2017 was a busy year regarding the development of our CNV tools. Since the release of the CNV caller, we have produced quite a bit of content tailored to assist our users with getting started. Here are some links: Robarts Research Institute CNV analysis on patients with familial hypercholesterolemia CNV annotations Common CNV questions CNV calling with shallow whole genome… Read more »
The recent release of VSClinical gives users the ability to evaluate variants based on the 33 criteria according to the American College of Medical Genetic and Genomics (ACMG) guidelines. This feature leverages a variety of variant sequencing evidence including population data, functional data, and computational predictions while providing rich visualizations and auto recommendations to help answer challenging criteria. This highly… Read more »
In our previous webcast, we discussed the splice site algorithms for clinical genomics within VSClinical. We took it a step further in yesterday’s webcast and looked at the functional predictions and conservation scores. We had a great turnout for this event with lots of great questions from the attendees. I’d like to recap our Q&A for anyone else who might… Read more »
Ready to take your analysis to the next level? Our Small-Lab VarSeq PowerPack enables users to move their analysis from FASTQ to clinical reporting through one streamlined pipeline. Here’s what’s included: VarSeq VarSeq is an intuitive, integrated software solution for tertiary analysis. With VarSeq you can automate your workflows and analyze variants for gene panels, exomes, and whole genomes. VS-CNV… Read more »
I hope you were able to join us for last week’s webcast where we invited first-place abstract competition winner Michael Iacocca to present on his submission “Using NGS to detect CNVs in familial hypercholesterolemia”. Today, I’d like to announce our second-place winner, Nicole Weaver, Clinical Geneticist at Cincinnati Children’s Hospital. Nicole adopted VarSeq into her research pipeline in 2015 and… Read more »
We have a lot to thank the 1000 Genomes project for in the genomics community. By the collaborate efforts of many researchers and organizations, the project produced not only the first catalog of rare human variation but in the process standardized many things we take for granted, such as the VCF and BAM file formats. The variant frequencies of the… Read more »
With the recent release of VarSeq 1.4.7, we have expanded the concepts of our popular assessment catalog to include CNV and other region-based records and not just variants. To match these capabilities, we have made a major update to VSWarehouse that supports these new record types in the centrally hosted and versioned Catalogs and Reports. Review of the VSWarehouse Genomic… Read more »
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 top this off, VarSeq 1.4.7 has been shipped with many… 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 »
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 »
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 »
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 »
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 »
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 »
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 data when opening the software? Answer: Yes, if you save your… 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 »
The new VSReports tutorial covers a basic VSReports workflow with an emphasis on understanding and exploring report customizations. This tutorial requires an active VarSeq license with the the VSReport feature included. You can go to Discover VarSeq or email info@goldenhelix.com to request an evaluation license with the VSReports functionality included. VS Reports provides the ability to generate clinical-grade reports. This feature enables VarSeq… 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 »
