Category Archives: Public data & annotations

A Simple Guide to Curating Genome Assemblies

         June 8, 2021
curate

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, Golden Helix has an SVS Tutorial available that walks users… Read more »

Orphanet Annotations in VarSeq

         March 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 this database is to provide a universal nomenclature to classify… Read more »

Lock in Annotation Source Versions to Increase Workflow Consistency

         February 25, 2021
Annoation Sources

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 and accuracy of results. In this blog, we are focusing… Read more »

What You Need to Know About Staging Annotations

         January 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 has curated over 100 annotation sources for human variant analysis… Read more »

ACGS Guidelines Now Available in VSClinical

         January 7, 2021
ACGS Guidelines Screen Shot

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 2015).  Very similar are the ACGS guidelines that were developed… Read more »

Adding Population Catalogs to VSClinical

         December 10, 2020
example population view

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. Now, users can implement population catalogs to VSClinical such as… Read more »

Updated Annotation: BRCA Exchange

         October 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 in BRCA, a tumor suppressor gene, it has been difficult… Read more »

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

         August 26, 2020
Clinical Genome Resource

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 like ClinGen. We recently participated in a survey and vetting… Read more »

Updating Somatic Annotation Catalogs: ICGC and COSMIC

         October 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 as always, increasing the number of mutations listed. The current… Read more »

Updated Annotations: The new and improved gnomAD 2.1.1

         September 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 samples were counted in the previous 2.0.2 release, the additional… Read more »

New and Updated Annotations

         December 7, 2017
Genotype Imputation

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 been updated to include sub-population allele frequencies and heterozygous and… Read more »

Annotation Education Series: CNV Annotations

         November 9, 2017
CNV Annotations

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. The types of CNV annotations vary and include frequency, clinical… Read more »

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

         October 26, 2017
VarSeq annotations

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 trying to capture rare variants known across multiple subpopulations in… Read more »

Annotation Education Series: Cancer Annotations

         October 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 is to make sure the variants contained in the database… Read more »

Golden Helix, Inc. – Your Annotation Curation Station

         June 15, 2017

The current reduced cost and increase availability of genome sequencing has been making academics, clinicians and individuals alike excited with the possibility of increased research depth, diagnosing capability and personal curiosity. And although a freshly sequenced genome is chock-full of tasty letter snippets, the real revelation and education occurs when comparing to an annotation foundation. In this post, I’ll review… Read more »

Coming Soon! The genome Aggregation Database (gnomAD)

         March 15, 2017
VarSeq Updated

Ever since the MacArther Lab announced the new gnomAD browser at last year’s ASHG conference, we have had many requests from our customers to make this new variant frequency source available within both VarSeq and SVS. This new dataset includes variants obtained from 123,136 exome sequences and 15,496 whole-genome sequences. In comparison to the original ExAC dataset which contained exomes… Read more »

ExAC CNVs: The First Large Scale Public Exome CNV Variant Set

         December 8, 2016
ExAC CNVs

ExAC CNVs were released publicly with a recent publication, providing the full set of rare CNVs called on ~60K human exomes. While there are many public CNV databases out there, this is the first one that was derived from exome data, and thus includes both extremely rare and very small CNV events. With the recent release of Golden Helix’s CNV calling… Read more »

GWAS Example Project Updated for SVS Viewer

         January 26, 2016
SVS 8

With the release of our updated GWAS E-book, we have recently updated the GWAS example project (SNP Genome-Wide Association Tutorial – Complete). This updated project includes more details about how spreadsheets were generated, how to generate plots and which images were used for the GWAS E-book. This information can be found in the User Notes view in the project navigator and… Read more »

Updates to dbNSFP – The Universal Remote of Annotation Sources

         December 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 variant. You can update to dbNSFP 3.0 using the built-in… Read more »

Analyze Your 23andMe Genotype Files with Golden Helix

         July 22, 2015
23andMe

I was definitely an early adopter when it comes to personal genomics. In a recent email to their customer base announcing their one millionth customer, they revealed that I was customer #44,299. And I have been consistently impressed with the product 23andMe provides through their web interface to make your hundreds of thousands of genotyped SNPs accessible and useful. It… Read more »