By Jim Shrine

Special To BioWorld Today

In its first significant collaboration since forming in May, Celera Genomics Corp. agreed to work with Paracel Inc. to develop high-resolution bioinformatics tools.

Rockville, Md.-based Celera, a unit of Perkin-Elmer Corp., and privately held Paracel, of Pasadena, Calif., anticipate developing tools to analyze genomic information. Celera — a venture involving Perkin-Elmer, sequencing pioneer Craig Venter, and The Institute for Genomic Research (TIGR), also of Rockville — is about six months into a three-year, $200 million effort to sequence the human genome. (See BioWorld Today, May 13, 1998, p. 1.)

The heart of Paracel's contribution is its GeneMatcher data analysis technology. Kwang-I Yu, Paracel's chairman, CEO and president, described GeneMatcher as a "massively parallel system for genetic data analysis pattern matching with high sensitivity and selectivity." One GeneMatcher contains more than 6,000 custom processors, implemented in application-specific integrated circuit technology. The processors perform a full range of programming algorithms, Yu said.

Brute Force Meets Sophistication

Company officials would not disclose specific terms of the collaboration, but said they will concentrate on expressed sequence tag clustering and whole genome data-mining capabilities, while leveraging technology for sequencing quality estimation and similarity searching.

"On the surface, [the collaboration] seems to make a lot of sense," said Mary Ann Gray, senior vice president of Raymond James & Associates, in New York. "The sequencing is a nuts-and-bolts, brute-force effort, but it requires sophisticated information systems to really make sense of all the information."

Yu said the companies already have begun joint development of software technologies for this area. Installation of a GeneMatcher at Celera is expected in a month, he said.

"Celera is trying to do a very large-scale shotgun sequence assembly of the human genome," Yu told BioWorld Today. "The Celera problem is well defined: mapping the human genome in three years. That's a very large-scale sequencing problem. Once sequenced, fragments then must be assembled together, like a very large jigsaw puzzle. Our competency lies in very high-end data analysis.

"Clearly this is an important partnership for us," Yu said. "As far as Paracel is concerned, this relationship is exclusive to the extent of the specific areas of joint development."

Perkin-Elmer, based in Norwalk, Conn., already had a relationship with Paracel through a July 1996 equity investment and through a 1992 relationship between Paracel and Foster City, Calif.-based Applied Biosystems Inc., which Perkin-Elmer acquired in 1992.

Paracel also was working at the time with the California Institute of Technology (CalTech), one of the partners in a January 1995 collaboration involving TIGR, Perkin-Elmer and the France-based Centre d'Etude du Polymorphisme Humain (CEPH). CalTech and CEPH are research centers that developed physical maps of the human genome.

Peter Barrett, Celera's chief business officer and a Perkin-Elmer vice president, said the collaboration should benefit both companies.

"The terms, and how the money flows, is less important than the value we're going to create for each company," Barrett said. "We are going to be creating the largest volume of genomic information in the world. We had a longstanding relationship with Paracel, and were looking to step up the scale of these genomics searches. By putting our heads together we will be able to help our process and they will get benefit by developing new products for their customer base."

Barrett said immediate goals are to understand how the GeneMatcher can best be used in Celera's facility and to determine the capabilities of a next-generation product.

"We want to test the limits of the technology and see how it can be improved," he said. "Data mining has never been done before." That approach is expected to produce DNA and protein-level comparisons of the sequence data.

The Paracel technology then will be used to extract value and knowledge from the sequencing information, Barrett said. That data next could be leveraged into areas such as databases, polymorphism information, assay services and gene discovery.

Perkin-Elmer's stock (NYSE:PKN) closed Friday at $69.187, up $0.625. *

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