evolgen

Watson’s Genome

Posted by RPM on April 20, 2008
(4)
More »

Last year, Craig Venter became the first single person to have his genome sequence published (doi:10.1371/journal.pbio.0050254). That genome was sequenced using the old-school Sanger technique. It marked the second time the complete human genome had been published (which led to some discussion as to whether the publication deserved to be published in a high profile journal like PLoS Biology), and the first time all of the sequence came from a single individual.

ResearchBlogging.org

This past week, Nature published the second complete genome sequence of a single individual (doi:10.1038/nature06884). Like Venter, this individual is also a famous scientists, known both within his field and to non-experts. His name is Jim Watson, he helped discover the structure of DNA, and he’s been eviscerated in the past few months because of some comments he made about racial differences. So, we can expect the publication of his genome to be received with conflicted emotions.

What makes the sequencing of Watson’s genome different from that of Venter’s? It’s the technology. Watson’s genome was sequenced using one of the next generation sequencing technologies (454), which allows much more sequencing bang for the buck. This isn’t a $1000 genome, but it’s a step in that direction.

Along with the article, Nature has published a News and Views piece on the Watson genome paper. The article takes many steps to point out that, while we are at the cusp of an era of personal genomics, there are many limitations as to what we can do with these data. Given our current knowledge, we can’t say much about Watson’s phenotype that we didn’t already know based on non-genomic information. Personal genomics needs not only data, but also ways of assigning genomic variants to particular phenotypes. At this point, we’re probably limited to advising a couple about the risks that their child will acquire a particular genetic disease based on sequencing of the mother and father’s genomes.

The real value of Watson’s genome sequence is a proof of principle. This project was completed at a low cost (relative to the previous methods of sequencing genome), but with high quality. They were able to identify not only sequence variation between Watson and the reference genomes, but also structural variation. To truly realize the potentials of personal genomics, we need many more of these genomes, with the phenotypic data on the individuals.

Levy S, Sutton G, Ng PC, Feuk L, Halpern AL, et al. 2007. The Diploid Genome Sequence of an Individual Human. PLoS Biol 5: e254 doi:10.1371/journal.pbio.0050254

Wheeler DA, Srinivasan M, Egholm M, Shen Y, Chen L, et al. 2008. The complete genome of an individual by massively parallel DNA sequencing. Nature 452: 872-876 doi:10.1038/nature06884

(4)
More »

Comments

  1. #1 Mary
    April 20, 2008

    You can look around at the sequence here, if you want:

    http://jimwatsonsequence.cshl.edu

    I know he said dreadful things, and I don’t condone that at all. But I would like to encourage people to consider that it is possible that his wiring isn’t quite what it used to be. From that link to his genome, the “about” page relates:

    The entire Watson sequence, with the exception of the ApoE gene, variants of which are associated with early-onset Alzheimer’s Disease, has been released to the public….

    I know he asked for this region to be redacted. There is Alzheimer’s in his family history. I don’t know Jim, I don’t know his family, I’m just saying…could be.

  2. #2 Joe
    April 20, 2008

    Meanwhile I’m wondering if they found the gene that makes you a racist, sexist asshole.

    @Mary: If you dig into it a little deeper, Watson has basically been a jerk his whole life. He’s been spewing that crap for decades and the lastest flap that finally brought him some shame, was more to do with him finally being in the wrong place at the wrong time and attacking black people, instead of his more regular fare of women and the disabled.

  3. #3 Mary
    April 20, 2008

    @Joe: Yes, as a woman in science I have been aware of this for a long time. I didn’t just fall off the turnip truck. In fact, I was pretty irritated that the recent stuff was suddenly deemed bad enough for everyone’s outrage when some of us have been hearing this stuff from “advanced” faculty members for years.

    But I’m saying that a little compassion may be in order. Being a victim of one’s genes would be a special terrible irony in this case.

    I’ve seen Alzheimer’s in people I have known for decades, and have been rather stunned at the lack of self-censoring that was happening in conversations. I hope you don’t have to see it. It can be rather sad and disturbing. But I can accept it for what it is. And forgive.

    I hope that we can learn from the genes and stop it.

  4. #4 Joe
    April 22, 2008

    You mean like the compassion he’s had in continually abusing Franklin both during her lifetime, and forever after? Just a few months ago he let rip another bunch of insults and called her autistic. It never stops with this guy. If he has Alzheimer’s I feel bad for him, of course, but nothing excuses his lifetime of atrocious behavior.