Search results for “annotation”

What’s Coming to VSClinical: Expanded Clinical Trial Search Results

May 17, 2022

While the interpretation of germline variants generally focuses on the pathogenicity of a variant for a specific disease, the interpretation of somatic variants is centered around each variant’s impact on clinical care. As a result, clinical trials play an important role in assessing the clinical significance of somatic biomarkers, with…

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Sentieon Updates: Now Supporting Long-Read Alignment and Calling

May 9, 2022

Here at Golden Helix, we’ve sought to develop top-quality bioinformatic software to handle not only high-throughput clinical next-gen sequencing pipelines but also cater to research groups exploring their cohorts. Our tools fit in this NGS pipeline by importing the VCF and BAM files for downstream filtration, annotation, and classification/interpretation as…

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Mining Curated Databases for Literature in VSClinical

Apr 29, 2022

Curated databases are a real time saver when compiling published evidence to support your variant evaluations and classifications. Leveraging the curated databases at your fingertips in our VSClinical variant interpretation hub is even more efficient. Not only does VSClinical provides users with automated variant classification for germline variants according to…

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Mining VarSeq Curated Databases for Literature – Raw Data Search in Variant Table or GenomeBrowse

Apr 21, 2022

An under-utilized use of VarSeq is the ability of mining raw variant data in GenomeBrowse for relevant literature. By bringing in various public and private annotation sources, GenomeBrowse allows the user to interface with raw variant data in a compressed and manageable view. This blog will show you how to…

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Review of VarSeq Export Options

Mar 10, 2022

Although best known for its auto-generation of custom reports, VarSeq comes with a slew of options for exporting your data. In this blog, we will review some of the lesser-known methods for exporting your data into usable formats. These four export options can all be found under the Export tab…

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How to Create Your Own CNV Frequency Catalog

Jan 20, 2022

Global population frequency catalogs like 1kG Phase 3, gnomAD, DGV, and others are excellent resources for identifying rare variants in your copy number variant (CNV) analysis. However, they are not exhaustive, and the reality is a lot of variants that are missing from global population frequency catalogs are still common…

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What to Expect From GnomAD v3.1.2

Jan 5, 2022

In this blog post, I am very excited to talk about The Broad Institute’s release of the latest version of gnomAD, v 3.1.2, which is now available for use as an annotation source in your SVS or VarSeq projects. For VarSeq users, I also want to point out that gnomAD…

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Using ACMG Secondary Findings v3.0 List in VarSeq and VSClinical

Dec 21, 2021

As the number of genes on a gene panel increases, there is the possibility of picking up variants of medical significance that are not related to the primary indication for the test. Especially with large gene panels, exomes, and genomes, it is medically and ethically important to report variants that…

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Highlights from Advanced Report Customization in VSClinical Webcast: Germline Reports

Dec 14, 2021

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…

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VarSeq 2.2.4 Release

Nov 30, 2021

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…

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Highlights From Our Golden Helix CancerKB Webcast

Nov 24, 2021

Thank you to everyone who attended Using Golden Helix CancerKB to Accelerate NGS Cancer Testing! I had a great time showing off Golden Helix 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…

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

Nov 18, 2021

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…

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Validating Your CNV Workflow

Nov 16, 2021

The VarSeq CNV calling algorithm, VS-CNV, is a powerful tool for calling CNVs from the NGS coverage data stored in your BAM files. However, before this algorithm can be deployed in a clinical setting, it must be tuned and validated using data that is representative of your lab’s NGS workflow.…

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Running VSPipeline from a Docker Container

Nov 10, 2021

As a lab or group scales the number of NGS samples analyzed, it is important to automate the sample analysis pipeline from the sequencer to the point where it is ready for a variant scientist or lab personnel to follow the interpretation workflow and draft a clinical report. VSPipeline leverages…

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Customer Publications in October 2021

Oct 28, 2021

The customer-published articles this October cite the range of Golden Helix’s VarSeq annotation range and capability. The following publications feature everything from annotating an Italian nobleman mummy, assisting in identifying mutations in primary congenital and juvenile glaucoma, new mutations associated with muscular dystrophinopathy, and germline variants associated with head and…

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Details of the Golden Helix CancerKB Database Update

Oct 21, 2021

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,…

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Customized Reports in VSClinical with New Output Types

Sep 23, 2021

Golden Helix VSClinical provides a guided workflow interface for following the ACMG and AMP guidelines to evaluate variants and CNVs for NGS tests. The output of this work is most often a lab-specific clinical report. Since it was introduced, we have provided a powerful Word-based templating system to allow labs…

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Updates to ClinVar Curation to Include More Pathogenic Variants

Sep 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…

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Merging VCFs in an Imperfect World

Sep 7, 2021

Merging variant records, VCFs, across samples is important when performing trio or family analysis as it ensures that hereditary relationships can be properly inferred. There are many ways to represent a single variant. Insertions and deletions may be right or left aligned, prefixes and suffixes can be added, and adjacent…

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Manage gene lists across projects with VarSeq and VSClinical

Aug 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…

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