Tuesday, September 4, 2007

Venter’s Genome: No Genome Is An Island

With the release of the research paper describing the personal genome of J. Craig Venter, ostensibly the first individual genome to ever be made public, we’ve got an incredible opportunity to muse about what we know so far about human genomes. And the answer is: not much today, but wait until tomorrow.

I don’t know about you, but finding out that Venter has the ear-wax characteristics of most Caucasians and has European ancestors isn’t that surprising to me. His risk for heart disease and Alzheimer’s was already known and could have been found out a lot quicker and cheaper using microarrays. And although we believe that in these early days of personal genomics, you haven’t really released all your sequence unless you’ve released the primary sequence reads with their quality score files, the release by Venter of his assembled sequences (even without the primary data) does at least allow some geno-dumpster diving. We’ll probably post a few nuggets of information about Venter that aren’t mentioned in the PLoS article in future blogs, but suffice it to say for the moment, Venter is mostly pretty normal for a white guy.

So where’s the beef? Think about any nascent network. Who did the very first people with telephones get to call? The first people establishing a network get – initially – very little benefit, aside from the well-deserved credits. The value to scientific research? Priceless. The value to the individual? Hardly.

Venter reports a lot of novel genetic variants, including copy number variations, deletions, insertions, duplications, you name it … and of course, since they are by definition novel, we don’t know what they mean other than at least they aren’t fatal or associated with obvious overt disease(s), given that Venter is alive and reasonably healthy.

For all the hoopla over the Human Genome Project, the reality is that we still know very little about the complex interplay between millions of genetic variations and environmental factors and lifestyle choices. It will take many, many individual genomes, and even more daunting, detailed comprehensive medical records, before we are able to make many of the correlations that will ultimately matter to us on a daily basis. Venter estimates a minimum of 10,000 individual genomes, and maybe, a million or more.

Let me put it another way. What’s it worth to you to get your own genome sequenced, compared to just using microarrays to determine your genotypes? Here’s my first rule of thumb: it’s worth one penny times the number of already released complete personal genomes that also have medical histories. So with Venter being #1 (OK, he actually hasn’t released any medical info really, but let’s cut him some slack), in just another 9,999 genomes I’d say your personal genome sequence will be worth about $100 more to you than whatever you could learn from genotyping yourself with microarrays (and using SNPedia, naturally).

One corollary to this is that it will be essential to get as many genomes sequenced as possible, and whether it’s from government support or celebrity genome sequencing shouldn’t matter. What matters is that the medical histories of the individuals are also made available. As is the case with genome association studies, both case-control (groups of patients with a disease; why not one of the patientslikeme.com communities?) and ‘genome cohort’ personal genome sequencing studies should be funded by whoever’s got the bucks. Comparative personal genomics, here we come!

I recall a joke that probably plenty of folks have told; I heard it from Francis Collins, the head of NIH’s Genome Project.

A previously-married woman heads to bed for the first time with her new beau, and to his surprise, she admits to being a virgin. When he wonders why, she says, “Well, I was married to a genome biologist, and every night, he just sat in bed and talked about how great our sex life would be someday.”

Someday personal genome sequences will be great for each of us to have, and it’s fantastic to have the first personal genomes coming out this year. As of today, it’s 1 (personal genome) down, at least 9,999 to go …

1 comment:

Drew Yates said...

I don't quite buy your network idea. It's not the number of people who get sequenced, but our ability to understand that sequence.

You are confusing a weak correlation between the number of people who have been sequenced with our ability to understand the genome.