NEW YORK – Take2 and the Chinese University of Hong Kong have sued Pacific Biosciences, alleging infringement of a patent covering methods to call methylated DNA bases.
In a Tuesday filing with the US Securities and Exchange Commission, PacBio disclosed the lawsuit, filed last December in the US District Court for the District of Delaware.
The plaintiffs, both associated with noninvasive prenatal testing pioneer Dennis Lo, alleged infringement of US Patent No. 11,091,794, titled "Determination of Base Modifications of Nucleic Acids." Specifically, they alleged that PacBio sequencing instruments carrying software that enables direct methylation detection infringe the patent. The software, released last year, is available for the Sequel IIe and the forthcoming Revio instruments.
The complaint seeks unspecified monetary damages and an order enjoining PacBio from infringing the '794 patent. The plaintiffs have alleged the infringement is willful and are thus seeking treble damages.
PacBio filed a motion to dismiss the case on Feb. 14. In an accompanying brief, the firm's attorneys argued that the patent is invalid. Specifically, the patent "claims a statistical model for calculating an allegedly better prediction as to whether a nucleic acid base is modified," they wrote. "A statistical model is ineligible subject matter because it is essentially math, even if it solves a problem of genetic prediction."
"We believe the infringement allegations in the complaint lack merit and we intend to vigorously defend [ourselves] in this matter," PacBio said in its SEC filing.
Neither the plaintiffs nor PacBio responded to a request for comment before deadline.
PacBio's sequencing method calls methylated bases by analyzing hiccups in polymerase activity during base incorporation at those and nearby bases. These irregularities show up as length of time between fluorescence pulses, or the interpulse duration (IPD). PacBio's algorithm uses these differences in IPD to make the epigenetic modification calls.
In early 2021, Lo's team at CUHK published a paper in the Proceedings of the National Academy of Sciences on its use of neural networks to improve methylation detection using PacBio sequencing data. At the time, Lo said Take2 Health, a cancer genetic testing and informatics company, would commercialize the technology, having secured an exclusive license.
Children's Mercy Kansas City has already begun using the new capability of PacBio's sequencers to generate methylation calls for rare disease cohorts.