ASHG Happenings

         October 8, 2014

It’s that time of year again. The mornings are chilly, the leaves are falling, and ASHG is right around the corner. This year will mark my very first ASHG and I am really looking forward to meeting some of the Golden Helix community! The team has been hard at work preparing for a great conference and I wanted to give you… Read more »

VarSeq: Making Variant Discovery and Gene Panels Easy

         September 29, 2014

Last week, our CEO Andreas Scherer announced our entrance into the clinical testing market with VarSeq. This week, I will be giving a webcast on Wednesday introducing this new tool and demonstrating its capabilities. (Register for the webcast) VarSeq’s focused purpose is making NGS gene testing and variant discovery efficient, scalable and accessible to users with a broad range of backgrounds and specialties. In this blog post, we will examine the use cases that VarSeq supports in more detail,… Read more »

Entering the Clinical Testing Market with VarSeq

         September 25, 2014

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 outcomes, and to choose the best possible care option for a patient. Our part here at Golden Helix is to essentially build the equivalent of an MRI for the genome. In this process the latest… Read more »

A few thoughts from IGES

         September 18, 2014

Late last month I had the opportunity to attend one of my favorite events: the annual meeting of the International Genetic Epidemiology Society (IGES).  This year’s conference was held in Vienna, in conjunction with the Genetic Analysis Workshop (GAW) and the International Society for Clinical Biostatistics (ICBS).  The program at IGES this year was very diverse, with content ranging from… Read more »

Top 3 Most Viewed Tutorials from Golden Helix

         September 12, 2014

Tutorials are ever-present in the world today, and for good reason. Why struggle through a complicated process yourself, when there is already a guide established to assist? While no one would suggest that a tutorial is the only way to complete a project, it is certainly a nice starting point. This rings true with genetic software as well. There are… Read more »

Tips and Tricks for Quality Control Metrics

         September 4, 2014

SVS offers options for performing many different QC functions on genomic data. This blog takes you through some of the most commonly applied filters for various analysis types. Filters for GWAS data vary depending on the type of association tests you are performing. A typical GWAS for a common variant usually requires filters to remove problematic or poorly called variants,… Read more »

False Positives in Big Data Analytics

         September 2, 2014

We had a lot to celebrate recently. Last year was the 300th anniversary of Jacob Bernoulli’s Ars Conjectandi. In this book he consolidated central ideas in probability theory, such as the very first version of the law of large numbers. It was also the 250th anniversary of  Bayes theorem named after Thomas Bayes (1701–1761), who first suggested using the theorem to update beliefs.

Updates to ClinVar and dbSNPs: Fresh charts for Cromonaughts!

         August 28, 2014

I’m sitting in the Smithsonian Air and Space Museum basking in the incredible product of human innovation and the hard work of countless engineers. My volunteer tour guide started us off at the Wright brother’s fliers and made a point of saying it was only 65 years from lift off at Kitty Hawk to the landing of a man on the moon…. Read more »

Top 5 Webcasts to Watch at GoldenHelix.com

         August 26, 2014

Genomic research is exploding. There is a plethora of new methods and workflows for research and clinical use. While we are a software company at heart, we find ourselves in the role of educators. Our customer interactions are about informing, teaching, and consulting. A few years back, we started with regular webcasts that took this idea to the next level…. Read more »

Genomic Prediction and How it’s Used

         August 21, 2014

Golden Helix is excited to host a webinar on Tuesday August 26th discussing the Genomic Prediction methods which were recently integrated into the SVS software. Genomic prediction uses several pieces of information when calculating its results. Genetic information is used to predict the phenotype or trait for the individuals. The phenotypic trait data can be provided for a subset or for all… Read more »

Leveraging SVS for NGS Workflows

         August 19, 2014

Over the last decade, DNA sequencing has made vast technological improvements. With the cost of sequencing decreasing significantly, sequencing technology has become a product for the masses. The sequencing technology and programs that were once used exclusively by major research institutions are now becoming available in many research facilities around the globe. These tools produce large amounts of data sets… Read more »

RefSeq Genes: Updated to NCBI Provided Alignments and Why You Care

         August 14, 2014

You probably haven’t spent much time thinking about how we represent genes in a genomic reference sequence context. And by genes, I really mean transcripts since genes are just a collection of transcripts that produce the same product. But in fact, there is more complexity here than you ever really wanted to know about. Andrew Jesaitis covered some of this… Read more »

Runs of Homozygosity Updated

         August 12, 2014

For the SVS 8.2 release we decided to improve upon the existing ROH feature. The improvements include new parameters to define a run and a new clustering algorithm to aide in finding more stringent clusters of runs. The improvements were motivated by customer comments and a recent research paper by Zhang 2013, “cgaTOH: Extended Approach for Identifying Tracts of Homozygosity,”… Read more »

SVS 8.2 – New Capabilities and Features

         August 7, 2014

Earlier this year we completed the marriage of SVS and GenomeBrowse. When we released Version 8 of SVS we completed a major engineering task. A lot of things under the hood of both products had been changed to create a seamless experience for our users. The new and improved SVS platform is based on a technology stack that allows us… Read more »

Have you ever had a bad experience with a VCF file?

         August 5, 2014

“Who has ever had a bad experience with a VCF file?” I like to ask that question to the audience when I present data analysis workshops for Golden Helix. The question invariably draws laughter as many people raise their hands in the affirmative. It seems that just about everybody who has ever worked VCF files has encountered some sort of… Read more »

And the winners are…

         August 1, 2014

Drumroll, please! Voting has come to a close for the 2014 Golden Helix T-shirt contest, and there were some clear favorites among the finalists. We are very excited at the wealth of creativity that came forward with this contest and are happy to announce that our final decisions have been made.

Guest Post: Population Structure & Genetic Improvement in Livestock by Dr. Heather Huson

         July 30, 2014

Genetic improvement in livestock, particularly dairy cattle, has been a priority for both industry and researchers for nearly a century.  While the animal itself is the foundation for improvement, our research and the implementation of improvement has progressed with developing technologies and priorities.  In terms of genetics, we have evolved from basic measures of heritability to identifying specific mutations and… Read more »

New MM-KBAC Method Explained

         July 29, 2014

Last month, June 2014, we announced a new method that Golden Helix developed–the soon to be available MM-KBAC. MM-KBAC, or Mixed Model Kernel Based Adaptive Clustering combines the KBAC method developed by Lui and Leal (2010) with a random effects matrix to adjust for relationships between samples. The KBAC algorithm takes a binary dependent variable and transformations are used to convert… Read more »