ALaMar Biosciences Inc v. Olink Proteomics Ab

1. Case Identification

• Case #: IPR2024-01353
• Patent #: 7,883,848
• Filed: August 23, 2024
• Petitioner(s): Alamar Biosciences, Inc.
• Patent Owner(s): Olink Proteomics AB
• Challenged Claims: 1-20

2. Patent Overview

• Title: Regulation Analysis by Cis Reactivity, RACR
• Brief Description: The ’848 patent discloses methods for detecting functional interactions between molecules of interest (MOIs). Each MOI is coupled to a nucleic acid moiety (NAM) containing both a unique identification sequence and a complementary association element, forming an "interactor." The association elements allow different interactors to bind, bringing the MOIs into proximity to enable a functional interaction, which produces a detectable trace that allows for subsequent identification of the interacting MOIs.

3. Grounds for Unpatentability

Ground 1: Obviousness over Kanan and Neri - Claims 1-15 and 17-20 are obvious over Kanan in view of Neri.

• Prior Art Relied Upon: Kanan (a 2004 article in Nature describing DNA-templated synthesis) and Neri (Application # 2004/0014090).
• Core Argument for this Ground:
  • Prior Art Mapping: Petitioner argued that Kanan disclosed a method for discovering bond-forming reactions between substrates tethered to DNA, which corresponds to the claimed method of detecting functional interactions. Kanan’s substrates are linked to oligonucleotides with both a coding region (identification element) and an annealing region (association element). However, Kanan’s method was inefficient because it required synthesizing a unique annealing region for each specific pair of substrates to be tested. Petitioner asserted that Neri disclosed using common "self-assembly sequences" on oligonucleotides to allow for combinatorial association between all members of two libraries, along with separate "sequence tags" to identify each member. The combination of Kanan and Neri allegedly taught every limitation of the independent claim.
  • Motivation to Combine: A person of ordinary skill in the art (POSA) would combine Kanan with Neri to improve the efficiency of Kanan's method. Synthesizing the library members in Kanan was a time-intensive, rate-limiting step. Neri’s use of common self-assembly sequences provided a known solution to this problem, allowing a POSA to screen much larger libraries faster and more efficiently by eliminating the need to synthesize unique annealing regions for every possible interaction.
  • Expectation of Success: A POSA would have had a reasonable expectation of success because both references taught libraries of oligonucleotides attached to substrates designed to associate and interact. Modifying Kanan’s specific annealing regions with Neri’s common self-assembly sequences was a predictable substitution of one known hybridization technique for another to achieve the known benefit of improved efficiency.

Ground 2: Obviousness over Baez and Landegren - Claims 1-8, 11-12, 14-15 are obvious over Baez in view of Landegren.

• Prior Art Relied Upon: Baez (Patent 6,511,809) and Landegren (WO 01/61037).

• Core Argument for this Ground:

  • Prior Art Mapping: This ground was argued based on the Patent Owner's litigation position that the claims cover proximity ligation assays (PLA). Petitioner asserted that Baez disclosed the foundational steps of PLA for detecting a known analyte, where two antibody-oligonucleotide conjugates (interactors) bind to a target, bringing the oligonucleotides into proximity for ligation. This ligation event was argued to be the claimed "functional interaction" producing a detectable trace. Landegren also taught PLA methods but added the use of unique identifier tags on the nucleic acids to enable multiplex assays and reduce background noise. Petitioner argued that adding Landegren's identification tags to Baez's conjugates would satisfy the claim limitation of having both an association element (the ligatable ends) and an identification element.
  • Motivation to Combine: A POSA would combine Baez and Landegren to improve Baez’s assay. Landegren expressly taught strategies to reduce background noise and enable multiplex protein detection, both of which were known goals in the field. A POSA would have been motivated to incorporate Landegren's use of unique identifier sequences into Baez's PLA method to create a more robust, specific, and high-throughput assay capable of screening multiple analytes simultaneously.
  • Expectation of Success: A POSA would have expected success because both references related to the same foundational PLA technology. Combining Landegren’s identification tags with Baez’s reporter conjugates was a straightforward addition of a known element to an existing system to achieve the predictable advantages of improved specificity and multiplexing capabilities.

• Additional Grounds: Petitioner asserted that claim 16 is obvious over Kanan, Neri, and Famulok (a 2002 article), where Famulok provided teachings on ligation. Petitioner also asserted that claims 14-15 are obvious over Baez, Landegren, and Freskgard (WO 2005/003778), where Freskgard provided teachings on identifying molecules by sequencing a nucleic acid identifier.

4. Arguments Regarding Discretionary Denial

• Fintiv Factors: Petitioner argued that discretionary denial under Fintiv is unwarranted because the parallel district court litigation is in its infancy. No scheduling order had been entered, no trial date was set, and fact discovery had not begun. Petitioner contended that a Final Written Decision (FWD) from the Board would issue long before any potential trial date, which is projected for January 2027.
• §325(d) Factors: Petitioner argued against denial under §325(d), asserting that the petition raised new art and arguments not before the Examiner. Specifically, the Examiner never considered Neri, Kanan’s Supplementary Information (which detailed the inefficiencies that Neri solved), or any PLA art like Baez or Landegren. Petitioner contended this art is material to patentability, especially given the Patent Owner’s litigation conduct of asserting the claims against a PLA-based product after disclaiming PLA during the original prosecution.

5. Relief Requested

• Petitioner requests the institution of an inter partes review (IPR) and the cancellation of claims 1-20 of the ’848 patent as unpatentable.