WOBURN, Mass. (AP) – It’s been three years since scientists completed a rough draft of the human genetic code, but nobody’s yet rushing out for a personal DNA analysis. That’s because the first one took 12 years and cost billions of dollars.

Today, the cost has fallen, but only to an estimated $50 million. The target remains orders of magnitude away: $1,000 for each complete sequence of an individual’s DNA.

That’s the price considered essential if scientists are to acquire the thousands of sequenced samples they need to fully understand how human genes work, and individuals are ever to make use of personalized DNA snapshots that can be taken in a doctor’s office.

Some scientists believe the old methods of sequencing DNA, though improving, will never produce a $1,000 genome, and they are exploring radically different ways to map the blueprint of human life.

Their methods remain far from proven. But lately there have been signs of headway on several fronts.

“It’s not clear which of these things will be the ultimate success, but I think these are all pieces of the puzzle moving us in the direction we need to go,” said Jeff Schloss, program director for technology development at the National Institutes of Health’s National Human Genome Research Institute. “There is real progress.”

The human genome project yielded the first complete sequence of the 3.2 billion base pairs that comprise the DNA molecule of a person (actually, it sequenced a composite of a few people). Each base is one of four chemicals, called A, G, C or T, the order of which governs a human being’s development.

But it was only a starting point. While the DNA of one person is 99.9 percent identical to another’s, it is the 0.1 percent of variation that interests many scientists because the differences may answer questions like why some people develop certain diseases and others do not.

To answer those questions, scientists must compare the DNA sequences of thousands of people. To get them, they must find a way to sequence DNA that, unlike the first sequencing, doesn’t require thousands of lab technicians and dozens of supercomputers.

“To actually deliver everybody’s genome, you can’t apply that kind of brute force strategy,” said George Church, a researcher at Harvard Medical School.

A $1,000 genome will also be necessary to make full use of what the scientists discover. If average patients can afford quick and cheap personal DNA snapshots, it could help doctors know which diseases they are at risk of developing – and help them take steps to avoid certain health problems.

For years, scientists sequencing DNA have relied on a lumbering technique called electrophoresis, in which DNA is copied and cut into snippets then raced through tiny corridors in an electrified gel. The bits of DNA settle in a way that shows scientists which base ends each snippet, allowing them to sequence a few hundred base pairs at a time.

It’s clever, but problematic. Automation has speeded the copying, but it still requires expensive chemicals. And it’s impossible to handle relatively long strings of DNA. A lab that could sequence 1,000 base pairs a day might be doing well, but at that speed, it would take almost 10,000 years to get through the 3.2 billion base pairs in human DNA.

The new techniques basically start from scratch.

In April, a group led by Caltech researcher Stephen Quake was the first to publish successful results from so-called “single molecule sequencing,” or reading DNA one base pair at a time.

When one strand of DNA is copied, free molecules around it are drawn to their opposite base – As to Ts, Cs to Gs – to make a mirror copy. Quake’s technique involves putting a fluorescent label on the free molecules, then tracking which ones are used in the copy. The technique works on only five base pairs at a time, but Quake says many sequences can be read at once.

“I think it’s sort of a landmark in the sense it is the first experimental demonstration that you can extract information from a single molecule,” Quake said. However, he acknowledged, it “is by no means a practical sequencing technology at this point.”

Meanwhile, in an article published in the August edition of Science, Church’s lab reported progress on another fluorescent method: bathing DNA in different frequencies of light, each illuminating one of the four types of base in separate colors. The goal is to produce a color-coded snapshot of an entire sequence, which a computer could be taught to interpret.

Daniel Branton, a Harvard colleague of Church’s, is working on a method Schloss considers among the most promising: shooting DNA through a tiny hole called a nanopore and measuring the electric signals each base pair emits.

And in another recent development, a Branford, Conn. company called 454 Life Sciences announced it had sequenced the genome of a virus – about 30,000 base pairs long – by dropping strands of DNA into tiny wells.

As opposites pair up, exposure to other chemicals triggers a light flash which is captured by a camera. The company is now working on bacteria – 2 million to 8 million base pairs – and hopes to work its way up to humans.

Other technologies, meanwhile, won’t “read” DNA, but they can compare one strand to a reference, like that provided by the human genome project, and highlight differences. That could help scientists identify the 99.9 percent of identical base pairs, and allow them to focus on the remaining 0.1 percent.

Woburn-based U.S. Genomics tags certain sequences then shoots them past a laser, which detects the tags as they go by. Another such technology is being developed by Solexa, a British spinoff of the University of Cambridge, that hopes to have a product for sale by 2006.

“This is all about detecting differences, because the differences are what are interesting,” said Tony Smith, Solexa’s chief technical officer.

Many of these techniques solve some shortcomings of electrophoresis, but none yet solves them all. One big challenge with fluorescence is making base pairs light up strongly enough to be seen, which requires copying, but not light up so strongly as to blur. Another challenge is finding computers that crunch all the numbers these methods produce.

One skeptic, Elaine Mardis, a genetics expert at Washington University in St. Louis, worries too many labs are releasing “data by press release” instead of subjecting them to serious, scientific peer review. She isn’t convinced that scientists are really solving problems like how to read longer DNA snippets and developing instruments that perceive flourescent light precisely enough.

“Honestly, it’s going to take us 10 or 15 years to get there,” she said of the $1,000 genome. “The non-scientific public is hearing this and saying that sounds really great, and people must be at that goal because they’re talking about it. That’s totally not the case. This is the plan for the future, and the future is not now.”

Schloss, who also believes the $1,000 genome is perhaps 10 years away, said NIH is supporting research both to improve electrophoresis and develop new methods, but added “I do think all the easy gains in electrophoretic methods have been achieved.”

“This is all great progress towards the goal of being able to do whole genomes in a miniaturized way,” said Dick Begley, 454’s president and CEO. “Obviously the bigger the organism, the bigger the challenge. It’s good progress, but it’s still an enormous challenge.”

—

On the Net:

Human Genome Project background: http://www.ornl.gov/TechResources/Human-Genome/project/info.html

Stephen Quake: http://thebigone.caltech.edu/quake/

George Church’s Work: http://arep.med.harvard.edu/Polonator/

Daniel Branton’s Work: http://mcb.harvard.edu/branton/index.htm

454 Life Sciences: http://www.454.com/

U.S. Genomics: http://www.usgenomics.com/

Solexa: http://www.solexa.com/

AP-ES-09-04-03 1345EDT