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 a row and are looking forward to seeing everyone there…. Read more »
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 & Engineering, Gabe Rudy, who reviewed the expanded capabilities of… Read more »
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 is to make sure the variants contained in the database… Read more »
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 and VP Research of Pacific Autism Family Network. She and… Read more »
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 that we wanted to share with the community. Question: Can I… Read more »
As VarSeq is quickly becoming the go-to variant analysis software for tertiary analysis, we want to give our readers the opportunity to examine completed projects from start to finish. As an addition to the currently available demonstration projects, we are pleased to provide users with a Single Exome Analysis example project. To access this project simply click here to download… Read more »
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 aggregates data from many disparate sources and normalizes it into… Read more »
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 clinical partners a specialized NGS-based CNV caller capable of detecting… Read more »
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 and identical results. Here are two fantastic white papers that… Read more »
We were incredibly impressed with the amount of creativity the GHI Community delivered for this year’s T-Shirt Design Competition! A big thank you to everyone who participated. We are pleased to announce our three prize winners: First Place – James Hadfield, PhD, Head of Genomics Core at the University of Cambridge Second Place – Pia Pulido, High School Student from… Read more »
Next-Gen Sequencing promised to be the ultimate paradigm when it comes to genetic research and clinical testing since it contains the complete genetic information. When it comes to the current reality in testing labs, there are still a number of additional testing paradigms used in an analysis, specifically, copy number variations. Among these, labs still widely use Chromosomal Microarrays and… Read more »
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 cover are seemingly limitless. In this webcast, we will focus… Read more »
The VarSeq clinical platform is built on a strong foundation of data curation and annotation algorithms to ensure the variants identified have all the information required to make the correct clinical assessments. It’s easy to make light of “variant annotation”, but the details run very deep into the roots of how we represent genomic data, how public data is aggregated, stored… Read more »
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 reviewed genetic variation in humans and looked at the key… Read more »
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 novel and extremely rare mutations in the GABA/glutamatergic pathways This… Read more »
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 integrates multiple metrics to determine if a CNV event is… Read more »
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 evolving platform, so everything you see in this webcast is… Read more »
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 analytics framework for next-gen sequencing data. There are a number of different approaches to CNV detection. The published algorithms share common strategies to solve the… Read more »
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 long running medical mystery. Audrey Lapidus knew there was something… Read more »
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. In Part I, we reviewed genetic variation in humans in general and looked at the key components of a systems architecture supporting this… Read more »