Search results for “annotation”

A Decade of Clinical Genomics in Curated Annotations

May 14, 2026

Effective use of data drives efficient, reliable analysis in next-generation sequencing. Users of the VarSeq suite are well-acquainted with the tools that VarSeq supplies to empower users, at the center of which lies a curated collection of clinical annotations that users can leverage in their own customized workflows. In the…

Read more →

Simplifying Custom PGx Annotations with VSWarehouse

Jan 15, 2026

In the rapidly evolving field of pharmacogenomics (PGx), laboratories often face a common challenge: balancing standardized guidelines with the need for specialized, lab-specific data. In the past, maintaining custom PGx annotations was difficult and time-consuming, with custom annotation tracks generated using bespoke curation scripts that merged internal data with VarSeq’s…

Read more →

Detect Cryptic Splicing Events with the New CI-SpliceAI Annotations in VarSeq

Dec 10, 2025

Aberrant splicing is a major cause of human disease, with an estimated 15–30% of pathogenic variants either disrupting an existing splice site or introducing a novel one [1]. While variants that alter the canonical AG/GT dinucleotides are straightforward to detect, those that affect the broader splice motif or activate cryptic…

Read more →

Enhanced Transcript Annotation: HGVS Repeat Notation Support in VarSeq

Jul 10, 2025

At Golden Helix, we’ve supported the HGVS variant nomenclature standard since the very first release of VarSeq. The HGVS standard provides a consistent and precise language for describing sequence variants in the context of gene transcripts and is a critical part of clinical genomics workflows. As with all living standards,…

Read more →

Best Practices for Variant Annotation and Filtration – Germline Variant Analysis

Jan 14, 2025

Golden Helix field application scientists curate a set of FAS templates that capture best practices for filtering, which we use when training and onboarding customers. In addition to the basic templates that come default with the software, these more fleshed-out templates are available upon request. This first blog in the…

Read more →

VarSeq Annotation and Filtering Use Cases

Sep 3, 2024

The following customer publications showcase the ability of VarSeq. Each study highlights how VarSeq simplifies variant annotation, filtering, and interpretation, supporting efficient NGS workflows in both clinical and research settings. Rare host variants in ciliary expressed genes contribute to COVID-19 severity in Bulgarian patients Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)…

Read more →

VarSeq PGx inputs: Annotation Tracks Required for PGx Analysis

Jul 16, 2024

The PGx Variant Detection and Recommendations algorithm is the driving force behind the pharmacogenomic analysis capabilities provided by VSPGx in VarSeq. This algorithm is used to identify pharmacogenomic diplotypes and annotate them against drug recommendations. In this blog post, we outline the steps involved in the process and explain the…

Read more →

LOVD Annotations in VarSeq for Variants and CNVs

May 23, 2024

The Leiden Open Variation Database (LOVD) is an online database designed to facilitate the collection and display of clinically classified variants. Since its initial release in 2004, LOVD has evolved significantly, with the latest version, LOVD 3.0, greatly expanding the number of annotated variants. Golden Helix is excited to announce…

Read more →

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

Feb 2, 2023

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…

Read more →

AMP Manual Deep Dive: VSClinical’s Interpretation for Cancer Biomarker Annotation

Jan 24, 2023

VSClinical AMP Matching of Interpretations  In this blog post, we will delve into the intricacies of the VSClinical AMP interpretation workflow. At the heart of this process lies the task of annotating cancer biomarkers with the correct interpretations based on the classification of the tumor and the type and scope…

Read more →

Annotation Updates: RefSeq and Ensembl gene tracks for GRCh38

Apr 20, 2022

I’d like to take a moment to announce the release of updated gene tracks for the GRCh38 genome assembly! Gene annotation tracks are essential to all VarSeq projects and workflows. Whether your favorite gene track is Ensembl or RefSeq, both sources have been updated and released and can be used…

Read more →

New Annotations Product Page

Mar 30, 2022

Golden Helix is always trying to add new helpful resources to aid in using Golden Helix products for NGS analysis. In today’s blog, I am very excited to introduce a new resource for Golden Helix users! A new resource that is now available is our Golden Helix Annotations product page…

Read more →

Integrating Custom Gene Panels for Variant Annotations Q&A Follow Up

Feb 16, 2022

Thanks to all those who attended the recent webcast by Dr. Rana Smalling, “Integrating Custom Gene Panels for Variant Annotations”. If you were unable to attend or would like to recap, here is a link to watch the broadcast. We covered a lot of content regarding virtual gene panels, and…

Read more →

Five Annotation Sources You Should Know

Oct 19, 2021

In addition to Golden Helix providing easy-to-use genomic software, we also provide value to our users by automating the curation of public databases used in our tools. These annotation sources serve multiple purposes not only leveraging key fields in the filter chain but also automatically supplying evidence for the ACMG…

Read more →

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

Sep 29, 2021

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…

Read more →

Highlights from “Reduce Turn-Around with Enhanced Cancer Annotations and Golden Helix CancerKB Updates”

Jul 22, 2021

We had a wonderful turnout for our recent webcast, “Reduce Turn-Around with Enhanced Cancer Annotations & Golden Helix CancerKB Updates.” Thanks so much to those who were able to join us! And not to worry, we have a link to the recording here just in case you weren’t able to make it. We covered…

Read more →

Merged gnomAD Genomes and Exomes Annotation Source

Jul 15, 2021

The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects (1). We have covered this annotation in-depth in other blog posts, but this resource…

Read more →

GenomeAsia 100K Variant Frequency Annotation

Mar 30, 2021

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…

Read more →

Orphanet Annotations in VarSeq

Mar 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…

Read more →

Lock in Annotation Source Versions to Increase Workflow Consistency

Feb 25, 2021

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…

Read more →