Golden Helix Newsletter

 
ASHG 2015
Tumor-normal demo project comes to VarSeq
by Jami Bartole,
FAS/Tech Support Rep


With the release of VarSeq 1.3.1 we have included a new demo project to showcase a single tumor-normal pair analysis workflow. The project can be accessed through VarSeq and VarSeq Viewer by going to File > Open Example Projects > Example Tumor-Normal Pair Analysis.

This project contains an exome pair (Normal-N990005 and Tumor-T990005) from the Gastric Cancer study Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes published in Nature Genetics.
Continue reading »

Summer Savings

Check out the new SNP GWAS project in SVS
by Cheryl Rogers,
Director Of Marketing


Interested in seeing what the SNP & Variation Suite (SVS) software can do? Download the free SVS Viewer! With the SVS Viewer, you can explore and interact with the workflows of a pre-built project. To get you started, we have included a SNP GWAS project for you to download.

And don't worry, it is as easy as pie! Learn More! »

VarSeq
Handling Singletons and Complex Pedigrees with Gene Count Algorithms
by Gabe Rudy,
VP of Product & Engineering


As VarSeq's adoption has grown among analysts using whole exome data to diagnose rare diseases, a couple of family designs outside of the common trio of an affected child and both parents have come up frequently.

While having both parents provides the maximum power to discover de novo mutations and recessively inherited variants, it is not always possible to contact or enlist parents in the diagnostic odyssey.
Continue reading »

VarSeq
Visualizing Meta-Analysis results with a Forest Plot
by Jami Bartole,
Senior Field Application Scientist


We have just released SVS version 8.4.2, and included in the release is a new script for visualizing Meta-Analysis results with a Forest Plot. You can find full details on all the new and updated features included with the update in our Release Notes. Release Notes from all our software products can be found on our Support Bulletin web page.

You can also find the release notes through SVS by going to Help > SVS Manual and selecting the Release Note section under the Contents menu, the most recent ones will always be at the top.
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Updates to dbNSFP
by Gabe Rudy,
VP of Product & Engineering


Probably one our most popular public annotation sources we curate and update is the database of Non-Synonymous Functional Predictions (dbNSFP). In it's recent update, it has expanded the predictions to include FATHMM-MKL and VarSeq now incorporates this new prediction into its voting algorithm of now 6 different discrete predictions per variant.

You can update to dbNSFP 3.0 using the built-in ability to move to the latest annotation in VarSeq 1.3.1 or later. Just click on the "information" icon on your variant table to see available updates and select one or all of them.
Continue reading »

VarSeq
GxE Mixed-Model Analysis Added in SVS
by Greta Linse Peterson,
Director of Services


After our announcement in August that we would be making GxE Regression available in SVS, we were pleased to receive feedback that this was exactly what our customers had been wanting. Being able to account for environmental effects or gene effects as interacting with the SNPs was essential to those researchers working with GWAS.

Unfortunately, this did not help our customers who were also working with related samples and known environmental interactions that needed to be tested. So, we were asked to add GxE interaction terms into Mixed-Model Analysis..
Continue reading »
 
   CEO Corner
Andreas Scherer
We at Golden Helix can look back at a very successful 2015. We were able to launch a slew of new products and features. We strengthened our filtering and annotation product, VarSeq, by adding capabilities such as the variant database, coverage statistics and many more. We launched VSPipeline that allows our clients to run any VarSeq defined workflow in a bioinformatics pipeline. This is crucial for larger labs with high throughput. Finally, we launched VSReports which simplifies the generation of clinical reports. This task is as simple as clicking a button with our product. On the SVS side we made numerous upgrades to our software and added new methods such as Meta-Analysis. We are very thankful for the great feedback and support from our customers and partners. On behalf of Golden Helix, I wish you a wonderful Holiday season and a successful start into the new year 2016.

   Special Software Offer!
Bundle Offer
VarSeq & SVS Bundle Offer

For a limited time, we have bundled VarSeq and the SVS software together to bring you HUGE savings!

This bundle offer provides an excellent package for small labs and research teams who work with a broad set of diagnostic and research problems.

VarSeq provides a powerful filtering and annotation engine to sift through large variant data sets, helping you to quickly and easily find the variants of importance, while SVS allows you to perform complex analyses and visualizations on genomic and phenotypic data - without programming experience.

•$6,995 for a 12 month, single-user license of VarSeq AND SVS!
•Access to OMIM, the most comprehensive annotation database for mendelian disorders is included!
•Access to OncoMD's more than 2.3 million annotated cancer variants is included!

Request your savings here! »

   Customer Success


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About Golden Helix
Golden Helix has been delivering industry leading bioinformatics solutions for the advancement of life science research and clinical and translational medicine for over 16 years. Our innovative technologies and analytic services empower scientists and healthcare professionals at all levels to derive meaning from the rapidly increasing volumes of genomic data produced from microarrays and next-generation sequencing. With our solutions, hundreds of the world's top pharmaceutical, clinical laboratories, biotech, and academic research organizations are able to harness the full potential of genomics to identify the cause of disease, improve the efficacy and safety of drugs, develop genomic diagnostics, and advance the quest for precision medicine. Golden Helix products and services have been cited in over 900 peer-reviewed publications.