PTAB

IPR2020-01200

Pacific Biosciences Of California Inc v. Personal Genomics Taiwan Inc

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1. Case Identification

2. Patent Overview

  • Title: Bioassay system including optical detection apparatuses, and method for detecting biomolecules
  • Brief Description: The ’441 patent describes a semiconductor-based biosensor system for identifying single biomolecules, such as DNA. The core of the claimed apparatus comprises a substrate with an integrated light detector, over which a "linker site" is formed to affix a biomolecule for detection, with the linker site positioned in close proximity (≤100 micrometers) to the detector.

3. Grounds for Unpatentability

Ground 1: Anticipation of Claims 1, 7, 10-16, 18-19, 21-22, 24, 27, and 30-36 under §102 by Hassibi

  • Prior Art Relied Upon: Hassibi (Application # 2004/0197793).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner argued that Hassibi, which describes methods for biomolecule detection and sequencing, discloses every element of the challenged claims. Hassibi teaches an apparatus with a substrate (silicon wafer) having a light detector (photodiode array), with reaction chambers serving as linker sites formed over the detectors. Hassibi explicitly teaches treating these sites to affix biomolecules (e.g., nucleic acids) and discloses that the distance between the detector and the chamber can range from 1 µm to 1 m, with a typical range beginning at 10 µm, which anticipates the claimed ≤100 µm distance. Hassibi also discloses arrays with over 10,000,000 apparatuses, anticipating the dependent claims.
    • Key Aspects: The core of this ground is that Hassibi, a single prior art reference not cited during prosecution, describes the exact architecture claimed in the ’441 patent, including the key spatial relationship between the detector and the biomolecule that was the basis for the patent's allowance.

Ground 2: Obviousness of Claims 17 and 20 under §103 over Hassibi in view of Korlach

  • Prior Art Relied Upon: Hassibi (Application # 2004/0197793) and Korlach (Patent 7,361,466).
  • Core Argument for this Ground:
    • Prior Art Mapping: This ground built upon the teachings of Hassibi. For claim 17, which requires affixing a nucleic acid via a polymerase molecule, Petitioner asserted that while Hassibi teaches using various binding moieties, Korlach explicitly teaches immobilizing a DNA polymerase to a support surface to anchor a target DNA molecule for sequencing. For claim 20, which requires labeling nucleotides on their terminal phosphate, Petitioner argued that Hassibi’s system detects pyrophosphate released during sequencing. Korlach, which is acknowledged prior art in the ’441 patent, expressly teaches fluorescently labeling the terminal phosphate of nucleotides to facilitate detection in such systems.
    • Motivation to Combine: A person of ordinary skill in the art (POSA) would combine Hassibi with Korlach because they address similar problems in DNA sequencing. Using Korlach’s method of immobilizing the polymerase would be a simple, known substitution that provides cost savings and higher throughput for Hassibi's system. For terminal phosphate labeling, a POSA would be motivated to use Korlach’s well-known technique to enhance the signal in Hassibi’s pyrophosphate detection scheme.
    • Expectation of Success: Given that both references describe highly interchangeable methods for DNA sequencing and Korlach’s techniques were well-known, a POSA would have had a high expectation of success in applying them to Hassibi's apparatus.

Ground 3: Anticipation of Claims 1, 2, and 6 under §102 by Blumenfeld

  • Prior Art Relied Upon: Blumenfeld (Application # 2002/0018199).

  • Core Argument for this Ground:

    • Prior Art Mapping: Petitioner argued that Blumenfeld, which describes imaging biological samples with an electronic light detector, also anticipates the key claims. Blumenfeld discloses a DNA chip (linker site) positioned over a detector array (light detector) on a substrate. It explicitly teaches that the light path from the sample to the detector is "most preferably, the light path is less than 15 microns," satisfying the ≤100 µm limitation. For dependent claim 2, Blumenfeld discloses an "aperture" that functions as the claimed "pinhole" in a "blind sheet." For dependent claim 6, Blumenfeld discloses an optional focusing lens between the sample and detector, meeting the "microlens" limitation.

  • Additional Grounds: Petitioner asserted additional challenges, including: obviousness of claims 1, 7, 10-16, 18-19, 21-22, 24, 27, and 30-36 over Hassibi in view of POSA knowledge; obviousness of claims 28 and 29 (reciting FRET and time-resolved fluorescence) over Hassibi in view of POSA knowledge; obviousness of claims 21, 22, and 24 over Hassibi in view of Cheeseman (Patent 5,302,509); and obviousness of claims 1, 2, and 6 over Blumenfeld in view of POSA knowledge.

4. Key Claim Construction Positions

  • "over": Petitioner argued that the term "over" describes the relative position of the linker site to the light detector (i.e., in parallel planes such that light travels from one to the other) and is not dependent on the absolute orientation of the device. This construction is critical to the argument that Hassibi's apparatus, even if depicted in a different orientation, would be seen by a POSA as teaching the claimed invention, as it could be simply rotated.
  • Preamble of Claim 1: Petitioner contended that the preamble "An apparatus for identifying a single biomolecule" is not a limitation but merely states an intended use for a structurally complete invention. Alternatively, if limiting, Petitioner argued the references still meet the limitation as they describe detecting signals from both single molecules and multiple copies of a single molecular species.

5. Arguments Regarding Discretionary Denial

  • Petitioner argued that this IPR should not be subject to discretionary denial. It noted the existence of co-pending litigation between the same parties involving the ’441 patent. Petitioner also disclosed a concurrently filed IPR petition against the same patent but asserted that this petition is not redundant because the two petitions challenge largely different claims and are based on different prior art, with minimal overlap.

6. Relief Requested

  • Petitioner requested that the Board institute an inter partes review of claims 1-2, 6-7, 10-22, 24, and 27-36 of the ’441 patent and cancel these claims as unpatentable.