Golden Helix Newsletter

Annotating Cancer mutataions
Annotating Cancer Mutations with CIViC
by Gabe Rudy
VP of Product & Engineering

While clinical assessments of germline mutations have been collected in ClinVar under the stewardship of the NCBI and the collaborate effort of many testing labs, the same type of resource has been missing for mutations that could informal clinical care in Cancer. Or at least, that is what I thought until I started to work with CIViC.

With the stewardship of Washington University in St Louis, an open source and iterative development model, an open access data licensing and a crowdsourcing but moderated wiki-like ability to submit, correct or comment on cancer mutations, it has the trajectory to become the ClinVar of Cancer.
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Genotype Imputation and Phasing Coming to SNP & Variation Suite
Gabe Rudy,
VP of Product & Engineering

One of the tools at the top of the toolbox for researchers working with microarray data is genotype imputation.Genotype imputation is the process of inferring the genotype of one or more markers based on the correlation pattern (aka linkage disequilibrium or LD) of the surrounding markers for which genotypes are known.

Last week, we announced the coming integration of a natively ported version of BEAGLE into Golden Helix's SVS software. This integration will make imputation and phasing a first-class feature. One which does not require leaving the comprehensive SVS platform to run as part of your micro-array workflow.
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Genotype Imputation
Exporting Data From VarSeq to Excel
by Hauwa Yusuf,
Field Application Scientist

True to its nature, VarSeq offers multiple data export options. You can export result tables from VarSeq to Text, VCF, a VarSeq annotation file and most importantly an XLSX (Excel) File. VarSeq's Excel export options provide a lot of flexibility in the information that is exported and preserve the formatting of data during the export process from VarSeq to Excel.

In the following example, we have performed a trio analysis on our data with 6 different inheritance patterns/workflows (De Novo Candidate, Compound Heterozygous, Recessive Homozygous, Dominant Heterozygous, X-Linked and Known Rare Pathogenic). We will explore how to use VarSeq's Excel Export option to export the data we want from VarSeq to Excel.
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We're in the news!
by Cheryl Rogers,
Director of Marketing

We are excited to announce that our CEO & President, Dr. Andreas Scherer, was featured in "The 50 Most Creative CEOs to Watch" issue of Insights Success magazine last month. The article is focused on how Dr. Scherer is leading Golden Helix to deliver top bioinformatics solutions to further enable Precision Medicine. Follow the link below to read his discussion on turning thoughts into reality.
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annotate variants
How To Annotate and Filter Variants in SVS
by Jami Bartole,
Field Application Scientist

The new Annotate and Filter algorithm is now available with the release of SVS 8.6.0, see the release notes for full details on all new and updated features. To access this new functionality, you simply need to update your SVS installation to the new version. The update can be done by clicking the Update Available link at the bottom of the Welcome Screen before opening a project.
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   CEO Corner
Andreas Scherer
This year has been fast and furious at Golden Helix. We were able to launch a number of new products such as VSWarehouse and VS-CNV. Our customer base continues to grow, in particular internationally. Since the beginning of this year, we have welcomed many new clients to the Golden Helix which we are extremely grateful for. We defined a few software packages to give those who are still on the fence a convenient starting point to work with us. Feel free to take a closer look at our end of the year offerings.

  2016 End of Year Pricing Specials!

This year we have added some very important features to our software including CNV calling in VarSeq and integrating our premium annotations into SVS. We have also made many improvements to our software's performance so that you can handle growing datasets with relative ease.

To thank our community for their support, we have annouced four special pricing offers:

�$14,995 for 2 seats of VarSeq with VSReports, CADD & OMIM.
�$35,995 for VSWarehouse with access to VSReports and VSPipeline.
�$6,995 for VarSeq with CNV Calling.
�$4,250 for SVS with CADD, OMIM and OncoMD!

Get the details & request your savings here! »

   Customer Success
We are ringing in the holidays with another round of customer's who've been published! Congrats to all for their hard work. Here are a few highlights:

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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 1,000 peer-reviewed publications.