Author Archives: Gabe Rudy

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.
Gabe Rudy

Analyze Your 23andMe Genotype Files with Golden Helix

I was definitely an early adopter when it comes to personal genomics. In a recent email to their customer base announcing their one millionth customer, they revealed that I was customer #44,299. And I have been consistently impressed with the … Continue reading

Posted in Personal genomics, Public data & annotations | Tagged , , , | Leave a comment
Gabe Rudy

The Clinical Genome Conference 2015 Highlights

This last week I had the pleasure of attending the fourth annual Clinical Genome Conference (TCGC) in Japantown, San Francisco and kicking off the conference by teaching a short course on Personal Genomics Variant Analysis and Interpretation. Some highlights of … Continue reading

Posted in Best practices in genetic analysis, Clinical genetics, Public data & annotations, Technology review | Tagged , , , , , , | Leave a comment
Gabe Rudy

VarSeq is a better ANNOVAR, snpEff and VEP

Yes, I said it. “Them be fighting words” you may say. Well, it’s worth putting a stake in the ground when you have worked hard to have a claim worth staking. We have explored the landscape, surveyed the ravines and … Continue reading

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Gabe Rudy

Accurate Annotations: Updates to the NHLBI Exome Sequencing Project Variant Catalog

Since its early release in early 2012, the population frequencies from the GO Exome Sequencing Project (ESP) – from the National Heart, Lung and Blood Institute (NHLBI) have been a staple of the genomic community. With the recent release of … Continue reading

Posted in Bioinformatic support | Tagged | 1 Comment
Gabe Rudy

Unique Labs, Common Tool: Making VarSeq Ready for Clinical Workflows

As VarSeq has been evaluated and chosen by more and more clinical labs, I have come to respect how unique each lab’s analytical use cases are. Different labs may specialize in cancer therapy management, specific hereditary disorders, focused gene panels … Continue reading

Posted in Best practices in genetic analysis, Clinical genetics | Tagged | Leave a comment
Gabe Rudy

Supercentenarian Variant Annotation: Complex to Primitive

In a previous blog post, I demonstrated using VarSeq to directly analyze the whole genomes of 17 supercentenarians. Since then, I have been working with the variant set from these long-lived genomes to prepare a public data track useful for … Continue reading

Posted in Public data & annotations | 2 Comments
Gabe Rudy

What TriCon 2015 Foreshadows for Clinical Genomics

I spent a very eventful week at the Molecular TriCon in downtown San Francisco, and have been pondering the very clear trends that emerged by attending the clinical and NGS focused talks. Cancer gene panels make sense economically and as … Continue reading

Posted in Big picture, News, events, & announcements | Tagged , , , , , , | 2 Comments
Gabe Rudy

In Pursuit of Longevity: Analyzing the Supercentenarian Whole Genomes with VarSeq

If you haven’t been closely watching the twittersphere or other headline sources of the genetics community, you may have missed the recent chatter about the whole genome sequencing of 17 supercentenarians (people who live beyond 110 years). While genetics only … Continue reading

Posted in Best practices in genetic analysis, Big picture, Clinical genetics | Tagged , | 103 Comments
Gabe Rudy

6 Population Catalogs Compared with the ExAC 61,486 Exomes

To say the announcement of Dan MacArthur’s group’s release of the Exome Aggregation Consortium (ExAC) data was highly anticipated at ASHG 2014 would be an understatement. Basically, there were two types of talks at ASHG. Those that proceeded the official … Continue reading

Posted in Big picture, Bioinformatic support, Clinical genetics, Uncategorized | Tagged , , , , | 7 Comments
Gabe Rudy

VarSeq: Making Variant Discovery and Gene Panels Easy

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 … Continue reading

Posted in Big picture, News, events, & announcements | Tagged , , , , | 2 Comments