VSWarehouse 3 as an Integration Platform

         December 5, 2024

Following up on our recent post about VSWarehouse 3’s Bring Your Own Cloud capabilities, we wanted to dive deeper into one of its most powerful features: our comprehensive workflow system. This system is designed to streamline genomic analysis pipelines while providing flexible integration with various cloud genomics providers. Understanding VSWarehouse 3 Workflows At its core, VSWarehouse 3’s workflow system is… Read more »

How Customers Are Using VarSeq to Drive Genetic Discoveries

         December 4, 2024

Golden Helix customers are at the forefront of genetic research, using VarSeq to tackle some of the most challenging questions in genomics. From identifying novel variants to uncovering the genetic basis of rare diseases, their work showcases the power of VarSeq in real-world applications. In this blog, we’re highlighting three recent publications that demonstrate how customers are using VarSeq to… Read more »

Complex Variants for Acid Reflux, Right in Time for Thanksgiving!

         November 26, 2024

It’s the big day, and you’ve spent hours preparing for the big old-fashioned family Thanksgiving. Keeping in mind that your Cousin Eddie likes to show up unannounced and eat you out of house and home, you have remembered our food allergy allele workflow from last year, and prepared a special menu. Right on time, Cousin Eddie arrives, family in tow…. Read more »

Webcast Follow-Up: Answering Your Questions on VSWarehouse 3 and Bring Your Own Cloud

         November 21, 2024

Thank you to everyone who attended our recent webcast, Bring Your Own Cloud: Clinical Testing at Scale with VSWarehouse 3. We’re thrilled about the level of engagement during the Q&A session and wanted to take the opportunity to elaborate on some of the key questions asked. Here’s a recap of the answers: 1. Is it more expensive to run on… Read more »

Golden Helix CancerKB 4.0 is Officially Released!

         November 19, 2024

Just in time for the holidays, CancerKB 4.0 is now available to incorporate into your cancer analysis workflows! We have termed this release “The Hematological release” as we boast of complete coverage of the NCCN Guidelines recommended therapies and FDA-approved therapies for all hematological cancers in our Drug Sensitivity Interpretations. We have also reviewed and synthesized the consensus from the… Read more »

Don’t Miss MITOMAP for Mitochondrial Variant Analysis in VarSeq

         November 12, 2024

Mitochondrial diseases, caused by mutations in mitochondrial DNA (mtDNA), represent a complex and diverse group of disorders. These conditions often affect organs with high-energy demands, such as the brain, heart, and muscles. Identifying mitochondrial DNA variants and understanding their clinical relevance is essential for diagnosing and treating these diseases. One of the most valuable resources in mitochondrial variant analysis is… Read more »

Golden Helix at AMP 2024: Advancing Precision Oncology and NGS Analysis

         November 12, 2024

Golden Helix is excited to announce our attendance at AMP 2024 in Vancouver, British Columbia, from November 21 to 23. Visit booth #1511 to discover how our latest advancements in cancer capabilities, automation, and clinical diagnostics can transform your genomic workflows and precision medicine applications. Live Demos: Experience the Latest Innovations Stop by our booth to see Golden Helix solutions… Read more »

Exploring Publicly Available NGS Data Sources

         October 31, 2024

Publicly available datasets play a crucial role in research and offer resources for validation and benchmarking of workflows. In this blog, I would like to point out and briefly discuss several notable, publicly available sources of NGS sequencing data. Each of these sources provides validated datasets that are invaluable for laboratories and institutions processing NGS samples. EPI2ME is an advanced… Read more »

Golden Helix at ASHG 2024: Come Say Hi and Check Out Our Latest Innovations!

         October 29, 2024

Guess what, Golden Helix users and interested parties? We will be front and center at the ASHG 2024 Annual Meeting in Denver, Colorado, from November 6-8—and we’ve got a ton to share with you. If you’re attending, make sure you swing by booth #959 because we’re bringing some great new information on our latest updates that are going to take… Read more »

Showcasing VarSeq: Empowering Groundbreaking Genetic Research

         October 29, 2024

Our VarSeq software continues to support cutting-edge research, enabling scientists worldwide to explore the depths of genetic variants with precision and accuracy. In this blog, we highlight recent publications that leveraged VarSeq for impactful discoveries in pharmacogenomics and familial cancer studies, showcasing the vital role of our tools in advancing personalized medicine and genetic research. Thai pharmacogenomics database −2 (TPGxD-2)… Read more »

Efficient Quality Control tools for an automated VarSeq pipeline

         October 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 further elucidate on how QC methods fit into the picture…. Read more »

GnomAD 4.1 Released: Improved Allele Frequency Data for VarSeq Users

         October 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 into the VarSeq data source library, we provide users with… Read more »

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

         October 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 external cancer kits in the form of a Genomic Signature,… Read more »

VarSeq 2.6.2 is Released!

         October 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 also talk about other exciting features and new algorithms that… Read more »

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 »