Search results for “annotation”

Genomenon’s Mastermind – Novel Splice Variant in PAH

Oct 16, 2025

As whole-genome sequencing becomes routine in clinical practice, variant interpretation remains both the opportunity and the obstacle. VarSeq users can efficiently process and report individual samples using extensive annotations and automated classification tools—but even the most comprehensive databases can leave gaps. Some variants simply aren’t found in ClinVar or ClinGen,…

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Ghosts in the Pipeline – Haunted by Incidental Findings

Oct 14, 2025

Every October, we prepare for spooky surprises — creaky doors, eerie whispers, and shadows that move when no one’s there. But in the world of genomics, at any given time and for any given analysis, there’s another kind of haunting that can appear: the ghost in the pipeline — the…

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New in VarSeq 3.0: Location Mapped Breakend Assessment Catalogs

Oct 8, 2025

Breakends (BNDs) represent the precise genomic coordinates where DNA is rearranged in structural variants such as translocations, inversions, and complex rearrangements. Analyzing breakends in NGS analysis is important because they capture the exact “breakpoints” of structural alterations, enabling accurate identification of gene fusions, large deletions, or other events that can…

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Reporting Short Tandem Repeats in VarSeq

Sep 30, 2025

Short Tandem Repeats (STRs) are increasingly recognized as clinically important genetic variants, contributing to a wide range of rare inherited disorders. Historically, the analysis and clinical reporting of STRs have been challenging due to limitations in both sequencing technologies and interpretation frameworks. With the advent of long-read sequencing technologies and…

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September Webcast Recap: Golden Helix + Genomenon

Sep 26, 2025

Golden Helix is excited to spread the word about our partnership with Genomenon, a genomic intelligence giant! We recently presented a joint webcast featuring Dr. Nathan Fortier, Director of Research, Dr. Rana Smalling (Field Application Scientist), members of the Golden Helix team, and Denice Belandres (Senior Manager of Customer Success)…

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Integrating Genomenon Mastermind Curated Variants in VarSeq and VSClinical

Sep 23, 2025

When performing variant classification using VarSeq’s ACMG classifier, a large number of variants inevitably fall into the category of variants of uncertain significance (VUS). This is because much of the evidence required for confident classification cannot be programmatically evaluated. Take PS3, for example, the criterion for functional evidence. This criterion…

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From Rare Disease to Cancer and Neurodegeneration: Customer Publications | September 2025

Sep 18, 2025

In recent years, the adoption of advanced bioinformatics platforms has enabled clinicians and researchers to identify novel variants, characterize complex inheritance patterns, and better understand the clinical impact of genetic disorders. Below are publications from customers in September 2025, showcasing the work built upon the trusted capabilities of our VarSeq…

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Using VSPipeline to Automate Tertiary Analysis in VSWarehouse

Sep 17, 2025

In this blog post, I’ll highlight the benefits of using VSPipeline to automate tertiary analysis in VSWarehouse. Users can now run VSPipeline project creation as a standalone task or a final step in a bioinformatic workflow without writing code. Simply use one of our shipped VarSeq projects or create your…

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VarSeq 3.0.0 to Bring a Major Overhaul to Assessment Catalogs

Sep 2, 2025

We’re thrilled to announce that VarSeq 3.0.0 is right around the corner, and with it comes one of the most exciting updates yet: a complete reimagining of the Assessment Catalogs system. Whether you’re curating clinically relevant variants, tracking tumor-specific calls, or building rich catalogs of sample information, the new system…

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Golden Helix and Genomenon Announce Strategic Partnership to Advance Clinical Diagnostics

Sep 2, 2025

Today, we announced a strategic partnership with Genomenon to integrate its Mastermind Genomic Intelligence Platform and Cancer Knowledgebase (CKB) into the Golden Helix software suite. This collaboration combines two industry-leading platforms to enhance genomic interpretation and deliver high-confidence, literature-backed insights to clinical laboratories worldwide. Through this integration, Golden Helix customers…

