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.
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.
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.
We know our software will exceed your expectations. But don't just take it from us, see what our customers have benefitted from it.
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 supplemental learning materials that are an excellent resource 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!
Read our eBook on how NGS has made its way into the clinic.
NGS-Based Clinical TestingRead Here
Follow along with a typical CNV workflow from a VarSeq user’s perspective.
CNV Analysis in VarSeq - A User's PerspectiveWatch Now
Request a free trial of VS-CNV:
4 GB of RAM
100GB of space available for annotations and projects
If you are working with whole exomes or genomes, especially if or hundreds to thousands of samples, we suggest a high-memory configuration and plenty of storage capacity:
16GB+ of RAM (32GB for Servers)
8+ CPU Cores
1TB of space available for annotations and projects
The following operating systems are supported:
64-bit Windows 7 or later (32-bit also supported, but not recommended)
Linux Ubuntu 14.04 or later (64-bit only)
Linux RHEL 6 or later, or equivalently CentOS 6 or later (64-bit only)
Mac OS X 10.9 or later
With a server license, you can install your Golden Helix software solution on a server with multi-user access and shared resources. You can launch any number of instances of the software on the same host, and are only limited by the natural CPU, Memory and Disk resources of the server.
For Windows, you would need to use ability for multi-user Remote Desktop only available on Windows Server. We support Windows Server 2008 or newer.
On Linux, clients can log in from any operating system using SSH and open the Golden Helix software using X11-tunneling to interact with the software. On windows, we suggest a solution like MobaXterm that provides a all-in-one SSH client and X11 server to enable easy logging in, file transfer and opening of remote GUI applications.
Golden Helix VarSeq and SVS can be configured to access the internet through a SOCKS5 or HTTP/HTTPS Tunneling Proxy. Go to Tools -> Proxy Settings… to configure.
The software only needs to make outgoing connections on standard HTTP/HTTPS ports and protocols. If a local firewall is installed that prevents these types of outgoing connections (this is very uncommon), firewall rules will need to be created to whitelist the software.
Note we have run into numerous issues where aggressive anti-virus programs prevent the product from performing normal operations such as opening files and logging in. You may need to whitelist Golden Helix executables or disable these tools to perform your analytics.