The genetics industry is undergoing a fundamental shift from a clinical science focus to a bioinformatics focus. Genetic services require a greater level of data analytics sophistication than is required for other laboratory testing. Currently, data generated by new tests can overwhelm information technology systems and human interpretation capabilities. Our VarSeq® software can bring speed and efficiency to genetic testing labs by simplifying the process of analyzing and interpreting the data. With an intuitive design, VarSeq allows you to create a high throughput environment by creating repeatable workflows.
At Golden Helix®, we provide our pharmaceutical customers with software that can quickly identify causal markers, test drug efficacy and assist in selecting patients for clinical trials. Our software brings both speed and efficiency to research and development efforts, reducing production costs and helping them get to market faster.
Support for Gene Panels
VarSeq includes the necessary features needed for both commercially available and custom gene panels. Variants can be filtered using the BED files provided by manufacturers which define the panel's amplicons and "hotspots." A wide array of annotation sources are available to provide additional information for both hereditary and somatic variants. Moreover, the VCF import process is optimized to produce variant representations which match those in annotation catalogs. Finally, variant blacklists can be created to filter variants that your lab has found to be inaccurate or not actionable.
Clinical Grade Variant Annotations
Included in VarSeq is functionality similar to SnpEff or Variant Effect Predictor. Each variant is mapped to all overlapping transcripts and information about the region where it is located (exon, intron, intergenic, etc.), sequence ontology (frameshift, synonymous, etc.), and HGVS notation (g dot, c dot, and p dot) is provided. You can choose to filter against the highest-impact annotation for each variant or the entire set of variant-transcript interactions.
VarSeq software provides a powerful filtering and annotation engine to sift through large variant data sets. Using a chain of filters, you can quickly narrow your list of variants down to those that are most likely to be of interest. After determining the parameters that work well for your analysis, you can save the state of your filters so that you can easily apply the same analysis to another dataset. The same automated workflow can be used for each batch of samples, making VarSeq an ideal solution for high-throughput environments. Real-time filtering gives you the power to quickly prototype and tune analysis workflows to the specific gene panels that your lab uses. Once the appropriate set of filters have been found, the workflow can be saved and applied to future sequencing outputs without having to re-enter any parameters.
Industry leading annotation sources
After data import, annotations are automatically applied based upon your pre-configured settings. Additional annotations can then be added at any time during the analysis process. The Golden Helix team curates a wide selection of public databases and updates these datasets on a quarterly basis. The specific annotations used in your analysis are stored locally with your data and are never changed without your explicit request. This ensures that your analysis is performed on a stable dataset and your results are reproducible and available in the future.
Family Based Workflows in VarSeq
Leading the charge in clinical variant analysis. See VarSeq in action with our free webcast. Read on to see what benefits our customers have gained from using our products!
We know our software will exceed your expectations. But don't just take it from us, see what our customers have benefitted from it.
Dr. Benjamin Darbro
Director, Shivanand R. Patil Cytogenetics and Molecular Laboratory
VarSeq had everything we were looking for with regards to annotation, filtering sources and an actual visual browser within the software itself. VSReports allows us to take it all the way to the report generation. But what really set it apart in retrospect is how intuitive it is.Read Dr. Darbro's Entire Case Study
Dr. Matthew McClure
Lead Geneticist, Irish Cattle Breeding Federation
Dr. Matthew McClure is a lead geneticist at the Irish Cattle Breeding Federation, and was previously at the Bovine Functional Genomics Lab at the USDA-ARS. In the case study, Dr. McClure talks about using SVS at the ICBF and the results he's been able to achieve. In the webcast, Dr. McClure describes his research at the USDA-ARS to identify causal mutations for Mendelian and complex traits.Read Dr. McClure's Entire Case Study
Dr. Chaim Jalas
Director, Genetic Resources & Services
Paying per sample fees is too much. I would rather buy a software program than to ever think twice before reanalyzing a sample. It also makes budgeting less of a hassle. And Golden Helix has been around for a long time. I know that you will not disappear in a few months.Read Dr. Jalas'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 VarSeq!
Check out our free eBooks on a variety of different topics:
Watch an informative webcast featuring VarSeq in action!
- End to end solution for clinical labs
- An exploration of clinical workflows
- CNV Analysis in VarSeq
- Identifying genetic variant