A Bioengineer Sequences His Genome
The first human genome sequenced using single molecule sequencing technology.
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:
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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.”
