioinformatic pipeline makes a huge difference in the quality of patient care and accuracy of results. In this blog, we are focusing… Read more »

Customer Publications February 2021: The Heart Edition

         February 23, 2021
heart

Welcome to our Customer Publications for February 2021. As we commemorate the 57th American Heart Month, it is important to remember why we are wearing red and using #OurHearts. Heart disease is the leading cause of death worldwide. The National Heart, Lung, and Blood Institute urges Americans to do what they can to be heart-healthy and mitigate the risks of… Read more »

New VSClinical ACMG Word Report Templates

         February 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. We will cover the three different report templates that ship… Read more »

New CNV Tools with VarSeq 2.2.2 Update

         February 16, 2021
copy number variant algorithm

Our latest release of the VarSeq software has had a major upgrade with the addition of the new CNV ACMG guidelines! Here are some recent webcasts we’ve given covering the new guideline tool: Family-Based Workflows in VarSeq and VSClinical A User’s Perspective: ACMG Guidelines for CNVs in VSClinical Not only does VarSeq 2.2.2 come with the new guideline tool, but… Read more »

Webcast Recap: Family-Based Workflows in VarSeq and VSClinical

         February 13, 2021
screen shot from webcast

Thank you for attending the webinar focused on implementing VarSeq and VSClinical for family-based workflows. If you would like to use the webinar as a reference or were not able to attend, you can access it using the following link to view ‘Family-Based Workflows in VarSeq and VSClinical. Here is a brief recap of what we discussed: This webinar demonstrated… Read more »

New Annotation: GnomAD – Gene Constraints

         February 10, 2021
GnomAd screenshot

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 Constraints. This provides various metrics for pathogenicity on a per… Read more »

Applying the Probability Segregation Algorithm for CNV Analysis

         February 4, 2021
Bioinformatics software

There is a multitude of interesting new features that have been incorporated into VarSeq 2.2.2. In this blog, I want to continue the discussion of these features and how each can be incorporated into your workflow, and also discuss the application of the Probability Segregation algorithm for copy number variation (CNV) analysis. The Probability Segregation algorithm is a new algorithm… Read more »

Updates on Splice Site Analysis

         February 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 effect prediction along with several other small improvements. Novel Splice… Read more »

January 2021 Publications

         January 28, 2021
Customer Publications

New discoveries using NGS data analysis are never-ending and are pushing precision medicine to the forefront. In this month’s customer publication blog, I am focusing on our VarSeq software as investigators harness its power to perform a variety of investigational study designs. From cancer to inherited rare disease research, VarSeq is the rising star in research and diagnostic tools. At… Read more »

New eBook Update: Precision Medicine – Third Edition

         January 27, 2021
Precision Medicine - Third Edition

I am pleased to share with you the official release of my updated eBook, “Precision Medicine“. Almost 2,500 years ago, Hippocrates captured one of the key principles underlying precision medicine. In the 21st century, we take an understanding of the individual characteristics of a person to a new level. By leveraging information about an individual’s genome, we are able to… Read more »

New Feature in VarSeq: Latest Sample Assessment Algorithm

         January 26, 2021

In continuation of our blog posts focusing on new features of VarSeq v2.2.2, here we will discuss the Latest Sample Assessment algorithm for both single nucleotide variants (SNVs) and copy number variants (CNVS). This algorithm annotates the variants of the project with the latest assessment from your variant catalog, which will show the history of interpretations made for the variants… Read more »

What You Need to Know About Staging Annotations

         January 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 has curated over 100 annotation sources for human variant analysis… Read more »

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 »

What to expect from Golden Helix in 2021

         January 1, 2021

Happy New Year! I hope you had an opportunity to relax over the holidays with your family and friends. It’s time to start talking about our plans for the New Year, but first, please allow me to review a few highlights from 2020 that helped build a foundation for our future. Growth: Golden Helix was named to the 2020 Inc… 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 »

VarSeq 2.2.2 Release Notes

         December 23, 2020
ClinVar

VarSeq 2.2.2 was released on December 17th, 2020 and the main feature that was added to VarSeq was that the VSClinical ACMG Guidelines workflow now has an additional CNV interpretation framework based on the ACMG/ClinGen guidelines. This product supports interpreting CNVs detected with VS-CNV or imported CNVs alongside variants and requires both a VSClinical ACMG license and a CNV license…. 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 »