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 »
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 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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
