February Newsletter
 Following the AMP Guidelines with VSClinical: Part I

New CNV Tools with VarSeq 2.2.2 Update
By Darby Kammeraad
Field Application Scientist

Not only does VarSeq 2.2.2 come with the new guideline tool, but also a number of new features related to CNV analysis. Any variant analysis is going to include the capability of excluding low-quality calls or artifacts. The CNV workflow in VarSeq has had this quality flag assessment since the introduction of our CNV computation. However, we added a new field to make this quality assessment even more thorough. Figure 1 shows our latest quality flag “Deletion Contains Heterozygous Variants”, and it works just like it sounds, to isolate... Read More

Automating & Standardizing Your NGS Workflow

Updates on Splice Site Analysis 
By Nate Fortier
Director of Research

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. Read More

Automating & Standardizing Your NGS Workflow

New Annotation: GnomAD - Gene Constraints 
By Darby Kammeraad
Field Application Scientist 

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... Read More

Automating & Standardizing Your NGS Workflow

New VSClinical ACMG Word Report Templates 

By Jake Patek
Software Developer

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... Read More

CEO Corner
New eBook: Clinical Variant Analysis for Cancer

We hit the ground running in 2021 with a fast and furious start to the year. We have seen tremendous adoption of our clinical solutions across the globe, specifically Europe and North America. Golden Helix is the distinguishable choice for our customers for the following reasons:

• We provide a comprehensive solution for clinical variant interpretation for both cancer and hereditary disease.

• Our industry-leading CNV solution, which includes the first commercially available tool with integrated ACMG guidelines for CNVs.

• The ability to deploy either on-premise or in a private cloud setting.

• A predictable, fixed-fee structure that is independent of sample-number sizes.

We are so appreciative of the strong support from our customers and prospective partners. We will continue to innovate and are eager to share with you all our new developments in the upcoming quarters.

Upcoming Webcast

VSWarehouse: Tracking Changing Variant Evidence and Classifications 
March 10, 2021 | 12:00 PM Eastern

In this webcast, we are going to explore the value and application of VSWarehouse. Our example variants will showcase a situation where variants of uncertain significance ultimately reach a pathogenic classification based on updates to ClinVar. This change will be presented not only in VarSeq with listings of previous samples but also shown directly from the VSWarehouse browser in a ClinVar classification tracker.

Customer Success

February is American Heart Month and we are raising awareness in our latest blog of heart research-related publications! To highlight just a couple:

Use of next-generation sequencing to detect LDLR gene copy number variation in familial hypercholesterolemia - Michael A. Iacocca,*, Jian Wang, Jacqueline S. Dron,*, John F. Robinson, Adam D. McIntyre, Henian Cao, and Robert A. Hegele1

Genetic determinants of circulating galectin‐3 levels in patients with coronary artery disease - Yu‐Huang Liao Ming‐Sheng Teng Jyh‐Ming J. Juang Fu‐Tien Chiang Leay‐Kiaw Er Semon Wu Yu‐Lin Ko

Evaluating Polygenic Risk Scores in “Lone” Atrial Fibrillation - Julieta Lazarte, Jacqueline S. Dron, Adam D. McIntyre, Allan C. Skanes,  Lorne J. Gula, Anthony S. Tang, Rafik Tadros, Zachary W. Laksman, Robert A. Hegele, Jason D. Roberts 

Read more about the articles published during February on our blog!

About Golden Helix

Golden Helix has been delivering industry-leading bioinformatics solutions for the advancement of life science research and translational medicine for over 20 years with 1,000s of users around the world. Their innovative technologies and analytic services empower scientists and healthcare professionals at all levels to derive meaning from the rapidly increasing volumes of genomic data produced from NGS sequencers and microarrays. With their solutions, hundreds of the world's top hospitals, testing labs, pharmaceutical, biotech, and academic research organizations can harness the full potential of genomics to identify the cause of disease, improve the efficacy and safety of drugs, develop genomic diagnostics, and advance the quest for personalized medicine.