Tag Archives: VSClinical

Highlights from Advanced Report Customization in VSClinical Webcast: Germline Reports

         December 14, 2021
germline clinical report blog

When it comes to clinical variant analysis for germline variants using ACMG guidelines, we understand that the clinical report is essentially the receipt for your services for the patient. In our recent webcast, Advanced Report Customization in VSClinical, we displayed several examples of report templates to show off the range of possibilities our users have to format their clinical report…. Read more »

Breaking Down ACMG CNV Guidelines in VSClinical

         November 25, 2021

In February 2020, the American College of Medical Genetics (ACMG) and the Clinical Genome Resource (ClinGen) published a joint consensus on standards for the interpretation and reporting of copy number variants (CNVs) ranging from large CNVs spanning multiple genes to small intragenic events1. The guidelines consist of over 80 different criteria which are arranged into five distinct sections. These extensive… Read more »

Highlights From Our CancerKB Webcast

         November 24, 2021

Thank you to everyone who attended Using Golden Helix CancerKB to Accelerate NGS Cancer Testing! I had a great time showing off CancerKB and how it can enhance NGS analysis in cancer, I certainly hope you enjoyed it! If you were unable to make the live session, we have added the on-demand recording to our site, or we would be… Read more »

Top FAS Tricks You Wish You Knew When Getting Started with VSClinical

         November 18, 2021
vsclinical top things to know

As a newer member of the Golden Helix FAS Team I, like many of our customers, went through a phase of learning the ins, outs, and shortcuts of clicking around the program. In an effort to expedite new users coming up to speed, or to teach some tricks to experienced users, I’ve compiled a list of the top things I… Read more »

Details of the Golden Helix CancerKB Database Update

         October 21, 2021
cancerkb updates

Recently we have released blog posts discussing updates to annotations in VarSeq such as ClinVar and COSMIC. Keeping with that trend, in this blog post, I will discuss the most recent updates to the Golden Helix CancerKB database. For those how may be unfamiliar with the Golden Helix CancerKB source, it is a professional curated set of interpretations for the… Read more »

Reviewing Clinical Studies for Novel Splice Variants in VSClinical

         October 12, 2021
DNA spliced site

In order to thoroughly assess a variant’s pathogenicity, it is important to take into account the variant’s effect on splicing. While the interpretation of variants that disrupt the pairs of bases at the beginning of a splice site is fairly straightforward, variants resulting in the introduction of a novel splice site are more difficult to interpret. In this blog post,… 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 »

VSClinical Customer Publications for August 2021

         August 31, 2021
customer

Welcome to the August edition of our customer publications blog post! Each month we spotlight a few recently published articles by our incredible Golden Helix customers. With users spanning both research and clinical spaces, the topics vary widely across many fields. This month, we will be highlighting VSClinical users and the guided workflow. Host Genetics and Antiviral Immune Responses in… Read more »

Manage gene lists across projects with VarSeq and VSClinical

         August 18, 2021

Clinical labs often maintain gene panels, which are lists of genes with evidence of disease association. These panels are used to prioritize variants and limit interpretations to a predefined set of test-specific genes. In general, gene panels should be stored independently of any specific project or interpretation, as it is common for an individual gene panel to be generally applicable… 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 »

Selecting Clinically Relevant Transcripts in VarSeq

         June 28, 2021

One of the many tricks of encoding so much functionality into so little space in eukaryotic genomes is the ability to produce multiple distinct mRNAs (transcripts) from a single gene. While one transcript is often the dominant one for a given tissue or cell type, there are, of course, exceptions in the messy reality of biology. It doesn’t take many… Read more »

Summer 2021 Software Specials

         May 25, 2021
Special Offer

Summer is quickly approaching, which heralds the return of our summer software specials! Golden Helix will be offering a limited number of the following deals through June 30th, 2021. Here is a snapshot of what is being offered: VarSeq w/ CADD & OMIM (3-users) – $8,995 | (3 available) Our filtering and annotating product, VarSeq, paired with premium annotations. VSClinical,… Read more »

Webcast Recap: Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Capabilities

         April 8, 2021
Exome CNV webcast

Thank you to those who attended the recent webcast, “Exome Analysis with VS-CNV & VSClinical: Updated Strategies & Expanded Capabilities”. For those who could not attend but wish to watch, here is a link to the recording. In this webcast, we covered the capabilities and updates that have been incorporated into VarSeq that enhance whole exome sequencing workflows. The new… Read more »

GenomeAsia 100K Variant Frequency Annotation

         March 30, 2021
genomeAsia

The GenomeAsia 100K Variant Frequency database is a pilot annotation source now available to our users. This valuable database offers a deep characterization of specific populations in Asia that can be used to drive genetic studies. GenomeAsia is comprised of whole-genome sequencing data of over 1,000 individuals from 219 populations across Asia. Using this as an annotation, users can analyze… Read more »

Orphanet Annotations in VarSeq

         March 18, 2021

Orphanet is a public database available in VarSeq that aims to improve the current understanding and treatment options for patients affected by rare diseases. This resource was established in France in 1997 and has gradually grown to cover a consortium of over 40 countries in Europe. The primary goal of this database is to provide a universal nomenclature to classify… Read more »

Customizing New VSClinical Report Templates

         March 9, 2021
VSClinical Word reporting

Clinical testing labs produce reports as the end product of the NGS variant detection and interpretation workflow. Necessarily, the content, detail, and presentation of the report needs to be specialized to each clinical lab, and potentially each offered test. Our last blog post introduced the new Word-based report templates in VSClinical. In this blog post, we will introduce and explore… Read more »

New eBook Update: Clinical Variant Analysis – Second Edition

         March 4, 2021

This morning I released a new version of my eBook “Clinical Variant Analysis – Second Edition.” The clinical interpretation of variants in Next-Gen Sequencing is a quickly evolving field. While the body of knowledge is growing exponentially, experts have to derive sound, clinical decisions leveraging an ever-expanding set of specialty databases, clinical publications, and algorithms that are designed to predict the… Read more »

Lock in Annotation Source Versions to Increase Workflow Consistency

         February 25, 2021
Annoation Sources

Next-generation sequencing generates an immense amount of data which is then subject to a multi-step process to establish a validated bioinformatic pipeline. From processing raw sequence data to the detection of genetic mutations, establishing a validated and consistent bioinformatic pipeline makes a huge difference in the quality of patient care and accuracy of results. In this blog, we are focusing… Read more »

New VSClinical ACMG Word Report Templates

         February 18, 2021

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. We will cover the three different report templates that ship… Read more »