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In Reversal, Helicos Appeals EPO Decision to Maintain lllumina Patent

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Helicos BioSciences has decided to appeal a European Patent Office decision to maintain, in an amended form, a sequencing-related patent owned by Illumina, Helicos said in a filing with the US Securities and Exchange Commission last week.

The legal challenge began in August 2006, when Helicos filed an opposition with the EPO against the patent, EP1105529 B1. After that, the EPO issued a preliminary non-binding opinion upholding the patent, which prompted Helicos to end its opposition in August 2008. Last October, the EPO maintained the patent in an amended form.

However, in an apparent reversal, Helicos in January filed a notice of appeal to the EPO's decision, according to the company's 10-K last week.

EPO records show that the patent, entitled "Arrayed Biomolecules and their Use in Sequencing," was granted in 2005 and was originally assigned to Solexa, which was acquired by Illumina in early 2007. The inventors include Solexa co-founders and University of Cambridge faculty members Shankar Balasubramanian and David Klenerman.

The patent appears to cover single-molecule arrays, which Helicos uses in its sequencing platform. According to the patent, the invention "is based in part at least on the realization that molecule arrays can be produced with sufficient separation between the molecules to provide distinct optical resolution." These arrays have "a surface density which allows each molecule to be individually resolved, e.g. by optical microscopy."

It was unclear how the Illumina patent might affect Helicos' ability to sell its Genetic Analysis System in Europe. Helicos President Steve Lombardi declined to comment on the proceeding, saying that the company does not comment on intellectual property issues.

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