Field Trip #2: Cincinnati Children's Hospital (CCH) DNA Sequencing Core
Speaker: Dr. David Fletcher, Director of DNA Sequencing Core
Time: 12:30 p.m. – 3:00 p.m.
Date: July 9, 2014
Venue: CCH Medical Center DNA Sequencing Facility - Location R1045A, 3333 Burnet
Avenue, Cincinnati, OH 45229
Prepared by:
Aaron Choi, University of Cincinnati, Cincinnati, OH
Davis Sneider, The George Washington University, Washington, D.C.
Saifuddin Aijaz, University of Cincinnati, Cincinnati, OH
Project # 3: A Biological Optoelectronic Nanopore for DNA Sequencing and Stochastic Sensing
It all started with the Human Genome Project. The quest to map the human genome has
captivated scientists for several decades. By discovering the code behind genetics, Major
advances in science would come forth. Since the 1990's DNA sequencing has relied mostly on
capillary-based semi-automated implementation of the Sanger biochemistry. Some methods
include: the "shotgun" method, the 454 pyrosequencing and even Illumina dye sequencing. With
the "shotgun" method, DNA is cloned into a plasmid and is used to transform bacteria for
sequencing. In 454 pyrosequencing, DNA is amplified inside water droplets in a process called
emulsion PCR with each drop containing a single DNA template attached to a single primercoated bead that forms a clonal colony. With Illumina dye sequencing, DNA and primers are put
on a slide, amplified with polymerase so DNA colonies can form. Then RT-bases are added and
a camera takes images of the labled nucleotides and then the dye is removed so that ne next cycle
can begin. In Children's there are DNA sequencing machines that can sequence up to 300
million base pairs per day. DNA sequencing has always been expensive so the average person
would not be able to afford to get their own DNA sequenced. In recent years, the cost of DNA
sequencing has dropped exponentially. It is a third of what Moore's Law states it should be.
Dr. David Fletcher, Talking about Capillary-based, Semi-automated Sanger Sequencing
The Human Genome Project took about 6 billion dollars over the course of six years and
now thanks to modern technology, Children's Hospital can do much more in about a week. DNA
sequencing has become much more common place due to rapid advancement in technology Dr.
David Fletcher, the director of the DNA sequencing center, acknowledged Oxford's
announcement of their nanopore technology although the method does not seem commercially
feasible yet. If nanopore technology does prove to be fruitful, then it would be a huge leap in
science. For now nanopores remain a second generation method meaning it still requires lots of
work and cost. Next gen sequencing aims to be cheaper and more proficient and currently
nanopores are not proficient enough to be commercially viable.
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The HiSeq 2500 Sequencing Machine is Pictured Above: Created by the Illumina
Company, it is the Standard Machine for DNA Sequencing Today
Nanopore sequencing is a technique that applies a voltage across a nanopore in a
membrane seperating two chambers containing a buffer solution. The resulting changes in the
ionic current can be measured by electrophysiological techniques to read DNA. It had high
hopes for reducing DNA sequencing to a few hundred dollars but early experiments have
provided disappointing results. Nanopore sensors don't require ligases, or nucleotides which
means it would be much cheaper than the Sanger method.
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Depicted above is the William Cooper Procter Research Center located in the Cincinnati
Children's Hospital Medical Center, DNA is sequenced in the building
The tour through the DNA sequencing center has revealed much about the sequencing
world. It has shown that although nanopores can be a promising innovation, they simply aren't
commercially viable with current technology. The cost of DNA sequencing has dropped
drastically, however, and brings high hopes for cheaper and more proficient methods for DNA
sequencing. By making DNA sequencing affordable to the general public, discoveries about the
human genome could surface. Curing genetic diseases could become a reality sooner than
expected. Cancer could even become a thing of the past similar to how Edward Jenner's vaccine
eradicated smallpox. All five groups have been given a glimpse into the field of DNA
sequencing. The number of applications and expectations for this study is quite high, which
means that if scientists find a way to make nanopore technology viable for people then there
would be massive amounts of scientific progress.