Search Results for: Catalog

What’s Coming to VSClinical: Expanded Clinical Trial Search Results

         May 17, 2022
Expanding-Clinical-Trial-Search-in-VSClinical

While the interpretation of germline variants generally focuses on the pathogenicity of a variant for a specific disease, the interpretation of somatic variants is centered around each variant’s impact on clinical care. As a result, clinical trials play an important role in assessing the clinical significance of somatic biomarkers, with the AMP Guidelines assigning a higher level of evidence to… Read more »

VarSeq Template Design Recommendations: Single Sample Variant Filtering

         April 6, 2022

When doing next-generation sequencing (NGS) analysis in VarSeq, the fundamental goal is to develop efficient ways to filter through your NGS data. If you are just getting started with Varseq, a pre-designed project template can really come in handy for variant filtering! This blog series will cover a number of template design recommendations for variant filtering on data types ranging… Read more »

Review of VarSeq Export Options

         March 10, 2022
varseq export options

Although best known for its auto-generation of custom reports, VarSeq comes with a slew of options for exporting your data. In this blog, we will review some of the lesser-known methods for exporting your data into usable formats. These four export options can all be found under the Export tab at the upper left corner of your VarSeq interface (Figure… Read more »

Highlights from Advanced Report Customization in VSClinical Webcast: Somatic Reports

         January 6, 2022
advanced somatic report customization in vsclinical

In our previous blog, we covered the highlights of our Advanced Report Customization in VSClinical webcast in the context of germline clinical reports. Now, we bring you the next of the series: somatic clinical reports. In the recent webcast, Advanced Report Customization, we covered a range of somatic-focused clinical reports, demonstrating how easy it is to create AMP guideline-based clinical… Read more »

Reviewing Clinical Studies for Novel Splice Variants in VSClinical

         October 12, 2021
DNA spliced site

In order to thoroughly assess a variant’s pathogenicity, it is important to take into account the variant’s effect on splicing. While the interpretation of variants that disrupt the pairs of bases at the beginning of a splice site is fairly straightforward, variants resulting in the introduction of a novel splice site are more difficult to interpret. In this blog post,… Read more »

Customized Reports in VSClinical with New Output Types

         September 23, 2021

Golden Helix VSClinical provides a guided workflow interface for following the ACMG and AMP guidelines to evaluate variants and CNVs for NGS tests. The output of this work is most often a lab-specific clinical report. Since it was introduced, we have provided a powerful Word-based templating system to allow labs the ability to generate customized reports to include specific content… Read more »

Updates to ClinVar Curation to Include More Pathogenic Variants

         September 14, 2021

In the September 2021 monthly update to our curated ClinVar track, we made some changes that will result in roughly another 7,000 Likely Pathogenic and Pathogenic variants being available for annotation and use in the ACMG auto-classification system.  Consensus Between Labs  ClinVar has nearly one million unique variant classification records that are curated into multiple annotation tracks used in VarSeq and VSClinical on a monthly basis. Clinical… Read more »

How a neonate’s rash can be one of your most important pieces of data: making phenotypic info statistically tractable for clinical diagnostics

         August 5, 2021

I remember visiting a patient in the NICU amongst the incubators, some glowing blue like tiny tanning beds to treat jaundice, all containing tiny humans – many smaller than a loaf of bread. Infants get admitted into the neonatal intensive care unit or NICU for many reasons ranging from elevated bilirubin, hypoglycemia, sepsis, and respiratory distress (RDS). Many are eventually… Read more »

Golden Helix’s Next-Gen Sequencing Data Analysis Solutions Explained

         June 22, 2021
VSClinical algorithm

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 »

VSPipeline Best Practices

         June 17, 2021

VSPipeline is becoming a very popular tool among VarSeq users as it is essential for creating repeatable clinical workflows that can be executed in automated fashion. Since VSPipeline is a command-line tool, I think it would be helpful to discuss some of the best practices along with helpful tips for getting the most out of VSPipeline.   Some of you may be less familiar with VSPipeline, so I want to cover how to set up the first run along with sharing the helpful tips as they arise.  … Read more »

