Golden Helix Newsletter

 
Jeff Rosenfeld
Bioinformatics Program Key in Precision Medicine
by Cheryl Rogers,
Director of Marketing


The Bioinformatics Program at Rutgers Cancer Institute of New Jersey, the state's only National Cancer Institute-designated Comprehensive Cancer Center, plays an integral part in the center's precision medicine program helping to bring personalized medicine to patients in a timely manner. The Program needs to determine what mutations from a tumor are relevant to a particular therapeutic option, bringing the right treatments to their patients faster.With over 14 years of experience in genomic science, bioinformatics expert, Jeffrey Rosenfeld, PhD is helping Rutgers Cancer Institute to lead this charge. Being a bioinformatics expert, Rosenfeld is tasked with helping to set up a clinical pipeline that best meets the testing needs of the facility.
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Variant Normalization: Underappreciated Critical Infrastructure
Gabe Rudy
VP of Product & Engineering


It may surprise you to learn that every variant in the human genome has an infinite number of representations! Of course, although true, I'm being a bit hyperbolic to prove a point.

Even seemingly simple mutations like single letter substitutions are legitimately represented differently in the local context of other mutations that can be described as a single complex substitution, or alternatively as multiple single letter changes mixed with insertions or deletions or even potentially equally represented along different sections of a repetitive reference sequence!
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VarSeq Reports Templates
Finding Rare Mutations at the Center for Rare Jewish Genetic Disorders
by Cheryl Rogers,
Director of Marketing


Since 1999, Bonei Olam has been providing large-scale funding for fertility treatment and research. The non-profit's mission is to provide whatever means or resources necessary to help childless couples achieve the dream of parenthood. Today, it is recognized in the worldwide medical arena for its leadership role at the forefront of reproductive medicine, research and technology. Specifically, Bonei Olam has brought the joy of parenthood to nearly 6,000 couples through a myriad of programs including financial assistance, work up, medication, high-risk pregnancy, pre-implantation, genetic diagnosis, pre-and-post cancer fertility, education, awareness, and adoption assistance.
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Custom Filtering using ClinVar Annotations
by Jami Bartole,
Field Application Scientist


ClinVar is one of our most used annotations sources for a variety of workflows. It is also the public annotation source that is updated most frequently of all the sources currently supported in VarSeq. ClinVar provides new versions of their database once a month in several formats (XML, VCF, TXT). We use custom Python scripts to convert the provided VCF and text data into annotation sources that can easily be used in any of the Golden Helix products.

ClinVar can be used for annotation purposes in addition to filtering your data. The most common filter choice for this source is using the Clinical Significance field. For example, in our Exome Trio Analysis Template, the Known Rare Pathogenic filter chain looks for only those rare variants classified as Pathogenic by ClinVar.
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Bonei Olam
Understanding the molecular genetics of hearing loss
by Cheryl Rogers,
Director of Marketing


Hearing loss is the most common sensory defect in humans. It affects roughly 1 in 500 newborns, and by the age of 80 approximately 50% of people have some type of hearing loss. Hearing loss has become an enormous burden in healthcare. Perhaps more importantly, studies have shown that hearing loss also affects one's quality of life, lowering social interactions as communication deteriorates. However, for Hela Azaiez, an associate research scientist at the University of Iowa, the commonality of hearing diseases is what makes them so interesting to study.
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   CEO Corner
Andreas Scherer
We continue to expand our footprint in testing labs that have to adhere to CLIA and CAP. Our clients have to be compliant with stringent requirements regarding the storage of input, intermediate and final data files generated by the bioinformatics pipeline. This includes BAM files, VCF files and clinical reports among other things. Our VSWarehouse solution allows our clients to store relevant information and make it retrievable via a simple user interface. Also, the information stored in the genetic data warehouse can be accessed via VarSeq. Please take a look at our most recent case study we developed in collaboration with the Center for Rare Jewish Genetic Disorders to learn more!

  Latest Webcasts
Warehouse
Using Clinical Reports as a part of a Gene Panel Pipeline

VarSeq Reports can be used as part of an automatic pipeline to quickly list variants with information that can be used to make actionable clinical decisions in a readable HTML format. Need to further filter the variants or add interpretation and recommendations? No problem! Clinical reports are easy to review, edit and prepare. This webcast will walk through preparing a template for automatic report generation, running new data through the pipeline and reviewing the generated report.

Watch here!

Using WES in Distant Relationships to Identify Cardiomyopathy Genes
Cardiomyopathy (DCM; MIM 115200) are myocardial diseases that are frequently hereditary, yet remain gene-elusive for 60% of affected families. Traditional gene discovery techniques dependent on multigenerational samples are difficult to apply. In this webcast, see how Dr. Hamilton uses whole exome sequencing and analysis in SVS for gene discovery among these families.

Watch here!

   Customer Success
We kicked off July with several new publications from our customers. As always there were several outstanding articles to choose from, but we wanted to share a few of the 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.