By Jim Nicholson
The Internet might provide a usefully, albeit simplistic, analogy
for the amazing technical advances happening at Washington University’s
Genome Sequencing Center. Dial-up was amazing as you were introduced
to the ever growing net. DSL was boggling as more and more information
arrived even faster. And higher speed service? Your net-cup
ran over as your computer filled with all the cyber goodies
you hadn’t anticipated receiving back in the recent past of
dial-up days presenting you a sudden need for increased memory
for the increasing items to be saved with the promise of even
greater advances in the indeterminate future.
The workings at the Genome Sequencing Center are a lot more
complicated than most lay people care to comprehend, but, as
very few of us can actually explain how the Internet works and
how a server delivers it to our computer, the PC analogy can
reduce the scientifically sublime to a fairly accessible lay-explanation.
The Center’s workhorse system (there are 130 of them in-house)
runs twenty-four hours a day, seven days a week and is capable
of twenty-four runs per day. The plate used in each run provides
384 wells to house each sample. There are 96 samples in each
run and each sample contains 700 base pairs of DNA.
The next system up the Sequencing ladder provides nano-scale
wells for each sample, thus allowing for more samples in a smaller
space. Its two runs per day provide more information (180 megabases)
per run than the workhorse system delivers in its seven.
The current top of the line system delivers a gigabase of DNA
data per three-day run. It delivers more data more cheaply than
either of the other systems with the result that the cost of
storing the data it delivers is on a par with the cost of generating
that data.
Until the advent of this system, generating information was
more expensive than storing that information. “Now we’re faced
with judgment decisions,” relates David Dooling, an assistant
director at the Center. “We have to decide what to store and
what we can regenerate.”
Dr. Dooling continues to point out that, with the vast amounts
of data being generated, analyzing that data becomes more expensive.
A process that used to be labor intensive is now ‘data precious’.
IT is both providing a solution and a challenge. “What used
to be largely a chemistry/biology problem,” Dr. Dooling states,
“is now a bioinformatics problem. The cart has been put in front
of the IT horse and the rest of the system is catching up.”
In its early stages, Dr. Dooling relates, the Human Genome Project
had its detractors. Those detractors have now been silenced
as the data has “really delivered on the promise of the Human
Genome Project” and science has benefited greatly from it. “We’re
now taking it from the realm of science to the next step, medicine.
We’re entering an age where we’re beginning to think about sequencing
people’s genomes as a matter of course.” Dooling emphasizes
that the key word is “thinking,” as “we’re not there yet.” One
can, however, envision a realistic time frame in which the Center
can apply its expertise to solving problems of human health.
Already, the Center, in conjunction with collaborators around
the world, is involved in several tumor-sequencing projects,
including the Cancer Genome Atlas, which has brain cancer as
its first target. “Everyone knows, or knows of, someone who
has had cancer,” Dr. Dooling states—a statement which becomes
all too real as soon as one inventories one’s own degree of
separation from the disease and comprehends how vast the one
degree list has become.
Taking a holistic approach and utilizing an iterative informed
view of the information fed back into the ever-increasing database
of genomic information, the Center forms further studies into
the disease. “We’re already discussing interesting new techniques
and both asking and answering different questions.”
“We’re poised at a precipice,” says Dr. Dooling. “With the explosion
of data, more and more emphasis is being placed on medical sequencing.
The challenge is making sense of it all.” As the price of the
technology continues to decrease, the next-logical step is personalized
medicine (another “IT nightmare,” Dooling anticipates with satisfaction).
The continuous evolution of the sequencing project has left
everyone—scientists, government regulators and politicians—playing
“catch up”.
As one of three such Centers in the United States, Washington
University’s Genome Sequencing Center impacts the metropolitan
BioBelt region in any number of ways. Its research attracts
highly-trained scientists, who are highly collaborative with
both the University’s Med School and its Danforth Campus. Its
presence impacts local BioTechnical companies and strengthens
the region as a Bio Tech hub. The true value of the Center,
however, is its work, which has the potential of impacting the
future medical well being of virtually everyone living in the
St. Louis metropolitan area.
