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 »

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 »

The added value of GenomeBrowse

         July 17, 2014

We released GenomeBrowse 2.0 earlier this year, allowing users to review all types of genomic data. Since then, it has received rave reviews from thousands of users around the world. Essentially, it’s the Google Earth app for genomic data. GenomeBrowse allows a user to sift through vast amounts of genomic data, and make it easy to focus on a single part… Read more »

Introducing Dr. Heather J. Huson

         July 16, 2014

It is with great excitement that we introduce our next webcast: Population Structure & Genetic Improvement in Livestock, presented by Dr. Heather J. Huson of Cornell University. Huson was one of the first place winners in this year’s research abstract competition. As part of the competition Huson has the opportunity to present her research in a webcast on Tuesday July… Read more »

Join us for a GWAS in Arabidopsis Thaliana

         July 8, 2014

Join us tomorrow, July 9th at 12PM EDT, for Ashley Hintz’s webcast on GWAS in a Model Organism: Arabidopsis Thaliana. Joining the Golden Helix team as a Field Application Scientist in April of 2014, Hintz is the perfect candidate to present on Arabidopsis Thaliana given her background in zoology and phylogenetics of planigales.

The State of Variant Annotation: A Comparison of AnnoVar, snpEff and VEP

         June 25, 2014

Up until a few weeks ago, I thought variant classification was basically a solved problem. I mean, how hard can it be? We look at variants all the time and say things like, “Well that one is probably not too detrimental since it’s a 3 base insertion, but this frameshift is worth looking into.” What we fail to recognize is… Read more »

2014 Golden Helix Summer School

         June 12, 2014

We are incredibly excited to sponsor the 2014 Golden Helix Summer School (not directly affiliated with Golden Helix, Inc. (us)), hosted on the island of Aegina, Greece, from September 11th-15th, 2014.  This year’s theme is “Pharmacogenomics and Genomic Medicine: Bridging research and the clinic” and will focus on disciplines within genomic medicine. The Golden Helix Summer School, conducted annually, is a… Read more »

Two New Regression Scripts

         May 29, 2014

We are excited to let you know about two new scripts to aid in Numeric Regression analysis. Don’t forget about the Technical Support Bulletins which keep you up-to-date on all the latest script news. You can stream this feed via an RSS reader, receive email updates, or see the latest on the SVS splash screen. Linear and Logistic Regression with… Read more »