Golden Helix Blog

Sentieon’s Secondary Analysis Tools Explained

Sep 12, 2017

We find ourselves talking about our partnership with Sentieon, a lot! More specifically, we are always extolling the powerful, comprehensive genomic data analysis solution we are able to offer our clients. Sentieon’s Secondary Analysis Suite made a significant improvement in runtime over BWA-MEM, GATK, Mutect, and MuTect2 while providing deterministic…

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Upcoming Webcast: Advantages of VarSeq’s Annotation Capabilities

Aug 31, 2017

September 13, 2017 12:00 PM, EST This month we’re branching out and covering a topic we’ve never explored before – annotation capabilities! Darby Kammeraad, Field Application Scientist at Golden Helix, will be giving us some insight into the advantages of VarSeq’s capability with annotations. The number of annotation topics to…

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Secondary Analysis 2.0 – Part V

Aug 22, 2017

An Example of an Integrated Clinical Workflow for CNVs and SNVs In this blog series, I discuss the architecture of a state of the art secondary pipeline that is able to detect single nucleotide variations (SNVs) and copy number variations (CNVs) in one test leveraging next-gen sequencing. In Part I, we…

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Customer Publications From Around the Globe

Aug 17, 2017

It’s fascinating to hear the various ways our products are being used by customers all around the world. This month we’re featuring publications citing VarSeq, SVS and HelixTree which cover studies from Schizophrenia, Multiple Sclerosis and more. We hope you enjoy! Exome sequencing in schizophrenic patients with high levels of homozygosity identifies…

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Secondary Analysis 2.0 – Part IV

Aug 15, 2017

Examples of CNV Calling What do CNV calls actually look like? What are some of the key metrics to determine an event? Part IV of the Secondary Analysis 2.0 blog series will answer these questions by walking through some examples of how our CNV caller, VS-CNV, identifies CNVs. Golden Helix…

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GWAS Workflows with SVS webcast Q & A

Aug 10, 2017

In case you missed our live event yesterday, I wanted to share a link to the webcast recording: New Enhancements: GWAS Workflows with SVS. There were several questions asked, so we’ve also shared the Q & A session below! Question: Are these enhancements priced as a separate feature?  Answer: No, SVS is a constantly…

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Secondary Analysis 2.0 – Part III

Aug 8, 2017

Detection of CNVs in NGS Data Our secondary analysis 2.0 blog series continues with Part III: Detection of CNVs in NGS Data. We will give you an overview of some design principles of a CNV analysis framework for next-gen sequencing data. CNV detection is one of the more nuanced challenges…

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UCLA Health Diagnoses Long Running Medical Mystery

Aug 3, 2017

We don’t just like hearing what our clients are up to … we love bragging about what they’re doing to the world as well! This week we’re showcasing Dr. Stanley Nelson, and his team at UCLA Health, who used next-generation sequencing and our VarSeq software to help diagnose a child’s…

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Secondary Analysis 2.0 – Part II

Aug 1, 2017

In this blog series, I will discuss the architecture of a state of the art secondary pipeline that is able to detect single nucleotide variations (SNV) and copy number variations (CNV) in one test leveraging next-gen sequencing. Modern NGS analysis pipelines integrate these steps to efficiently process high-throughput sequencing data.…

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Webcast: New Enhancements – GWAS Workflows With SVS

Jul 27, 2017

We are dedicating our August webcast to explain the latest and greatest enhancements with GWAS workflows in SVS. Below you can find further details and registration information. We hope you can attend! Wednesday, August 9th, 2017 12:00 PM EST In this webcast, we will focus on the recent improvements to…

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Frequently Asked Questions: CNV analysis in VarSeq

Jul 20, 2017

The support team at Golden Helix is always here to help with your SVS and VarSeq needs. Often, we receive some excellent questions that should be shared with the rest of our users. This blog will answer some common questions we’ve been seeing lately regarding VarSeq CNV. I’ve noticed there is a version 2…

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Secondary Analysis 2.0 – Part I

Jul 18, 2017

Human genetic variation makes us unique. On average, humans are to 99.9% similar to each other. Understanding in detail what the nature of the difference in our genetic make-up is all about allows us to assess health risks, and eventually enables Precision Medicine as we determine treatment choices. Furthermore, it…

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Clinical Workflows Webcast Q&A

Jul 13, 2017

In case you missed our live event yesterday, I wanted to share the Q&A session and a link to the webcast recording: An Exploration of Clinical Workflows in VarSeq. Question:You mentioned saving projects as templates, will it save GenomeBrowse plots in the project template or do you have to replot the…

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Our customer’s recent publications!

Jul 11, 2017

Summer is in full swing, and we are kicking off July with an excellent round of articles our customer’s published citing our SVS software. Check out the snippets below, there may be one in there that peaks your interest! Curtis Van Tassell of the USDA and colleagues published Whole genome structural…

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GHI’s Annual T-Shirt Design Competition

Jul 5, 2017

We’re gearing up for ASHG and kicking off our annual T-Shirt Design Competition! This one goes out to all the clever, witty genomic jokesters out there … here’s your chance to cash in on those DNA punchlines you’ve been practicing! Here’s how the T-Shirt Design Competition works: Draw it out or write…

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Webcast: An Exploration of Clinical Workflows in VarSeq

Jun 29, 2017

Our July webcast presentation will be focused on clinical workflows in VarSeq. We wanted to share the full details with you and hope you are able to attend! Wednesday, July 12th 12:00 PM EST This month’s webcast is a VarSeq exploration, featuring several example workflows and helpful features in VarSeq…

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Understanding Your GWAS Signal with LD Scores

Jun 27, 2017

When studying complex diseases that may have multi-genic contributions from across the genome, it is not uncommon to see what may appear like elevated correlation between your trait or other test variable and the SNPs across the genome. The problem is at first glance you won’t be able to tell…

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CNV Caller Updates and More with VarSeq 1.4.5

Jun 22, 2017

We have been heads down doing the detailed and careful work to improve our CNV caller algorithm in the past three months since our we launched our Exome capable CNV caller and are very excited about the massive step forward we have made with the VarSeq 1.4.5 release. Additionally, we…

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Calling Cytogenetic CNVs from Shallow Whole Genomes

Jun 21, 2017

Low read depth? Great! We are excited to introduce our new CNV calling algorithm for low and ultra-low read depth Whole Genome Sequencing (WGS) data. This algorithm is designed to call large cytogenetic events with high confidence from low read depth whole genome data, with as few as one million…

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Golden Helix, Inc. – Your Annotation Curation Station

Jun 15, 2017

The current reduced cost and increase availability of genome sequencing has been making academics, clinicians and individuals alike excited with the possibility of increased research depth, diagnosing capability and personal curiosity. And although a freshly sequenced genome is chock-full of tasty letter snippets, the real revelation and education occurs when…

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