Tag Archives: VarSeq

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

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

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

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!

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

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

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

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

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

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

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 »

Analyzing a Unique Family Structure in VarSeq 1.1.1

I am constantly on the lookout for fun or interesting datasets to analyze in SVS or VarSeq and recently came across a study looking into inherited cardiac conduction disease in an extended family (Lai et al. 2013). The researchers sequenced the exomes from five family members including three affected siblings and their unaffected mother and an unaffected child of one… Read more »

Call for Abstracts!

      Delaina Hawkins    December 11, 2014    1 Comment on Call for Abstracts!

As Andreas Scherer mentioned in his post last Tuesday, we will kick off our 2nd annual Abstract Challenge Monday, December the 15th. Here are the details. All academic, government, and commercial organizations world-wide working with genetic data (regardless of species) are invited to apply. Your project should be using DNA-Seq, RNA-Seq, SNP, or CNV methodology, as well as testing gene panels or searching… Read more »

VarSeq: A bioinformatics Swiss Army knife

If you’ve seen the recent webinars given by Gabe Rudy and Bryce Christensen, you’ve no doubt been impressed by the capabilities of VarSeq when it comes to annotation and filtering. However, we sometimes forget that the power that enables all this complex analysis can also be used in more mundane tasks like VCF subsetting. And although these day-to-day tasks don’t… Read more »

6 Population Catalogs Compared with the ExAC 61,486 Exomes

To say the announcement of Dan MacArthur’s group’s release of the Exome Aggregation Consortium (ExAC) data was highly anticipated at ASHG 2014 would be an understatement. Basically, there were two types of talks at ASHG. Those that proceeded the official ExAC release talk and referred to it, and those that followed the talk and referred to it. Why is this… Read more »

Don’t miss the VarSeq user experience webcast tomorrow!

We are shortly approaching the public launch (November 5th!) of our first clinical product, VarSeq. We could not have predicted how well the market would accept VarSeq – but we couldn’t be happier! For those of you who have not yet seen our newest product in action, I invite you to register for tomorrow’s webcast: The Golden Helix VarSeq User Experience.

Final thoughts on ASHG14

      Andreas Scherer    October 28, 2014    No Comments on Final thoughts on ASHG14

To make a long story short, we had a blast at ASHG14. The traffic at our booth was terrific. Every day we had scheduled presentations on VarSeq, SVS, and GenomeBrowse which were very well attended. And of course, there were our new t-shirts. The new designs were well received. If anything we promise to bring more next year. In particular more… Read more »

A new chapter for Golden Helix

      Delaina Hawkins    October 14, 2014    No Comments on A new chapter for Golden Helix

In our latest webcast (which introduced our newest product, VarSeq), Dr. Andreas Scherer, President and CEO of Golden Helix, announced the completion of 2 e-Books; one entitled Clinical Next-Gen Sequencing Analysis and one GWAS. Dr. Scherer published these e-books as part of Golden Helix’s continued effort to provide educational content to our clients and the genetic community as well as to put a… Read more »

ASHG Happenings

      Delaina Hawkins    October 8, 2014    No Comments on ASHG Happenings

It’s that time of year again. The mornings are chilly, the leaves are falling, and ASHG is right around the corner. This year will mark my very first ASHG and I am really looking forward to meeting some of the Golden Helix community! The team has been hard at work preparing for a great conference and I wanted to give you… Read more »

Looking forward to ASHG

      Andreas Scherer    October 2, 2014    1 Comment on Looking forward to ASHG

The 64th annual ASHG meeting is coming up in just a few short weeks in San Diego. This year’s event will be an exciting one for Golden Helix as we present VarSeq, with the first demonstration on Sunday at 11:30 am in booth 422. After the demonstration we will have some great VarSeq t-shirts to give away – you will not… Read more »

VarSeq: Making Variant Discovery and Gene Panels Easy

Last week, our CEO Andreas Scherer announced our entrance into the clinical testing market with VarSeq. This week, I will be giving a webcast on Wednesday introducing this new tool and demonstrating its capabilities. (Register for the webcast) VarSeq’s focused purpose is making NGS gene testing and variant discovery efficient, scalable and accessible to users with a broad range of backgrounds and specialties. In this blog post, we will examine the use cases that VarSeq supports in more detail,… Read more »