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Spec Tech: Your Genome Sequence is (Almost) Here

July 22, 2010

Moore’s law describes how the cost of transistors for computer integrated circuits has halved every two years, laying the groundwork for the idea that computing power increases at an exponential (rather than at a linear) rate. Applied across all areas of technology, the idea of exponential change leads to the concept of The Singularity, a point in the near future at which what happens next becomes wildly unpredictable.

In my own field of biology, DNA sequencing best exemplifies the exponential growth rate of a technology. The cost of sequencing DNA is dropping so quickly that within ten years most of you reading this will have had your own genomes sequenced. By that time the cost probably won’t be that much different from having your teeth cleaned. So I want to consider some of the repercussions of this information. The key point is that we aren’t just talking about near future in this discussion, but near near future, where for some people the future has already arrived.

The haploid human genome is 3 billion base pairs and encodes about 25,000 genes. The publicly funded project to sequence the human genome began in 1990, but it wasn’t until 2003 that a completed human genome sequence was published. The estimated cost for this project was $3 billion. But, as I said, the cost of sequencing is constantly dropping. A private company called Celera embarked on their own human genome-sequencing project in 1998 and completed the project more quickly than the publicly funded project, and at a ten-fold lower cost.

But although one can say that we have sequenced the human genome, all this has done is lay out the general blue-print for a human being. It isn’t the specific combination of gene sequences that make you the special you that we all know and love. There are different versions (alleles) of genes spread throughout the population. For example, different versions of the genes that dictate eye color are what give you blue, green, hazel, or brown eyes. In addition to the common variants, there may be mutant versions of genes. For example, a mutation in the gene encoding hemoglobin (the protein that transports oxygen in our bodies) results in the genetic disease called sickle cell anemia. Another example: a mutation in the gene CCR5 has the benefit of protecting against smallpox and HIV infection, but makes one more susceptible to the West Nile virus. The point here is that knowing the specific sequence of your own genome can say a lot about who you are, not everything mind you—it’s not just nature, it’s also nurture—but enough that you and other folks might be interested in knowing your personal genome sequence.

That these DNA sequencing technologies are actually starting to impact people at a personal level was brought home to me at a science conference this past spring. Over dessert and many cups of coffee, one of the scientists mentioned that he had recently had his genome looked at. He hadn’t had his genome fully sequenced, but he had used an approach called SNP (for small nucleotide polymorphisms) to examine 500 or so of his genes to see if he had any variants of interest. He took another sip of his coffee—his third cup of the evening I might mention—and said there was one variant that really stood out: it was in a gene for the enzyme that helps you metabolize caffeine.

No surprise there in retrospect.

Right now, if you want, you can have a similar genetic analysis performed by any one of a host of personal genomics companies. These include deCODEme, 23andMe, and Nvigenics. These companies will look at your genetic risk for various diseases (e.g. cancer, cardiovascular) or your ancestry based on different gene variants. Costs typically range from $500 to $2000 depending on the extensiveness of the testing. And all it takes is a cheek swab.

But that’s not quite the same as a whole genome sequence, you may be thinking to yourself. How much does it cost to get my full genome sequenced, not just pieces of a few hundred genes?

Well, personal genome sequencing is also being performed. It’s not quite as cheap as the analyses described above but it is happening.

In 2007, Knome became the first company to sequence the genome of a private customer.

In October 2008, Complete Genomics offered to sequence human genomes at a cost of $5000 each (not including cost of labor and computer analysis), and by September 2009 had sequenced genomes for 14 customers. Furthermore, they plan to sequence 5000 human genomes in 2010 and a million human genomes by 2014.

And these companies aren’t even using the newer, better, and faster sequencing technologies being developed. Take a look at this video showing the new sequencing method developed by Pacific Biosciences, a methodology that I find beautiful in concept and awe-inspiring in terms of the nano-scale technology that brings it off. Think, tiny nanowells containing zeptoliter (yes, zeptoliter!) quantities of reagents, and thousands of DNA fragments being sequenced simultaneously based on tiny puffs of fluorescence. I repeat, check out the video. It’s amazing.

So, given the technologies that are available and the rapidly dropping cost, I don’t think it takes any great stretch of the imagination to say that your own genome will have been sequenced within the next decade. That is, if you want to have it sequenced. There’s always that. So lets consider some of the repercussions of having a genome sequenced. What is gained and what is lost?

Just a couple of weeks ago, a group of Boston University scientists, announced they had identified 150 genetic markers that correlate with extreme longevity. These represent allelic variations of at least 70 different genes that allow one to identify those people more likely to live past 100 years old. Do you want to know this? Or, what about all those genes linked to health? I already mentioned that you can have your genetic propensity for different genetic diseases characterized right now for a few hundred dollars. Do you plan to send in your cheek swab? Maybe you want to know this information. Maybe not. Maybe you won’t have a choice. But, Boy Howdee, don’t you just know the insurance companies are slavering at the chops to get this kind of info, and to take it into account when setting rates if the law will ever allow it. Think identity theft at the genomic level. Think about genomic information being sold to those who could most profit from the knowledge.

Or think about the desire and ability to change one’s genetic make-up. At the simplest, and most publicly approved level, this would mean ‘fixing’ those mutations that result in genetic diseases. There’s plenty of medical research currently exploring such methods of gene therapy, the preferred approach being to incorporate the human gene of interest into a virus, and to then use the virus to infect and deliver it’s DNA payload into the cells of the patient. But, where does one draw the line? What about so-called ‘gay’ genes? Or genes involved in intelligence?

One thing you can’t really expect is to make much money off of knowing your own genome sequence. There is money to be made, but it involves having access to many genomes. The genetic markers for longevity I mentioned earlier were identified by working with a population of individuals, in this case more than 1000 people over the age of 100. This points to the power of working with populations in terms of identifying key genes that influence traits. At the individual level your genome sequence is practically useless for such a purpose. But aggregated with a bunch of other human genome sequences it becomes part of a pool with which a scientist can perform statistical analysis, and from this make the correlations between allelic variations and specific characteristics. So it doesn’t usually make sense for you to try to sell your genome sequence—I am sorry to say it, but you are probably just not that special—but it does potentially make sense for a population to sequence their genomes and sell access to the information.

And that’s just what some groups are doing. Back in 1998, the parliament of Iceland passed a law that established a database of genetic information for its populace and sold rights of access to the company deCODE genetics. That name should sound familiar. Earlier on, I mentioned how you could have your genetic analysis performed by several companies. One of those was deCODEme. The similarity of names is not a coincidence.

Again, we’re not talking near future here, we’re talking near near future, and now.

Readings:
1. THE SINGULARITY IS NEAR, by Ray Kurzwell (An easily accessible non-fiction book addressing the concept of the singularitry).
2. ACCELERANDO, by Charles Stross (A fun exploration of the singularity following three generations of a family).
3. “We, In Some Strange Power’s Employ, Move On a Rigorous Line,” by Samuel R. Delany (This short story explores what happens when a group opts out of a technological ‘improvement’).

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