Golden Helix Newsletter

CNV Calling
Why Call CNVs: Getting More from your NGS Data
by Gabe Rudy
VP of Product & Engineering

Copy Number Variants have been important to clinical genetics for quite a while now. So, what has made now the right time to be looking at calling CNVs from NGS data? Well, there are a number of good reasons. The dominant one is simply that the NGS data you are already creating for calling variants can be used in many cases to make high-quality CNV calls. So why not use it, and potentially save the time and resources on not doing additional tests to call CNVs?
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CADD, OMIM and OncoMD Coming to SVS
Alison Figueira
Software Engineer

For our upcoming SVS 8.6.0 release, we've updated our Annotate and Filter Variants feature to utilize our powerful VarSeq annotations. Annotations can be run against gene, interval, variant, and tabular tracks, including RefSeq, ClinVar, CADD, OMIM and OncoMD. The new streamlined dialog allows users to select track specific options and to set up custom filters.

While our public annotation repository has been previously available in SVS, they are now more powerfully integrated with more advanced filter and annotation control.New in this release will be our licensed premium annotation sources including CADD pathogenicity scores, full OMIM gene and variant annotations and the curated cancer mutation, gene and drug targeting mutation data from OncoMD.
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NGS-based clinical testing
Quality Management in Clinical Testing
by Andreas Scherer,
President & CEO

Any validated bioinformatics pipeline must be continuously monitored. Quality management in clinical testing labs ensures that any divergence from predefined quality metrics during the analysis of clinical samples is investigated. For example:
  • There is an insufficient number of sequence reads that passed the predefined base quality score threshold
  • The number of variants identified in a data set may deviate substantially from an expected value
An appropriate quality management system is designed to provide the framework to deep dive into any divergences from the designed analytical process.
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Final thoughts on ASHG 2016
by Andreas Scherer,
President & CEO

ASHG 2016 is in our rear mirror. Again, it was bigger and better than the previous year. The conference hosted over 9,000 visitors from 66 countries. This gave the event a level of vibrancy that was evenly matched by the wonderful ambiance of the city of Vancouver. Nestled in between the two conference centers was a little pier offering spectacular views. For us as a company, the conference was a success. Our booth was well attended over the three days, and we had four demos every day on several topics.
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Sergey Kornilov
Using GWAS to investigate neurodevelopmental disorders
by Cheryl Rogers,
Director of Marketing

Dr. Sergey Kornilov, a Duncan Scholar in Molecular and Human Genetics at Baylor College of Medicine, combines his broad psychology background with genetics to research the genetic basis of neurodevelopmental disorders with a unique dual perspective. Neuro-developmental disorders, for example, those of the spoken and written language, affect many worldwide � up to 10% of preschool children. In most cases, these disorders persist into adulthood which brings about a host of negative outcomes seen academically, occupationally and interpersonally.
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   CEO Corner
Andreas Scherer
The month of October was a very busy one! We had to get ready for ASHG in Vancouver, which was a huge success for us. Please read my summary here. We also launched our premium annotation sources including OMIM, CADD and OncoMD within SVS. We have received tremendous interest from our customer base. You can read more in this blog. Last but not least, we announced the ability to conduct CNV analysis within VarSeq. This is an important area that we will continue to invest R&D resources into going forward. Our ultimate goal is to create a platform that can conduct most if not all tests currently covered by CMAs within VarSeq, so stay tuned.

  Latest Webcasts
Getting More from your NGS Data: CNV Calling of Target Regions

Copy Number Variations (CNVs) play an important role in human health and disease, and the detection of CNVs in clinical samples has the potential to improve clinical diagnoses and inform treatment decisions. Yet until now, if you wanted to have CNVs on your targeted gene samples, you would need an alternative assay such as Chromosomal Microarrays (CMAs).

While we consider the handling of the variety of target panels and exome capture scenarios a process of iterative improvement, we will demonstrate the high precision characteristics of our algorithm on our clinical validation data sets.

Watch here!

   Customer Success
Every month we see customer's publishing and October was no exception! Please check out what a few of them have accomplished:

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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.