How To’s & Advanced Workflows

Loss-of-Function Splice Variant in MTHFR

Nov 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. VarSeq supports end-to-end rare disease analysis, from panel-level filtering to clinical variant…

Read more →

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

Nov 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.…

Read more →

Example De Novo CNV in Cardiomyopathy Panel

Oct 20, 2020

In a recent webcast, users were exposed to some new features upcoming in the next release of VarSeq. In this update, we will use an example de Novo CNV in a cardiomyopathy panel in VarSeq. There is a long list of new tools and polishes to the software but one…

Read more →

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

Oct 1, 2020

A common discussion with our customers includes the challenges with tertiary analysis of 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…

Read more →

Controlling Your Preferred Transcripts for Clinical Interpretation

Sep 24, 2020

Did you know you can control your preferred transcript settings for clinical interpretation in VSClinical? Your lab is analyzing the DNA of a tissue sample from a patient with small cell lung cancer. The lab technician has imported the patient data into VSClinical to detect clinically relevant variants and evaluate…

Read more →

Advanced Plotting Capabilities with GenomeBrowse

Sep 22, 2020

In this blog update, I’ll be walking you through some of the advanced plotting capabilities with GenomeBrowse. The strategy with any next-gen sequencing analysis is to filter down to interesting variants for either research or clinical conclusion. Golden Helix produces powerful software specifically tailored for this efficient and comprehensive search…

Read more →

Golden Helix’s NGS-Solutions for Clinical Variant Analysis: VarSeq’s CNV Frequency Assessment Catalogs

Aug 20, 2020

Our software solutions and partners have brought dramatic improvements to the secondary and tertiary analysis stages of variant evaluation. Regarding secondary analysis, we’ve discussed increased efficiencies in speed and overall accuracy in the variant calling process with Sentieon. On the tertiary analysis side, we have explored numerous workflows in VarSeq…

Read more →

Exporting Genes as Exon Regions in VS-CNV

Jun 16, 2020

We have had many customers come to us over the years with a simple problem: they have BAM files for whole exome or gene panel data and would like to call CNVs using VarSeq’s powerful CNV calling capabilities, but they don’t have a bed file defining the target regions for…

Read more →

Auto-Updating Template Sources

May 21, 2020

In VarSeq 2.2.1, you can enable auto-updating for template annotation sources, ensuring they always reflect the latest available version. Previously, VarSeq templates were frozen in time. Now, each new project created from a template would use the same source that was used when the template was created. When you save…

Read more →

The New ACMG-Based Trio Tutorial

Apr 3, 2020

Our Support Team curates a variety of tutorials to help orient new users to the capabilities of VarSeq. We are happy to announce the team’s new release of the trio tutorial that places emphasis on using the ACMG guidelines. This tutorial gives insight into the proper setup of pedigree structure…

Read more →

Updated VSReports Project Templates

Mar 10, 2020

Generating a clinical report is the final step of most NGS pipelines and is important as it relays results and information to legacy systems, physicians and ultimately the patient. Golden Helix’s clinical reporting capabilities are designed to integrate seamlessly into laboratory workflows, reducing manual effort and supporting consistent, standards-based output.…

Read more →

VarSeq Cancer Gene Panel Tutorial

Mar 3, 2020

At Golden Helix, we want our new users to hit the ground running with VarSeq and not spend oodles of time getting started building and automating their workflows. To achieve this goal, our team has generated blogs, webcasts, and tutorials that explain and demonstrate workflows that are possible with VarSeq.…

Read more →

VarSeq Copy Number Variant Caller Tutorial

Feb 20, 2020

Since the initial release of the copy number variant algorithms in VarSeq, our team has created a variety of content to help users get started with building their copy number variant projects. In our webcast library, you can find a few of our recent webcasts in 2019 covering CNV workflows…

Read more →

Updated GRCh38 VarSeq Project Templates

Feb 4, 2020

As many of our users know, GRCh38 VarSeq project templates come preloaded with the software and are designed to give users a baseline workflow to streamline their NGS analysis. These templates are tailored for various applications including tumor-normal, trios, cancer and hereditary gene panels, and ACMG Guidelines workflows. The templates…

Read more →

The New VSClinical ACMG Guidelines Tutorial

Nov 21, 2019

Our tutorials are a popular resource for prospective users. We have added a tutorial to help introduce customers to the ease and utility of the ACMG Guidelines incorporated in VSClinical. The ACMG Guidelines are a collection of 33 criteria that are used to determine a variant’s level of pathogenicity. VSClinical…

Read more →

All New VSClinical AMP Workflow Tutorial

Nov 5, 2019

We have recently added a tutorial to help introduce customers to the ease and utility of the AMP Guidelines incorporated in VarSeq’s VSClinical package. The AMP Guidelines allow users to sort through available clinical evidence in a streamlined fashion to arrive at final classification and interpretation and then transfer that…

Read more →

Copy Number Variants Using AMP Guidelines

Oct 10, 2019

The common approaches to detecting copy number variants (CNVs) are chromosomal microarray and MLPA. However, both options increase analysis time, per sample costs, and are limited to the size of CNV events that can be detected. VarSeq’s CNV caller, on the other hand, allows users to detect CNVs from the…

Read more →

Automating & Standardizing Your NGS Workflow: Part IV

Sep 10, 2019

We have covered a lot of ground in this Automating & Standardizing Your Workflows blog series. First, we saw how to perform secondary analysis with Sentieon to generate the necessary VCF and BAM files for tertiary analysis in Part I. The implementation of VSPipeline allowed for rapid import and project…

Read more →

Automating & Standardizing Your NGS Workflow: Part III

Sep 3, 2019

In our last part of this series, we showed how to run a pre-built workflow template via VSPipeline to automatically import and filter sample variants to streamline the search for clinically relevant variants. Now, we can deep-dive into our filtered, pathogenic variants to fully understand and capture their final classification…

Read more →

Automating & Standardizing Your NGS Workflow: Part II

Aug 29, 2019

VSPipeline: Automating your Tertiary Workflows The first part of this “Automating & Standardizing your NGS Workflow” blog series covered the secondary analysis steps of read alignment and variant calling in a broader NGS analysis pipeline with Sentieon. The next step is to transition into the tertiary analysis via utilization of…

Read more →