New SVS Meta-Analysis Example Project The latest version of the GWAS E-book featured a chapter on Meta-Analysis. We are pleased to make the project used in this chapter available as an example project for SVS (SNP & Variation Suite). This blog post will walk you through the analysis steps used in the example project. This information is also contained in… Read more »
Yesterday, it was my pleasure to share in a live webcast our integrated solution for genetic data warehousing, VSWarehouse. If you missed the webcast live, feel free to check out the recording. Although we had a great set of questions at the end of our presentation, we didn’t have time to answer all of them, so here is a selection of… Read more »
Compound Heterozygous Workflows: Including a 2nd Affected Child Looking for Compound Heterozygous regions for a trio is fairly straight forward in VarSeq, we include this workflow in our shipped Exome Trio Template. An example of which is included with our Example Projects which can be found by going to File > Example Projects > Example YRI Exome Trio Analysis. But… Read more »
Hope everyone’s new year is off to a great start! Golden Helix has been having wonderful start and have so much to look forward throughout the year. We wanted to share with you the list of our first round of customer publications for 2016, enjoy! Petra Werner of the Children’s Hospital of Philadelphia and colleagues published MESP1 Mutations in Patients with Congenital… Read more »
With the release of our updated GWAS E-book, we have recently updated the GWAS example project (SNP Genome-Wide Association Tutorial – Complete). This updated project includes more details about how spreadsheets were generated, how to generate plots and which images were used for the GWAS E-book. This information can be found in the User Notes view in the project navigator and… 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 was named one of the Top 10 Analytics Solutions Providers for 2016 by Pharma Tech Outlook! We are very excited to be honored in this month’s issue of Pharma Tech Outlook as one of 2016’s top ten Analytics Solutions Providers. Read the interview with our CEO, Andreas Scherer here: Empowering Biologists to Perform Complex Analyis We want to… Read more »
I hope your 2016 is off to a good start! We at Golden Helix have been busy preparing and planning new and updated content for the community. First up is an updated GWAS ebook which includes a sample Meta-analysis example project. In the 2nd edition, we start with an introduction to GWAS exploring its biology and origins as well as… Read more »
There is no doubt that we have big data in the field of genomics in general and Next Generation Sequencing specifically. Illumina’s latest HiSeq X can produce 16 genomes per run, resulting in terabytes of raw data to crunch through. Yet all that crunching is not the hard part. So, what is the main obstacle to scientists being able to… Read more »
The holiday season has come to a close and we are headed to sunny San Diego for PAG XXIV! This year, our President and CEO Andreas Scherer along with Greta Linse Peterson our Director of Services and Mary Makris our Operations and Marketing Manger, will be manning the Golden Helix booth, so stop by booth 129 to say “Hi!”. Since PAG XXIII,… 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 »
Recent Customer Publications We hope everyone had a Merry Christmas! The Golden Helix team is looking forward to the start of a new year, but first we wanted to share our last round of customer publications from 2015. Here’s to many more in 2016! Bishwa Sapkota and Dharambir Sanghera of the Oklahoma University Health Sciences Center and colleagues published The Genome-wide Association Study of… Read more »
Like most, we at Golden Helix love this time of year! It is a time to spend with family and friends, creating memories and reflecting on the past year. From all of us here, to you and yours, we wish you a very happy holiday and a prosperous 2016!
As part of our ongoing commitment to empower genetic research, it is time to announce our third annual abstract challenge. Here at Golden Helix, we are dedicated to creating powerful software that enables researchers to complete complex analysis. This competition allows us to enable discovery by awarding software to those making an impact in the field. The competition has been very… Read more »
The most common use of the VarSeq Match Gene List algorithm of course is to determine if the variants in your data set are contained within your genes of interest. As an example of this, say you are working with a whole exome trio and only want to consider those variants that are contained within the 56 genes recommended by… Read more »
We have just released SVS version 8.4.2, and included in the release is a new script for visualizing Meta-Analysis results with a Forest Plot. You can find full details on all the new and updated features included with the update in our Release Notes. Release Notes from all our software products can be found on our Support Bulletin web page… Read more »
Probably one our most popular public annotation sources we curate and update is the database of Non-Synonymous Functional Predictions (dbNSFP). In it’s recent update, it has expanded the predictions to include FATHMM-MKL and VarSeq now incorporates this new prediction into its voting algorithm of now 6 different discrete predictions per variant. You can update to dbNSFP 3.0 using the built-in… Read more »
As VarSeq’s adoption has grown among analysts using whole exome data to diagnose rare diseases, a couple of family designs outside of the common trio of an affected child and both parents have come up frequently. While having both parents provides the maximum power to discover de novo mutations and recessively inherited variants, it is not always possible to contact… 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 »
From the Golden Helix family to you and yours, we wish you a happy Thanksgiving!
