Search results for “annotation”

Analyzing a Single Sample Exome in VarSeq

Oct 22, 2015

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…

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Clinical Reporting comes to VarSeq

Sep 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…

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Introducing VarSeq Viewer!

Sep 10, 2015

With our latest release of VarSeq last Thursday, we are proud to offer the VarSeq ® Viewer to the community, for free! When you download VarSeq ® Viewer, you can explore pre-built projects to interact with the annotations and filters the project provides, visualize selected variants with pile-ups, and export data to…

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Dr. Scherer is a Keynote Speaker at Genomics 2015

Sep 8, 2015

A widely attended conference that is coming up on September 21-23 is the third international conference on Genomics 2015 in San Antonio, Texas. The theme of this year’s conference is “Implications and Impacts of Genomic Advances on Global Health“, which promises to provide some interesting presentations and discussions. Current issues in…

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OMIM Coming to VarSeq

Sep 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…

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Between Two Bases: Coordinate Representations for Describing Variants

Aug 27, 2015

Have you ever scratched your head when looking up a variant and it seems like the number you have for its position is one off from what it looks like in the file or database? You may be running into the dreaded world of 1-based versus 0-based coordinate representation! If…

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Coverage Statistics Come to VarSeq

Aug 20, 2015

A prerequisite for clinical NGS interpretation is ensuring that the data being analyzed is of high enough quality to support the test results being returned to the physician. The keystone of this quality control process is coverage analysis. Coverage analysis has two distinct parts. Ensure that there is sufficient coverage…

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Analyze Your 23andMe Genotype Files with Golden Helix

Jul 22, 2015

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…

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Tumor/Normal Pair support now available in VarSeq!

Jul 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…

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Top 5 things you need to know about VSPipeline

Jul 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,…

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Comparing Variants using a Venn Diagram

Jul 7, 2015

One of the lesser known functions in SVS allows the user to create Venn diagrams comparing variants found in multiple spreadsheets. These different spreadsheets could come from individuals samples, a case vs. control group or several variant databases. It is a helpful tool for visually comparing different variants. Start by…

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The Clinical Genome Conference 2015 Highlights

Jun 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…

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Partnership with MedGenome

Jun 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…

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Frequently Asked Questions about VarSeq

Jun 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…

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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…

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VarSeq as a Clinical NGS Platform Q&A

Apr 21, 2015

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…

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

Apr 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…

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Question and Answers: Cancer Gene Panels Webcast

Mar 17, 2015

Last week we conducted a webcast on “Cancer Gene Panels”. We had some excellent questions which we answered during the webcast and a few more that we didn’t get to in the allotted time. Please find answers to those questions here: 1. Are Cancer Gene Panels just another stepping stone on…

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Analyzing a Unique Family Structure in VarSeq 1.1.1

Mar 12, 2015

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…

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Tri-Con 2015 – just 5 days away!

Feb 10, 2015

In just 5 days, the 22nd International Molecular Medicine Tri-Conference (Tri-Con) will kick off in San Francisco. This year, Tri-Con will offer over 3,000 attendees 6 symposia, over 20 short courses, and 17 conference programs focused on drug discovery, genomics, diagnostics, and information technology surrounding, molecular medicine. Both Dr. Andreas Scherer, CEO…

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