Golden Helix Newsletter

Clinical Lab Architecture
Golden Helix announces Partnership with Sentieon
by Andreas Scherer
President & CEO

Today, we are happy to announce a multi-year partnership with Sentieon, a company that develops bioinformatics secondary analysis tools to process genomic data. This partnership will integrate Sentieon's secondary analysis tools with Golden Helix software to provide users with a comprehensive solution for genomic data analysis. Sentieon's suite of secondary analysis tools made significant improvement in runtime over BWA-MEM, GATK, Mutect, and MuTect2 while providing deterministic and identical results. There are some very cool white papers that describe the performance improvement in more detail. You can find those here.
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Clinical Lab Architecture
Golden Helix's End-to-End Architecture for Clinical Testing Labs
by Andreas Scherer
President & CEO

Precision Medicine and the usage of Next-Gen Sequencing to conduct genetic tests is rapidly growing. NGS based tests are increasingly used in therapeutic areas such as oncology, pediatrics and newborn screening and rare diseases.

There is also strong potential in areas such as diabetes and cardiac disorders, as well as in pharmacogenomics to determine safety, efficacy and cost of care. New applications of genetic testing will result in changes to current care, teams and processes. This trend reshapes how pathologists, clinicians, geneticists, genetic counselors, biostatisticians and bioinformaticians work together. The genetic testing technology and infrastructure has evolved quickly.
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Annotating with gnomAD
Annotating with gnomAD: Frequencies from 123,136 Exomes and 15,496 Genomes
by Gabe Rudy,
VP of Product & Engineering

When the Broad Institute team lead by Dan MacArthur announced at ASHG 2016 that the successor to the popular ExAC project (frequencies of 61,486 exomes) was live at, I thought their servers would have a melt-down as everyone immediately jumped on and started looking up their favorite genes and variants.But although the web interface was up, it would be a long four months until the downloadable bulk variant frequencies were made available.

We have just recently finished our curation and QC of these tracks, and have made them available today for usage in VarSeq, SVS and GenomeBrowse.
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New Tutorial: VSReports
by Steve Hystad,
Field Application Scientist

The new VSReports tutorial covers a basic VSReports workflow with an emphasis on understanding and exploring report customizations. This tutorial requires an active VarSeq license with the the VSReport feature included. You can go to Discover VarSeq or email to request an evaluation license with the VSReports functionality included.
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ESHG 2017
ESHG 2017 � Heading to Copenhagen!
by Mary Makris,
Marketing & Operations Manager

In just a few days, Golden Helix will arrive in Copenhagen, Denmark to attend the 2017 European Society of Human Genetics Conference (ESHG). We are excited to be returning to ESHG for the second year in a row! It's always a pleasure to see our European customers and meet some new faces in the community.

We will host a series of demos in booth #312 over the course of the three days that the exhibit hall is open. The demos will span both research and clinical workflows and range in topics from GWAS and imputation to clinical testing and data warehousing. Directly after our demos, we will hand out our famous Golden Helix t-shirts.

See the full demo schedule here »
   CEO Corner
Andreas Scherer
We have made tremendous progress with our CNV analytics. With the upcoming release of VarSeq and VS-CNV, we will provide comprehensive CNV analysis for gene panels, clinical exomes and whole genomes. In addition, we entered into a strategic partnership with Sentieon. This gives our clients access to a powerful alignment and variant calling technology. Combined, we have now an industry-leading secondary analysis stack. What excites us most is that this is not only very valuable for our clinical clients; the same product combination adds significant value to our customers focusing on human, plant and animal research.

  Latest Webcast
The Sentieon Genomic Tools - Improved Best Practices Pipelines for Analysis of Germline and Tumor-Normal Samples

The Sentieon Genomics Tools provide identical results to the GATK pipelines with a 10x reduction in runtime, a robust software implementation, and deterministic data processing. This webcast will explore the benefits of the Sentieon Genomics Tools including a discussion of the results of the PrecisionFDA Truth and Consistency challenges and the ICGC-TCGA DREAM Mutation Calling Challenge for somatic SNV, indel, and structural variants. In this webinar, Dr. Andreas Scherer delves into Golden Helix's new partnership with Sentieon and Dr. Donald Freed explains the genomic tools. Watch here.

P.S. Here is some Q&A from the webcast you can read here!

   Customer Success
As usual, we would like to share some of the articles that our clients have published recently citing our software. These articles are incredibly diverse and interesting, and we hope you enjoy browsing through them:

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About Golden Helix
Golden Helix� is a global bioinformatics firm founded in 1998. Our largest outside investor is GlaxoSmithKline who invested early on into the company. We develop and sell an industry leading clinical solution that supports the analysis of sequencing data and the creation of clinical reports. Clinicians and researchers worldwide trust our solution. Over all these years we have accumulated a significant customer base conducting business with over 350 organizations globally with thousands of users leveraging our various analytics products. Our customers fall into five categories: Large Hospitals, Genetic Testing Labs, Pharmaceutical companies, major research organizations, and government organizations here in the US and internationally. Our work his referenced in over 1,100 publications such as Science, Nature and Nature Genetics.