PTAB

IPR2014-00333

Ei Du Pont De Nemours Co v. Monsanto Technology LLC

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Petition
petition

1. Case Identification

2. Patent Overview

  • Title: High Throughput Methods for Sampling Seeds
  • Brief Description: The ’143 patent discloses a high-throughput method for analyzing individual seeds for a transgene of interest. The method involves removing a tissue sample from a seed while preserving the seed’s germination viability, depositing the sample into a tray, extracting DNA, and analyzing the DNA for the transgene.

3. Grounds for Unpatentability

Ground 1: Anticipation of Claims 1 and 9 under 35 U.S.C. §102 by Sangtong

  • Prior Art Relied Upon: Sangtong (V. Sangtong et al., a 2001 journal article on detecting transgenes in maize kernels).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner argued that Sangtong disclosed every element of claims 1 and 9. Sangtong described a nonlethal sampling method for maize kernels (seeds) that allows the kernels to be subsequently germinated. The method involved grinding endosperm tissue, transferring the powder to a 96-well plate (a sample tray), adding extraction buffers to obtain DNA, and analyzing the DNA via PCR for a specific transgene. Petitioner asserted that Sangtong’s use of a 96-well format for processing over 2,000 kernels constituted a high-throughput method. Claim 9, which specifies the seed can be maize, was also explicitly taught.
    • Key Aspects: This ground asserted that a single reference taught the entire claimed method, including the high-throughput nature, the preservation of viability, and the specific steps of DNA extraction and analysis for a transgene.

Ground 2: Obviousness of Claims 1 and 9 under 35 U.S.C. §103 over Horigane 1 in view of Sangtong

  • Prior Art Relied Upon: Horigane 1 (A. Horigane et al., a 2003 journal article on kernel analysis) and Sangtong (a 2001 journal article).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner contended that Horigane 1 disclosed a high-throughput method for removing tissue samples from a population of seeds while preserving germination viability. Horigane 1’s method used a computer-controlled cutting device to prepare analytical samples from up to 100 wheat grains at a time. While Horigane 1 taught automated high-throughput sampling, it was silent on the specific DNA extraction and transgene analysis steps. Sangtong was argued to supply these missing elements by teaching a well-known high-throughput method for DNA extraction from seed tissue using 96-well plates and subsequent analysis for a transgene of interest.
    • Motivation to Combine: A POSITA would combine Horigane 1 and Sangtong because both references addressed the same field of high-throughput seed analysis and shared the common goal of preserving seed viability. A POSITA seeking to improve the efficiency of seed analysis would have been motivated to combine Horigane 1’s automated sampling system with Sangtong’s established high-throughput DNA analysis protocol.
    • Expectation of Success: A POSITA would have reasonably expected success in applying Sangtong's standard molecular biology techniques to samples obtained via Horigane 1's mechanical method, as there was no incompatibility between the two processes.

Ground 3: Obviousness of Claims 2-8 under §103 over Sangtong in view of Chunwongse, He, and Lipman

  • Prior Art Relied Upon: Sangtong (a 2001 journal article), Chunwongse (J. Chunwongse et al., a 1993 journal article on genotypic screening), He (Lei He & Kai Wang, a 2002 protocol on plate-based DNA preparation), and Lipman (a 1934 journal article on seed tolerance to cold).
  • Core Argument for this Ground:
    • Prior Art Mapping: Petitioner argued that the base method of Sangtong could be modified with well-known techniques to arrive at the methods of dependent claims 2-8.
      • For claims 2-4 and 8 (adding Chunwongse): Sangtong taught adding buffer after the sample. Chunwongse taught pre-loading microcentrifuge tubes with PCR buffer before adding half-seed samples for analysis. Chunwongse also taught that after analysis, the remaining viable half-seeds could be selected and germinated.
      • For claims 5 and 6 (adding He): Sangtong used 96-well plates. The He protocol explicitly taught optimizing DNA preparation methods to accommodate higher-throughput 384-well microtiter plates and sealing the plates with aluminum tape, a standard practice to prevent evaporation and cross-contamination during vortexing and incubation.
      • For claim 7 (adding Lipman): Lipman, though very old, taught that seeds could be stored at liquid-air temperatures (down to -193°C) for extended periods without damaging their viability. This made it obvious to store tissue samples at cold temperatures, such as the claimed -80°C, to preserve them for later analysis.
    • Motivation to Combine: A POSITA would combine these references to optimize Sangtong's method. Combining with Chunwongse was a simple design choice of when to add a buffer. Combining with He was a predictable step to increase throughput, as explicitly suggested by He’s protocol. Combining with Lipman was motivated by the basic scientific principle of cold storage for sample preservation.
    • Expectation of Success: All proposed modifications involved applying routine, predictable, and standard laboratory procedures to the Sangtong method, leading to a high expectation of success.
  • Additional Grounds: Petitioner asserted additional obviousness challenges, including that claims 2-8 are obvious over the combination of Horigane 1, Sangtong, and the secondary references, and that claims 10-11 (automating the process) are obvious over Horigane 1, Sangtong, and Horigane 2 (Application # 2004/0074822).

4. Key Claim Construction Positions

  • “high-throughput method for analyzing individual seeds in a population of seeds”: Petitioner argued this phrase, undefined in the ’143 patent, should be construed to mean "a method that enables analysis of a larger number of seeds in a population of seeds per unit time than does a completely manual method." This construction was deemed critical as the prior art references (e.g., Sangtong’s 96-well plate system, Horigane 1’s automated cutter) met this definition, whereas a narrower construction might not.

5. Relief Requested

  • Petitioner requested institution of an inter partes review and cancellation of claims 1-11 of the ’143 patent as unpatentable.