Tag Archives: VSClinical

When Negative Findings are a Good Thing to Report: Leveraging VarSeq’s VSClinical AMP

         May 25, 2023

Explore the importance of negative findings in genomic medicine through the lens of VarSeq’s VSClinical AMP. When analyzing a somatic sample in VarSeq, users have the option to report on several types of biomarkers with VSClinical AMP. In addition to your usual mutational biomarkers such as small variants, your copy number variants, and structural variants, we support the analysis of… Read more »

VarSeq 2.4.0 Has Been Released!

         May 24, 2023

Greetings VarSeq users! VarSeq 2.4.0 has officially been released. VarSeq 2.4.0 is a significant release that focuses on enhancing the VSClinical ACMG workflow by introducing new features and noteworthy improvements. The major highlights of the release are: 1. Welcoming structural variant support to the VSClinical ACMG workflow 2. ACMG workflow automation has been enhanced via the application of evaluation scripts… Read more »

Transitioning to Broad-Scale Genomics: From Gene Panels to Whole Genome Sequencing

         May 16, 2023

Explore the evolving landscape of genomic analysis, transitioning from targeted gene panels to whole genome sequencing. A recent trend with our customers has been to expand their workflows from small panel sequencing analyses to larger whole exome and genome sequencing analyses. The decreasing cost of sequencing has made this a rather common request. Although more data allows for a greater… Read more »

ACMG STRIKES BACK

         May 4, 2023

Use the force of evaluation scripts to automate and customize your VSClinical ACMG workflow in VarSeq 2.4.0. VarSeq 2.3.0 came packed with new features! Most notably, VarSeq variant analysis expanded to support the import and annotation of structural variant files, and the AMP cancer workflow in VSClinical gained new functionality with the addition of evaluation scripts which help automate and… Read more »

Managing the Scope of Somatic Variants Reported in VSClinical

         April 13, 2023
Managing the Scope of Somatic Variants Reported in VSClinical

Discover the power of VSClinical’s Interpretation Match Behavior options for managing the scope of somatic variants in cancer reporting, enabling clinical teams to make informed treatment decisions. Multiple interpretations can apply to a single biomarker or tumor type. In some circumstances, a clinical team may only want to report the most relevant and significant biomarker, treatment, diagnosis, or prognosis interpretations… Read more »

WES Prenatal Workflow Examples: Exploring Duchenne Muscular Dystrophy, Gaucher Disease, and Fabry Disease in Genetic Screening

         April 11, 2023

Discover powerful WES prenatal workflow examples showcasing the detection of Duchenne Muscular Dystrophy, Gaucher Disease, and Fabry Disease through advanced genetic screening techniques. Our recent Prenatal Genetic Screening with VarSeq webcast focused on using whole exome sequencing for prenatal genetic analysis. This webcast was a hit with our customers, who asked for more information on different filtering chains to identify… Read more »

Unraveling the Genetics Behind Orofacial Clefts and Achromatopsia: Two Inspiring Studies Using Golden Helix Products

         March 30, 2023
Discover how Golden Helix products contribute to groundbreaking research on orofacial clefts and achromatopsia, showcasing their versatility in advancing our understanding of these rare genetic conditions.

Explore how Golden Helix products aid groundbreaking studies on orofacial clefts and achromatopsia, showcasing their versatility and enhancing our understanding of these rare conditions. We are always humbled and thrilled to learn how Golden Helix products are being used in the arena of human genetic testing.  This month is no exception, as we showcase two very interesting studies.  In the… Read more »

Maximizing Structural Variant Detection with Soft Clip Visualization

         March 27, 2023

Discover how soft clip visualization can help you identify structural variants in your research and improve the accuracy of your findings. Soft clipping is a common technique in sequence alignment used to remove bases from the ends of reads that do not align with the reference sequence. Removing these bases typically improves alignment accuracy. However, when multiple reads are soft… Read more »

Prenatal Genetic Screening with VarSeq Webinar Highlights

         March 16, 2023

Explore the cutting-edge capabilities of VarSeq in prenatal genetic screening as we delve into real-life cases, expert analysis, and efficient strategies to quickly assess Whole Exome Sequencing (WES) samples for genetic abnormalities in our recent webinar. Thank you all to those who attended our VarSeq webinar covering prenatal genetic screening! We had a great turnout and loved hearing from our… Read more »

Decoding Complex Fusion Representations: A Deep Dive into VCF Breakend Notation and its Impact on Gene Analysis

         March 14, 2023
Decoding Complex Fusion Representations A Deep Dive into VCF Breakend Notation and its Impact on Gene Analysis Icon