Variant Filtration and Interpretation

         June 3, 2021

I learned about Batten disease from a childhood friend’s Facebook post. Over the course of a few months, her 8-year-old, Eva, the oldest of 4 daughters – Emily, Lucy, and Carly – was rapidly going blind. Baffled, doctors ran a genetic panel that returned a devastating result – the diagnosis of Juvenile Neuronal Ceroid Lipofuscinosis or Batten disease. A broad… Read more »

VarSeq NGS Workflow Design: Clinical vs. Research

         April 22, 2021
NGS Clinical Research

In many cases, VarSeq users design their next-gen sequencing workflows for a clinical application. One of the major values of using VarSeq is the standardization of sample analysis via project templates for filtering down to rare variants and isolate any clinically relevant variant. However, VarSeq also doubles as a robust research application as well. There are specific algorithms that can… Read more »

Using Gene Preferences in VarSeq and VSClinical

         April 20, 2021

With the latest release of VarSeq, we have made significant updates to our handling of the interaction of variants and genes. This includes the support for non-coding transcripts, improved splice site predictions, and updates to gene and transcript annotations. We received several questions regarding how decisions are made in the software regarding genes and transcripts with these gene-related changes. This… Read more »

GenomeAsia 100K Variant Frequency Annotation

         March 30, 2021
genomeAsia

The GenomeAsia 100K Variant Frequency database is a pilot annotation source now available to our users. This valuable database offers a deep characterization of specific populations in Asia that can be used to drive genetic studies. GenomeAsia is comprised of whole-genome sequencing data of over 1,000 individuals from 219 populations across Asia. Using this as an annotation, users can analyze… Read more »

Webcast Recap: VSWarehouse: Tracking Changing Variant Evidence and Classifications

         March 11, 2021
VSWarehouse

Thank you to those who attended the recent webcast, “VSWarehouse: Tracking Changing Variant Evidence and Classifications”. For those who could not attend but wish to watch, here is a link to the recording. The webcast covered some general highlights of VSWarehouse value but also presented some specific capabilities covering the ClinVar classification tracker. Golden Helix provides complete solutions to handle… Read more »

Implementation of ClinGen Dosage Sensitivity in VSClinical

         March 4, 2021
Clin Gen CNV

The collaboration between the Clinical Genome Resource (ClinGen) consortium and the American College of Medical Genetics (ACMG) recently developed published guidelines for the interpretation of CNVs called on next-generation sequencing data. These new guidelines are the first to provide a robust set of rules for the interpretation of small intragenic deletions and duplications and are now automated in VSClinical.  … Read more »

Webcast Recap: Family-Based Workflows in VarSeq and VSClinical

         February 13, 2021
screen shot from webcast

Thank you for attending the webinar focused on implementing VarSeq and VSClinical for family-based workflows. If you would like to use the webinar as a reference or were not able to attend, you can access it using the following link to view ‘Family-Based Workflows in VarSeq and VSClinical. Here is a brief recap of what we discussed: This webinar demonstrated… Read more »

January 2021 Publications

         January 28, 2021
Customer Publications

New discoveries using NGS data analysis are never-ending and are pushing precision medicine to the forefront. In this month’s customer publication blog, I am focusing on our VarSeq software as investigators harness its power to perform a variety of investigational study designs. From cancer to inherited rare disease research, VarSeq is the rising star in research and diagnostic tools. At… Read more »

New Feature in VarSeq: Latest Sample Assessment Algorithm

         January 26, 2021

In continuation of our blog posts focusing on new features of VarSeq v2.2.2, here we will discuss the Latest Sample Assessment algorithm for both single nucleotide variants (SNVs) and copy number variants (CNVS). This algorithm annotates the variants of the project with the latest assessment from your variant catalog, which will show the history of interpretations made for the variants… Read more »

VarSeq 2.2.2 Release Notes

         December 23, 2020
ClinVar

VarSeq 2.2.2 was released on December 17th, 2020 and the main feature that was added to VarSeq was that the VSClinical ACMG Guidelines workflow now has an additional CNV interpretation framework based on the ACMG/ClinGen guidelines. This product supports interpreting CNVs detected with VS-CNV or imported CNVs alongside variants and requires both a VSClinical ACMG license and a CNV license…. Read more »