Powerful Genome Barcoding System Reveals
Large-Scale Variation in Human DNA

Genetic variation on the order of thousands to hundreds of
thousands of DNA's smallest pieces -- large swaths varying in length or
location or even showing up in reverse order -- appeared 4,205 times in
a comparison of DNA from just four people, according to a new study.
(Credit: iStockphoto/Andrey Prokhorov)
ScienceDaily (June 1, 2010) — Genetic
abnormalities are most often discussed in terms of differences so
miniscule they are actually called "snips" -- changes in a single unit
along the 3 billion that make up the entire string of human DNA.
"There's a whole world beyond SNPs -- single nucleotide polymorphisms
-- and we've stepped into that world," says Brian Teague, a doctoral
student in genetics at the University of Wisconsin-Madison. "There are
much bigger changes in there."
Variation on the order of thousands to hundreds of thousands of DNA's
smallest pieces -- large swaths varying in length or location or even
showing up in reverse order -- appeared 4,205 times in a comparison of
DNA from just four people, according to a study published May 31 in the
Proceedings of the National Academy of Sciences.
Those structural differences popped into clear view through computer
analysis of more than 500 linear feet of DNA molecules analyzed by the
powerful genome mapping system developed over nearly two decades by
David C. Schwartz, professor of chemistry and genetics at UW-Madison.
"We probably have the most comprehensive view of the human genome ever,"
Schwartz says. "And the variation we're seeing in the human genome is
something we've known was there and important for many years, but we
haven't been able to fully study it."
To get a better picture of those structural variations, Schwartz and his
team developed the Optical Mapping System, a wholly new type of genome
analysis that directly examines millions of individual DNA molecules.
Common systems for analyzing genomes typically chop long DNA molecules
into fragments less than a couple thousand base pairs long and multiply
them en masse, like a copy machine, to develop a chemical profile of
each piece.
Reading such small sections without seeing their place in the larger
picture of DNA leaves out critical understanding. To make matters worse,
interesting parts of the human genome are often found within DNA's
trickiest stretches.
"Short pieces could really come from so many different locations,"
Teague says. "An enormous part of the genome is composed of repeating
DNA, and important differences are often associated with areas that have
a lot of repeated sections."
It's a problem inherent to the method that has irked Schwartz for a long
time.
"Our new technology quickly analyzes huge DNA molecules one at a time,
which eliminates the copy machine step, reduces the number of DNA
jig-saw pieces and increases the unique qualities of each piece,"
Schwartz says. "These advantages allow us to discover novel genetic
patterns that are otherwise invisible."
The genome mapping system in Schwartz' lab takes in much larger pieces,
at least millions of base pairs at a time. Sub-millimeter sections of
single DNA molecules -- thread-like and, in full, 4 to 5 inches long in
humans -- are coaxed onto treated glass surfaces.
The long strands of DNA straighten out on the glass, and are clipped
into sections by enzymes and scanned by automated microscopes. The
pattern of these cuts along each molecule thread produces a unique
barcode, identifying the DNA molecule and revealing genetic changes it
harbors.
The scan results are passed along to databases for storage and
retrieval, and handled by software that stitches collections of
bar-coded molecules together with others to reconstitute the entire
strand of DNA and quickly pinpoint genetic changes.
"What we have here is a genetic version of Google Earth," Schwartz says.
"I could sit down with you and start at chromosome 1, and we could pan
and zoom through each one and actually see the genetic changes across an
individual's genome."
To Teague, the Optical Mapping System provides access to a new frame of
reference on human genetic variation.
"I've got a whole folder of papers on diseases that are ascribable to
these structural differences," he says. "If you can see the genetic
basis for those diseases, you can figure out the molecular differences
in their development and pick drug targets to treat or cure or avoid
them altogether. We fit into that storyline right up at the front."
It's been a long story.
"We've been thinking about these large structural variations for
decades," says Schwartz, whose work is funded by the National Institutes
for Health and the National Science Foundation. "The problem was that
the system for discerning large structural variants was not available.
So we had to build it."
The integrative building process included studying the behavior of
fluids at microscopic scale, manipulating large DNA molecules and
placing barcodes on them, automating high-powered microscopes to analyze
single molecules, organizing the computing infrastructure to handle the
data and algorithms to analyze whole human genome, and more.
And after notable turns analyzing the DNA of corn, parasites, bacteria
and even the mold that caused the 19th-century potato famine in Ireland,
Schwartz has arrived at the human genome, his original target.
"It's like you spend years making a telescope, and then one day you
point it at the sky and you discover things that no one else could see,"
he says. "We've integrated so many scientific problems together in a
holistic way, which lets us solve very hard problems."
The result is a 30-day turnaround for one graduate student to analyze
one human genome, but that's just a waypoint. Schwartz's team isn't just
pointing at the sky. They are aiming for the stars by building new
systems for personal genomics.
"This will go even further," says Konstantinos Potamousis, the lab's
instrumentation innovator and a co-author on the study, which included
researchers from UW-Madison, Mississippi State University, the
University of Pittsburgh, the University of Southern California and the
University of Washington. "Our systems scale nicely into the future
because we've pioneered single molecule technologies. The newer systems
we are building will provide more genetic information in far less time."
With development complete on new molecular devices, software and
analysis, a large piece of the system is already in place.
And the speed of innovation will synergize the pace of genome analysis.
"Our newer genome analysis systems, if commercialized, promise genome
analysis in one hour, at under $1,000," Schwartz says. "And we require
that high speed and low cost to power the new field of personal
genomics."
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