Golden Helix Blog

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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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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Plotting CNV Metrics in VarSeq

Jun 11, 2024

Golden Helix has a long history of developing a high-quality NGS-based CNV caller. This has become even more apparent with our latest publication, where we teamed up with Twist Bioscience to demonstrate VarSeq capability of calling large copy number variants utilizing their clinical whole exome sequencing data. You can access…

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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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Webcast Recap: Introducing VarSeq Dx as a Medical Device in the European Union

May 23, 2024

This last Wednesday we introduced VarSeq Dx Mode which enables customers to use VarSeq as a CE marked in vitro diagnostic medical device! If you missed our live webcast, no problem! You can watch the recording here. In brief, we started out discussing IVDR and that it establishes standardization for…

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LOVD Annotations in VarSeq for Variants and CNVs

May 23, 2024

The Leiden Open Variation Database (LOVD) is an online database designed to facilitate the collection and display of clinically classified variants. Since its initial release in 2004, LOVD has evolved significantly, with the latest version, LOVD 3.0, greatly expanding the number of annotated variants. Golden Helix is excited to announce…

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Golden Helix at ESHG 2024 in Berlin, Germany!

May 21, 2024

We are excited to participate in the European Human Genetics (ESHG) 2024 conference, where we will showcase our latest advancements in genetic analysis software. Attendees can visit Booth #428 to explore tools like VarSeq, VS-CNV, VSClinical, VSPipeline, and VSWarehouse. These solutions, aligned with ACMG and AMP Guidelines, offer powerful options…

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