When a variant shows up as rare in the general “healthy” population, as indicated by low frequency or absence in one or more commonly referenced population catalogs such as GnomAD Exomes or 1000 Genomes, this indicates by proxy that the variant may be pathogenic. However, several factors determine the frequency threshold below which a variant is considered rare enough to… Read more »
How long did it take to run coverage regions? Did my colleague update the filter chain like he said he would? Which import options did I use? Where did I save this project? These questions and more can be answered with our little-used VarSeq Log tab. Periodically, our customers come to us with questions in the realm of record keeping,… Read more »
Get your year started off right with Golden Helix’s new VarSeq Onboarding and Training Program! Analysis of NGS data comes with several challenges, but mastery of the data analysis software does not have to be one of them. With this in mind, Golden Helix is pleased to announce that VarSeq Onboarding and Training tools are now available to all our… Read more »
Last month, the researchers at Google DeepMind announced the release of AlphaMissense, a new missense prediction algorithm that leverages the protein structure prediction model AlphaFold to distinguish between benign and pathogenic missense variants (Cheng et al., 2023). AlphaFold is a model for the prediction of protein structures from amino acid sequences. During the development of AlphaMissense, the AlphaFold model was… Read more »
Discover how to enhance collaboration in VSClinical by sharing variant scores and assessment catalogs through the strategic relocation of the AppData folder. A subtle but powerful utility of VSClinical concerns the ability to share variant scores between users on the same account. What I mean by that is, leveraging the location of the AppData folder, so that users are writing… Read more »
Unlocking the Potential of CRAM Files: The New VarSeq 2.3.0 Release for Enhanced Plotting, Coverage Analysis, and CNV Detection The CRAM (Compressed Reference-oriented Alignment Map) file format was conceived in 2011 as a more space-efficient way to store alignment data. It saves space over the previous standard BAM (Binary Alignment Map) by only storing the differences between each read and… Read more »
Golden Helix provides extensive resources to help our users who are just getting started and address any issues they may encounter as they become more familiar with our software. Our resources are constantly updated and are tailored to the needs of our users. If you’re facing a problem, it’s likely that others have encountered it as well, and we’ve included… Read more »
Thank you to those who attended the recent webcast, “High Precision Exome CNV Detection with VS-CNV”. For those who could not attend but wish to watch, here is a link to the recording. This webcast delved into the complex world of CNV calling for whole-exome samples, which presents unique challenges that require specific considerations and strategies. Over the past several months,… Read more »
Webcast Recap In the recent webcast “Exploring New Features and Clinical Reports in the ACMG Guideline Workflow”, Gabe and I took viewers through an evaluation with CNVs and SNVs according to the ACMG Guidelines where we generated and customized a clinical report. Along the way, we highlighted many new features that will soon be available in the upcoming VarSeq release…. Read more »
Thank you to everyone who joined our webcast, “Whole Genome Trait Association in SVS.” If you missed the live event and are interested in knowing what we talked about, you may access the recorded event below: Our Live Q&A generated a lot of great questions. Unfortunately, we were unable to answer them all, but we have compiled some of the… Read more »
Thank you all for tuning in to yesterday’s webcast, “Simplify Your GWAS & Genomic Prediction with SVS”. I hope you all enjoyed it as much as I did! If you didn’t get a chance to join us for this live webcast, you can watch the recording below. We covered a lot of topics in so little time, but you all… Read more »
This webcast generated some great questions! If you have any other questions for me that are not answered below, please feel free to ask those by emailing [email protected]. To what level does the Warehouse scale? We have tested multiple instances of Warehouse in-house and on the cloud and it scales incredibly well to tens of thousands of samples and 100s… Read more »
In my recent webcast, I demonstrated how VS-CNV users can detect high-quality copy number variant events. If you didn’t have a chance to join, you can view the recording below! This webcast generated a lot of great questions! If you have any other questions about the content covered in this webcast that is not answered below, please feel free to… Read more »
Our “Processing Hereditary Cancer Panels in VarSeq” webcast was a great lesson for viewers to learn more about the functionality of our software. If you didn’t have a chance to join us for the live event, you can watch the recording on our site here. Q: What is the best place to get clinical interpretations of breast cancer variant interpretations?… Read more »
In our previous webcast, we discussed the splice site algorithms for clinical genomics within VSClinical. We took it a step further in yesterday’s webcast and looked at the functional predictions and conservation scores. We had a great turnout for this event with lots of great questions from the attendees. I’d like to recap our Q&A for anyone else who might… Read more »
This week we launched VSClincial with our first webcast to show our powerful new way to perform variant interpretation following the ACMG guidelines. Our audience asked a lot of great questions on the new product and I’d like to highlight a few here. Can VSClinical run on a laptop and/or a locked down environment? Like all of Golden Helix products, you have… Read more »
Sentieon TNscope is a platform dedicated to the identification of tumor-normal somatic variants including single nucleotide variation (SNV), indel, as well as structure variations (SVs). In our recent webcast, Dr. Donald Freed, Bioinformatics Scientist at Sentieon, gave viewers an exclusive overview of the platform. The webcast generated a lot of great questions which I would like to share with you… Read more »
First-place Abstract Competition Winner, Michael Iacocca, shared his research with the Golden Helix Community during our February webcast ‘Using NGS to detect CNVs in familial hypercholesterolemia‘. In this webcast, he gave a great explanation on how our CNV caller aided his team in their research. If you were unable to join us for the event, you can find a recording… Read more »
Yesterday’s webcast, Genomic Prediction Methods in SVS, gave attendees a chance to see how the principles of genomic prediction are applied within SVS, predicting phenotypes for both plant and animal species. You can find a recording of the webcast on our site here should you be interested in checking it out or sharing with a colleague! The webcast garnered a… Read more »
This month we hosted two, incredible webcasts officially announcing the latest CNV annotation capabilities our Software Engineering Team has been hard at work on for the past couple of months. Our first webcast, Comprehensive Clinical Workflows for Copy Number Variants in VarSeq, was presented by Golden Helix’s VP of Product & Engineering, Gabe Rudy, who reviewed the expanded capabilities of… Read more »
