Search results for “annotation”

Updating VarSeq’s Transcript Annotation along with NCBI RefSeq Genes Interim Release

Mar 30, 2017

It may be possible to say that annotating a variant correctly and accurately against gene transcripts is the most important job of a variant annotation and interpretation tool. We take it very seriously at Golden Helix as we support VarSeq and its use by our customers in both research and…

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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 genome sequencing data 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…

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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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Pharmacogenomic Variants That Differ Across Populations

Jun 9, 2026

Pharmacogenomic (PGx) testing tailors drug selection and dosing to a patient’s genetic profile, reducing adverse drug reactions and improving therapeutic outcomes. The clinical recommendations that drive PGx, published by the Clinical Pharmacogenetics Implementation Consortium (CPIC) and the FDA, are evidence-based and guideline-backed. However, many of the most clinically important PGx…

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Cryptic Splice Site Detection: How CI-SpliceAI and Whole Genome Sequencing Uncover What Exome Panels Miss

Jun 4, 2026

Aberrant splicing is one of the most consequential and least visible mechanisms driving human genetic disease. While variants disrupting the canonical GT/AG dinucleotides at exon–intron boundaries can be easily detected, some variants silently reshape splicing from deep within introns, far from the regions that targeted panels and whole exome sequencing…

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From Ovarian Cancer to Rare Genetic Disorders: Customer Publications | May 2026

May 28, 2026

In three published studies from this month, researchers used our genetic analysis software to investigate diverse and challenging genetic questions: identifying potential ovarian cancer susceptibility linked to germline ATRIP variants, expanding the clinical and molecular understanding of VPS35L-related Ritscher–Schinzel syndrome, and exploring the genomic landscape of early-onset oral tongue squamous…

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Long Read Part 3: Repeat Expansions

May 19, 2026

Short tandem repeats (STRs) are among the most challenging variants to characterize with traditional sequencing technologies. Many clinically significant STR expansions span hundreds or thousands of base pairs, far exceeding the read lengths of short-read platforms. As a result, countless disease-causing repeat expansions have historically gone undetected in genomic workflows,…

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Long-Read Part 1: Structural Variant Analysis

Apr 28, 2026

End-to-End Structural Variant Analysis for Long-Read Data with VarSeq and VSWarehouse Long-Read Data Long-read sequencing technologies like PacBio HiFi have transformed our ability to detect structural variants (SVs) with greater accuracy and resolution than ever before. Unlike short-read sequencing, which often struggles to span the repetitive or complex genomic regions…

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Webcast Recap: CI-SpliceAI for Splice Site Prediction and Variant Interpretation in VarSeq

Apr 16, 2026

We’re grateful to everyone who tuned in for our April 15th webcast, “CI-SpliceAI for Splice Site Prediction and Variant Interpretation in VarSeq,” with presenter Nathan Fortier. If you weren’t able to attend live, here’s a quick overview of what was covered: the ClinGen SVI Splicing Subgroup has released evidence-based recommendations…

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Precision Medicine in Action: Why Testicular Cancer Awareness Month Matters 

Apr 6, 2026

April is Testicular Cancer Awareness Month. This is an opportunity not only to emphasize early detection, but to reflect on how far oncology has advanced in the era of precision medicine. Testicular cancer represents one of the most curable solid tumors in modern oncology. Yet its management illustrates a broader truth: outcomes improve when early clinical vigilance is…

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March 2026 Customer Publications

Mar 26, 2026

March’s Clinical Genomic Insights Across immunodeficiency syndromes, oculocutaneous albinism, and ocular genetics 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 March explored immunodeficiency syndromes, oculocutaneous…

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March is Colorectal Cancer Awareness Month:

Mar 24, 2026

How VarSeq Helps Explore the Therapeutic Landscape for CRC Patients Colorectal Cancer Awareness Month for CRC Patients In honor of Colorectal Cancer Awareness Month, we’re taking a close look at how VarSeq’s VSClinical AMP workflow and evidence from Genomenon and Golden Helix CancerKB  can expose the right treatment strategies for…

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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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