InTelligent Bio Systems Inc v. IlLuMina CambRidge Ltd

1. Case Identification

• Patent #: 7,057,026
• Filed: January 29, 2013
• Petitioner(s): Intelligent Bio-Systems, Inc.
• Patent Owner(s): Illumina Cambridge Limited
• Challenged Claims: 1-8

2. Patent Overview

• Title: Labelled Nucleotides
• Brief Description: The ’026 patent is directed to modified nucleotides and nucleosides for use in nucleic acid sequencing. The invention's core is a molecule featuring (i) a base linked to a detectable label via a cleavable linker, and (ii) a sugar moiety with a protecting group on the 2' or 3' oxygen atom, wherein the key limitation is that the cleavable linker and the protecting group are "cleavable under identical conditions."

3. Grounds for Unpatentability

Ground 1: Anticipation of Claims 1-6 under 35 U.S.C. §102(b) over Stemple

• Prior Art Relied Upon: Stemple (WO 00/53805) and Anazawa (WO 98/33939), which is incorporated by reference into Stemple.
• Core Argument for this Ground:
  • Prior Art Mapping: Petitioner argued that Stemple discloses every element of claims 1-6. Stemple teaches a sequencing-by-synthesis method using nucleotides with a detachable labeling group attached to the base via a cleavable linker and a detachable protecting group on the 3' position of the sugar moiety.
  • Key Aspects: The petition emphasized that Stemple directly teaches the ’026 patent's central limitation by disclosing that "both the labeling group and the blocking group" can be removed "by exposure to light of the appropriate frequency." This single treatment constitutes "identical conditions." For claim 3, which requires a deazapurine base, Petitioner argued that Stemple's express incorporation of Anazawa for label attachment methods necessarily teaches this limitation, as Anazawa discloses attaching a label to a 7-deaza-guanine base.

Ground 2: Anticipation of Claims 1-6 under 35 U.S.C. §102(b) over Tsien

• Prior Art Relied Upon: Tsien (WO 91/06678) and Prober (a 1987 article in Science), which is incorporated by reference into Tsien.
• Core Argument for this Ground:
  • Prior Art Mapping: Petitioner asserted that Tsien, which was not considered during prosecution, anticipates claims 1-6. Tsien describes a sequencing-by-synthesis method using 3'-OH blocked nucleotides where a fluorescent tag is attached to the nucleotide base via a cleavable tether.
  • Key Aspects: The argument centered on Tsien's explicit disclosure that the fluorescent tag "may be chemically cleaved... simultaneously with the deblocking step." Petitioner contended this language is a direct and unambiguous teaching of the "cleavable under identical conditions" limitation. Similar to the Stemple ground, Petitioner argued that Tsien's incorporation of Prober to teach methods for preparing nucleotides with fluorescent tags anticipates the deazapurine limitation of claim 3.

Ground 3: Obviousness of Claims 1-8 over Ju, alone or in combination with Stemple, Tsien, Dower, and CEQTM User's Guide

• Prior Art Relied Upon: Ju (Patent 6,664,079), Stemple (WO 00/53805), Tsien (WO 91/06678), Dower (Patent 5,547,839), and CEQTM User’s Guide.

• Core Argument for this Ground:

  • Prior Art Mapping: Petitioner argued that Ju alone renders the claims obvious. Ju teaches nucleotides with cleavable linkers and 3'-OH capping groups, and discloses that both can be cleaved by a means selected from a group including physical, chemical, heat, or light methods. A person of ordinary skill in the art (POSITA) would have found it obvious to select the same condition for both cleavages to improve reaction efficiency—a stated motivation in the ’026 patent itself.
  • Motivation to Combine: A POSITA seeking to improve the sequencing methods disclosed in Ju would naturally look to other known, similar methods. References like Stemple, Tsien, and Dower, which explicitly teach simultaneous cleavage, would provide a clear roadmap for modifying Ju's method to improve efficiency. For kit claims 7 and 8, a POSITA would find it obvious to package the nucleotides and polymerases taught by Ju into a kit, a common practice for convenience, as demonstrated by commercial products like the one described in the CEQTM User’s Guide.
  • Expectation of Success: A POSITA would have a high expectation of success in making these combinations, as all references relate to the same field of sequencing-by-synthesis and employ analogous chemical principles. The goal of increasing efficiency by reducing process steps is a routine and predictable optimization in organic chemistry.

• Additional Grounds: Petitioner asserted additional anticipation challenges against claims 1-6 based on Ju and Dower, and further obviousness challenges building on each primary reference (Tsien, Dower) in various combinations. These grounds relied on similar arguments that the references taught simultaneous or same-condition cleavage of the linker and protecting group.

4. Key Technical Contentions (Beyond Claim Construction)

• Petitioner advanced an inherency argument regarding the Ju reference. It contended that even if Ju did not explicitly teach using identical conditions, the specific chemical structures disclosed in Ju inherently possess this property. Petitioner argued that the chemical conditions taught by Ju for removing the 3'-OH allyl protecting group would necessarily also cleave the disclosed carbamate linkers, based on well-established chemical principles known to a POSITA.

5. Relief Requested

• Petitioner requests that an inter partes review be instituted for claims 1-8 of the ’026 patent and that those claims be found unpatentable and subsequently cancelled.