Golden Helix Newsletter

Precision Medicine
Command-line Interface added to Golden Helix's VarSeq Software
by Cheryl Rogers,
Director of Marketing

Golden Helix recently announced the addition of VSPipeline to our VarSeq software. VSPipeline is a command-line interface that will allow high throughput environments the ability to tap the full power of VarSeq's algorithms and flexible project template system from any command line context, including existing bioinformatics pipeline.

VSPipeline supports the need to efficiently generate VarSeq projects from workflow-encoding project templates. Out of these automated pipelines will come fully produced VarSeq projects, ready for the technical and medical staff to jump into variant interpretation and reporting.
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Precision Medicine � Part VI - The Educational Challenge
by Dr. Andreas Scherer,
President & CEO

Precision medicine will fundamentally change how health care is practiced. Of course, we have a long way to go. For most practitioners today, their knowledge of the human genome was established many years ago. However, new therapies and diagnostic methods are pouring in on a daily basis. So, how do we make sure that the current and future health care workforce understands the complexities and intricate details of this field?

A starting point is a better understanding of how to use an individual's genomic information to determine targeted treatment options, tailored to the individual patient. This requires:
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Golden Helix's VarSeq Software to Incorporate MedGenome's OncoMD
by Dr. Cheryl Rogers,
Director of Marketing

Today at Golden Helix, we are proud to announce our collaboration with MedGenome through an integration of OncoMD into our VarSeq software. Now VarSeq's streamlined process of annotating and filtering variants will offer an added dimension.

OncoMD is a comprehensive knowledge base of cancer-specific genetic alterations, and by incorporating it into VarSeq, users can access to 2 million plus annotated cancer variants. Not only does this addition allow users to quickly prioritize actionable variants, but also make clinical decisions based on the sensitivity of variants to approved drugs and enrollment to open clinical trials.
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What's in a Name: The Intricacies of Identifying Variants
by Andrew Jesaitis,
Prodcut Manager & Senior Software Engineer

There's a strong desire in the genetics community for a set of canonical transcripts. It's a completely understandable and reasonable thing to want since it would simplify many aspects of analysis and especially the downstream communicating and reporting of variants. Unfortunately, biology isn't so tidy as to provide a clear answer for which transcript is the important one. Consequently, there isn't a single resource that lists the "canonical" transcript for each gene. And while there have been some attempts to label important transcripts, like Ensembl's "Gold" identifier, ultimately the issue is punted downstream to the lab.
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Baby Genes is raising the bar for Newborn Screening
by Cheryl Rogers,
Director of Marketing

It is standard practice for newborns to be screened for genetic diseases before leaving the hospital to assess for serious medical conditions that, left untreated, can cause lifelong health problems or in some cases, early death. What is not standard is which and how many conditions are screened for in each state. And in many states, the number of conditions screened simply isn't enough.

This means there are children all over the United States who are not being screened for serious genetic diseases they may have. By the time parents or physicians recognize the condition, serious, sometimes irreparable damage may already have been done. Baby Genes, a CLIA certified clinical laboratory formed in 2013 in Colorado, is trying to change this.
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   Latest Webcast
Using VarSeq to Improve Variant Analysis Research Workflows
Many questions must be answered when analyzing DNA sequence variants: How do I determine which variants are potentially deleterious? Is the sequencing quality sufficient? How do I prioritize the results? Which annotation sources may help answer my research question?

This webinar reviews workflow strategies for quality control and analysis of DNA sequence variants using the VarSeq software package from Golden Helix. VarSeq is a powerful platform for analysis of DNA sequence variants in clinical and translational research settings. VarSeq provides researchers with easy access to curated public databases of variant annotation information, and also enables users to incorporate their own local databases or downloaded information about variants and genomic regions.

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About Golden Helix
Golden Helix has been delivering industry leading bioinformatics solutions for the advancement of life science research 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, 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 personalized medicine. Golden Helix products and services have been cited in over 850 peer-reviewed publications.