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Solexa Mixes PhDs, Financing to Develop Massively Parallel Sequencing Technology


What can a group of more than two dozen PhDs produce in two years?

Solexa, a Cambridge, U.K. based startup firm, hopes that its stellar team of PhDs, including a large number of nucleotide chemists, can produce a prototype for a massively parallel genomic sequencing array.

The company is creating a high-density (targeting at least 108 sites per square centimeter) microarray, where each feature comprises one molecule – a fragment of sample DNA. This apparatus would enable the simultaneous sequence analysis of millions of different DNA fragments.

Additionally, the company is creating its own chemistry, specifically four fluorescently labeled nucleotides to use in the sequencing process. The innovation in Solexa’s concept comes from being able to erase the flourescence produced after each cycle of sequencing. The prototype is on schedule for rollout by 2004, company officials said.

Solexa is not alone in attempting to develop a massively-parallel scheme for genomic analysis – Illumina, US Genomics, and others are on its heel – and observers say it’s a competitive field with no clear winner. ”There is a whole cottage industry in doing massively parallel short sequencing to the reference genome,” said Ryn Miake-Lye, assistant director of the center for scientific affairs at the Whitehead Institute. ”Solexa looks like a lot of good smart people working on this, but there are others too. The jury is still out.”

The technology was developed by Shankar Balasubramanian and David Klenerman, two chemists at Cambridge University. They have collaborated on a paper published in 2000 in Analytical Chemistry – ”Single-molecule analysis of DNA immobilized on microspheres” – but neither they nor the company have published on Solexa’s particular technology.

The two scientists, and the university, hold equity stakes in the company, with Balasubramanian and a university representative sitting on the company’s board of directors.

Like many other companies attempting to commercialize a concept developed in academia, Solexa finds that there is no rulebook for how to run an enterprise of this type.

However, unlike most other early-stage startups in a time of economic uncertainty, Solexa has an advantage in a well-stocked treasure chest. It has $23 million from seed and Series A investors, providing a cushion of two years to shepherd a technological concept into a prototype ultra-high throughput genome sequencing application.

The firm, originally created in 1998 with university support and seed funding provided by venture capital firm Abingdon Capital, has grown to 40 employees in a 12,000-square-foot workspace in Chesterford Research Park, Little Chesterford, an hour by train from London.

"Getting a technology from the lab to the market, that is the biggest challenge – the organization has to make the transition too,” Nick McCooke, Solexa’s chief executive officer said. McCooke was president of Seattle-based Rapigene, a genomics firm acquired by Qiagen in 1999, and was brought in by investors to head Solexa. At 49, and with prior experience with Innovex and Celltech, McCooke stands like a conductor with a baton directing an ensemble of researchers, administrators, and financiers. He is joined by Tony Smith, hired earlier this year as chief technology officer from his post as vice president of research and development at Amersham Pharmacia Biotech, now Amersham Biosciences.

In a field where innovation and change are constants, the goal is to produce a technology that will still be commercially viable four years from now. ”We are developing a broadly-applied technology that is very robust,” said McCooke. ”If we were building a focused application, I would be worried that the sands would shift and we would have nothing in three to four years’ time.”

Stephen Benkovic, a chemistry professor at Penn State University, and an advisor to Solexa, said he thinks the company can do what it needs to do to create a viable commercial prototype. ”I’ve consulted for biotech companies that have had people who were bright as button[s] and they are no longer around,” Benkovic said. ”Solexa has good scientific people and the business types who know how to organize to get this done internally and externally. And, they have the funding to have a real shot at it.”


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