CRACKING THE CODE.

Byline: SUE VORENBERG

New Mexico is a state that understands the concept of speed.

Not only do we have the world's fastest supercomputer, Roadrunner at Los Alamos National Laboratory, and the world's fastest sled-track record, 6,416 mph at Holloman Air Force Base -- but now we also have the world's fastest genetics equipment at Santa Fe's National Center for Genome Resources.

In mid-January, equipment at NCGR broke a speed barrier by cataloging 20 billion DNA base pairs -- the letters G for guanine, A for adenine, T for thymine and C for cytosine used to define genes -- in 10 days on its Illumina Genome Analyzer.

The feat isn't something you'll find in the Guinness World Records, but as far as he knows, it's the fastest time in which such a test has ever been completed, said Stephen Kingsmore, NCGR's director and CEO.

"The actual number is a bit arbitrary, but there's a lot of potential behind this," Kingsmore said. "Everybody is trying to sequence the genome in a cost-effective way, and when we can get the speed to a certain level, genetic sequencing will go mainstream."

Experts think when the price of a test gets down to $1,000, most people will be able to afford to get their genes sequenced.

That, in turn, could spur a health care revolution in something called personalized medicine -- a sort of preventative medicine based on genetic risk factors, Kingsmore said.

"It will start to change the emphasis from waiting for disease to crop up, to sharing your sequence with the doctor and asking 'what do you recommend here?' " Kingsmore said. "You could go to a genetic counselor to determine your risks. For example, if you've got four alcoholism genes, you probably want to stay away from booze. If you have none, it's probably safe to have a drink."

Right now, NCGR can sequence and analyze a person's DNA for about $150,000, Kingsmore said.

That might sound like a lot of money, but the cost has come down rapidly as the speed of testing has increased, he said.

"The first one we did cost $120 million, and that was in 2004," Kingsmore said, adding that he thinks the cost will drop to about $100,000 by the end of this year.

Early last year, NCGR was sequencing about 500 million base pairs in 10 days. By last fall, that jumped to 4 billion. And by the first week of January, the equipment sequenced about 12 billion base pairs in 10 days, Kingsmore said.

"Our best has been going up by the month," Kingsmore said.

If progress continues at about the same pace, the price for a test could drop to $10,000 in two years and to $1,000 in about five years, he said.

NCGR has partnered with New Mexico Tech and Illumina on the technology and genetic research.

Rebecca Reiss, a biology professor at Tech, agrees that the price of a test could come down to about $1,000 in five to 10 years. But some of the ethical issues around DNA sequencing could slow progress toward personalized medicine, she said.

"There's a lot of bioethics involved in this," Reiss said. "There's a lot of potential for preventative medicine there, but there's also a lot of potential for abuse."

The problems revolve around who has access to a person's DNA sequence.

In 2008, Congress passed the Genetic Information Nondiscrimination Act, or GINA, aimed at preventing discrimination based on a person's genetic information when it comes to health insurance and employment.

But that doesn't mean social stigma or other problems could occur if genetic information about a person is easily accessible, Kingsmore said.

"One big issue is how do you keep the information confidential?" Kingsmore said. "What if you have something with a social stigma and people find out about it? Nobody's found one yet, but what if there were a gene associated with child molesters? If you had that, you could see the potential for discrimination."

A $1,000 test would put personalized medicine in the hands of many in First World countries, but what about those in poor nations? If that sort of medicine changed health care, Third World countries could face bigger problems in terms of access to drugs or care that has become tailored to those who can afford to know what their genetic predispositions are, Reiss said.

"Are there ways that this information can help people in Third World countries? Could we find drugs that work better? I don't know," Reiss said. "This may be more of a lifestyle problem, but at the same time I think we can say for sure that personalized medicine is happening."

Also, just because health-insurance companies aren't legally allowed to discriminate against a person because of genetic factors doesn't necessarily mean that they wouldn't hike rates for people with certain predispositions, Reiss said.

"And then, if you can test prenatally for some of these genetic risks, what happens? Do we start selecting our children?" Reiss said.

Still, with the risks come benefits. Cancer, for instance, is a genetic disease that can target a person's DNA in different ways. By understanding an individual's DNA, doctors could better target treatments and increase the likelihood of survival, Kingsmore said.

One could also look at the genes to determine personal strengths and weaknesses, such as genes associated with fast running or other skills, Kingsmore said.

"It's almost like inventing nuclear energy," Kingsmore said. "It's got tremendous potential to benefit society, but also if it's not handled right, it has tremendous potential to harm."

And while the day when personalized medicine becomes commonplace is getting closer, there are still some technical issues that must be resolved first, the two said.

"I think the speed of the tests might not be the biggest problem, but the price of some things you need to do those tests like reagents," Reiss said. "The price of reagents is coming down, but they're still very expensive."

Another technical problem is that the faster the tests run, the more likelihood there is for error. The NCGR milestone, for instance, had an error rate of 0.91 percent, which is low, but still something to consider.

With the error rate, companies will have to run a person's DNA sequence, which includes about 3 million of those genetic letters, several times to make sure the result is correct, Kingsmore said.

And, beyond the technological constraints, the ethical issues should be looked into more deeply before the medical revolution takes place, Reiss said.

"My personal opinion is that we're messing with evolution, and I'm uncomfortable with that," Reiss said. "We need to look before we leap."

That said, though, pushing the technology and bringing down the price isn't a bad thing. It can enable more genetic research and could be a boon for mankind if handled properly, Kingsmore said.

"The upside is hopefully the whole face of medicine will change to prevention," Kingsmore said. "Getting to 20 billion base pairs is a big step forward, but we're certainly not there yet. We'll keep plugging away."

Contact Sue Vorenberg at [e-mail].