Category Archives: Software Update

Unlocking Clinical Evidence: A Deep Dive into the Supporting Data Sources of VSClinical AMP Workflow

         February 7, 2023
Unlocking Clinical Evidence: A Deep Dive into the Supporting Data Sources of VSClinical AMP Workflow Icon

Discover the innovative clinical evidence search of the VSClinical AMP workflow, where patient biomarkers and tumor types are matched to the most relevant data from top sources like CIViC, DrugBank, and Clinical Trials. One of the core features of the VSClinical AMP interpretation workflow is the ability to search third-party data sources to find clinical evidence that matches the patient’s… Read more »

A New Comprehensive Template for Somatic Variant Annotation and Filtering in VarSeq

         February 2, 2023
A New Comprehensive Template for Somatic Variant Annotation and Filtering in VarSeq icon

Revolutionize Your Somatic Variant Analysis with Our Cutting-Edge Template for Annotation and Filtering in VarSeq Golden Helix is excited to share our new Comprehensive Cancer Template for somatic variant annotation and filtering, along with the latest version of our software VarSeq 2.3.0! Our latest VarSeq update was specifically focused on getting up to speed with multiple aspects of somatic variant… Read more »

VarSeq 2.3.0: A Comprehensive Look at the Revolutionary Cancer Genomic Profiling Solution’s New Features and Advancements

         January 18, 2023

Discover the latest advancements in cancer genomic profiling with the release of VarSeq 2.3.0 We are very excited to announce the release of VarSeq 2.3.0! This release was one of the largest VarSeq releases yet, as it includes a large refactor to the VSClinical AMP cancer module. A primary motivation for the release was focused on the availability and increased… Read more »

Improve Your Research with the Latest Cancer Ontology Updates

         January 10, 2023

Learn about the latest cancer ontology software updates and how they can enhance your research and work. Cancer Ontology An important feature of the VSClinical AMP workflow is the ability to select the correct tumor type for a given evaluation. The selected tumor type is used to identify relevant clinical evidence, including drug sensitivities, resistances, and previous biomarker interpretations. This… Read more »

Large Scale PCA Analysis in SVS – Webcast Q&A Follow Up

         January 26, 2022
Large Scale PCA Analysis in SVS - Webcast Q&A Follow Up

Thank you to those who attended our recent webcast by Gabe Rudy, Large Scale PCA Analysis in SVS. For those who could not attend, you can find a link to the recording here. While this webcast discussed methods for principal components analysis (PCA) in SVS, including the new capability for performing principal components analysis on large sample sizes, it also… Read more »

SVS 8.9.1 Release

         December 28, 2021
svs 8.9.1 release

We would like to announce that a new version of SVS has been released! The headlining feature of the SVS 8.9.1 release was new functionality for Large Data Principle Component Analysis. A detailed description of this new feature can be explored in this recent blog post: Finding a Few Principal Components Quickly from Data with Thousands of Samples. However, there… Read more »

VarSeq 2.2.4 Release

         November 30, 2021
varseq2.2.4

We are very excited to announce that just last week, we released VarSeq 2.2.4! In the past few months, we have been building the excitement for the 2.2.4 version of VarSeq with several webcasts in which we describe some of the headlining features in detail such as the new support for Gene Panels and Gene Lists, PhoRank Clinical, and Customized… Read more »

VarSeq Advanced Reporting Customizations: Part 1

         November 9, 2021
BLOG-11.9.21-VarSeq-Custom-Reports-Part-1

As we move towards the end of the year, our FAS Team is excited to announce our short blog series highlighting some of the Customization Features in our up-and-coming VarSeq release! The goal of this blog series is to show examples of how generating a clinical report can be customized to accommodate a wide range of functionality. Our December webcast,… Read more »

Updates to Somatic Variant Annotation and a New Way to Evaluate Fusions in VSClinical

         September 29, 2021
ClinVar

With the release of VarSeq 2.2.4 just around the corner, I want to detail some new 2.2.4 features that will enhance somatic variant annotation and fusion analysis within VSClinical. A webcast back in July showed some of these updates in action, so if you are looking for some more content on this topic, I would highly recommend checking out the… Read more »

Updates to ClinVar Curation to Include More Pathogenic Variants

         September 14, 2021

In the September 2021 monthly update to our curated ClinVar track, we made some changes that will result in roughly another 7,000 Likely Pathogenic and Pathogenic variants being available for annotation and use in the ACMG auto-classification system.  Consensus Between Labs  ClinVar has nearly one million unique variant classification records that are curated into multiple annotation tracks used in VarSeq and VSClinical on a monthly basis. Clinical… Read more »

Leveraging expert-curated variant interpretations using VSClinical

         July 27, 2021
Clinical Genome Resource

This blog post will cover an exciting new VSClinical feature in the upcoming VarSeq release. The ACMG Previously Interpreted Variants feature allows users to integrate databases of expert-curated variant interpretations into their VSClinical workflows. These data sources store variant-level interpretation data, including the classification, associated disorders, interpretation text, and scored criteria for each variant, along with notes providing a justification… 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 »

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 »

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 »

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 »

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 »

SVS 8.9.0 Release Notes

         August 24, 2020
Eigenvalue Decomposition

SVS 8.9.0 was released on August 19th and features a new GBLUP by Bin feature and a new utility to find the LD scores of markers and categorize them into bins, along with several mixed-model upgrades and many other upgrades, fixes, and polishes. The two new features LD Score Computation and Binning and Compute GBLUP Using Bins, while they can… Read more »

Coming to SVS: LiftOver Capability

         July 23, 2020

The world has been making a shift to use GRCh38 human genome reference coordinates, but the transition has not been fast. Many of the mainstay human catalog projects are changing to use native GRCh38 catalogs, or are remapping their current data to GRCh38 coordinates. While this seems to be the advancing goal, it is leaving researchers and analysts with the… Read more »

CADD Scores: New and Improved v1.4 and v1.5

         June 18, 2020

The University of Washington’s Combined Annotation Dependent Depletion (CADD) algorithm measures the deleteriousness of genetic variants. This includes single nucleotide polymorphisms (SNVs) and short insertions and deletions (indels) throughout the human reference genome assembly. This algorithm was introduced in 2014 and has since become one of the most widely used tools to assess human genetic variation. Since 2014, the algorithm has been… Read more »