2022 Innovation Awards

         December 1, 2021

We at Golden Helix love seeing our software and solutions out in action. Whether it is to find a clinical solution or to assist in academic research, seeing YOU use our tools to the best of their ability gets us excited to continue developing industry-leading software. For the 2022 Innovation Awards we would like to see all the creative and… Read more »

VarSeq 2.2.4 Release

         November 30, 2021
varseq2.2.4

We are very excited to announce that just last week, we released VarSeq 2.2.4! In the past few months, we have been building the excitement for the 2.2.4 version of VarSeq with several webcasts in which we describe some of the headlining features in detail such as the new support for Gene Panels and Gene Lists, PhoRank Clinical, and Customized… Read more »

Breaking Down ACMG CNV Guidelines in VSClinical

         November 25, 2021

In February 2020, the American College of Medical Genetics (ACMG) and the Clinical Genome Resource (ClinGen) published a joint consensus on standards for the interpretation and reporting of copy number variants (CNVs) ranging from large CNVs spanning multiple genes to small intragenic events1. The guidelines consist of over 80 different criteria which are arranged into five distinct sections. These extensive… Read more »

Top Things You Wish You Knew When Getting Started with VSClinical

         November 18, 2021
vsclinical top things to know

As a newer member of the Golden Helix FAS Team I, like many of our customers, went through a phase of learning the ins, outs, and shortcuts of clicking around the program. In an effort to expedite new users coming up to speed, or to teach some tricks to experienced users, I’ve compiled a list of the top things I… Read more »

Validating Your CNV Workflow

         November 16, 2021
VS-CNV Blog Validation

The VarSeq CNV calling algorithm, VS-CNV, is a powerful tool for calling CNVs from the NGS coverage data stored in your BAM files. However, before this algorithm can be deployed in a clinical setting, it must be tuned and validated using data that is representative of your lab’s NGS workflow. In the past, this validation process could be difficult, as… Read more »

Running VSPipeline from a Docker Container

         November 10, 2021
VSPipeline Docker Container BLOG

As a lab or group scales the number of NGS samples analyzed, it is important to automate the sample analysis pipeline from the sequencer to the point where it is ready for a variant scientist or lab personnel to follow the interpretation workflow and draft a clinical report. VSPipeline leverages the core VarSeq capability to create reproducible test-specific workflows through… Read more »

VarSeq Advanced Reporting Customizations: Part 1

         November 9, 2021
BLOG-11.9.21-VarSeq-Custom-Reports-Part-1

As we move towards the end of the year, our FAS Team is excited to announce our short blog series highlighting some of the Customization Features in our up-and-coming VarSeq release! The goal of this blog series is to show examples of how generating a clinical report can be customized to accommodate a wide range of functionality. Our December webcast,… Read more »

Customer Publications in October 2021

         October 28, 2021
varseq customer publications October 2021

The customer-published articles this October cite the range of Golden Helix’s VarSeq annotation range and capability. The following publications feature everything from annotating an Italian nobleman mummy, assisting in identifying mutations in primary congenital and juvenile glaucoma, new mutations associated with muscular dystrophinopathy, and germline variants associated with head and neck cancer. In each of these cases, VarSeq was utilized… Read more »

Details of the Golden Helix CancerKB Database Update

         October 21, 2021
cancerkb updates

Recently we have released blog posts discussing updates to annotations in VarSeq such as ClinVar and COSMIC. Keeping with that trend, in this blog post, I will discuss the most recent updates to the Golden Helix CancerKB database. For those how may be unfamiliar with the Golden Helix CancerKB source, it is a professional curated set of interpretations for the… Read more »

Five Annotation Sources You Should Know

         October 19, 2021
Golden Helix Annotation Blog Featured Image

In addition to Golden Helix providing easy-to-use genomic software, we also provide value to our users by automating the curation of public databases used in our tools. These annotation sources serve multiple purposes not only leveraging key fields in the filter chain but also automatically supplying evidence for the ACMG and AMP classifications reviewed in VSClinical. Supporting the curation of… 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 »

Customer Publications in September 2021

         September 30, 2021
customer

September’s published articles citing Golden Helix software serve as a testament to our product’s broad applications and utility in NGS data analysis. We are always proud of our customers and the contributions they make to advancing scientific discovery and are grateful to be included in their research. This month, we were treated to publications from all over the globe showing… Read more »

Updates to Somatic Variant Annotation and a New Way to Evaluate Fusions in VSClinical

         September 29, 2021
ClinVar

With the release of VarSeq 2.2.4 just around the corner, I want to detail some new 2.2.4 features that will enhance somatic variant annotation and fusion analysis within VSClinical. A webcast back in July showed some of these updates in action, so if you are looking for some more content on this topic, I would highly recommend checking out the… 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 »

Customizing VSClinical Reports 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 to customize reports to include specific content and branding. Recently… 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 »

Case Study with LifeCell International: Transforming Precision Medicine in India

         September 13, 2021

Established in 2004 and headquartered in Chennai, India, with regional centers across the country, LifeCell runs India’s largest stem cell bank and has also diversified into diagnostics and tissue therapeutics. They employ roughly 2,000 people, providing genetic services to customers in the mother and baby space. Phani Nagaraja Setty is working as a scientist at LifeCell. Setty obtained his Master’s… Read more »

Merging VCFs in an Imperfect World

         September 7, 2021

Merging variant records across samples is important when performing trio or family analysis as it ensures that hereditary relationships can be properly inferred. There are many ways to represent a single variant. Insertions and deletions may be right or left aligned, prefixes and suffixes can be added, and adjacent variants in the same sample may be combined or split at… Read more »

2021 T-Shirt Design Competition Winners

         September 2, 2021
T-Shirt Design Competition

We would like to thank everyone who participated in our 2021 t-shirt design competition. It was great to see the amount of creativity our community expressed and was certainly a tough decision to make! We are pleased to announce this year’s winners: First Place – Bruce Eng For over 35 years, Bruce Eng has partnered with businesses, educational institutions, and… Read more »