Saturday, March 1, 2014

Blogging My Genome, episode 1: parting with my blood (and treasure)

After learning about Illumina's Understand Your Genome (UYG) program at ASHG 2013, I decided to go ahead and sign up to get my genome sequenced. This is the first in a series of blog posts I'll write about my own adventure in very personal genomics!

UYG gets you:
  • "Deep" whole-genome squencing (WGS) from a blood sample
  • Bioinformatics and clinical interpretation through Illumina's CLIA lab
  • Report sent to your clinician
  • Raw data on a portable hard drive
  • Day-long workshop with other participants
  • iPad with the MyGenome app
...for $5,000, which isn't too bad given what's included. The pricing probably reflects that the program is mainly an outreach effort aimed at subject matter experts.

It seemed a little too easy to use Illumina's online form to put five grand on my credit card, but I suppose airline tickets can get up in that range too. (I can only presume X Ten purchasing is another matter!) Anyway, shortly thereafter the kit you see at the right appeared on my doorstep. We have some literature and forms, a blood sample collection tube, and a return shipping box addressed to Illumina's lab in San Diego.

Despite being charged to your credit card, UYG is not a direct-to-consumer (DTC) operation, so the sample collection and results delivery must be coordinated through a clinician - ideally one with genetic counseling resources - which is not included in the $5,000. I first tried sending my primary care physician an e-mail through kp.com, which produced a (very understandably) perplexed reply. I was also able to get in touch with KP's genetics department in San Francisco, which generated some interest and curiosity, but this also fell through. None of this is very surprising given that we're in the really early days of clinical WGS, especially in the absence of medical indications.

Fortunately, Illumina put me in touch with Dr. Euan Ashley at Stanford, who studies and practices clinical genome sequencing for cardiovascular conditions. We set up an appointment with a genetic counselor he works with - also one of the few with WGS experience - who patiently interviewed me at the Stanford medical center to make a pedigree of my extended family, annotated with any potentially genetic health issues therein. After that, I went downstairs to the lab:

Needle technology has gotten quite interesting over the years.

I'm curious about the prospects for DTC here given that saliva samples are not preferred for WGS. Exome sequencing and SNP-chips, in contrast, are just fine with saliva - which tends to have more contaminant DNA compared to blood or tissue - since their protocols involve powerful steps to purify the desired human DNA. Anyway, there's a much bigger issue facing DTC WGS today, namely its extremely limited actionability above and beyond those less expensive options - but we'll get to that in this series.

Once my sample was shipped off there was a three-month wait, during which Illumina sent a few generic e-mail updates about the process. Next episode: I get my results!