Golden Helix Newsletter

CIO Review
Diagnosing Rare Disease at King Abdulaziz Medical City
by Cheryl Rogers,
Director of Marketing

Dr. Majid Alfadhel and Dr. Ahmed Alfares are two well established and recognized scientists working in Riyadh. Both doctors are focused on applying NGS technology to diagnose rare diseases, specifically focusing on health issues resulting from consanguineous marriages in Saudi Arabian populations.
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Variants to GRCh38

Bridging Two Worlds: Lifting Over Your Variants to GRCh38
Nathan Fortier
Senior Software Engineer

When the new human reference genome was released over two years ago, it was hailed as a significant step forward for next generation sequencing. Compared to GRCh37, the new GRCH38 reference assembly fixed gaps, repaired incorrect sequences and offered access to sections of the genome that had been previously unaccounted for.

Despite these improvements, adoption of the new assembly has proven to be a headache for many researchers. Whether due to the lack of required annotations, or the weight of their archived data on GRCh37, some organizations have chosen to simply stick with the old assembly while others have begun using GRCh38 on new projects leading to data that can not be compared between the different versions.
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VarSeq Reports Templates
VSPipeline Tips and Tricks
by Aiden Bickford,
Software Engineer

The power of VSPipeline is in it's ability to automate VarSeq workflows. Using VarSeq to create a pipeline template is great because it allows you to dial in the applied filters as well as interactively organize the annotations and applied algorithms. Automating a workflow with VSPipeline is straightforward when beginning with an existing project. However, there are several steps that can be taken to make the process even easier and give you more control over the final results. Here are a few�
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Whole Exome Sequencing workflows in VarSeq
by Jami Bartole,
Field Application Scientist

Whole exome sequencing workflows using SNP & Variation Suite (SVS) was presented in a recent webcast, by Dr. Robert Hamilton from the Hospital for Sick Kids. In particular, he performed some filtering on his data to look for only heterozygous variants in his sample of interest, removed variants with allele frequency less than 0.005% based off of the ExAC Variant Frequency catalog and lastly performed some filtering based on coding classifications determined by the variant classification algorithm.

All of these annotation and filtering options can also be performed using our VarSeq software, and once the workflow is complete in VarSeq you can easily replicate the workflow on new samples using the available templating options. We will take a look at each filter options between the two products.
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GBS Workflows
Using Pharmacogenomics to teach Intro to Chemistry
by Cheryl Rogers,
Director of Marketing

Since our introduction of the mixed model methods in SVS, along with GBLUP, we have been very pleased to see it used by a number of customers working with human and agri-genomic data. As these customers have grown their genomics programs, the number of samples they have for a given analysis has been growing, and at times exponentially!

Up to this point, scaling these algorithms has just been about doing the analysis on an adequately large computer (specifically one with sufficient memory to hold these large N2 matrices, where N is the number of samples).
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   CEO Corner
Andreas Scherer
We are happy to announce that this week we launched our Golden Helix online store. Allowing customers to purchase our software online is a step forward towards providing global prospects easy-access to our products. By using the online store, potential customers can follow a simple order process and make an electronic payment. We hope this will help remove the often complex process of generating a PO. Additionally, to lower the large, upfront capital investments that can be a barrier to entry for many customers who need our software solutions, we will allow some of our packages to be purchased on a monthly payment plan to help spread out the cost over time. Please feel free to browse the online store here!

  Special Offer!
Bundle Offer
Limited Time Offer on VarSeq Packages

From research labs to NCI cancer labs to clinical testing labs, VarSeq has been gaining significant traction. VarSeq saves labs time and money by providing a proven and integrated testing pipeline from VCF to clinical report.

This entire solution is offered at an affordable annual subscription license. Our users are gaining efficiency and saving tens of thousands of dollars by avoiding per sample charges. In times of uncertain funding and tight budgets, we are providing unbeatable offers to bring efficiency and savings to your lab.

Small Lab Starter Package - Save with a VarSeq & SVS bundle!
VSReporting Package - Access to VSReports and 2 seats of VarSeq with CADD, OMIM & OncoMD included!
Warehouse Package - VSWarehouse, VSReports and VSPipeline all bundled into one to create a fully integrated analytics solution!

See the details & pricing for all three special offers here!

   Customer Success
The final month of spring brings another round of customer publications. Our talented clients continue to do ground-breaking research, and we are happy to be a small part of it! Here are a few interesting pubs from June:

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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.