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 »

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 »

2020/21 Abstract Competition

         November 24, 2020
Recent Customer Publications

We encourage you to share how you are utilizing Golden Helix software in your clinical research work! Golden Helix strives to enable precision medicine by developing powerful software to support researchers and clinicians with complex analyses. One of my favorite events of the year is our abstract competition. This competition allows us to help our community by recognizing innovative ways… 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 »

New Algorithm: Variants Matching Current Sample

         November 12, 2020
New Algorithm: Variants Matching Current Sample

Those of you who have been attending our recent webcasts have learned about our upcoming VarSeq release. A part of that release will be an additional algorithm that will annotate variants matching the current sample. If you are not familiar with these webcasts, here are several on-demand webcasts I recommend to get you familiar with these new features: Evaluating Copy… 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 »

Updated Annotation: BRCA Exchange

         October 30, 2020

Our team is regularly updating and curating annotations, most recently the BRCA Exchange. Breast cancer is known to occur in approximately 10% of the female population and if there is a damaging mutation in the breast cancer gene (BRCA), that rate increases to 65%. Although genetic testing can identify mutations in BRCA, a tumor suppressor gene, it has been difficult… 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 »

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

         October 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 sneak peek by looking at some of our most recent… Read more »

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

         October 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 recent webcast was dedicated to breaking down these new guidelines… Read more »

Annotate your VarSeq Projects with REVEL

         October 6, 2020

Typically, researchers are looking for rare variants in their next generation sequencing datasets. However, most of the nonsynonymous variants have unknown significance because there is an inherent difficulty in validating large numbers of rare variants or even detecting rare variants with high statistical power. In lieu of this issue, computational tools are needed as they accurately predict the pathogenicity of… Read more »

VarSeq’s NGS Panel Workflow: COL4A2 Variant from an Intellectual Disability Panel

         October 1, 2020

A common discussion with our customers includes the challenges with the tertiary stage of analyzing next-gen sequencing data. This is the stage where all data from gene panels, exome, or whole genome scale pass through filters to quickly isolate the clinically relevant variant contributing to a patient disorder. Golden Helix has recognized these challenges in the scale of data and… Read more »

Discoveries in Human Medicine Continue Amid the Ongoing Pandemic

         September 29, 2020
customer

As the world is consumed by the ongoing pandemic, it is easy to forget that there are investigators all around the globe that continue to make important discoveries in human medicine. Below are a few examples that remind us there are those that persevere in their chosen fields of study despite the trying times. At Golden Helix, we continue to… Read more »