Intelligent Bio Systems Inc v. Illumina Cambridge Ltd

1. Case Identification

• Case #: IPR2013-00128
• 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 relates to modified nucleotides and nucleosides for nucleic acid sequencing. The claimed molecules feature a base linked to a detectable label via a cleavable linker and a sugar moiety with a protecting group, where the linker and protecting group are cleavable under identical conditions.

3. Grounds for Unpatentability

Ground 1: Claims 1-6 are anticipated by Stemple under 35 U.S.C. §102(b).

• Prior Art Relied Upon: Stemple (WO 00/53805).
• Core Argument for this Ground:
  • Prior Art Mapping: Petitioner argued that Stemple, which was not considered during prosecution, discloses every element of claims 1-6. Stemple teaches a sequencing-by-synthesis method using nucleotides with a detachable label attached to the base via a cleavable linker and a detachable protecting group at the 3' position. Stemple explicitly teaches that both the linker and the protecting group can be removed "enzymatically, chemically, or photolytically."
  • Key Aspects: Crucially, Petitioner asserted that Stemple discloses embodiments where the linker and protecting group are the same chemical moiety (a 2-Nitrobenzyl group), which are removed simultaneously by "exposure to light of the appropriate frequency." This directly teaches the key limitation of being "cleavable under identical conditions," which Petitioner noted was the primary basis for allowance of the ’026 patent over the prior art of record.

Ground 2: Claims 1-6 are anticipated by Ju under 35 U.S.C. §102(e).

• Prior Art Relied Upon: Ju (Patent 6,664,079).
• Core Argument for this Ground:
  • Prior Art Mapping: Petitioner contended that Ju teaches nucleic acid sequencing using 3'-OH capped, chain-terminating nucleotide analogs with a fluorescent label attached to the base through a cleavable linker. Ju explicitly discloses that both the linker and the 3'-OH protecting group are cleavable by a means selected from a group including heat and light, thus satisfying the "identical conditions" limitation.
  • Key Aspects: Petitioner also advanced an inherency argument, stating that the chemical structures disclosed in Ju inherently possess the claimed functional property. The argument centered on the assertion that chemical conditions taught by Ju to remove the allyl protecting group (using TMSi-I) would necessarily also cleave the disclosed carbamate linkers, based on well-established chemistry known to a person of ordinary skill in the art (POSITA).

Ground 3: Claims 7-8 are obvious over Stemple in view of the CEQTM User's Guide or Canard under 35 U.S.C. §103(a).

• Prior Art Relied Upon: Stemple (WO 00/53805), CEQTM User's Guide (a Beckman Coulter manual from June 2000), and Canard (Patent 5,798,210).

• Core Argument for this Ground:

  • Prior Art Mapping: Petitioner argued that claims 7 and 8, which add kit limitations ("packaging materials," "an enzyme and buffers") to the nucleotide of claim 1, are obvious. Stemple was argued to teach the use of the claimed nucleotides with a polymerase in a sequencing reaction. The CEQTM User's Guide and Canard were cited as evidence that packaging reagents for DNA sequencing, including polymerases and modified nucleotides, into a kit was conventional and well-known in the art before the patent's filing date.
  • Motivation to Combine: A POSITA would combine the nucleotides of Stemple with the kit format of the CEQTM User's Guide for the predictable purpose of convenience and efficiency in performing sequencing reactions.
  • Expectation of Success: The expectation of success in creating such a kit would have been high, as it represented a routine practice in the field for standardizing and simplifying laboratory procedures.

• Additional Grounds: Petitioner asserted numerous additional anticipation and obviousness challenges. These included anticipation of claims 1-6 by Tsien (WO 91/06678) and Dower (Patent 5,547,839), as well as various obviousness combinations based on Ju, Tsien, and Dower, alone or in combination with references like Prober (a 1987 journal article) and Anazawa (WO 98/33939).

4. Key Technical Contentions (Beyond Claim Construction)

• Inherent Cleavage Conditions in Ju: A central technical argument was that the specific chemical structures disclosed in Ju inherently meet the "cleavable under identical conditions" limitation, even if not explicitly stated for every combination. Petitioner's expert contended that a POSITA would recognize that the reagents taught by Ju to cleave the 3'-OH protecting group (e.g., an allyl group) would, based on fundamental chemical principles, necessarily also cleave the disclosed linkers (e.g., carbamate groups) in the same step.

5. Relief Requested

• Petitioner requested the institution of an inter partes review and cancellation of claims 1-8 of the ’026 patent as unpatentable under §§ 102 and 103.