This year’s annual Abstract Challenge was once again a successful event. We want to thank all that participated. This year we had nearly 50 submissions and our decision was a difficult one. Here are the selected winners. This year, we had dual first place winners; Reza Sailani and Jingga Inlora of the Michael Snyder lab in the Department of Genetics at… Read more »
With a properly defined wet-lab and bioinformatics process, we are able to zero in on clinically relevant variants. How does a lab report on the outcome of their analysis? We find that most laboratories conduct their variant classification based on the guidelines formulated by the American College of Medical Genetics (ACMG) for inherited diseases. The ACMG guidelines for variant classification… Read more »
Acute lymphoblastic leukemia (ALL) is the most frequently diagnosed cancer in children and one of the leading causes of death due to disease in children. Dr. Daniel Sinnett, along with Pascal St-Onge and their colleagues at Sainte-Justine University Health center have been investigating the molecular determinants of the disease to improve detection, diagnosis and treatment. One particular area of study… Read more »
Clinical labs need to be able to process samples down to a short list of variants and publish a professional report. VSReports helps scientists and clinicians alike create timely, actionable reports that can improve clinical decision making and streamline patient care by seamlessly incorporating the results of tertiary analysis into a customizable clinical report. To include the VSReports functionality in… Read more »
Dr. Laura Li and her colleagues at the Children’s Hospital Los Angeles (CHLA) are working to determine the underlying genetic causes of Optic Nerve Hypoplasia (ONH), which is still unclear. ONH is the absence or under-development of the optic nerve and is currently the leading ocular cause of vision impairments and blindness in young children. ONH can also be combined… Read more »
December’s webcast will provide the Golden Helix community with a more in-depth look at CNV analysis in VarSeq. On December 7th, Dr. Nathan Fortier will discuss the challenges and metrics surrounding CNV detection and then demonstrate VarSeq’s new capability from VCF to clinical report. Wednesday, December 7th @ 12:00 PM, EST Numerous studies have documented the role of Copy Number Variations (CNVs)… Read more »
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… Read more »
After the Wet Lab process has been completed, the bioinformatics analysis of the sequencing data work begins. The next three blogs will focus on three aspects of this process. The building blocks of a bioinformatics pipeline, documentation and validation (today’s topic) Quality Management Clinical Reporting The Building Blocks of an NGS PipelineThe bioinformatics process to analyze NGS data occurs in three… Read more »
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 »
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 »
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 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 »
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 »
Submit directly to N-of-One from VarSeq If you or your lab uses N-of-One solutions for clinical annotations, here’s some good news: You can now submit directly to N-of-One from VarSeq! N-of-One’s set of preferred transcripts may differ from those outputted by our algorithms in VarSeq, so our solution was built with that in mind. Our slick, easy to use, and… Read more »
Clinical reports come in all shapes, sizes and flavors. With that in mind, our clinical reporting interface VSReports was built to be highly customizable and flexible. With a little Javascript and HTML know-how, your clinical reports can be customized to meet the needs and goals of your lab. With a little Javascript and HTML know how, you can customize yours as… Read more »
Dr. Folefac Aminkeng, first place winner in this year’s Abstract Challenge, will present his work to the community via a live webcast on Wednesday, April 20th at noon EDT. Dr. Aminkeng is a Postdoctoral Fellow at The Centre for Molecular Medicine and Therapeutics (CMMT) at the University of British Columbia in Vancouver, BC. Aminkeng’s research focus is the pharmacogenomics of adverse… Read more »
So, why are we launching a new data warehouse product? Why did we build VSWarehouse? According to Grand View Market Research, the next generation sequencing (NGS) market size was $2.0 billion (USD) globally in 2014. This number is expected to grow from 2015 to 2022 at an annual rate of about 40%. What drives this phenomenon is the increasing number… Read more »
Golden Helix in 2016 We had a terrific year 2015. It was the year in which we got serious about the clinical testing market. We successfully continued on the path of attracting more referenceable clients such as University of Iowa, Baby Genes, Prevention Genetics and many more. We rounded out our VarSeq suite by adding more clinically relevant features and… Read more »
With the release of VarSeq 1.3.1 we have included a new demo project to showcase a single tumor-normal pair analysis workflow. The project can be accessed through VarSeq and VarSeq Viewer by going to File > Open Example Projects > Example Tumor-Normal Pair Analysis. This project contains an exome pair (Normal-N990005 and Tumor-T990005) from the Gastric Cancer study Exome sequencing of… Read more »
The Golden Helix® team is gearing up for ASHG 2015 in Baltimore as I would guess many of you are too. I for one am super excited since I grew up in the Baltimore area and have a fondness for Inner Harbor and crabs! This year, you will find Ashley Hintz (our Field Application Scientist) and myself just inside the… Read more »
