Golden Helix Blog

VarSeq Updated with CNV Annotations, CNV PhoRank and Region Assessment Catalogs

Oct 19, 2017

VarSeq Updated with CNV Annotations, CNV PhoRank, and Region Assessment Catalogs This year we have released multiple advances to support CNV analysis in VarSeq, expanding our target region based VS-CNV caller to handle exomes and low-depth genomes as well as additional supporting algorithms like calling Loss of Heterozygosity regions. To…

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Goodbye snow … hello Orlando!

Oct 17, 2017

We look forward to seeing you all at ASHG 2017! Golden Helix is leaving the snowy mountains of Bozeman, MT and heading for the sunny streets of Orlando, FL to attend the 2017 American Society of Human Genetics Conference (ASHG)! We’re excited to be returning for the 12th year in…

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All of your VS-CNV annotation questions answered

Oct 12, 2017

This month we hosted two, incredible webcasts officially announcing the latest CNV annotation capabilities our Software Engineering Team has been hard at work on for the past couple of months. Our first webcast, Comprehensive Clinical Workflows for Copy Number Variants in VarSeq, was presented by Golden Helix’s VP of Product…

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Annotation Education Series: Cancer Annotations

Oct 5, 2017

CIViC The Clinical Interpretations of Variants in Cancer, better known as CIViC, is an open access open source, community-driven web resource available to all VarSeq users. Nature Genetics published an article that states, “CIViC accepts public knowledge contributions but requires that experts review these submissions”. Fundamentally, the focus behind CIViC…

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Case Study: iTARGET Autism Project

Oct 3, 2017

Dr. Suzanne Lewis is a Clinical Professor in the Department of Medical Genetics at University of British Columbia (UBC) and Senior Investigator at British Columbia Children’s Hospital Research Institute (BCCHR), Vancouver, Canada. She is also the Chair of the iTARGET Autism Project and Vice-Chair of Autism Canada Chief Medical Officer…

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CNV Annotation Clinical Workflows Webcast: Q&A

Sep 28, 2017

  Gabe Rudy gave a fantastic presentation yesterday on the latest additions to VS-CNV annotations. If you weren’t able to join us for the live event, you can access the recording and webcast slides here: Comprehensive Clinical Workflows for Copy Number Variants in VarSeq. Additionally, there were many great questions asked…

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Annotation Education Series: Clinical Assessment Tracks

Sep 21, 2017

Clinical Assessment Tracks Golden Helix provides a large catalog of annotation sources for our research and clinical clientele. Making these public data repositories available to all our users is no easy task. As Cody Sarrazin mentioned in his blog post, annotation curation is a complex data science pipeline. This process…

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Upcoming Webcast: Comprehensive Clinical Workflows for Copy Number Variants in VarSeq

Sep 14, 2017

September 27, 2017 12:00 PM, EDT While Copy Number Variants are important to detect and interpret in many clinical genetic tests, labs have been without a comprehensive solution that integrates the annotating and reporting of high-quality CNV alongside their existing NGS variants. Golden Helix has developed and validated with our…

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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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