August 6, 2007

Scifoo day three: Genome Voyeurism with Lincoln Stein

On day three of Science Foo Camp (scifoo) biologist Lincoln Stein (picture right) gave a presenation on what he calls “genome voyeurism”, using Jim Watsons genome as an example. This session demonsrated the current and future possibilities of individuals having their own DNA sequenced, what has been called “personal genomics“.

Unlike the session on genomics yesterday on day two, where George Church, Eric Lander, 23andme, Sergey and Larry (and even Sergey’s pet dog) are all present, today they are conspicuously absent.

Lincolns presentation starts with a video (see youtube video below) of Jim Watson receiving his genome on a disk from Baylor College of Medicine, Houston. Lincoln tells how Jim puts his genome (stored on a hard drive) next to his Nobel prize medallion in his office. After all the press publicity, Jim deposits the data in GenBank, and it becomes available worldwide.

What this means is that anyone can go and look up the differences and similarities between Jim and the original reference sequence in GenBank. The only thing excluded is the data on the ApoE gene, which is implicated in alzheimers disease. Jim is now 79 years old, most of the diseases for which there are know gene(s), Jim would have died of by now. Or as Lincoln puts it “Jim has so far dodged the bullet”. All this leads into Genetic Association Mapping: where control populations can be genotyped and compared with case populations (e.g. alzheimers) for different alleles, which gives a likelihood score of developing a particular disease.

DISCLAIMER: some of what follows is in note form, best to post it now, and tidy up later if I get the chance. Release early, release often 🙂

It turns out that 500,000 SNPs is enough for genotyping much of the population, these variants can act as proxies for 85% of all common variants. This only gives you *some* knowledge of susceptibility to associated diseases. Lincoln has put together a genome browser at http://jimwatsonsequence.cshl.edu. This browser allows users to search and browse jim’s genome, the “jimome” if you like.

Out of 2 million sequence variants identified: 90% of them are SNPs seen in others, 10% rare (see HapMap). A small number of these (around 2 dozen) probably unique to Jim Watson. The Jimome browser hooks into OMIM by means of a simple mashup. However, you do not necessarily want to believe everything in the data, unless you can trace its provenance and have the necessary training to understand all the implications. Less scrupulous people might not make this type of uncertainty clear.

We can look at jims genotype for eosinophilic esophagitis, and SNPS like rs420259 (bipolar disease) and it would be possible to put together a story, if you wanted. Lincoln doesn’t want to support this browser, its just a demo to show what is possible. “Anyone” (with the right knowledge and skills) can do this because all the data is public.

Summary: Ethics, politics and legality of personal genomics?

The discussion that followed Lincolns presentation focussed on the ethical, legal and political issues which are all a bit shady right now. For example, when Jim published his genome, he also published half of his sisters genome and half of his sons genome. Who owns the data? Is it ethical to publish data that doesn’t just belong to you, but has implications for other (younger) members of your family? As the costs of sequencing fall, there are lots of healthcare, pharmaceutical, insurance and genealogy companies ready to financially exploit this kind of data, and could draw all sorts conclusions that are scientifically questionable. This is sounding rather worryingly like Gattaca, where is all this technology going? Currently, these issues only really affect the rich and the famous, as they are the only ones who can afford to sequence their genomes. But as the technology gets better, cheaper and faster more people will be able to do it. Imagine you sequenced your genome, how would you protect that data and how would you choose who you share it with?


  1. Glyn Moody (2004) Googling the Genome: The ability to digitally store, and search, personal genetic data raises a series of difficult ethical questions The Grauniad 2004-04-15
  2. Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. (2007) The Diploid Genome Sequence of an Individual Human (Craig Venter). PLoS Biol 5(10): e254 doi:10.1371/journal.pbio.0050254
  3. Anon (2007) J. Craig Venters genome, The Seven Stones Molecular Systems Biology Blog.
  4. This post originally on nodalpoint

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