Customer Questions

From the Inbox: Leveraging the Transparency and Flexibility of VSClinical for ACMG Guidelines

Mar 19, 2024

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…

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The Log Tab in VarSeq

Jan 11, 2024

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…

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VarSeq Onboarding and Training Program Now Available!

Jan 4, 2024

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…

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Evaluating DeepMind’s AlphaMissense Classifier

Oct 20, 2023

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…

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Moving the AppData Folder – A Look At Sharing Assessment Catalogs

Jul 3, 2023

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…

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Exploring the CRAM File Format in VarSeq 2.3.0

Jan 17, 2023

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…

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4 Essential Support Resources for Golden Helix Software Users

Jan 5, 2023

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…

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Webcast Recap: High Precision Exome CNV Detection with VS-CNV

May 7, 2021

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…

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Webcast Recap: Exploring New Features and Clinical Reports in the ACMG Guideline Workflow

Dec 3, 2020

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…

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Webcast Recap: Whole Genome Trait Association in SVS

Jul 21, 2020

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…

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GWAS & Genomic Prediction Webcast Q&A

Dec 5, 2019

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…

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Storing your Copy Number Variant & ACMG Results in VSWarehouse – Webcast Q&A

Oct 11, 2018

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…

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Using VS-CNV to Detect High-Quality Copy Number Variant Events

Sep 14, 2018

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…

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Processing Hereditary Cancer Panels in VarSeq: Webcast Q&A

Aug 16, 2018

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…

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Functional Predictions & Conservation Scores in VSClinical

May 17, 2018

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…

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VSClinical Webcast Q&A

Apr 20, 2018

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…

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Exclusive Look at Sentieon TNscope Q&A

Mar 1, 2018

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…

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Using NGS to detect CNVs in familial hypercholesterolemia Q&A

Feb 19, 2018

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…

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Genomic Prediction Methods in SVS Q&A

Dec 14, 2017

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…

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All of your VS-CNV annotation questions answered

Oct 12, 2017

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…

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