Features
Clinical genetic testing often requires looking for and interpreting Copy Number Variants (CNVs) as well as small point mutations. While NGS based gene panels and exome tests have become the best practice assay for many types of genetic tests, CNVs must be acquired using a different paradigm.
Golden Helix has pioneered an industry leading CNV calling algorithm that operates on existing clinical NGS gene panel, exome and whole genome NGS data. Along with the calling of CNV events, the entire workflow is managed inside VarSeq’s clinical interpretation workflow. This integration enables CNV events to be considered alongside the annotated and filtered NGS small variants and incorporated into clinical reporting using VSReports.
Detect CNVs
VS-CNV is able to detect CNVs in your NGS data sets. It ascertains multiple metrics from samples along with matched controls to make CNV calls with high and consistent accuracy and sensitivity to meet the thresholds for clinical validation and adoption.
Operates on all NGS Data
Our CNV calling algorithm operates on existing clinical NGS gene panel, exome, and whole genome NGS data. The entire workflow is managed inside VarSeq’s clinical interpretation workflow. This integration enables CNV events to be considered alongside the annotated and filtered NGS small variants and incorporated into clinical reporting using VSReports.
Integrated Clinical Workflow
The entire workflow is managed inside VarSeq’s clinical interpretation workflow. This integration enables CNV events to be considered alongside the annotated and filtered NGS small variants and incorporated into clinical reporting using VSReports.
Germline & Cancer Tests
With VS-CNV the following can be achieved for germline and cancer tests: Call CNV events that range from 200bp single exons to multi-megabase and chromosomal aneuploidy, replace multiple assays such as MLPA, qPCR and CMAs with a single NGS test, use the NGS data already generated to call small SNPs and InDels variants to call CNVs, and integrate Loss of Heterozygosity (LOH) with CNV calling to distinguish Copy-Neutral LOHs from LOH events that support Heterozygous Deletion CNV calls.
Use Cases
Detect Structural Variations
Structural variations such as copy-number variation and deletions, inversions, insertions, and duplications account for much more genetic variation than single nucleotide diversity.
Major genomic mutations in germline cells will likely result in inviable or cause human diseases such as Down syndrome, Turner Syndrome and many other diseases result from aberrations of entire chromosomes. Cancer cells frequently have aneuploidy of chromosomes, as well as other major structural variations.
Traditionally, labs conduct their CNV analysis outside of NGS workflows by deploying methods such as quantitative PCR, multiplex ligation-dependent probe amplification (MLPA) or chromosomal microarrays. Conducting this analysis leveraging NGS data has the potential to simplify clinical workflows. It goes without saying that this approach can potentially reduce costs in running a CNV analysis substantially.
Case Studies
We know our software will exceed your expectations. But don't just take it from us, see what our customers have benefitted from it.
James Weber
CEO, Prevention Genetics
We are highly impressed with both the sensitivity and specificity of the Golden Helix CNV detection software. Sensitivity ... in many cases exceeds chromosomal microarrays and rivals custom arrays...Read Dr. Weber's Entire Case Study
Dr. Jeffrey Rosenfeld
Bioinformatics Scientist, Rutgers Cancer Institute of New Jersey
We could have taken a few tools and wrapped them together, but then we are responsible to maintain the system. By choosing a commercial solution, I can count on an entire team of programmers to keep the system updated. On top of that, the cost of an additional high-end programmer to help support an in-house system is more than the cost of a commercial solution.Read Dr. Rosenfeld's Entire Case Study
Dr. Laura Li
Associate Director, Children's Hospital Los Angeles
VarSeq is pretty user-friendly. Also the support team is very helpful. They know the VarSeq software in and out and the tech support has helped me to quickly learn VarSeq.Read Dr. Li's Entire Case Study
Recommended Learning Materials
We have a variety of materials for anyone interested in the industry or our software solutions. Here are some of our recommended materials for you to check out related to VS-CNV!
eBooks
Read our eBook on how NGS has made its way into the clinic.
NGS-Based Clinical Testing
Read HereWebcasts
Check out some of our previously recording webcasts featuring VSClinical in action!
CNV Analysis in VarSeq - A User's Perspective
Watch NowOther Resources
Explore a clinical workflow in VarSeq or follow along with a VS-CNV tutorial!
VarSeq Viewer:
Download Here
VS-CNV Caller Tutorial:
Download Here
Try VS-CNV for Free
Did you know we offer complimentary trials of our software? No restricted features, no sample data - you get to try all the features of VS-CNV with your data and see how it works!
If you are interested in a trial, please fill out the form below, and we will send you the details!
Technical Specifications
VarSeq is on-premises software, ensuring full control over installation and data management. It is compatible with various deployment environments including workstations, server setups with remote desktop access, and private cloud servers.
The software is optimized for operation within strict corporate firewalls. It seamlessly integrates with existing web proxy configurations, ensuring uninterrupted functionality in secured network infrastructures. VarSeq's internet connectivity requirements are minimal. It only needs to connect to a select group of Golden Helix servers. This connection is essential for license verification and accessing annotation data updates.
See System Requirements for more details of hardware and operating systems requirements based on planned workflows.