Genotyping by Sequencing (GBS) Workflows in SVS

         March 29, 2016

Did you know you can analyze your Genotyping by Sequencing (GBS) data in SVS? Well you can! You can combine tools for both GWAS quality control and analysis with tools for NGS data analysis to either identify SNPs in your dataset or to identify differences between populations or sub-species. If your species has a reference sequence or even if you… Read more »

Getting Started with VSWarehouse – The User Experience

         March 24, 2016
VSWarehouse Updates

Wednesday, April 6th 12:00 pm EDT As the number of samples and associated data volume in a testing lab increases, it becomes imperative for labs to leverage state of the art warehousing technology that not only organizes data, but also aides and enables researchers and clinicians to perform further analysis, and ongoing research. Built on the algorithms and high-performance storage… Read more »

Golden Helix reached the 1,000 citations mark!

         March 22, 2016

Customer success is very important to us at Golden Helix. Every month we showcase their success by putting together a blog post highlighting the most recent publications. We have been compiling this list since 2003 (you can find the full list here). Today, I am very honored to announce that the Golden Helix software has assisted in one thousand publications. We have enjoyed… Read more »

Concepts and Relevance of GWAS

         March 17, 2016
Genome-Wide Association Studies

Concepts and Relevance of Genome-Wide Association Studies Genome-Wide Association Studies continue to be a very effective method for determining the underlying cause of disease, Golden Helix is happy to share our long-standing knowledge with the community. We are very happy to announce that “Concepts and Relevance of Genome-Wide Association Studies”, a paper surrounding GWAS was recently published in Science Progress… Read more »

Practical VarSeq Example – Cancer Gene Panel

         March 15, 2016

Recently, we were excited to find a new example data set for cancer gene panels. We have included this example data in the latest e-book by Dr. Andreas Scherer, Genetic Testing for Cancer as well as in the latest cancer webcast . This data is from Illumina’s MiniSeq sequencer and the TruSight Cancer panel. The BAM and VCF files for three samples… Read more »

Cancer eBook – 2nd Edition

         March 10, 2016

In 1914, the German cytologist Theodor Boveri coined the phrase “Cancer is a disease of the genome”. At this time, his ideas were as equally revolutionary as they were highly contested. Fast forward. More than a hundred years later, Next-Generation Sequencing effectively permits a highly sensitive analysis of cancer cells. It can help us to understand mutations associated with cancer… Read more »

Customer Spotlight – Dr. Kazima Bulayeva

         March 8, 2016

We, at Golden Helix, would like to take the time to highlight one of our long time customers on her recent success. Since the beginning of 2015, Dr. Kazima Bulayeva of the Vavilov Institute of General Genetics (VIGG), has published in 10 scientific publications including two times Nature Genetics. We are very excited to share the research she is performing using the… Read more »

Recent Customer Publications

         March 1, 2016
Recent Customer Publications

We want to say congratulations to all of our customers who have recently published! It’s always great to see all the new research and advancements our clients are doing, and how the Golden Helix software is assisting in that. With that, here are the most recent customer publications for the month! L. Nguyen and Russel Lyons of the University of… Read more »

3rd Annual Abstract Challenge Winners!

         February 25, 2016

Thank you to all who submitted an abstract in the 2016 Abstract Challenge, it was a great success! With more than 30 submissions and a wide variety of topics, selecting only 3 winners very difficult! With that being said, here are the top 3 winners for this year’s Abstract Challenge: Our 1st place winner is Dr. Folefac Aminkeng, Postdoctoral Fellow… Read more »

Case Study: Clinical Testing at the University of Iowa

         February 23, 2016
Dr. Benjamin Darbro

Benjamin Darbro, MD, PhD at the University of Iowa, uses VarSeq® software for Clinical Testing Founded by Hans Zellweger in the 1960’s, The Shivanand R. Patil Cytogenetics and Molecular Lab at the University of Iowa has a long history of clinical testing, seeing 45 years of advancements. Today, the lab is mainly focused on oncology, pre and post-natal genetics testing… Read more »

Cancer Workflows in VarSeq

         February 19, 2016
VCF file format

Wednesday, March 2nd 12:00 pm EST Clinical labs must have the ability to go from a collection of samples and associated variants to a professional report documenting a short list of clinically relevant variants. Cancer Gene Panels are a common clinical application for genetic tests. In this webcast we will show how VarSeq and VSReports can be used to go… Read more »

Quality Assurance Sample Statistics Added To VarSeq

         February 18, 2016
VarSeq

As VarSeq continues its adoption amongst clinical labs and researchers looking for reproducible workflows for variant annotation, filtering and interpretation, we have continued to prioritize the addition of features to assess the quality of the upstream data at a variant, coverage and now sample level. The  Importance of Quality Assurance Sample prep and sequencing problems are difficult to detect through the analysis… Read more »

The Golden Helix Soccer Team

         February 16, 2016
Golden Helix Soccer Team

The Golden Helix Soccer Team I recently received a very special email from a long time Golden Helix customer, Dr. Vanessa Hayes of the Garvan Institute of Medical Research in Sydney, Australia. In 2010 Dr. Hayes, then of the J. Craig Venter Institute, joined several colleagues in collaboration on The Southern African Genome Project. The project was aimed at including African genomes in existing… Read more »

Scaling is in our DNA: Making Genomics Accessible

         February 11, 2016
Scalable Data

Scaling is in our DNA: Making Genomics Accessible One of the things I absolutely love about the work we do at Golden Helix is keeping up with the changes in data analysis driven by the iterative and generational leaps in technology. But one thing has always been a constant since day one: we break preconceived notions of what scale of… Read more »

Genetic Data Warehousing e-Book

         February 10, 2016
Genetic Data Warehouse

Genetic Data Warehousing e-Book In our webcast last week, we announced the upcoming release of VSWarehouse, a scalable genetic data warehouse for VarSeq. Genetic data warehousing becomes more important as Next-Generation Sequencing is taking off in the clinic, creating significant data management issues for clinicians, scientists and IT professionals alike. How can we retain the massive amounts of data coming out… Read more »

New SVS Meta-Analysis Example Project

         February 9, 2016
SVS 8

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 »

Q&A from the VSWarehouse Launch Webcast

         February 4, 2016
VSWarehouse Updates

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

         February 2, 2016
VarSeq

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 »

Recent Customer Publications

         January 28, 2016
published

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 »