Tag Archives: VarSeq

Analyzing a Single Sample Exome in VarSeq

         October 22, 2015
Exome

While VarSeq comes with a number of starter workflows that are stored as templates, customers also have the option of creating filter chains from scratch; analyzing a single exome may require you to do exactly that. In this blog, I’ll go through analyzing a single exome and generating a list of variants for further study. After importing the variant data… Read more »

What to expect from ASHG 2015

         September 29, 2015

The 65th annual ASHG in Baltimore will be another exciting one. We at Golden Helix have been very busy this year making great improvements to both SVS and the VarSeq software and we look forward to showcasing them during our in-booth demos. In particular, we will launch two new additions to the VarSeq software suite; VSReports and VSWarehouse. VSReports brings highly customizable clinical… Read more »

VSReports – Highlights from yesterday’s webcast

         September 24, 2015
Exome

Yesterday, our VP of Product and Engineering, Gabe Rudy, presented VSReports to the Golden Helix community for the first time in a live webcast; Authoring Clinical Reports in VarSeq. It was an excellent presentation. Gabe highlighted VSReports’ ability to take the output of tertiary analysis to a customized clinical grade report in one click. He also gave an overview of… Read more »

Clinical Reporting comes to VarSeq

         September 17, 2015

The next release of VarSeq will ship a new product that is highly relevant to our customers in clinical testing labs. Via VSReports, VarSeq now has the ability to generate clinical-grade reports. These reports are fully customizable, containing focused and actionable data. VS Reports ships with report templates that are modeled off of the ACMG guidelines, the de-facto gold standard… Read more »

OMIM Coming to VarSeq

         September 1, 2015

When it comes to down to it, the genomic variants we collect in a research and clinical setting are impossible to interpret without that important link of how genes are related to phenotypes. Indisputably, the Johns Hopkins project to catalog all evidence related to inheritable Mendelian diseases is our best repository of this evidence. Online Mendelian Inheritance in Man (OMIM)… Read more »

Analyze Your 23andMe Genotype Files with Golden Helix

         July 22, 2015
23andMe

I was definitely an early adopter when it comes to personal genomics. In a recent email to their customer base announcing their one millionth customer, they revealed that I was customer #44,299. And I have been consistently impressed with the product 23andMe provides through their web interface to make your hundreds of thousands of genotyped SNPs accessible and useful. It… Read more »

Fulgent Diagnostics Implements VSPipeline to Speed Analysis & Interpretation

         July 22, 2015

Today, we are proud to announce our collaboration with Fulgent Diagnostics, a CLIA certified molecular diagnostics lab. Fulgent offers more than 4,000 single gene tests among others and will implement VSPipeline to help speed up their analysis and interpretation process. On our quest to enable precision medicine, we look forward to working with Fulgent and other diagnostics labs in the… Read more »

Tumor/Normal Pair support now available in VarSeq!

         July 16, 2015

VarSeq now supports analysis of paired Tumor/Normal samples! Tumor/Normal support has been one of the most common feature requests for VarSeq since it was launched late last year, and we are excited to make this functionality available to all of our VarSeq users in the latest update (version 1.1.4). VarSeq is a powerful platform for annotation and filtering of DNA… Read more »

Top 5 things you need to know about VSPipeline

         July 14, 2015

Recently, Golden Helix, Inc. announced the addition of VSPipeline to our VarSeq software suite. VSPipeline is a command-line interface that will allow 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 existing bioinformatics pipeline. So, what is the big deal? Here are the top five… Read more »

The Clinical Genome Conference 2015 Highlights

         June 30, 2015

This last week I had the pleasure of attending the fourth annual Clinical Genome Conference (TCGC) in Japantown, San Francisco and kicking off the conference by teaching a short course on Personal Genomics Variant Analysis and Interpretation. Some highlights of the conference from my perspective: Talking about clinical genomics is no longer a wonder-fest of individual case studies, but a… Read more »

