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 »
In this month’s Customer Publication blog, I will highlight four studies that provided further insights into conditions that are typically identified in early childhood. As you will see as you read the summaries of each publication, both Golden Helix software platforms (VarSeq and SNP & Variation Suite or SVS for short) were instrumental in exploring the genetic factors that influence… Read more »
This blog post will cover an exciting new VSClinical feature in the upcoming VarSeq release. The ACMG Previously Interpreted Variants feature allows users to integrate databases of expert-curated variant interpretations into their VSClinical workflows. These data sources store variant-level interpretation data, including the classification, associated disorders, interpretation text, and scored criteria for each variant, along with notes providing a justification… Read more »
We had a wonderful turnout for our recent webcast, “Reduce Turn-Around with Enhanced Cancer Annotations & Golden Helix CancerKB Updates.” Thanks so much to those who were able to join us! And not to worry, we have a link to the recording here just in case you weren’t able to make it. We covered the gamut of new and updated annotation tracks available in VarSeq along… Read more »
We are honored to be selected as MirrorReview’s 10 Innovative Biotechnology Solution Companies for 2021. This award would not be possible without the incredible support from our customers and partners. Thank you to our entire community! If you are interested in reading our story, and why we were selected for this award, you can access the publication here: https://www.mirrorreview.com/golden-helix-pioneering-bioinformatics-solutions/. “Biotechnology… Read more »
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 »
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 »
It’s everyone’s favorite time of the year; Golden Helix’s Annual T-Shirt Design Competition is starting! If you’d like to participate, simply send a sketch of your design to marketing@goldenhelix.com. Don’t forget about the sweet prizes we’re handing out for the top three designs: First Place: $300 Second Place: $200 Third Place: $100 Deadline: August 25, 2021 How It Works Draw it… Read more »
Golden Helix’s solutions are leveraged in a wide variety of scientific fields. As always, we are thrilled to showcase some of the newly published articles written by our customers. Here are a few that utilized VarSeq’s powerful scalability analyzing whole exome sequencing data. WES can identify variations in the protein-coding region of any gene. Since most known mutations that cause… Read more »
One of the many tricks of encoding so much functionality into so little space in eukaryotic genomes is the ability to produce multiple distinct mRNAs (transcripts) from a single gene. While one transcript is often the dominant one for a given tissue or cell type, there are, of course, exceptions in the messy reality of biology. It doesn’t take many… Read more »
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 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 »
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 to convert the data running through an initial mapping to… Read more »
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 years since the algorithm’s development. The PhoRank Algorithm When performing… Read more »
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, Golden Helix has an SVS Tutorial available that walks users… Read more »
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 »
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 »
In this month’s customer publication 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 scientific discoveries in Agrigenomics and human health and wellness. Read… Read more »
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 and analyzes multiple whole exome samples for copy number variations,… Read more »
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 »