Up until a few weeks ago, I thought variant classification was basically a solved problem. I mean, how hard can it be? We look at variants all the time and say things like, “Well that one is probably not too detrimental since it’s a 3 base insertion, but this frameshift is worth looking into.” What we fail to recognize is… Read more »
SVS 7.6.7 features new tools for filtering sequencing data based on functional predictions and allele frequencies. To complement these new features, new annotations tracks have been uploaded to our data server and are now available for our customers! Below you will find descriptions of the new tools and the related annotations track(s).
At Golden Helix, we’re proud to see how VarSeq is transforming the landscape of genetic research and clinical diagnostics. From variant annotation and filtering to in-depth visualization, VarSeq’s powerful suite of tools helps researchers uncover critical genetic insights with confidence and efficiency. In this blog post, we’re excited to showcase recent publications where VarSeq played a pivotal role in identifying… Read more »
We are excited to announce the addition of CADD 1.7 as an annotation track in VarSeq. The latest release of CADD incorporates a variety of new annotations into its model, resulting in significant improvements in variant scoring. This includes the integration of Meta ESM scores and improved performance on non-coding variants. Meta AI Evolutionary Scale Model One of the most… Read more »
Next-generation sequencing (NGS) has transformed our ability to detect the genetic causes of diseases. VarSeq is a key tool in this process because it helps users sift through large numbers of genetic variants to find those most likely to cause or contribute to disease. The below publications have demonstrated VarSeq’s usefulness in discovering new gene variants related to neurodevelopmental disorders,… Read more »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
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 »
VarSeq enables users to import structural variants for annotation, filtration, and subsequent clinical or other analyses. Structural variants are often called during secondary analysis as belonging to two broad categories – Copy Number Variants (CNVs) with the file suffix “…_CNV.vcf” and Breakends with the file suffix “…_SV.vcf”. This blog will give some insight into how structural variants are triaged when… Read more »
In this blog post, we will explore the nuances of variant calling and import in the context of VSPGx. We will discuss the importance of integrating must-call variant definitions into the calling processes and provide guidance on incorporating copy number variants (CNVs) and structural variations (SVs) into your PGx analysis workflow. Must Call Variant Files To ensure the optimal performance… Read more »
