Author Archives: Golden Helix

Questions from Webcast: Evaluating Cloud vs On-Premises for NGS Clinical Workflows

         May 23, 2022

In the era where cloud-based solutions are the default for the modern office, it may not be obvious why many laboratories and testing centers choose to host their data and analysis pipelines on-premises or on self-managed cloud services. In the recent webcast Evaluating Cloud vs On-Premises for NGS Clinical Workflows, I explored the topic of how to make infrastructure decisions… Read more »

2021 End of Year Pricing Packages

         September 28, 2021
VarSeq PowerPack

For the third year in a row, Golden Helix has been included on the Inc 5000 List. Without our amazing customers and partners, this award would not have been possible. We all know that the world is seeing significant increases in daily expenses. Our company has been able to absorb these increases by expanding its market share around the world. We… Read more »

ESHG 2021 Corporate Satellite Talks

         August 26, 2021

Join the Golden Helix team at this year’s ESHG 2021 Virtual Conference! We will be presenting two different talks on our different product solutions and fielding any questions you might have. VSClinical: a comprehensive NGS clinical solution The first talk, VSClinical: a comprehensive NGS clinical solution, will be on Sun, 29 August, 14:00-15:00. This will be moderated by Golden Helix… 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 »

Merged gnomAD Genomes and Exomes Annotation Source

         July 15, 2021
CNV Annotations

The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects (1). We have covered this annotation in-depth in other blog posts, but this resource contains over 125,000 exome sequences and around 16,000 whole genome… Read more »

An end to diagnostic odysseys?

         July 13, 2021

Could leveraging CNV analysis for whole exome or genome sequencing help provide answers for the undiagnosed? Roughly 4% of the world’s population shares one common desire – a diagnosis (1). Though it may seem counterintuitive, a diagnosis, no matter how grim, can provide relief, validation, the chance to make plans, and have a discernible sense of future for individuals and… 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 »

Importing CNVs using VSPipeline

         June 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 and annotating your data, which can help streamline your analysis… Read more »

Summer 2021 Software Specials

         May 25, 2021
Special Offer

Summer is quickly approaching, which heralds the return of our summer software specials! Golden Helix will be offering a limited number of the following deals through June 30th, 2021. Here is a snapshot of what is being offered: VarSeq w/ CADD & OMIM (3-users) – $8,995 | (3 available) Our filtering and annotating product, VarSeq, paired with premium annotations. VSClinical,… 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 post will elaborate on these capabilities and demonstrate how they… Read more »

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

         April 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 a robust set of rules for interpreting intragenic deletions and… Read more »

GenomeAsia 100K Variant Frequency Annotation

         March 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 across Asia. Using this as an annotation, users can analyze… Read more »

Orphanet Annotations in VarSeq

         March 18, 2021

Orphanet is a public database available in VarSeq that aims to improve the current understanding and treatment options for patients affected by rare diseases. This resource was established in France in 1997 and has gradually grown to cover a consortium of over 40 countries in Europe. The primary goal of this database is to provide a universal nomenclature to classify… Read more »

2021 Abstract Competition Winners

         March 16, 2021
2020 Abstract Competition Winners

We would like to thank everyone who entered our 2021 Abstract Competition. It is wonderful to read about the different ways Golden Helix software is being applied around the world. It is our pleasure to announce this year’s winners! First Place: Viney Gupta – All India Institute of Medical Sciences – AIIMS Digenic Inheritance in Juvenile Open-AngleGlaucoma Sign up for… 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 »

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 »

Webcast Recap: VSClinical: A Complete Clinical Workflow Solution

         January 15, 2021

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 »

ACGS Guidelines Now Available in VSClinical

         January 7, 2021
ACGS Guidelines Screen Shot

Golden Helix offers a market-leading bioinformatics solution that allows users to evaluate next-generation sequencing variants according to the ACMG and now ACGS guidelines. The ACMG guidelines were created in 2015 and are widely accepted as best practice for the interpretation of sequencing variants throughout the United States (Richard et al 2015).  Very similar are the ACGS guidelines that were developed… Read more »

Adding Population Catalogs to VSClinical

         December 10, 2020
example population view

Our previous webcast demonstrated some of the new functionalities of VSClinical, including the ability to add ACMG frequency sources for the ACMG BA1, BS1, and PM2 criteria. This new feature was spurred by the feedback from our users, which requested supporting frequency tracks other than gnomAD Exomes and 1kG Phase3. Now, users can implement population catalogs to VSClinical such as… Read more »