Golden Helix Blog

Efficient Quality Control tools for an automated VarSeq pipeline

Oct 29, 2024

Optimizing sample throughput while maintaining quality control is, arguably, the crux of any profitable lab performing a high volume of analysis. We’ve discussed in great detail the flexibility of VSPipeline, our command line automation tool, as well as our full-stack FASTQ to report automation capabilities, and today I’d like to…

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GnomAD 4.1 Released: Improved Allele Frequency Data for VarSeq Users

Oct 22, 2024

We’re excited to announce the release of gnomAD 4.1 variant frequencies as an annotation track in VarSeq. This latest release addresses key issues from previous versions and introduces joint variant frequencies curated directly from gnomAD. Additionally, we’ve refined our liftover process, offering more accurate GRCh37 tracks. By incorporating this data…

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Flexible Biomarker Reporting Capabilities with VarSeq: Somatic Interpretation Made Easy!

Oct 15, 2024

Reporting on Cancer Biomarkers may seem like a daunting task, both in determining the scope of what a biomarker can encompass and which information to include. Biomarkers can come in the form of small variants (SNPs and INDELs), copy number variants, and structural variants. Biomarkers can also be sourced from…

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VarSeq 2.6.2 is Released!

Oct 8, 2024

I am pleased to announce that VarSeq 2.6.2 is now available! VarSeq 2.6.2 comes jammed-packed with new features and capabilities to advance your NGS analysis workflows. In this blog, I will describe the major changes to the VSPGx workflow, which were the main focus of the release, and I will…

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Compound Heterozygosity Between Variant Classes

Oct 4, 2024

Compound heterozygosity describes the relationship between two alternate alleles when they are located within the same gene but at different loci within that gene. Compound heterozygosity is particularly relevant in a recessive disorder when the presence of these alleles in combination confers an increased risk of disease, similar to a…

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How VarSeq Powers Research in Inherited Diseases and Cancer

Sep 25, 2024

Exome and genome sequencing have advanced genetic research, but data analysis remains complex. VarSeq simplifies this by helping researchers identify key genetic changes in rare diseases and cancer, improving screening and diagnosis. Here are recent customer publications that highlight VarSeq usage. Expanded carrier screening for inherited genetic disease using exome…

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Combined Impact: New Tools in VarSeq Follow Up Blog

Sep 19, 2024

Thank you to all our audience members who attended our recent webcast, Combined Impact: New Tools to Assess Complex and Compound Heterozygous Variants with VarSeq. If you would like to view the webcast, follow the link above! As the title suggests, this webcast was all about breaking down the new…

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VarSeq Early Capabilities for Analyzing DNA Methylation

Sep 12, 2024

DNA methylation is becoming more relevant as a clinically important biomarker, and long-read pipelines are making it easy to get this information in the same sequencing run as small variants and larger structural variants. Even though there are no official guidelines for addressing DNA methylation, it is still useful to…

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Collapse Phased Variants in VarSeq

Sep 12, 2024

In a recent blog post, we explored how phased genotypes provide crucial insights by separating variants into distinct haplotypes—groups of alleles inherited together from a single parent. We also discussed how the combined impact of multiple variants within the same gene can significantly differ from their individual effects. However, accurately…

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Golden Helix CancerKB’s Focus on Hematological Cancer Interpretations

Sep 6, 2024

You might have noticed an uptick in the number of interpretations associated with hematological cancers within the Golden Helix CancerKB database over the past several months. This is because the Golden Helix CancerKB curation team has been focused on bolstering our drug sensitivity, diagnostic, and prognostic interpretations. This project has…

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Sneak Peek: Force Calling Reference Alleles

Sep 3, 2024

In the upcoming release of VarSeq 2.6.2, we have added the ability to force call reference alleles using the BAM files associated with the sample. This feature extends the current force call functionality, which allows filling in reference alleles from GVCFs. This is an important option to enable when running…

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VarSeq Annotation and Filtering Use Cases

Sep 3, 2024

The following customer publications showcase the ability of VarSeq. Each study highlights how VarSeq simplifies variant annotation, filtering, and interpretation, supporting efficient NGS workflows in both clinical and research settings. Rare host variants in ciliary expressed genes contribute to COVID-19 severity in Bulgarian patients Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)…

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Webcast Q & A: Integrating Long and Short Read Sequencing for Comprehensive NGS Analysis

Aug 22, 2024

Our webcast on Integrating Long and Short Read Sequencing for Comprehensive NGS Analysis was a timely review of a topic. We discussed how users are leveraging both short and long-read sequencing modalities for comprehensive NGS analyses, reviewing the differences between long and short-read sequencing, the benefits and limitations of each modality,…

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The Power of Phased Genotypes in Variant Analysis

Aug 20, 2024

Phased genotypes provide crucial information that allows us to separate variants into distinct haplotypes, representing the sequence of alleles inherited together from a single parent. This information can offer profound insights into inheritance patterns, the combined functional effects of variants, and the identification of specific genetic profiles such as pharmacogenomic…

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What’s Wrong with My Computer? The Value of a Self-Diagnostics Test

Aug 13, 2024

Periodically, our FAS team will see a situation where a customer has installed VarSeq on a new machine…but something is not entirely right. Perhaps a VCF will not load, annotations cannot download, or a long-running process like coverage regions will not complete. Any of these issues alone can be tricky…

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The Versatility of VarSeq: Local and Cloud Deployment Options

Aug 6, 2024

Cloud computation is a hot topic across industries that require scalable software solutions to enable growth, and for good reason. The cloud, in all its mystical appeal, has so mellifluously penetrated the zeitgeist that experts engaging with new software solutions are often eager to hear how they fit into the…

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Our New Pharmacogenomic Tutorial is Hot Off the Press!

Aug 1, 2024

Our customers asked for a step-by-step tutorial for navigating a pharmacogenomic (PGx) workflow in VarSeq, and we are happy to have it delivered! Our brand new PGx tutorial can be found on our website, along with our other VarSeq tutorials. Like our other famous tutorials, this one will provide example…

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Pioneering Precision Medicine: Recent Publications Showcasing the Impact of VarSeq

Jul 30, 2024

This month, we saw overwhelming customer publications with great use cases of VarSeq. Explore the publications below of our amazing customers continuing to pioneer precision medicine. The polygenic implication of clopidogrel responsiveness: Insights from platelet reactivity analysis and next-generation sequencing Clopidogrel is widely used worldwide as an antiplatelet therapy in…

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A Hidden Gem Inside Golden Helix CancerKB

Jul 18, 2024

The FDA approved the first medical therapy for desmoid tumors only a few months ago! What’s the big deal, right? Desmoid tumors are non-cancerous and can’t even metastasize. Well, in this blog post, I want to discuss these interesting tumors, and you will find that not only are these tumors…

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VarSeq PGx inputs: Annotation Tracks Required for PGx Analysis

Jul 16, 2024

The PGx Variant Detection and Recommendations algorithm is the driving force behind the pharmacogenomic analysis capabilities provided by VSPGx in VarSeq. This algorithm is used to identify pharmacogenomic diplotypes and annotate them against drug recommendations. In this blog post, we outline the steps involved in the process and explain the…

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