Compound Heterozygosity Between Variant Classes

         October 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 traditional homozygous recessive combination of alleles. The detection of compound… Read more »

How VarSeq Powers Research in Inherited Diseases and Cancer

         September 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 and genome sequencing The goal of this study was to… Read more »

Combined Impact: New Tools in VarSeq Follow Up Blog

         September 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 variant analysis tools in the upcoming VarSeq 2.6.2 release and… Read more »

VarSeq Early Capabilities for Analyzing DNA Methylation

         September 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 analyze and evaluate this data, so we would like to… Read more »

Collapse Phased Variants in VarSeq

         September 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 assessing the joint impact of these in-phase variants is a… Read more »

Golden Helix CancerKB’s Focus on Hematological Cancer Interpretations

         September 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 CancerKB curation team has been focused on bolstering our drug sensitivity, diagnostic, and prognostic interpretations. This project has had the team reading through the NCCN Guidelines, WHO Guidelines and International… Read more »

Sneak Peek: Force Calling Reference Alleles

         September 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 pharmacogenomics pipelines with VarSeq, as it allows for inferring the… Read more »

VarSeq Annotation and Filtering Use Cases

         September 3, 2024

The following customer publications showcase the ability of VarSeq. Each study demonstrates the abilities of VarSeq’s annotation and filtering of variants and the ease of identifying with our software. Rare host variants in ciliary expressed genes contribute to COVID-19 severity in Bulgarian patients Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), a pneumonia with extremely heterogeneous clinical… Read more »

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

         August 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, and how they complement each other. The theme was how… Read more »

The Power of Phased Genotypes in Variant Analysis

         August 20, 2024
The Power of Phased Genotypes in Variant Analysis

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 diplotypes. In this blog post we describe how phased genotypes… Read more »

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

         August 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 to troubleshoot, whether due to a permissions block, a lack… Read more »

The Versatility of VarSeq: Local and Cloud Deployment Options

         August 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 cloud computing ecosystem. In the world of next-generation sequencing (NGS),… Read more »

Our New Pharmacogenomic Tutorial is Hot Off the Press!

         August 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. You can also follow this link. Like our other famous tutorials, this one will provide example data, or you may… Read more »

Pioneering Precision Medicine: Recent Publications Showcasing the Impact of VarSeq

         July 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 patients with acute coronary disease. Genetic factors influence interindividual variability… Read more »

A Hidden Gem Inside Golden Helix CancerKB

         July 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 anything but benign, but Golden Helix CancerKB has you covered… Read more »

VarSeq PGx inputs: Annotation Tracks Required for PGx Analysis

         July 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 annotation tracks utilized by the algorithm at each stage of… Read more »

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

         June 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 versatility of VarSeq in various research domains, from neurodegenerative diseases… Read more »

Where are my structural variant calls? – Highlighting the Breakends Table

         June 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 partners at PacBio will provide an additional VCF containing copy… Read more »

Plotting CNV Metrics in VarSeq

         June 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 the recent publication here: Analyzing Performance of Twist Bioscience Exome… Read more »

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 Bioscience Exome Enrichment with Spike-in CNV Backbone Panels at Various… Read more »