Golden Helix Blog

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

Jun 22, 2021

Next-gen sequencing (NGS) comprises many sophisticated steps that are often compressed into three major sections: library prep, sequencing, and data analysis. Understanding each stage of NGS data analysis is essential for building efficient clinical workflows. Obviously, the goal is to simplify each of these steps, but more often than not,…

Read more →

VSPipeline Best Practices

Jun 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, supporting everything from variant filtering to clinical reporting. 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…

Read more →

Harmonizing Next-Generation Sequencing Data: VarSeq Liftover Tool

Jun 15, 2021

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…

Read more →

Highlights from our PhoRank 2.0 Webcast

Jun 10, 2021

Thank you to those who attended our recent webcast, “PhoRank 2.0: Improved Phenotype-Based Gene Ranking in VarSeq”. For those who could not attend, you can find a link to the recording here. This webcast covered upcoming improvements to the PhoRank phenotype-based gene ranking algorithm based on literature published in the…

Read more →

A Simple Guide to Curating Genome Assemblies

Jun 8, 2021

A common feature request from Golden Helix customers is to curate and make available genome assemblies for different plant and animal species. These requests commonly come from SVS users as many research projects are being carried out, and having the genome assembly available for analysis is essential. That being said,…

Read more →

Variant Filtration and Interpretation

Jun 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…

Read more →

Importing CNVs using VSPipeline

Jun 2, 2021

VSPipeline is a command-line interface that will provide high throughput environments the ability to tap the full power of VarSeq’s algorithms and flexible project template system from any command-line context, including the existing bioinformatics pipeline. This feature is a great resource for analyzing large sample volumes as it automates importing…

Read more →

Customer Publications – May 2021

May 25, 2021

In this month’s customer publications blog, both of our flagship software platforms are shown hard at work to cover many scientific investigational topics. You will get a glimpse of how VSClinical can be used to dive deeper into a specific gene associated with breast cancer and how SVS is enabling…

Read more →

Easily Edit Algorithms in VarSeq Projects with a Quick Right-Click

May 20, 2021

Thanks for checking out this blog on how to to get more out of your VarSeq projects! The best way to show off one of my favorite new features that have been incorporated into the latest VarSeq 2.2.3 release is with a scenario: You work in a lab that processes…

Read more →

VS-CNV Updates in VarSeq v2.2.3

May 18, 2021

Golden Helix has just released VarSeq v2.2.3. In this update, there are notable changes that can improve CNV calling capabilities covered in this webcast. The topics discussed included: Accounting for GC content Improvements to CNV quality flags Using target filtering Updates to the CNV sensitivity and precision settings This blog…

Read more →

Case Study – Hannover Medical School

May 11, 2021

Dr. Auber is the team leader for the molecular genetic diagnosis of hereditary diseases at the Institute for Human Genetics at Hannover Medical School (MHH). MHH is one of the largest hospitals in northern Germany, with one of the largest outpatient clinics for individuals and families dealing with hereditary cancer…

Read more →

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…

Read more →

Golden Helix Customer Publications – April 2021

Apr 29, 2021

Researchers and clinicians alike benefit from the powerful capabilities of Golden Helix’s software. Our tools are continuously validated, and we like to showcase a few articles each month that demonstrate the multitude of use cases and advancements in science. For our April 2021 customer publication installment, I would like to…

Read more →

VarSeq 2.2.3 Released!

Apr 27, 2021

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…

Read more →

VarSeq NGS Workflow Design: Clinical vs. Research

Apr 22, 2021

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…

Read more →

Using Gene Preferences in VarSeq and VSClinical

Apr 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…

Read more →

VarSeq Update: Support for the Interpretation of Non-coding and Splice Site Variants

Apr 15, 2021

While VarSeq has always had excellent support for variant interpretation and analysis, we continue to find new edge cases in the clinical literature that improve our interpretation capabilities. In this blog, we will be covering some of the new improvements in VarSeq to support the interpretation of non-coding and splice…

Read more →

Featured in The Journal of Precision Medicine: Implementing the ACMG Guidelines for CNV in a Commercial Software Solution

Apr 8, 2021

We are excited to share our latest publication with The Journal of Precision Medicine, “Implementing the ACMG Guidelines for CNV in a Commercial Software Solution”. “In 2020, ACMG in collaboration with the ClinGen working group developed a new set of guidelines for the clinical interpretation of CNVs. While theseguidelines provide…

Read more →

Webcast Recap: Exome Analysis with VS-CNV and VSClinical: Updated Strategies and Expanded Capabilities

Apr 8, 2021

Thank you to those who attended the recent webcast, “Exome Analysis with VS-CNV & VSClinical: Updated Strategies & Expanded Capabilities”. For those who could not attend but wish to watch, here is a link to the recording. In this webcast, we covered the capabilities and updates that have been incorporated…

Read more →

GenomeAsia 100K Variant Frequency Annotation

Mar 30, 2021

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…

Read more →