Search results for “annotation”

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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Precision Medicine – Part V – Bioinformatics Pipelines and Systems Infrastructure

May 7, 2015

Bioinformatics Pipelines and Systems Infrastructure The genetics industry is undergoing a fundamental shift from a clinical science focus to a bioinformatics focus. Genetic services require a greater level of data analytics sophistication than is required for other laboratory testing. Currently, data generated by new tests overwhelms current information technology systems…

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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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SVS, Population Genetics, and 1000 Genomes Phase 3

Jan 27, 2015

One frequent question I hear from SVS customers is whether whole exome sequence data can be used for principal components analysis (PCA) and other applications in population genetics. The answer is, “yes, but you need to be cautious.” What does cautious mean? Let’s take a look at the 1000 Genomes…

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VarSeq: A bioinformatics Swiss Army knife

Dec 5, 2014

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…

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Don’t miss the VarSeq user experience webcast tomorrow!

Nov 4, 2014

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…

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New Plugin for Ion Torrent Server

Oct 21, 2014

Golden Helix is proud to announce the release of the Golden Helix GenomeBrowse Plugin for Ion Torrent server. The new plug-in enables adding selected BAM files from Torrent Server reports directly into GenomeBrowse. The BAM files remain on the torrent server and are streamed from the server on demand using…

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Variant Notation: In simplicity we find complexity

Oct 9, 2014

Recently, I have been thinking a lot about Human Genome Variation Society (HGVS) notation — you know “G dot”, “P dot”, and “C dot”. HGVS has quickly become one of the most common ways to represent variants.  It’s no wonder that HGVS nomenclature is used so widely. It provides an…

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ASHG Happenings

Oct 8, 2014

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…

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Updates to ClinVar and dbSNPs: Fresh charts for Cromonaughts!

Aug 28, 2014

I’m sitting in the Smithsonian Air and Space Museum basking in the incredible product of human innovation and the hard work of countless engineers. My volunteer tour guide started us off at the Wright brother’s fliers and made a point of saying it was only 65 years from lift off at Kitty…

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RefSeq Genes: Updated to NCBI Provided Alignments and Why You Care

Aug 14, 2014

You probably haven’t spent much time thinking about how we represent genes in a genomic reference sequence context. And by genes, I really mean transcripts since genes are just a collection of transcripts that produce the same product. But in fact, there is more complexity here than you ever really…

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