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 »
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 »
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 enables scientists to better understand ancient human migrations. It gives… Read more »
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 it down; we accept either illustrated or written designs. Email… Read more »
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 comparing to an annotation foundation. In this post, I’ll review… Read more »
Yesterday’s monthly webcast featured our end-to-end solution for clinical labs. In case you missed it, you can watch the webcast here! There were a number of questions asked in the live event, so in today’s blog post I wanted to recap the Q&A session. Can you go over the requirements for the CNV algorithm in more detail? If you are… Read more »
We are back from another exciting trip to ESHG, hosted in Copenhagen, Denmark last week. We were delighted by the number of researchers and clinicians we were able to connect with. Needless to say, the weather was outstanding in Copenhagen, which made our stay even more pleasant! Even though this was a European event, it was great to be able to speak with… Read more »
As usual, we would like to share some of the articles that our clients have published recently citing our software. These articles are incredibly diverse and interesting, and we hope you enjoy browsing through them. Fielding Hejtmancik and Lin Li of the NIH-NEI and colleagues published Homozygosity Mapping and Genetic Analysis of Autosomal Recessive Retinal Dystrophies in 144 Consanguineous Pakistani… Read more »
We are ending the first half of the year with a webcast featuring our entire clinical software stack: Golden Helix’s End-to-End Solution for Clinical Labs. This webcast is scheduled for Wednesday, June 7th at noon EST, and it’s not one you’ll want to miss! Here are the full details: Wednesday, June 7th 12:00 pm EST In this webcast we will provide an… Read more »
In just a few days, Golden Helix will arrive in Copenhagen, Denmark to attend the 2017 European Society of Human Genetics Conference (ESHG). We are excited to be returning to ESHG for the second year in a row! It’s always a pleasure to see our European customers and meet some new faces in the community. This year the Golden Helix team will be… Read more »
Yesterday we had an excellent webcast presentation featuring Sentieon’s Dr. Donald Freed. Golden Helix recently partnered with Sentieon to integrate their secondary analysis tools into our software stack, and this presentation is an introduction to their genomic tools. Please check the webcast out here if you missed it! There were a number of questions asked in the live event, so in… Read more »
Today, we are happy to announce a multi-year partnership with Sentieon, a company that develops bioinformatics secondary analysis tools to process genomic data. This partnership will integrate Sentieon’s secondary analysis tools with Golden Helix software to provide users with a comprehensive solution for genomic data analysis. Sentieon’s suite of secondary analysis tools made the significant improvement in runtime over BWA-MEM, GATK,… Read more »
We had lots of customers publish their work using our SVS software, and I wanted to share their work with you. Congrats to all! Here are some of the highlights: Francesca Fernandez of the University of Wollongong along with colleagues published Effects of common GRM5 genetic variants on cognition, hippocampal volume and mGluR5 protein levels in schizophrenia in Brain Imaging and… Read more »
Nathan Fortier’s webcast yesterday, CNV Analysis in VarSeq – A User’s Perspective, was an excellent demonstration of our CNV capabilites, so check it out here if you missed it. There were a number of questions asked in the live event, so in today’s blog post I wanted to recap the Q&A session. Question: Do the reference samples have to be from the… Read more »
Recently, we added a natively supported Genotype Phasing and Imputation capability in SNP & Variation Suite 8.7.0. Since then we have had fantastic feedback and adoption as folks take advantage of the BEAGLE 4.0 and 4.1 algorithms from within their existing SNP GWAS and agrigenomic workflows. One piece of feedback we heard from our time at PAG, ACMG and our… Read more »
