Bioinformatic Support

Your Variant Knowledge Base

Apr 9, 2026

Getting the Most from Assessment Catalogs in VSWarehouse One of the most frequent questions from our customers is some version of: “How do we keep our team from re-evaluating the same variant every time it shows up in a new sample?” The answer, in nearly every case, is assessment catalogs and more…

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Automating Couple’s Carrier Screening Workflows with VarSeq

Dec 16, 2025

Carrier screening, also referred to as preconception genetic screening, helps individuals and reproductive partners understand their risk of passing along autosomal recessive and X-linked genetic conditions to their children. This method is being increasingly adopted as a preventive, population-level health intervention that specifically benefits couple’s or individuals in the family…

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Integrating Genomenon Cancer Knowledgebase (CKB) into VarSeq and VSClinical

Nov 19, 2025

Golden Helix’s VSClinical AMP guidelines platform, powered by our Golden Helix CancerKB has long been trusted by clinicians and researchers for generating report-ready clinical cancer biomarker interpretations. To further elevate the coverage and currency of our somatic variant evaluation capabilities, we’ve integrated Genomenon’s Cancer Knowledgebase (CKB) into both VarSeq and…

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November Webcast: Simplifying Complex Cancer Data into Actionable Knowledge

Nov 6, 2025

As precision oncology evolves, clinicians and laboratories need tools that can both handle massive genomic datasets and translate those findings into clear, clinically actionable guidance. In our recent webcast, “Simplifying Complex Cancer Data into Actionable Knowledge with Golden Helix CancerKB,” we walked through how Golden Helix CancerKB can take clinical…

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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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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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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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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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Improving the Quality of CNV Analysis in VarSeq

Aug 13, 2025

High-quality copy number variant (CNV) analysis begins with a well-designed assay and optimized sequencing workflow. Foundational quality measures deployed in VarSeq include building an appropriate reference set for coverage normalization, ensuring sufficient sequencing depth, and maintaining consistency in both the sequencing platform and library preparation methods. These steps help ensure…

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Leveraging VarSeq for NGS Quality Control

Jul 24, 2025

A crucial step in any next-generation sequencing (NGS) analysis is quality control, which is essential for confirming the validity of potentially clinically relevant findings before proceeding with any subsequent variant interpretation or reporting. While Golden Helix does not directly provide NGS validation services, our VarSeq software provides robust analysis tools…

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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,…

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Visualization With IGV

Jun 5, 2025

Modern genomics workflows often require multiple specialized tools working in concert. In the upcoming VarSeq release, we are excited to announce the option for tighter integration with IGV. Genomics researchers and clinicians are well-versed in using IGV as a visualization tool for their genomic data. This new option will allow…

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Compute Fields to the Rescue: Creating Additional Fields from Your VCF

Mar 11, 2025

We on the FAS Team recently had a case we wanted to share where Compute Field could help a customer navigate filtering a unique edge case. This edge case coincides with the rising popularity of filtering on a specific value for the Alternate of the Allelic Depths Column. Said another…

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Bringing Phasing Information from Long-Read Data into a Trio Analysis

Feb 11, 2025

Golden Helix customers continue to push the boundaries of genomic research and clinical applications, leveraging VarSeq to analyze complex genetic data and uncover previously uncatalogued variants. With advancements in long-read sequencing and our recent updates to the VarSeq software, clinicians can now harness phasing information to distinguish between inherited and…

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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…

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Complex Variants for Acid Reflux, Right in Time for Thanksgiving!

Nov 26, 2024

It’s the big day, and you’ve spent hours preparing for the big old-fashioned family Thanksgiving. Keeping in mind that your Cousin Eddie likes to show up unannounced and eat you out of house and home, you have remembered our food allergy allele workflow from last year, and prepared a special…

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Don’t Miss MITOMAP for Mitochondrial Variant Analysis in VarSeq

Nov 12, 2024

Mitochondrial diseases, caused by mutations in mitochondrial DNA (mtDNA), represent a complex and diverse group of disorders. These conditions often affect organs with high-energy demands, such as the brain, heart, and muscles. Identifying mitochondrial DNA variants and understanding their clinical relevance is essential for diagnosing and treating these diseases. One…

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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…

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Demystifying the Representation of Structural Variants Imported into VarSeq

May 20, 2024

VarSeq enables users to import structural variants for annotation, filtration, and subsequent clinical or other analyses. Structural variants are often called during secondary analysis as belonging to two broad categories – Copy Number Variants (CNVs) with the file suffix “…_CNV.vcf” and Breakends with the file suffix “…_SV.vcf”. This blog will…

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