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January 4, 2011

Genetic Barcodes

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Understanding Genetics

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Doctors are learning to tailor disease treatments to individuals' genetic makeups, but will customized medicine really be available to all? The inventor of DNA barcodes hopes that a cheap test will soon give anyone speedy access to their personal blueprint. This ScienCentral News video explains.

Your Own Personal Genome

A barcode scan takes only a moment to tell you what you're buying and how much it costs - it would be pretty tedious to check out if cashiers had to manually enter every single item. Now, University of Wisconsin genome researcher David Schwartz hopes that DNA barcodes will be a similar shortcut for getting information about our health.

"You can take DNA molecules, which tend to be very long, and you can put a barcode onto these molecules very much the same way you can put a barcode onto frozen pizza in the supermarket," says Schwartz.

As reported in Proceedings of the National Academy of Sciences, Schwartz’s system for putting barcodes on DNA is a little more complicated than just printing an ink pattern onto a box. But in important ways, it's simpler than conventional sequencing, which was the method used in the Human Genome Project.

To use an analogy, if our genome is a long book, "sequencing" that book would involve carefully reading and transcribing every letter (of the 3 billion base pairs that make up our own genetic code). Rather than coming up with an individually sequenced genome for everyone, Schwartz's system checks a sentence every few pages and also measures the distance between these landmark sentences. This creates a customized genome-wide scan, revealing the areas of the genome that vary between individuals. Fortunately, we already have a copy of that book in our libraries to check against - the fully sequenced Human Genome.

Schwartz's team begins by sticking all six feet of the DNA molecules extracted from a cell onto a glass surface and allowing the DNA strands to elongate. The DNA is immobilized in this position and then exposed to restriction enzymes - biochemical scissors that cut DNA at very specific, recognized sequences of base pairs. Every place that the DNA is cut causes a gap to form. The result is a strand of DNA that has been dotted with a "barcode" pattern of gaps, which can be photographed and analyzed by computers running specially-designed software.

"With modern computers, it's become very simple for us to take these pictures and analyze them," says Schwartz.
Comparing these "barcode" patterns against the sequenced genome gives a snapshot of the differences hidden in our personal genetic blueprints.

"There are trivial differences in terms of hair color, eye color, skin color," explains Schwartz, "but sometimes DNA is altered so that it can give rise to disease."

He says that using these barcode-like scans correctly could help doctors pick the best treatments for their patients, or even identify people at high risk for certain diseases. Schwartz says that even though this method doesn't provide every single letter of an individual's genome, it provides enough information to personalize certain medical treatments - like deciding for or against chemotherapy based on individual genetic odds of success.

He says the goal now is to make these barcodes cheap enough for everyone to get.

"The idea is to drive the cost down so that this becomes a tool that every doctor can have a chance to use," he says.

He estimates that they'll be commercially available within five years, with a fairly affordable price tag - well below a thousand dollars each. Not bad when you compare it to the 2.7 billion dollars the Human Genome Project is estimated to have cost.

Schwartz's latest research was published in the October 24th issue of the Proceedings of the National Academy of Sciences and funded by the National Cancer Institute, the National Science Foundation, and the National Human Genome Research Institute.

       email to a friend by Eva Gladek

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