Search results for “annotation”

Customer Publications Throughout June 2020

Jun 25, 2020

As I prepared to write the Customer Publication blog for June 2020, I was excited by the number of recently published papers that stood as examples of how both VarSeq and SVS software are employed to advance diagnostics and treatments in human medicine. We often think of SVS as the…

Read more →

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

Jun 18, 2020

The University of Washington’s Combined Annotation Dependent Depletion (CADD) algorithm, now available in CADD v1.4 and CADD v1.5, 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…

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 →

Updates to Default Transcripts and Gene Preferences in VarSeq

Jun 9, 2020

An under-appreciated area of complexity when looking into the field of genetics from the outside can be found in genes and transcripts. Alternative splicing allows eukaryotic species to have a wonderfully powerful genetic code, resulting in multiple protein isoforms being encoded in a single section of DNA. But when it comes to…

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 →

Clinical Variant Analysis for Cancer eBook – Second Edition

May 14, 2020

At Golden Helix, we’re committed to advancing precision oncology through robust software solutions that streamline clinical workflows. As the field of cancer genomics continues to evolve, staying informed about the latest best practices and tools is more important than ever. That’s why we’re excited to announce the release the second…

Read more →

Webcast Recap: Next-Gen Sequencing of the SARS-CoV-2 Virus with Golden Helix

May 13, 2020

Thank you to everyone who joined me for our latest webcast, “Next-Gen Sequencing of the SARS-CoV-2 Virus with Golden Helix.” If you missed the live event and are interested in knowing what we talked about, you may access the recorded event below: Our Live Q&A generated a lot of great…

Read more →

Detecting de Novo Copy Number Inheritance and Family Segregations

Apr 23, 2020

In trio workflows, one of the most important factors in scoring a variant is understanding how that variant is inherited from the parents. Likewise, when looking at extended families, the segregation, or presence of the variant among the affected versus unaffected individuals provides evidence for its pathogenicity for a given…

Read more →

VarSeq 2.2.1 Release Notes

Apr 10, 2020

VarSeq 2.2.1 was released on April 1st and features an upgraded gene annotation capability with new RefSeq genes tracks and an AMP workflow addition: the Drugs and Trials tab. The new RefSeq human genome genes tracks contain updated gene names and the recognition of any MANE (Matched Annotation from NCBI…

Read more →

Webcast Recap: Using VarSeq Templates to Advance and Customize Variant Analysis

Apr 9, 2020

Thank you to everyone who joined me for yesterday’s webcast, Using VarSeq Templates to Advance and Customize Variant Analysis, I hope you all enjoyed it. If you missed the live event and are interested in knowing what we talked about, good news, you can watch the recorded version right here!…

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 →

Customer Publications March 2020: Spotlight on Congenital Defects and Early Development

Mar 31, 2020

In these very uncertain times, it has been uplifting to read the wonderful work Golden Helix customers have been doing across the globe! In March 2020, the focus of this blog is on published articles relating to congenital defects and early development. Congratulations to all our customers who have published…

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. As reporting is a valuable process, Golden Helix offers reporting capabilities according to the ACMG and AMP guidelines but also as…

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 →

Cyber Security Strategies for NGS Testing Labs: Part IV

Feb 13, 2020

Golden Helix is in a unique position to provide a secure on-premise analysis solution. This capability is based on two enablers. First, we build our software solutions from scratch and from the ground-up with the assumption that it should run on any operating system and potentially behind firewalls or even without internet access. Second, we provide these…

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 →

Customizing Your VSClinical Workflow: Part II

Jan 27, 2020

In the first part of this series, we covered how VarSeq supports customizing ACMG guidelines in VSClinical to streamline the clinical analysis workflow. VSClinical’s various customization parameters within the ACMG Guidelines workflow includes the choice of how the internal knowledge base of previous variant interpretations are stored and what considerations…

Read more →

Cyber Security Strategies for NGS Testing Labs: Part I

Jan 23, 2020

Hospitals and testing labs are undergoing a digital transformation like any other business in our time. They deal with personal data in categories with the highest level of security requirements: personal identity and medical records. The architecture chosen to store and analyze this data is critical to provide the best…

Read more →

Introducing Drugs and Trials for Cancer Diagnostics

Jan 23, 2020

When interpreting a variant using the AMP guidelines for somatic variant interpretation, clinicians must determine whether the variant can be considered a biomarker that affects clinical care by predicting sensitivity, resistance, or toxicity to a specific therapy. Such a determination requires the investigation of multiple evidence sources, including clinical trials,…

Read more →