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New Affymetrix Patent Could Cause Trouble for Next-Gen Sequencing Players

NEW YORK (GenomeWeb News) - The US Patent and Trademark Office recently issued Affymetrix a patent that could have significant implications for the next-generation sequencing field. The patent relates to sequencing by synthesis or hybridization strands of nucleotides attached to a substrate using fluorescent detection.
US Patent 7,056,666, entitled "Analysis of surface immobilized polymers utilizing microfluorescence detection" with William Dower and Stephen Fodor listed as inventors, was issued to Affymetrix on June 6. As described in its abstract, the patent covers "means for simultaneous parallel sequence analysis of a large number of biological polymer macromolecules."
The patent is a continuation of an earlier patent issued to the same inventors at then-Affymax Technologies in 1996. Despite that earlier intellectual property, Affymetrix has not announced publicly any plans to enter the sequencing arena.
The new patent differs from its parent, which also related to the sequencing of polymers immobilized on a surface using fluorescent detection, primarily through:
  • addition of density requirements -- the new patent relates to high-density surfaces with at least 1,000 oligos per square centimeter;
  • allowing for more than one fluorescent label in the detection process with labels of different wavelength;
  • and a switch from a silicon substrate to one made of silicon, glass, ceramic, or plastic.
This type of technology is similar to next-gen DNA sequencing devices made or under development by several organizations, the best known of which are Solexa and Helicos Biosciences, as well as any number of more nascent efforts underway in academic labs. Companies such as Curagen subsidiary 454 Life Sciences and Agencourt Biosciences, which rely on bead-based reactions instead of matrix-like substrates, will likely be unaffected by this patent, according to people familiar with the technology.
Representatives of Solexa and Helicos could not be reached for comment.
If Affymetrix chooses to enforce this latest patent, it could mean a shift in the landscape of the emerging sequencing market. However, it is unclear how much impact this particular patent will have; as a continuation of a previous patent, its priority date harks back to 1990 (the original filing date of the parent patent) - giving this new one a shelf life of just four years before it expires, according to patent experts. Any legal challenge related to this patent could conceivably be tied up in court long enough to make it moot.
Also, the history of this patent leaves some question about its teeth. While it is common for patent applications to be rejected once, the history of this particular patent indicates that it was given three so-called final rejections before it was finally amended to the satisfaction of its examiner.
An Affymetrix spokesperson declined to comment on the matter, and company attorneys could not be reached for comment.

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