Category Archives: Clinical genetics

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

         January 13, 2015

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 explains 20-30% of the longevity of those with average life-spans, it turns out there is a number of good reasons… Read more »

6 Population Catalogs Compared with the ExAC 61,486 Exomes

         November 13, 2014

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 ExAC release talk and referred to it, and those that followed the talk and referred to it. Why is this… 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 »

The New Human Genome Reference and Clinical Grade Annotations: It’s All About the Coordinates

         February 17, 2014

On my flight back from this year’s Molecular Tri-Conference in San Francisco, I couldn’t help but ruminate over the intriguing talks, engaging round table discussions, and fabulous dinners with fellow speakers. And I kept returning to the topic of how we aggregate, share, and update data in the interest of understanding our genomes. Of course, there were many examples of… Read more »

Why You Should Go To TCGC

         June 12, 2013

In a couple of short weeks, Gabe is headed off to TCGC in San Francisco where he will be giving part of a short course. He was super excited about it last year and is even more so this year. I sat down with him yesterday to find out why. Jessica: What’s TCGC? Gabe: Last year I got to attend… Read more »

GATK is a Research Tool. Clinics Beware.

         December 3, 2012

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. So recently, I was happy to see a message in my inbox from the 23andMe exome team saying they had… Read more »

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

         October 22, 2012

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 diagnosis he named Ogden Syndrome. Being so close to data that comes directly from clinical settings got me thinking about… Read more »