A Bioengineer Sequences His Genome

Stephen Quake, a bioengineer at Stanford University, has sequenced his genome–the first human genome generated using single molecule sequencing technology, according to results published in the current issue of Nature Biotechnology. Quake joins a handful of others with public genome sequences, including genomics’ luminaries Craig Venter and James Watson, and several anonymous subjects.

Quake, who was named one of Technology Review’s top young innovators in 2002, cofounded Helicos BioSciences in 2003. Quake used the company’s commercial sequencer, called the HelioScope, to read his DNA. Unlike other advanced sequencing technologies currently in use, which simultaneously read multiple copies of the same piece of DNA, thus boosting the signal, the HelioScope can read the sequence from a single molecule. Quake says this approach will allow for faster and cheaper sequencing.

According to an article in Bio-IT World:

Apart from being a major milestone in single-molecule sequencing (SMS), Quake says his group’s paper points to the democratization of genomic research. “This is the first case you haven’t needed a genome center to sequence a human genome,” Quake told Bio-IT World on the eve of his landmark publication. “What we’ve shown is that you can do it with a pretty modest set of resources–a single professor’s lab, one person doing the sequencing, one instrument, lower cost. Those are all order-of-magnitude improvements over what’s been published recently.” (See accompanying interview, “The Single Life: Stephen Quake Q&A.”)

Quake wrote in an opinion piece that appeared in the New York Times in March that he was inspired to sequence his DNA in part to try to understand his children’s peanut allergies:

I became fascinated with trying to find out whether there is useful information in my genome that might affect my lifestyle choices, or explain why my children have such vicious allergic reactions to peanuts. So, having helped invent an ultra-high-throughput sequencing machine, I used it to sequence my genome.

The sequencing itself was amazingly easy–it took a single machine operator two weeks to get tenfold coverage of my genome (it turns out that for technical reasons it is not sufficient to sequence the equivalent of one genome of DNA; one must over-sample by 10- to 30-fold in order to be sure there aren’t too many gaps). The actual analysis of the data has taken several more weeks as we have built up our computer infrastructure, but it is essentially complete. The hardest part is to interpret what it means.

For the nitty gritty on Quake’s genome analysis, see Daniel MacArthur’s blog on the paper. MacArthur says that, “while this paper is a promising taste of things to come, the genome sequence itself is in many ways a disappointment.”