NGS-Based Clinical Testing: Part II

         August 25, 2016
ngs-based clinical testing

We have come a long way since Next-Generation Sequencing (NGS) evolved as a set of technologies in the 1970s. The higher throughput and rapid reduction of costs associated with NGS have lead to the accelerated adoption of clinical testing that we are experiencing today. Currently, it is applied to analyze inherited diseases, tumors, hematologic malignancies and infectious diseases. It is… Read more »

Personalized Medicine through Tumor Sequencing

         August 23, 2016
Tumor Sequencing

Join us for a guest presentation Personalized Medicine through Tumor Sequencing by Dr. Jeffrey Rosenfeld! Wednesday, September 7th 12:00 pm EDT The identification of medications that target specific gene mutations is one of the major recent advances in cancer therapy. In 2001 Gleevec was approved to treat patients with the BCR-ABL fusion in chronic myelogenous leukemia (CML). Since then many more drugs… Read more »

FAQ: Creating Repeatable Clinical Workflows

         August 18, 2016
Repeatable clinical workflows

Question: Now that I’ve added annotation sources for my sample, filtered down to a list of interesting variants, flagged those variants and generated a clinical report, can I save or copy the annotation sources and filters for use on another sample? Short Answer: Yes! Long Answer: VarSeq was created with ease and efficiency in mind. In VarSeq, once you’ve defined… Read more »

NGS-Based Clinical Testing: Part I

         August 16, 2016
NGS Testing

The adoption of genetic services is key to our ability to provide personalized medicine in the future. The goal is to better diagnose diseases, predict their outcome, and choose the best possible care option for a patient. We still have a long way to go to achieve this goal. While there is agreement about the ultimate goal, there is still… Read more »

Guest Webcast by Dr. Rohan Palmer

         August 4, 2016

Dr. Rohan Palmer presents: Investigating Shared Additive Genetic Variation for Alcohol Dependence Wednesday, August 10th @ 12pm EDT Abstract: Molecular genetic research has supported the use of a multivariate phenotype representing alcohol dependence in studies of genetic association. One recent study found that additive genetic effects on Diagnostic and Statistical Manual of Mental Disorder version four (DSM-IV) alcohol dependence criteria overlap,… Read more »

Compute Kinship Matrices & GBLUP on Very Large Sample Sets

         August 2, 2016
Binary Data

Now available in SVS! Increasingly important in the analysis of the genotype to phenotype relationship is accurately accounting for the relatedness of samples. This is especially important to model correctly in plant and animal populations where man-directed breeding shapes the relationship structure. Along with trait association, one of the high-value use cases for genotyping animals and plants is to estimate… Read more »

Recent Customer Publications

         July 28, 2016
published

It’s that time of the month again! As usual, we have several new customer publications we would like to recognize and share with you. Please check out a few of our favorite articles: In Biological Psychiatry, Ariel Martinez and Marucio Arcos-Burgos of the National Institute of Health, as well as colleagues, published An Ultraconserved Brain-specific Enhancer within ADGRL3 (LPHN3) Underpins… Read more »

Precision Medicine leverages innovative tech advances

         July 26, 2016

We are excited to announce that earlier this month an article by our CEO, Dr. Andreas Scherer, was featured in Chronicle Pharmabiz. The article is focused on how Precision Medicine is becoming a reality by leveraging the advances in technology. The excerpt below is courtesy of Chronicle Pharmabiz. Almost 2,500 years ago, Hippocrates captured one of the key principles underlying… Read more »

Our 5 Most Watched Webcasts

         July 21, 2016
5 Most Watched Webcasts

Every month hundreds of clinicians and researchers access the variety of free resources on the Golden Helix website. Our resource library hosts eBooks, webcasts and tutorials to keep the community apprised of new methods, informed on best practices and to help our customers get the most out of their software purchase. Here is a list of the 5 most watched webcasts… Read more »

Custom Filtering using ClinVar Annotations

         July 19, 2016
ClinVar

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… Read more »

Finding Rare Mutations at the Center for Rare Jewish Genetic Disorders

         July 14, 2016
Bonei Olam

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… Read more »

Variant Normalization: Underappreciated Critical Infrastructure

         July 7, 2016
Variant Normalization

Variant Normalization: Underappreciated Critical Infrastructure 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… Read more »

Using Clinical Reports in a Gene Panel Pipeline

         June 30, 2016
Gene Panel

Upcoming Golden Helix Webcast: Using Clinical Reports as part of a Gene Panel Pipeline Wednesday, July 13th @ 12:00 pm EDT 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… Read more »

Understanding the molecular genetics of hearing loss

         June 28, 2016
Hela Azaiez

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… Read more »

June’s Customer Publications

         June 23, 2016
published

As spring ends and summer begins here in Montana, we wanted to share another round of customer publications. It’s so important to us that our software plays a role in our client’s success, and we love to display the fruit of their hard efforts each month. Here are a few of the publication highlights: Bradley Aouizerat of UCSF and colleagues published… Read more »

Bioinformatics Program Key in Precision Medicine

         June 21, 2016
Jeffrey Rosenfeld

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… Read more »

Launch of the Golden Helix eCommerce Store

         June 16, 2016
Golden Helix eCommerce

Today, we launched our eCommerce Store. With this capability we respond to our customers requesting a simplified way to conduct business with us. Here is the background on this latest development. As we continue to grow in the genomics space, the needs of our clients fall really into two categories. On one hand, there are clients who want convenient access to our… Read more »

Whole Exome Sequencing workflows in VarSeq

         June 14, 2016
Whole Exome Sequencing Workflows

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… Read more »

Diagnosing Rare Disease at King Abdulaziz Medical City

         June 9, 2016
King Abdulaziz Medical City

King Abdulaziz Medical City (KAMC) in Riyadh commenced its operations in May 1983. Since then, it has continued expanding, while providing services for a rapidly growing patient population in all of its catchments areas. Today, King Fahad National Guard Hospital has evolved to be part of the King Abdulaziz Medical City with many other prominent medical centers. Since its inauguration… Read more »

Bridging Two Worlds: Lifting Over Your Variants to GRCh38

         June 7, 2016
GRCh38

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… Read more »