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Companies race to put genes on a chip

Biotech companies are upping the ante in the competition to develop microarrays that match medicines to your genetic code.
Affymetrix's GeneChip contains vital pieces of the 30,000 genes that make up the human genetic code. Several other companies and research teams have developed similar technologies.
Affymetrix's GeneChip contains vital pieces of the 30,000 genes that make up the human genetic code. Several other companies and research teams have developed similar technologies.
/ Source: The Associated Press

The lofty goal of “personalized medicine” is one step closer to reality, with two companies announcing that they have successfully placed vital bits of humankind’s estimated 35,000 genes on a small glass chip.

Rivals AffymetrixInc. and Agilent Technologies produced so-called gene chips — dime-size pieces of glass infused with genetic material. Until Thursday, Affymetrix and Agilent needed two chips to hold the same genetic material.

Chips with portions of the genome are now indispensable in biology laboratories around the world. Now, Affymetrix says researchers can buy the entire genome for between $300 and $500 each — roughly half the old price.

“It’s a significant milestone,” said Affymetrix chief executive Stephen Fodor.

Employing semiconductor manufacturing technology, workers “print” genes one molecule at a time onto the glass until they stand up like microscopic skyscrapers, each about 25 molecules high.

Researchers then drop onto the chips specially tagged RNA, which serves as the messenger between DNA blueprints and a cell’s protein-making machinery. The portion of a chip on which genes interact with the RNA will be fluorescent, highlighting bad genes that may need a closer look.

Rivals in the gene chip industry
The dueling announcements Thursday come on the heels of similar breakthroughs by Applied Biosystems of Foster City and Madison, Wis.-based NimbleGen Systems, both of which said in July they had each created a genome on a chip. In addition, a research team from two German science institute made a similar announcement last year.

Because Affymetrix owns 80 percent of the commercial market, however, its announcement was greeted as an industry turning point.

The continued packing of more genes into smaller spaces leads many to believe the gene chip industry will follow its own Moore’s Law, which holds that the processing power of semiconductor chip doubles every 18 months.

While no one believes gene chips will evolve that quickly, many still expect big things.

Even the chips touted Thursday don’t contain whole genes on them. Instead, they contain vital pieces of each gene. But more genetic detail is expected to be added to the chips in coming years, making them more powerful and versatile.

Today, researchers mostly use the chips to do basic genetic research.

Scientists believe many diseases are caused by genes “turning on” when they shouldn’t. Knowing this, researchers can design drugs to attack suspect genes.

Until gene chips came into vogue about five years ago, genetic scientists slogged slowly through their research, often investigating one gene at a time. Now they can analyze thousands of genes simultaneously, more quickly identifying disease causes.

“We can now look 35,000 at a time,” said Harvard Medical School’s Dr. Scott Armstrong. “But we are not using to dealing in that.”

‘Sending shivers up my spine'
Some researchers even envision a day when pediatricians and other physicians are armed with these chips, technically called microarrays. The hope is that a drop of a newborn’s blood can quickly be converted into a genome on a chip. From there, a doctor can determine the baby’s predilection to disease and other genetic traits.

“This is starting to get really cool and it’s sending shivers up my spine in a good and bad way,” said Dietrich Stephan of the nonprofit Translational Genomics Research Institute in Scottsdale, Ariz.

Discovering somebody is likely to suffer an incurable disease is rife with ethical and philosophical implications, he said.

Stephan is already using gene chips to help determine the chances of relapse for children whose leukemia is in remission.

Armstrong and other researchers at Harvard also used gene chips to show that childhood leukemia comes in at least two distinct forms, and a human experiment is under way to test a new drug’s effectiveness against the newly discovered form.

Armstrong isn’t as bullish as Stephan because he doesn’t envision the chips being used in the doctor’s office anytime soon. But he does see pathologists and other doctors soon using gene chips to tailor medicines to individual genetic makeup.

“That’s where this is all going,” he said.

Armstrong said it will take some time for scientists to figure out how to interpret all the data that the gene chips equipped with the complete genome can spit out.