Public Data & Annotations

CADD 1.7 in VarSeq Enables Enhanced Prioritization of Missense and Non-Coding Variants

Jan 28, 2025

We are excited to announce the addition of CADD 1.7 as an annotation track in VarSeq. The latest release of CADD incorporates a variety of new annotations into its model, resulting in significant improvements in variant scoring. This includes the integration of Meta ESM scores and improved performance on non-coding…

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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…

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Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer

Jul 25, 2023

While the analysis of gene fusions is crucial for understanding the genetic basis of cancer, the process of interpreting these mutations can be challenging. One important component of fusion interpretation is the identification of relevant publications. To aid researchers in the search for publications related to specific gene fusions, Felix…

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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…

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What to Expect From GnomAD v3.1.2

Jan 5, 2022

In this blog post, I am very excited to talk about The Broad Institute’s release of the latest version of gnomAD, v 3.1.2, which is now available for use as an annotation source in your SVS or VarSeq projects. For VarSeq users, I also want to point out that gnomAD…

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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…

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A Simple Guide to Curating Genome Assemblies

Jun 8, 2021

A common feature request from Golden Helix customers is to curate and make available genome assemblies for different plant and animal species. These requests commonly come from SVS users as many research projects are being carried out, and having the genome assembly available for analysis is essential. That being said,…

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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…

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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…

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What You Need to Know About Staging Annotations

Jan 22, 2021

Annotating genomic variants is a very complex process but perhaps the most important part of next-generation sequencing variant analysis. Here at Golden Helix, we recognize the importance and value of having the most up-to-date sources available and curating new annotation sources as they become available for variant analysis. Golden Helix…

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ACGS Guidelines Now Available in VSClinical

Jan 7, 2021

Golden Helix offers a market-leading bioinformatics solution that allows users to evaluate next-generation sequencing variants according to the ACMG and now ACGS guidelines. The ACMG guidelines were created in 2015 and are widely accepted as best practice for the interpretation of sequencing variants throughout the United States (Richard et al…

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Adding Population Catalogs to VSClinical

Dec 10, 2020

Our previous webcast demonstrated some of the new functionalities of VSClinical, including the ability to add ACMG frequency sources for the ACMG BA1, BS1, and PM2 criteria. This new feature was spurred by the feedback from our users, which requested supporting frequency tracks other than gnomAD Exomes and 1kG Phase3.…

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Updated Annotation: BRCA Exchange

Oct 30, 2020

Our team is regularly updating and curating annotations, most recently the BRCA Exchange. Breast cancer is known to occur in approximately 10% of the female population and if there is a damaging mutation in the breast cancer gene (BRCA), that rate increases to 65%. Although genetic testing can identify mutations…

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Golden Helix gets full marks in ClinGen’s list of Genomic Analysis Software Platforms

Aug 26, 2020

The potential of genetic testing to impact a patient’s life has been greatly accelerated by the sharing of variant interpretations done by clinical labs in public repositories such as ClinVar. This is not an inevitable outcome, but the persistent work and advocacy of people like Dr. Heidi Rehm and organizations…

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Updating Somatic Annotation Catalogs: ICGC and COSMIC v89

Oct 28, 2019

Golden Helix works to keep incorporating and updating great somatic annotation catalogs for our VSClinical users. We currently have the updated version of one of the largest cancer databases from the International Cancer Genome Consortium, or ICGC. Version 28 has been improved by integrating ClinVar and CIViC clinical annotations, and…

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Updated Annotations: The New and Improved gnomAD 2.1.1

Sep 19, 2019

The Broad Institute team led by Dan MacArthur announced the release of gnomAD version 2.1 at last year’s ASHG conference. This new version boasted data from 125,748 exomes and 15,708 genomes, but the greater updates were the improved QC refinement and more discrete sub-population break downs. Although the majority of…

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New and Updated Annotations

Dec 7, 2017

Golden Helix is excited to announce a new round of novel and updated annotations; including a frequency track, a region track, and a gene track. All three of these tracks were created with the use of VarSeq and its Convert Wizard functionality. First, the expansive 1000 genomes track (1kG) has…

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Annotation Education Series: CNV Annotations

Nov 9, 2017

With the recent upgrade to VarSeq 1.4.7, users gain access to some new great features. Among the additions are new CNV annotations (Figure 1). In this final chapter of the annotation blog series, we are going to provide descriptions of the new CNV annotations and how they can be used.…

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Annotation Education Series: Frequency, Functional Prediction, and Gene Annotations

Oct 26, 2017

In our final chapter of this variant annotation blog series, we will discuss additional annotations that provide powerful variant filtering and analysis capability. Golden Helix curates many annotations in a way that allows for simple analysis and saves the users the hassle of all this data management. Whether you are…

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Annotation Education Series: Cancer Annotations

Oct 5, 2017

CIViC The Clinical Interpretations of Variants in Cancer, better known as CIViC, is an open access open source, community-driven web resource available to all VarSeq users. Nature Genetics published an article that states, “CIViC accepts public knowledge contributions but requires that experts review these submissions”. Fundamentally, the focus behind CIViC…

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