Author Archives: Gabe Rudy

Gabe Rudy

About Gabe Rudy

Meet Gabe Rudy, GHI’s Vice President of Product Development 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 and wife. Follow Gabe on Twitter @gabeinformatics.

The State of NGS Variant Calling: DON’T PANIC!!

Posted on March 25, 2013 by Gabe Rudy

I’m a believer in the signal. Whole genomes and exomes have lots of signal. Man, is it cool to look at a pile-up and see a mutation as clear as day that you arrived at after filtering through hundreds of … Continue reading →

Posted in Assessment of new methods, Technology review | 4 Comments

What Can Exomes Tell Us About the Pathology of Complex Disorders?

Posted on February 26, 2013 by Gabe Rudy

My investigation into my wife’s rare autoimmune disease I recently got invited to speak at the plenary session of AGBT about my experience in receiving and interpreting my Direct to Consumer (DTC) exomes. I’ve touched on this before in my … Continue reading →

Posted in Personal genomics | 5 Comments

GATK is a Research Tool. Clinics Beware.

Posted on December 3, 2012 by Gabe Rudy

In preparation for a webcast I’ll be giving on Wednesday on my own exome, I’ve been spending more time with variant callers and the myriad of false-positives one has to wade through to get to interesting, or potentially significant, variants. … Continue reading →

Posted in Best practices in genetic analysis, Clinical genetics, Personal genomics | 17 Comments

Upcoming Webcast: 23andMe Variant Analysis of My Personal Exome

Posted on November 28, 2012 by Gabe Rudy

Join me on December 5th for a one-hour webcast as I explore my personal exome provided by the Exome Pilot project of 23andMe. Exome sequencing has seen many success stories in the realm of diagnosing highly penetrant monogenic disorders as … Continue reading →

Posted in News, events, & announcements, Personal genomics | 2 Comments

To Find a Killer Variant: Successes and Challenges on the Journey to Mass Adoption of NGS in the Clinic

Posted on October 22, 2012 by Gabe Rudy

Recently, I have been spending some time analyzing real patient data. I’m preparing for a webcast I’ll be giving in which I will walk through the process of replicating the findings of Dr. Gholson Lyon‘s study on the novel disease … Continue reading →

Posted in Big picture, Clinical genetics | 2 Comments

A Conversation with 1000 Genomes Analysis Group Member: Jeffrey Rosenfeld

Posted on August 14, 2012 by Gabe Rudy

After my latest blog post, Jeffrey Rosenfeld reached out to me. Jeff is a member of the Analysis Group of the 1000 Genomes Project and shared some fascinating insights that I got permission to share here: Hi Gabe, I saw … Continue reading →

Posted in Best practices in genetic analysis | Leave a comment

One Track to Rule Them All: Close but not quite from the 1000 Genomes Project

Posted on July 31, 2012 by Gabe Rudy

I recently curated the latest population frequency catalog from the 1000 Genomes Project onto our annotation servers, and I had very high hopes for this track. First of all, I applaud 1000 Genomes for the amount of effort they have … Continue reading →

Posted in Best practices in genetic analysis | 6 Comments

My 23andMe Trio Exomes Arrived: Sneak Peek

Posted on July 18, 2012 by Gabe Rudy

There is nothing cooler than having something arrive that you have been excitedly waiting for: last week I got an email notification that my 23andMe exome results were ready. Actually, I got 3 emails that my exome results were ready. … Continue reading →

Posted in Personal genomics | 8 Comments

Exaggerating your number of controls or being precise? “Variant not found in over 10,000 chromosomes from EVS…”

Posted on June 22, 2012 by Gabe Rudy

Reading through the last release of AJHG I saw a couple papers mention that the putative rare variant they were investigating was “not present in over 10,000 control chromosomes from the EVS”. My first reaction was, “What? Do they mean … Continue reading →

Posted in Paper review | 4 Comments

Admixture in Reference Populations: 1000 Genomes Uses African Americans in African Reference Group

Posted on June 22, 2012 by Gabe Rudy

Today I ran into an interesting fact about how a prolifically used catalog of population controls classifies African Americans with potential impacts on research outcomes. The 1000 Genomes Project is arguably our best common set of controls used in genomic … Continue reading →

Posted in Technology review | Leave a comment