Command-line Interface added to Golden Helix’s VarSeq Software

         June 18, 2015

Golden Helix recently announced the addition of VSPipeline to our VarSeq software. VSPipeline is a command-line interface that will allow 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 existing bioinformatics pipeline. VSPipeline supports the need to efficiently generate VarSeq projects from workflow-encoding project templates…. Read more »

Partnership with MedGenome

         June 17, 2015

Just a few weeks ago we announced our partnership with MedGenome. The news was covered by a number of outlets including: Financial Express Pharmabiz Let me expIain the importance and impact of this announcement. Since Varseq was released, we have received strong interest from testing labs that are leveraging our product to implement cancer diagnostic pipelines. Please feel free to take… Read more »

Frequently Asked Questions about VarSeq

         June 16, 2015

The support team at Golden Helix is always on-hand to help with your SVS and VarSeq needs. We get some questions more often than others, and this blog will answer some of the most common questions we’ve been seeing lately regarding VarSeq. A common question we receive is if data can be filtered from a locally kept set of variants… Read more »

New and Updated Annotation Tracks Now Available!

         June 11, 2015

In recent months we have been updating our public annotation library to include the most recent versions of existing sources as well as include new sources. Each of these annotation sources are compatible with our three major products (SVS, GenomeBrowse and VarSeq) and can be used for visualization, annotation and filtering. NHLBI ESP6500SI-V2-SSA137 Exomes Variant Frequencies 0.0.30, GHI Annotations are… Read more »

VarSeq is a better ANNOVAR, snpEff and VEP

         June 9, 2015

Yes, I said it. “Them be fighting words” you may say. Well, it’s worth putting a stake in the ground when you have worked hard to have a claim worth staking. We have explored the landscape, surveyed the ravines and dangerous cliffs, laboriously removed the boulders and even dynamited a few tree stumps. Stake planted. Ok, so now I’m going… Read more »

Baby Genes is raising the bar for Newborn Screening

         May 28, 2015

Today we wanted to share a recent client case study to demonstrate how VarSeq has been implemented in a CLIA certified clinical laboratory. Please feel free to contact us if you have questions or if you would like to discuss VarSeq further at info@goldenhelix.com. It is standard practice for newborns to be screened for genetic diseases before leaving the hospital to… Read more »

Golden Helix’s VarSeq Software to Incorporate MedGenome’s OncoMD

         May 27, 2015

Today at Golden Helix, we are proud to announce our collaboration with MedGenome through an integration of OncoMD into our VarSeq software. Now VarSeq’s streamlined process of annotating and filtering variants will offer an added dimension. OncoMD is a comprehensive knowledge base of cancer-specific genetic alterations, and by incorporating it into VarSeq, users can access to 2 million plus annotated… Read more »

What’s in a Name: The Intricacies of Identifying Variants

         May 26, 2015

There’s a strong desire in the genetics community for a set of canonical transcripts. It’s a completely understandable and reasonable thing to want since it would simplify many aspects of analysis and especially the downstream communicating and reporting of variants. Unfortunately, biology isn’t so tidy as to provide a clear answer for which transcript is the important one. Consequently, there… Read more »

VarSeq as a Clinical NGS Platform Q&A

         April 21, 2015
CNV User

Our VarSeq as a Clinical Platform webcast last week highlighted some recent updates in VarSeq that support gene panel screenings and rare variant diagnostics. The webcast generated some good questions, and I wanted to share them with you. If the questions below spark new questions or need clarification, feel free to get in touch with us at info@goldenhelix.com. Question: Should… Read more »

Unique Labs, Common Tool: Making VarSeq Ready for Clinical Workflows

         April 9, 2015

As VarSeq has been evaluated and chosen by more and more clinical labs, I have come to respect how unique each lab’s analytical use cases are. Different labs may specialize in cancer therapy management, specific hereditary disorders, focused gene panels or whole exomes. Some may expect to spend just minutes validating the analytics and the presence or absence of well-characterized… Read more »