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'Cheap' genome sequencing now possible
Friday, August 5, 2005; Posted: 10:50 a.m. EDT (14:50 GMT)
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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.
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