August 4, 2005

‘Cheap’ genome sequencing now possible- scientists

By Maggie Fox, Health and Science Correspondent

WASHINGTON (Reuters) - Want your own personal genome
sequenced? Researchers said they had found a faster and cheaper
way to do it that would cost only about $2.2 million.

George Church and colleagues at Harvard Medical School hope
eventually to reduce the cost further to $1,000 per genome --
the entire DNA code of a person, plant or other organism.

Their new method, described in a report in the journal
Science, bypasses the traditional gel-based technology for
analyzing DNA and instead uses color-coded beads, a microscope
and a camera. It is considerably cheaper than the current
methods, which cost an estimated $20 million for a human
genome.

"We are finding needles in a haystack very accurately,"
Church said in a telephone interview.

They said it costs about one-ninth the current cost of
sequencing a genome, which involves using E.coli bacteria as an
incubator to generate the genetic material, separating it out,
breaking it apart and laying it onto a gel.

DNA, short for deoxyribonucleic acid, is made up of repeats
of four nucleotide bases called A,C,T and G for short.

Each nucleotide carries a slightly different charge and
thus can be filtered using a process called electrophoresis.
Modern sequencing uses dyes to make it easy to pick out each
one, but the process can take hours.

"Electrophoresis is slow. You can't really speed it up,"
Church said. "But with a digital camera, you can go as fast as
electronics can go."

Church's team replicated thousands of DNA snippets at once,
each snippet on its own tiny bead just one micron in diameter.

They packed 14 million of these beads into an area the size
of a fingerprint.

"Each camera frame is filled with beads each of which has
one of four colors corresponding one of the four bases of DNA
(A,C,G,T)," Church said.

One of four fluorescent dyes corresponding to the four DNA
bases attaches, depending on which base is present.

"As the computer controls the chemicals flowing in, the
colors of the beads change to reveal which base (A,C,G, or T)
is present at each sequential position of the DNA," Church
said.

Right now the system must use an existing genome map as a
reference -- it cannot sequence a new genome from scratch. But
it worked to show the genetic differences between a new kind of
E. coli bacterium and the existing E. coli genome map that has
been published, Church said.

The idea is to produce a technology that could be used to
compare one person's genome, for example, to the existing human
genome map and find an individual's differences.

"There are needs for personal genomic data already," Church
said.

"If you are a cancer patient there are quite a number of
therapies which can only be used if you have a specific genetic
component."

Harvard has licensed the technology to Agencourt Bioscience
Corporation and Church and his colleagues would collect
royalties on any commercial application.

It would be inexpensive to set up their system, the
researchers said.

"Our integrated liquid-handling and microscopy setup can be
replicated with off-the-shelf components at a cost of
approximately $140,000," they wrote.