By Randall Osborne

West Coast Editor

Perlegen Sciences Inc., the genomics venture formed last fall by Affymetrix Inc., said it completed $100 million in private financing, and is marching ahead with its plan to scan 50 genomes.

"We'll get those done in about a year," said Brad Margus, Perlegen's CEO.

The key is wafers. Affymetrix and Perlegen have been developing and using the former's wafers, which hold up to 60 million probes. In contrast, the commercial GeneChip arrays ordinarily provided by Affymetrix have only 400,000 probes per chip.

"It's pretty amazing," Margus said. "The advanced version of Affymetrix's technology that we have can't read the sequence of a new genome at all, but once you have one, it can look at many, many more, and tell you whether they match. We needed two things - Affymetrix's technology, and the publicly available human genome."

Ultimately, Perlegen plans to inspect the entire genomes of specific patient populations provided by pharmaceutical partners, seeking to associate patterns and health factors.

"What we're building is a tool with which we can scan thousands of genomes," Margus said. "We want to scan thousands of people who have diseases, and thousands of people who don't. We'll also be doing genetic association studies internally, by collaborating with people who have clinical information and DNA [data]."

As the Series B financing closed, Affymetrix turned over assets and intellectual property rights to Perlegen in exchange for Series A shares. Affymetrix owns 52 percent of Perlegen, or a little over $138 million worth, Margus told BioWorld Today.

"The post-money valuation [of Perlegen] is $266 million," he said. "We went out saying it was already worth $165 million, and investors put in an additional $100.8 million."

Since last year, when the arrangement was disclosed, "we haven't slowed down a bit on the science, and we continued to spend Affymetrix's money. Not until late January or early February did we start to market the financing," Margus said. (See BioWorld Today, Oct. 4, 2000.)

Affymetrix has not contributed cash "other than what they've spent to get us to this point - $10 million or $12 million," he added.

Perlegen has agreed to buy whole-wafer DNA arrays from Affymetrix, and the two firms entered into cross-licensing deals letting Perlegen use the technology exclusively, while granting Affymetrix the right to commercialize products that contain content discovered by Perlegen.

"We're using [the wafers]," Margus said. "We're not allowed to make them ourselves."

Affymetrix also will provide Perlegen, which has 41 employees, with administrative support and facilities. For now, the company is located with Affymetrix in Santa Clara, Calif.

"We're here through the end of the year," Margus said.

Affymetrix's stock (NASDAQ:AFFX) closed Tuesday at $24.625, down $1.50. n

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