Author Archives: Gabe Rudy

About Gabe Rudy

Meet Gabe Rudy, GHI’s Vice President of Product and Engineering and team member since 2002. Gabe thrives in the dynamic and fast-changing field of bioinformatics and genetic analysis. Leading a killer team of Computer Scientists and Statisticians in building powerful products and providing world-class support, Gabe puts his passion into enabling Golden Helix’s customers to accelerate their research. When not reading or blogging, Gabe enjoys the outdoor Montana lifestyle. But most importantly, Gabe truly loves spending time with his sons, daughter, and wife. Follow Gabe on Twitter @gabeinformatics.

  

Genomic Data is Big Data, But That is not the Hard Part

Big Data

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 »

Updates to dbNSFP – The Universal Remote of Annotation Sources

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 »

Handling Singletons & Complex Pedigrees with Gene Count Algorithms

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 »

A New and Unexpectedly Powerful VarSeq Feature

With the release of VSReports, we added the ability to “select” rows of your filtered output (often variants, but potentially things like coverage regions or genes) with a new feature dubbed “Record Sets”, but more often described as “colored checkboxes” for your tables. Although necessary for the important task of marking primary, secondary or other sets of variants for a… Read more »

OMIM Coming to VarSeq

      Gabe Rudy    September 1, 2015    7 Comments on OMIM Coming to VarSeq

When it comes to down to it, the genomic variants we collect in a research and clinical setting are impossible to interpret without that important link of how genes are related to phenotypes. Indisputably, the Johns Hopkins project to catalog all evidence related to inheritable Mendelian diseases is our best repository of this evidence. Online Mendelian Inheritance in Man (OMIM)… Read more »