Search results for “annotation”

Custom Filtering using ClinVar Annotations

Jul 19, 2016

ClinVar is one of our most used annotations sources for a variety of workflows. It is also the public annotation source that is updated most frequently of all the sources currently supported in VarSeq. ClinVar provides new versions of their database once a month in several formats (XML, VCF, TXT).…

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Updates to dbNSFP – The Universal Remote of Annotation Sources

Dec 8, 2015

Probably one our most popular public annotation sources we curate and update is the database of Non-Synonymous Functional Predictions (dbNSFP). In it’s recent update, it has expanded the predictions to include FATHMM-MKL and VarSeq now incorporates this new prediction into its voting algorithm of now 6 different discrete predictions per…

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Supercentenarian Variant Annotation: Complex to Primitive

Mar 19, 2015

In a previous blog post, I demonstrated using VarSeq to directly analyze the whole genomes of 17 supercentenarians. Since then, I have been working with the variant set from these long-lived genomes to prepare a public data track useful for annotation and filtering. Well, we just published the track last…

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The State of Variant Annotation: A Comparison of AnnoVar, snpEff and VEP

Jun 25, 2014

Up until a few weeks ago, I thought variant classification was basically a solved problem. I mean, how hard can it be? We look at variants all the time and say things like, “Well that one is probably not too detrimental since it’s a 3 base insertion, but this frameshift…

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New 1kG, dbNSFP, and ESP6500 Annotation Tracks and Associated Filters

Jul 16, 2012

SVS 7.6.7 features new tools for filtering sequencing data based on functional predictions and allele frequencies. To complement these new features, new annotations tracks have been uploaded to our data server and are now available for our customers! Below you will find descriptions of the new tools and the related…

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CI-SpliceAI High Confidence Regions

Mar 17, 2026

Introducing CI-SpliceAI High Confidence Regions track Last year, we introduced genome-wide precomputed CI-SpliceAI scores for VarSeq, enabling the detection of splice-altering variants outside of canonical splice motifs. These scores make it significantly easier to identify cryptic splice gains, splice losses, and other splicing events that may be missed by traditional…

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Customer Publications February 2026

Feb 24, 2026

February’s Clinical Genomics Insights Across Brain Tumors, Rare Missense Variants, and Genetic History of Cattle Each month, we highlight new research from the scientific community that advances our understanding of complex genetic diseases and showcases the tools researchers rely on for precise variant interpretation. Our customer publications in February explored…

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Customer Publications January 2026 | Customer Publications: Clinical Genomics Insights Across Pharmacogenomics and Human Immunology

Jan 29, 2026

Each month, we highlight new research from the scientific community that advances our understanding of complex genetic diseases and showcases the tools researchers rely on for precise variant interpretation. January’s customer publications explore pharmacogenomics testing and variants that reveal how specific genetic mechanisms shape human immune responses. Together, these studies…

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December 2025 | Customer Publications: Clinical Genomics Insights Across Infectious Disease, Pharmacogenomics, and Rare Kidney Disorders

Dec 30, 2025

December 2025 brings a diverse set of customer publications highlighting how advanced genomic analysis is being applied to real clinical and population-scale challenges, from infectious disease susceptibility to pharmacogenomics and rare kidney disorders. Together, these studies underscore the growing importance of integrated variant interpretation, scalable sequencing strategies, and rigorous clinical…

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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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VSWarehouse for Genome Centers: Scalable, Secure Whole-Genome Infrastructure for Modern Sequencing Programs 

Dec 12, 2025

Thank you to everyone who joined our recent webcast, “VSWarehouse for Genome Centers: Scalable, Secure Whole-Genome Infrastructure for Modern Sequencing Programs,” presented by Gabe Rudy on December 10, 2025. We appreciate the strong attendance and the excellent questions regarding the operational and security needs of modern genome centers.  For those…

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Integrating PacBio Somatic Workflows into VSWarehouse 3.0

Nov 21, 2025

As long-read sequencing solidifies its role in clinical and translational research, labs are increasingly seeking streamlined methods to transition from raw data to actionable results. With the release of VSWarehouse 3.0, Golden Helix now supports a fully integrated implementation of PacBio’s somatic workflow, providing users with a powerful, centralized environment…

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Golden Helix to Attend AMP 2025 in Boston

Oct 30, 2025

Golden Helix is excited to exhibit at the Association for Molecular Pathology (AMP) 2025 Annual Meeting in Boston, Massachusetts, where we’ll showcase our newest advancements in variant interpretation, enterprise genomics, and scalable software deployment. Visit us at Booth #543 to explore how VSWarehouse and our Bring Your Own Cloud (BYOC)…

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October 2025 | Customer Publications: Driving Genomic Innovation with VarSeq

Oct 28, 2025

At Golden Helix, we’re proud to see how researchers worldwide continue using our software to accelerate discovery and improve clinical decision-making. These October 2025 publications highlight how VarSeq is advancing genetic research across cancer, hereditary disease, and molecular diagnostics. From identifying new variant mechanisms to expanding our understanding of genotype–phenotype…

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Clinical Variant Interpretation at Scale: Reflections from ASHG 2025

Oct 27, 2025

Recently, Golden Helix attended the ASHG 2025 conference, where we had the opportunity to showcase our partnership with Genomenon. This collaboration took center stage at both our booth and Genomenon’s CoLab session, Automating Genomic Workflows: Cutting Interpretation Time, Accelerating Turnaround, and Increasing Diagnostic Yield. Our discussions centered on a problem…

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October Webcast: Scaling NGS Analysis into Institutional Knowledge with VSWarehouse

Oct 24, 2025

As Next-Generation Sequencing (NGS) becomes central to modern clinical diagnostics, laboratories are managing more data than ever before, and turning that data into actionable insight requires both precision and scalability. In our recent webcast, Next-Gen Sequencing at Scale: Transforming Per-Sample Outcomes into Institutional Knowledge with VSWarehouse, we explored how Golden…

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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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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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