By Julia Karow
This article, originally published Sept. 1, has been updated with additional information from the US Patent and Trademark Office.
Opening another front in the IP battle between Helicos BioSciences and other developers of next-generation sequencing platforms, Life Technologies has been granted a request for reexamination of a patent licensed to Helicos.
Also, the USPTO has maintained its initial rejection of the claims of another Helicos patent that is currently undergoing reexamination in a so-called "action closing prosecution."
The patent that Life Tech asked to be reexamined is part of a recent expansion of Helicos' license of intellectual property from Arizona State University (IS 8/30/2011), and covers a broader range of sequencing methods than the original license, including technology underlying the Ion Torrent PGM, according to Helicos CEO Ivan Trifunovich.
Trifunovich said that Life Tech requested the reexamination even before Helicos gained the rights to the patent, US Patent No. 7,875,440, and that Helicos has not sued Life Tech for infringing the patent as of now. "The fact that Life preemptively tried to invalidate this patent tells you that they are quite worried about this patent," he told In Sequence.
Life Technologies declined to comment on the patent reexamination request.
Helicos said that the new license from Arizona Technology Enterprises, the tech transfer arm of Arizona State, gives it the rights to several patents covering sequencing-by-synthesis methods, including those that do not rely on optical detection of labeled nucleotides, like Ion Torrent's.
The '440 patent, entitled "Method of determining the nucleotide sequence of oligonucleotides and DNA molecules," issued in January of this year and is assigned to the Arizona Board of Regents. According to Helicos, the patent derives from "an existing foundational invention" with a priority date of May 1998.
The patent describes a method for sequencing nucleic acids through real-time detection of the incorporation of nucleotides by a DNA polymerase. For the detection, the abstract mentions "any of a variety of methods, including but not limited to" fluorescence, chemiluminescence, and microcalorimetic detection of heat.
In its inter partes reexamination request, filed in early June and granted by the USPTO on Aug. 17, Life Tech questioned the patentability of claims 1, 3, 4 and 12 of the patent, citing several patent applications with earlier publication dates. The patent remains valid while the reexamination is proceeding.
According to Trifunovich, Helicos' patent estate keeps growing – this year so far, the company has had eight patents issued or allowed, and filed more than a dozen patent applications. The '440 patent, as well as another patent, US Patent No. 7,897,345 "contain very broad claims that cover the very core chemistry of most major next-generation sequencing platforms," according to a company statement, and another patent, US Patent No. 7,948,625, covers a lighting system with two light sources for sample detection.
The new patents provide the company with new ammunition for its strategy to assert its IP rights against competitors. Last year, Helicos sued Pacific Biosciences, Life Tech, and Illumina for infringing four of its patents. The three defendants countersued, saying the patents are invalid and unenforceable. A magistrate judge ordered a mediation conference for Aug. 31 (IS 7/26/2011), but Trifunovich said the conference was postponed until further notice due to the recent hurricane on the East Coast. He said Helicos has not decided yet whether it will assert the '440 patent in the ongoing litigation.
Separately, PacBio requested the reexamination of the four patents — US Patents No. 7,645,596; 7,037,687; 7,169,560; and 7,767,400 — earlier this year, which the USPTO granted this spring, rejecting all their claims in a non-final office action (IS 5/10/2011). Again, these patents' claims remain valid during the reexamination.
In an "action closing prosecution" issued earlier this month, the USPTO maintained the rejection and reexamination of all 12 claims of the '560 patent, following responses by both Helicos and PacBio to the initial non-final office action. Helicos can now comment on the decision within 30 days. As of this week, the USPTO had not filed equivalent decisions for the other three patents.
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