Search results for “annotation”

Webcast Recap and Q & A: Introducing VSPGx: Pharmacogenomics Testing in VarSeq

Mar 14, 2024

Thanks to all of you who were able to attend the live webcast introducing the newest genomic analysis tool within VarSeq, VSPGx! For those of you who could not make it to the live presentation and demonstration, I will fill you in on what we covered. If you would like…

Read more →

We Are Heading to Toronto!

Feb 27, 2024

Join Golden Helix at the American College of Medical Genetics and Genomics (ACMG) 2024 conference and discover the latest advances in genetic research. This premier event brings together leading researchers, clinicians, and industry experts to share their insights on cutting-edge topics in medical genetics. Stop by our booth for a…

Read more →

Incorporating gnomAD V4 into the ACMG Auto-Classifier

Feb 14, 2024

We at Golden Helix are thrilled with our recent release of gnomAD v4! The curation of this massive database was a huge undertaking for our development team, but with the addition of new features, we believe it was well worth the wait. This annotation track contains allele frequencies from a…

Read more →

GnomAD v4 Released: Enhanced Data and Golden Helix Curation for VarSeq Users

Feb 7, 2024

The Broad Institute’s release of gnomAD v4 needs no introduction as the data in this release is highly sought after by professionals in the genetics community, and the v4 release has a lot to boast about! The v4 release is roughly five times larger than the v2 and v3 releases…

Read more →

Exploring the Genetic Frontier: Advances in Understanding Eye Disorders

Jan 30, 2024

Welcome to the exploration of groundbreaking genetic research in ophthalmology. Recent studies have unveiled fascinating insights into the complex interplay between genetics and eye disorders, offering hope and new directions for understanding and treating these conditions. From novel genetic variants linked to microphthalmia and glaucoma to the long-term implications of…

Read more →

Using Liftover to Curate GnomAD v4 for GRCh37

Jan 25, 2024

We are excited to announce the release of our gnomAD v4 annotation tracks for VarSeq. This version of the GnomAD database represents a significant leap forward, including data from an impressive cohort of over 800,000 individuals — a remarkable 5x expansion compared to the previous releases. Notably, this dataset is…

Read more →

Advanced Techniques for GenomeBrowse Customization

Jan 23, 2024

Today, we will be exploring the indispensable role of GenomeBrowse in your VarSeq workflows. This blog aims to guide you through various customization options, including color preferences, filtering techniques, display modifications, numeric value plotting, and additional tips. I hope to enhance your GenomeBrowse experience and enable you to gain valuable…

Read more →

Webcast Recap: VarSeq, the Complete Tertiary Platform for Short and Long-Read NGS Data

Jan 18, 2024

Many thanks to those who came to view our most recent webcast, From Panels to Genomes with VarSeq: The Complete Tertiary Platform for Short and Long-Read NGS Data. This was a great opportunity for us to showcase the breadth of our workflows, from short-read to long-read, panels to genomes, singleton…

Read more →

Managing Gene Preferences and Preferred Transcripts in VarSeq

Jan 16, 2024

There are several contextual factors to consider when analyzing genomic data for NGS analyses. A variant may have divergent impacts depending on which transcript of the gene is being considered, or the impact of a variant could be weighed more or less heavily depending on the disease context. Evidently, the…

Read more →

The Log Tab in VarSeq

Jan 11, 2024

How long did it take to run coverage regions? Did my colleague update the filter chain like he said he would? Which import options did I use? Where did I save this project? These questions and more can be answered with our little-used VarSeq Log tab. Periodically, our customers come…

Read more →

VarSeq in Action: Deciphering Complex Genetic Puzzles in Immune Thrombocytopenia, Glaucoma, and Rare Syndromes

Dec 31, 2023

In this blog, we explore the impactful applications of VarSeq in genetic research and diagnostics. Through case studies, we examine its role in diverse conditions like Immune Mediated Thrombocytopenia (ITP), glaucoma, and Cri du Chat syndrome. These studies demonstrate VarSeq’s capability in identifying genetic variants and influencing diagnosis and treatment…

Read more →

Polygenic Risk Scores Analysis in SVS 8.10 Release

Dec 21, 2023

Thank you to those who attended our recent webcast on Golden Helix’s SNP & Variation Suite (SVS) and its new capability related to Polygenic Risk Scores (PRS). If you were unable to attend, a recording can be found via this link. For common diseases, PRS can provide a predictive value…

Read more →

Management of Large-Scale Genomic Data with VarSeq Warehouse

Dec 14, 2023

VarSeq Warehouse is the solution provided by Golden Helix for management of large-scale genomic data. It serves a centralized, indexed variant repository that stores variants and assessments from selected samples or projects. Management of large-scale genomic data with VSWarehouse enables entire teams, including collaborators, to oversee key aspects of their…

Read more →

VarSeq 2.5.0 Released!

Nov 14, 2023

As many of you may already know, we just released VarSeq version 2.5.0 this month! We have talked about the two headlining features a bunch, but we have not focused on what else has changed in VarSeq 2.5.0 that might also strike your fancy. For those of you who might…

Read more →

Evolution of Multi-Allelic Calls in VarSeq: Before and After Version 2.5.0

Nov 9, 2023

It may come as a surprise to our long-standing users that the multi-allelic import and representation in VarSeq is slated to have different import options with the 2.5.0 upgrade. As the software grows and evolves, we strive to meet the changing needs of our users, and this is one area…

Read more →

Evaluating DeepMind’s AlphaMissense Classifier

Oct 20, 2023

Last month, the researchers at Google DeepMind announced the release of AlphaMissense, a new missense prediction algorithm that leverages the protein structure prediction model AlphaFold to distinguish between benign and pathogenic missense variants (Cheng et al., 2023).  AlphaFold is a model for the prediction of protein structures from amino acid…

Read more →

Accessing Report Templates and Simple Modifications

Sep 18, 2023

Your variants of interest have been identified, the SVs annotated, and the CNVs classified. Once the manifest has been imported (and here is a great blog on the subject), the last step is to bring all of this information into a report template! In this blog, we will go over…

Read more →

Evaluation scripts in VSPipeline: We heard you like automation…

Sep 12, 2023

…so we added some automation to your automation so you can automate while you automate! Automation has been a hot topic recently and for all the right reasons. As we (proudly) watch our customers increase their sample and data volume, we are constantly seeking to provide tools to reduce click…

Read more →

VarSeq Assessment Catalogs for Beginners

Aug 29, 2023

Variant interpretation is a critical aspect of any clinical NGS workflow. VarSeq assessment catalogs are a tool used to save variants and associated variant information for easy tracking and retrieval of completed variant interpretations. As variant interpretations stack up and classifications are saved, storing in assessment catalogs makes it easy…

Read more →

Get More Out of Assessment Catalogs by Storing and Tracking Variant Artifacts

Aug 8, 2023

Assessment catalogs are a way for VarSeq users to save variants and variant information for clinically relevant variants, so when you come across this variant again in another sample, all of the work to analyze and classify the variant is already done! But there is more than meets to the…

Read more →