Search results for “annotation”

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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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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Optimizing the Capture of Tier II Evidence in VSClinical AMP

Jul 18, 2023

VarSeq 2.3.0 unleashed a whole new way to select, process, analyze, and report cancer variants through complete workflow automation, application of evaluation scripts, and enhanced annotation. Single nucleotide variants, copy number variants, structural variants, and genomic signatures could be added to a single patient evaluation, and Golden Helix CancerKB came…

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Moving the AppData Folder – A Look At Sharing Assessment Catalogs

Jul 3, 2023

Discover how to enhance collaboration in VSClinical by sharing variant scores and assessment catalogs through the strategic relocation of the AppData folder. A subtle but powerful utility of VSClinical concerns the ability to share variant scores between users on the same account. What I mean by that is, leveraging the…

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Data Viewing with VarSeq: Plotting Tracks!

Jun 26, 2023

In recent weeks, GenomeBrowse capabilities have had a sudden resurgence of interest among our customers. To support this, the FAS team wanted to share with you several under-utilized GenomeBrowse plotting tricks. First, let’s cover plotting a BED file for easy track viewing. The first step is launching a GenomeBrowse window…

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We are Headed to AMP Europe 2023!

Jun 12, 2023

Discover the Latest Developments in Variant Classification and Interpretation Tools at Golden Helix’s Booth at AMP Europe 2023 in Milan, Italy We are thrilled to announce that Golden Helix will be participating in the AMP Europe 2023 conference in Milan! We are eagerly looking forward to connecting with leading healthcare…

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