Unlocking the intricacies of fusion representations is crucial for understanding the impact of complex genetic rearrangements on gene function and disease development. In the most recent release of VarSeq, we added support for the import of complex rearrangements from VCF files, which typically encode rearrangements using breakend notation. This powerful notation is capable of describing the full spectrum of structural… Read more »

VarSeq Customization and Automation with VSCode

         March 9, 2023
VarSeq Customization and Automation with VSCode Blog

Enhancing VarSeq Customization and Automation with Visual Studio Code: A Guide to Evaluation and Reporting Scripting Are you as excited as we are about the new automation and customization features we’ve been rolling out with VarSeq’s most recent release, VarSeq 2.3.0? Do your eyes light up at the prospect of automated integration of various data sources into VarSeq’s evaluation and… Read more »

Revolutionizing Whole Exome Sequencing: VarSeq Powers Complex Analysis Data in Recent Publications!

         February 23, 2023
Revolutionizing Whole Exome Sequencing VarSeq Powers Complex Analysis Data in Recent Publications! icon

Recent publications have highlighted how Golden Helix’s VarSeq suite of products is enabling researchers and clinicians to conduct complex whole exome sequencing studies, once considered ‘out of reach,’ with ease and precision, resulting in the discovery of new biomarkers and personalized treatment options. It is always with pride that we feature recent publications citing Golden Helix software; this month is… Read more »

Automated FASTQ to Reports with VarSeq Suite: A fast, flexible solution

         February 16, 2023
Automated FASTQ to Reports with VarSeq Suite

Discover the Thrilling Automation Capabilities of VarSeq Suite for NGS Testing and Learn How We’re Tackling Contemporary Lab Challenges First off, I’d like to thank everyone who joined us for our February webcast on the automation capabilities of the VarSeq software suite through VSPipeline. For those of you who joined us, I’m sure it’s obvious that automation is a topic… Read more »

Unlocking Clinical Evidence: A Deep Dive into the Supporting Data Sources of VSClinical AMP Workflow

         February 7, 2023
Unlocking Clinical Evidence: A Deep Dive into the Supporting Data Sources of VSClinical AMP Workflow Icon

Discover the innovative clinical evidence search of the VSClinical AMP workflow, where patient biomarkers and tumor types are matched to the most relevant data from top sources like CIViC, DrugBank, and Clinical Trials. One of the core features of the VSClinical AMP interpretation workflow is the ability to search third-party data sources to find clinical evidence that matches the patient’s… Read more »

Maximizing Cancer Care with Golden Helix CancerKB 2.0: Unveiling the Latest in Precision Medicine

         January 26, 2023
Maximizing Cancer Care with Golden Helix CancerKB 2.0 Unveiling the Latest in Precision Medicine icon

Our recent webcast, Maximizing the Benefits of Comprehensive Genomic Testing in Cancer Care with Golden Helix CancerKB 2.0, was an opportunity to unveil Golden Helix CancerKB v2.0. Our latest VarSeq release was designed to address the changing landscape of cancer genomics, and in this webcast, we discussed the application of our very own Golden Helix CancerKB in the context of… Read more »

AMP Manual Deep Dive: VSClinical’s Interpretation for Cancer Biomarker Annotation

         January 24, 2023

VSClinical AMP Matching of Interpretations  In this blog post, we will delve into the intricacies of the VSClinical AMP interpretation workflow. At the heart of this process lies the task of annotating cancer biomarkers with the correct interpretations based on the classification of the tumor and the type and scope of the biomarker. This is a crucial step in understanding… Read more »

VarSeq 2.3.0: A Comprehensive Look at the Revolutionary Cancer Genomic Profiling Solution’s New Features and Advancements

         January 18, 2023

Discover the latest advancements in cancer genomic profiling with the release of VarSeq 2.3.0 We are very excited to announce the release of VarSeq 2.3.0! This release was one of the largest VarSeq releases yet, as it includes a large refactor to the VSClinical AMP cancer module. A primary motivation for the release was focused on the availability and increased… Read more »

Exploring the CRAM File Format in VarSeq 2.3.0

         January 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 Map) by only storing the differences between each read and… Read more »

Improve Your Research with the Latest Cancer Ontology Updates

         January 10, 2023

Learn about the latest cancer ontology software updates and how they can enhance your research and work. Cancer Ontology An important feature of the VSClinical AMP workflow is the ability to select the correct tumor type for a given evaluation. The selected tumor type is used to identify relevant clinical evidence, including drug sensitivities, resistances, and previous biomarker interpretations. This… Read more »

4 Essential Support Resources for Golden Helix Software Users

         January 5, 2023
4 Essential Support Resources for Golden Helix Customers BLOG Image

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 »