Thank you to those who attended our webcast on the user perspective of our automated AMP guidelines! Furthermore, let me express our appreciation for those particularly engaged users who posed some very thoughtful questions. While we weren’t able to answer all of them live, I hope to shed some light on some pertinent details of somatic analysis here. Let’s start… Read more »
Manually converting FASTQs to VCFs, importing these into VarSeq, and building projects from scratch is adequate when you have only a handful of cases per week. But as you start ramping up production, the key to your lab’s success quickly becomes how quickly and efficiently you can get to the reporting of your analysis. This blog will explain how you… Read more »
Next-gen sequencing (NGS) comprises many sophisticated steps that are often compressed into three major sections: library prep, sequencing, and data analysis. Obviously, the goal is to simplify each of these steps, but more often than not, there is a need for multiple tools to complete each one. Regarding the data analysis, Golden Helix seeks to provide simple yet comprehensive solutions… Read more »
One of the inherent realities of next-generation sequencing is the ongoing updates to the human reference genome—one of the strongest recommendations to take the original sequencing data and remap to the latest genome assembly. However, there are several reasons why remapping may be impractical. So, an alternative solution is needed to convert the data running through an initial mapping to… Read more »
I want to take this opportunity to highlight and briefly discuss some of the key features and updates that have been incorporated into VarSeq 2.2.3. Some of you may have attended the webcast that covered the prominent new features added to VarSeq, which are the updates to improve whole-exome analysis workflows, namely improved CNV calling in whole-exome datasets. However, there… Read more »
Didn’t catch the webcast live? No worries! We cover ‘VSClinical: A Complete Clinical Workflow Solution’ Q&A’s in this blog post. The webcast, ‘VSClinical: A Complete Clinical Workflow Solution’ demonstrated how solutions provided by Golden Helix can be implemented to cover all requirements of a clinical workspace. Specifically, this webcast focused on a detailed workflow from a bioinformatician, geneticist, and lab… 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 »
Golden Helix has been committed to making sure our community has the tools and resources they need during this pandemic. We have developed several different assistance programs, such as our home office licenses for current users and our software discounts for COVID-19 related projects, to name a few. We have been approached by a number of labs not working with COVID-19… Read more »
VarSeq 2.2.1 was released on April 1st and features an upgraded gene annotation capability with new RefSeq genes tracks and an AMP workflow addition: the Drugs and Trials tab. The new RefSeq human genome genes tracks contain updated gene names and the recognition of any MANE (Matched Annotation from NCBI and EMBL-EBI) identified transcripts. VarSeq has been updated to be… Read more »
Thank you to everyone who joined me for yesterday’s webcast, I hope you all enjoyed it. If you missed the live event and are interested in knowing what we talked about, good news, you can watch the recorded version right here! There were so many great questions asked during our Live Q&A that I was unable to answer all of… Read more »
Introducing Drugs & Trials for Cancer Diagnostics VSClinical offers enormous simplicity and consistency in evaluating biomarkers and providing treatment options. Last month, we announced our newest feature to now include the automated collection of relevant clinical trials. The new capability was unveiled in our “Introducing Drugs & Trials for Cancer Diagnostics” webcast with Nathan Fortier, Ph.D., Director of Research, showing… Read more »
Golden Helix is in a unique position to provide a secure on-premise analysis solution. This capability is based on two enablers. First, we build our software solutions from scratch and from the ground-up with the assumption that it should run on any operating system and potentially behind firewalls or even without internet access. Second, we provide these solutions on a licensing model based on training and supporting users, not… Read more »
As clinical genetic tests have been adopted as a critical enabler of precision medicine, the number of tests offered by clinical labs and the volume of tested patients has grown by orders of magnitude in the past five years. The Gene Testing Registry, managed by the NIH, documented a rise from 13,000 to 60,000 tests offered in the US market… Read more »
We have covered a lot of ground in this Automating & Standardizing Your Workflows blog series. First, we saw how to perform secondary analysis with Sentieon to generate the necessary VCF and BAM files for tertiary analysis in Part I. The implementation of VSPipeline allowed for rapid import and project generation for a predefined cancer gene panel project template in… Read more »
In our last part of this series, we showed how to run a pre-built workflow template via VSPipeline to automatically import and filter sample variants to streamline the search for clinically relevant variants. Now, we can deep-dive into our filtered, pathogenic variants to fully understand and capture their final classification and interpretation. Filtered Germline Variants for ACMG Guidelines The VSPipeline… Read more »
VSPipeline: Automating your Tertiary Workflows The first part of this “Automating & Standardizing your NGS Workflow” blog series covered the secondary analysis steps of read alignment and variant calling with Sentieon. The next step is to transition into the tertiary analysis via utilization of our workflow automation tool, VSPipeline. VSPipeline operates as a command-line tool meant to simplify the deployment… Read more »
Secondary Analysis with Sentieon: Rapid and Accurate Variant Calling This blog post will cover the utilization of secondary analysis tools to produce a list of high-quality variants and associated coverage data. This data will serve as the main, importable content for the tertiary stage of analysis where variants are interpreted and classified for their impact on a patients’ disorder. We… Read more »
As our regular customers may know, we write our blogs to provide relevant content to any NGS-based analysis with VarSeq. Our goal here at Golden Helix is to provide top quality software and guidance on how to use the software efficiently to perform variant analysis. However, this blog series will take a more general perspective and supply some insight into… Read more »
In the previous two articles, we explored the different steps of a clinical workflow. The first post covered the automated analysis that creates a VarSeq project. While the second post covered the interpretation steps and generation of a clinical report. These posts illustrated the ease with which these complex tasks can be carried out. Today we’ll dig a little bit… Read more »
Automating a clinical workflow creates a stable and repeatable clinical analysis. Automation reduces the potential to introduce human error, helps in regulatory compliance, and improves the precision of the clinical results. It is important to know that if you run a sample through your clinical pipeline, you are going to get the same results today as you will in 6… Read more »