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August 2025 Customer Publications: Applications in Cancer, Prenatal Testing & Rare Disease

Aug 26, 2025

At Golden Helix, we get to see firsthand how our software enables groundbreaking research around the world. Our tools are central to real-world discoveries, from cancer studies and prenatal diagnostics to uncovering new genetic links in rare diseases. These publications from August 2025 showcase how VarSeq and VSPipeline are helping…

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Defining HLA Diplotypes for Pharmacogenomics

Aug 14, 2025

In the dynamic field of pharmacogenomics (PGx), the human leukocyte antigen (HLA) system stands out as a critical factor in personalizing drug therapies, particularly in avoiding severe adverse reactions. However, as highlighted in a comprehensive review on the HLA system’s genetics and clinical testing, these genes are notoriously challenging to…

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5 Things I Wish I Knew When Getting Started With VarSeq

Aug 7, 2025

As a new member of Golden Helix’s Field Application Services team, I’ve recently been diving into the capabilities of VarSeq and our broader software suite – an experience every new VarSeq user goes through. If I could schedule a training call with my former self, there are some key points…

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Take Control Over Your Variant Assessment Catalogs

Aug 5, 2025

Over the past several months, we’ve highlighted the powerful new capabilities introduced with VarSeq Warehouse 3.0. Today, I’d like to focus on a familiar feature that’s been thoughtfully enhanced, assessment catalog record management. This update significantly improves data quality, role-based collaboration, and regulatory compliance. Variant assessment catalogs have always been…

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Precision in Practice: VarSeq and VSClinical in Recent Peer-Reviewed Studies | July 2025

Jul 31, 2025

As next-generation sequencing (NGS) becomes more embedded in clinical diagnostics and research workflows, the ability to confidently interpret and report on genomic findings is more critical than ever. In July 2025, Golden Helix’s software suite continued to play a central role in variant annotation and classification, with publications spanning diverse…

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Implementing Data Freedom Practices in Your Genomics Workflows

Jul 17, 2025

In the world of genomics, data ownership and portability are fundamental principles that every researcher and clinician should embrace. With the increasing complexity of genomic datasets and the critical importance of long-term data accessibility, having the ability to export your data in multiple formats is not just convenient, it’s essential.…

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The Breakend Catalog Format for VarSeq 3

Jul 8, 2025

New to VarSeq 3 is support for breakend catalogs. Breakends represent the junction points of structural variants, which include complex genomic rearrangements like translocations, inversions, and large deletions that play crucial roles in cancer genomics and rare disease analysis. These catalogs are unique as they must save two genomic positions…

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June 2025 Customer Publications: Variant Classifications for Cancer & HHT

Jun 27, 2025

This month, our team at Golden Helix is proud to highlight a series of standout customer publications demonstrating the real-world impact of next-generation sequencing and variant analysis. Featured articles from June 2025 showcase the power of the VarSeq platform in supporting high-quality research across hereditary and somatic disease. From integrating…

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The CoLoRS Database: Enhancing Your Long-Read Sequencing Analysis

Jun 17, 2025

Here at Golden Helix, we continue to develop top-quality bioinformatic software to support high-throughput clinical next-gen sequencing pipelines, including long-read whole-genome-sequencing (WGS) workflows. WGS long-read technologies like PacBio HiFi and Oxford Nanopore offer improved variant calling for SNVs, Indels, structural variants, tandem repeats and repeat expansions, and epigenetic modifications. Each…

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Reduce, Reuse, Recycle: Creating Automatable Workflow Templates with VarSeq

Jun 10, 2025

Next-generation sequencing (NGS) data analysis often involves multiple steps from variant annotation, filtering, interpretation, visualization, and report generation. Repeating these steps manually for each new project can be error-prone and inefficient. In clinical bioinformatics and regulated environments, we recognize that consistency is critical. That’s why VarSeq offers robust support for…

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