Our final webcast presentation in the series of winners from our Annual Abstract Challenge is first place recipient Dr. Sergey Kornilov. A Postdoctoral Associate in the Child Study Center at Yale University’s School of Medicine, Dr. Kornilov’s submission focused on the genetic basis of developmental language disorders in a geographically isolated Russian-speaking population. Next week on October 14th, he will present his team’s research on SETBP1 as a novel candidate gene for these neurodevelopmental disorders (Join the webcast). If you are interested in learning more about Dr. Kornilov’s background and research, keep reading!
While stand-alone SVS is an amazing statistical software package for genomics analysis, adding additional Python scripts to the program can expand SVS’s genomic analysis capabilities. In this post, I’ll take you through the most frequently downloaded Add-On Scripts for SVS and the top five were not what I expected!
Coming in at Number Five is the script Convert Dosages to Genotypes. This script converts allelic dosage values to genotypes based on user-specified thresholds. The dosage data may be in Single or Double-Dosage format. The Single-Dosage format usually has data ranging from 0-2, while the Double-Dosage format has values from 0-1.
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 main doors to the exhibit hall floor in booth 311. During demos, you will also find Andreas Scherer (our President & CEO) as well as Gabe Rudy (our VP of Product and Engineering). As always, we will be giving away our somewhat famous Golden Helix t-shirts. To get yours, simply come to one of the demos below!
The 65th annual ASHG in Baltimore will be another exciting one. We at Golden Helix have been very busy this year making great improvements to both SVS and the VarSeq software and we look forward to showcasing them during our in booth demos. In particular, we will launch two new additions to the VarSeq software suite; VSReports and VSWarehouse.
VSReports brings highly customizable clinical report functionality to VarSeq, allowing you to convert the output of your tertiary analysis into a customized clinical report in one click. We presented VSReports in a webcast just last week.
Yesterday, our VP of Product and Engineering, Gabe Rudy, presented VSReports to the Golden Helix community for the first time in a live webcast; Authoring Clinical Reports in VarSeq. It was an excellent presentation. Gabe highlighted VSReports’ ability to take the output of tertiary analysis to a customized clinical grade report in one click. He also gave an overview of how our customers implement VarSeq in clinical testing workflows as well as recent updates to VarSeq. Here are a few of the key takeaways:
This month we wanted to highlight four publications from a few of our valued customers. Congrats to all!
- Zuemei Ji and Christopher Amos of Dartmouth University published The Role of Haplotype in 15q25.1 Locus in Lung Cancer Risk: Results of Scanning chromosome 15 in the Oxford Journals which analyzed lung cancer patients and a control study to determine that rs588765-rs16969968 may be a genetic marker to lung cancer risk.
- In the Expert Review of Hematology, Maria Skerenova and Jan Stasko of Comenius University, along with colleagues, published Genetic variations of the GP6 regulatory region in patients with sticky platelet syndrome and miscarriage. The study used light transmission aggregometry to establish platelet hyperaggregability, and found a higher occurrence of 3 SNPs in patients with platelet hyperaggregability and a history of miscarriage. Continue reading
The next release of VarSeq will ship a new product that is highly relevant to our customers in clinical testing labs. Via VSReports, VarSeq now has the ability to generate clinical-grade reports. These reports are fully customizable, containing focused and actionable data. VS Reports ships with report templates that are modeled off of the ACMG guidelines, the de-facto gold standard for clinicial reporting.
Templates for both hereditary and cancer analysis are included free of charge. They should cover most clinical relevant scenarios, but our Services Organization is happy to work with you to design templates specific to your needs. Additionally, reports can be branded and styled to match the documents that your lab typically produces. With tight integration to your analysis results, you can pull in additional annotation sources relevant to the sample tested.
“It’s far more important to know what person the disease has than what disease the person has.” – Hippocrates (460 BC – 370 BC)
Almost 2,500 years ago, Hippocrates captured one of the key principles underlying precision medicine. In the 21st century we take the understanding of the individual characteristics of a person to a new level. By leveraging information about an individual’s genome we are able to increase the effectiveness of medical treatments. The goal is to have more successful outcomes by providing targeted therapies.
With our latest release of VarSeq last Thursday, we are proud to offer the VarSeq ® Viewer to the community, for free! When you download VarSeq ® Viewer, you can explore pre-built projects to interact with the annotations and filters the project provides, visualize selected variants with pile-ups, and export data to widely used formats. To get you started, we have included a TruSight Cardio Gene Panel project.
The best part? Getting started is EASY!
A widely attended conference that is coming up on September 21-23 is the third international conference on Genomics 2015 in San Antonio, Texas. The theme of this year’s conference is “Implications and Impacts of Genomic Advances on Global Health“, which promises to provide some interesting presentations and discussions. Current issues in the field to be addressed include next-gen sequencing, clinical and cancer genomics, parmacogenomics, bioinformatics and biotechnology. A main focus of the conference is to deliver recent achievements and scientific advancements in each of these respective fields to the attendees.