Search results for “annotation”

Exploring Cutting-Edge Genetic Research with VarSeq: Recent Publications Highlighting Innovation and Discovery

Jun 26, 2024

At Golden Helix, we are proud to support researchers and clinicians worldwide who push the boundaries of precision medicine. Our VarSeq software continues to be instrumental in the analysis and interpretation of genetic data, enabling groundbreaking discoveries and advancements. Recently, several papers have been published that showcase the power and…

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Where Are My Structural Variant Calls? – Highlighting the Breakends Table

Jun 25, 2024

In the last year, we have seen a surge in customers moving to whole genome sequencing. Not only does whole genome sequencing provide unparalleled gene coverage compared to whole exome, but depending on the kind of sequencing, you may expect to see additional file types as well. For example, our…

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Preprints, Posters, and Golden Helix Authors

May 30, 2024

We continue to make significant contributions to the field of genomic analysis through collaborative studies, innovative software solutions, and robust data interpretation methodologies. This blog highlights four recent contributions from our team and collaborators, showcasing the breadth of our research and its implications for clinical practice. Analyzing Performance of Twist…

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Demystifying the Representation of Structural Variants Imported into VarSeq

May 20, 2024

VarSeq enables users to import structural variants for annotation, filtration, and subsequent clinical or other analyses. Structural variants are often called during secondary analysis as belonging to two broad categories – Copy Number Variants (CNVs) with the file suffix “…_CNV.vcf” and Breakends with the file suffix “…_SV.vcf”. This blog will…

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Variant Calling and CNV Import in PGx Genes using VSPGx

Apr 18, 2024

In this blog post, we will explore the nuances of variant calling and import in the context of VSPGx. We will discuss the importance of integrating must-call variant definitions into the calling processes and provide guidance on incorporating copy number variants (CNVs) and structural variations (SVs) into your PGx analysis…

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Computed Fields in VarSeq: The Ultimate Customization Tool

Apr 2, 2024

Bioinformatic freedom is core to the user experience with Golden Helix software, a topic with which you will be well-versed if you’ve kept up on our recent blogs. We are constantly endeavoring to provide our users with powerful tools to tackle complex and impactful next-generation sequencing (NGS) workflows while maintaining…

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VarSeq 2.6.0 is Released!

Mar 26, 2024

We have been building up to the final release of VarSeq 2.6.0 for a couple of weeks now, but we are excited to announce that 2.6.0 is officially available! VarSeq 2.6.0 is an exciting release as this version of VarSeq features the introduction of VSPGx, offering a complete pharmacogenomic workflow,…

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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…

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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…

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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…

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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…

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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…

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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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