QIAGEN Sciences LLC v. Tecan Group AG

1. Case Identification

• Case #: IPR2025-00026
• Patent #: 11,098,357
• Petitioner(s): QIAGEN Sciences, LLC
• Patent Owner(s): Tecan Genomics, Inc.
• Challenged Claims: 1-10

2. Patent Overview

• Title: Methods for Detecting Duplicate Nucleic Acid Sequences
• Brief Description: The ’357 patent discloses methods for identifying duplicate nucleic acid sequences generated during Polymerase Chain Reaction (PCR) amplification in high-throughput sequencing. The invention involves ligating adaptors containing a unique identifier site to nucleic acid fragments before amplification, allowing for subsequent identification and removal of PCR duplicates.

3. Grounds for Unpatentability

Ground 1: Anticipation of Claims 1-3 and 5-10 under 35 U.S.C. §102

• Prior Art Relied Upon: Porreca (Application # 2012/0165202).
• Core Argument:
  • Prior Art Mapping: Petitioner argued that Porreca discloses every limitation of the challenged claims. Porreca teaches a method for detecting duplicate sequencing reads by ligating adaptors to nucleic acid fragments. These adaptors contain "differentiator tag sequences" which serve as the claimed "unique identifier" (disclosing lengths up to 8 nucleotides) and "barcodes" to identify individual samples, which meet the "indexing site" limitation. Porreca explicitly teaches amplifying the tagged fragments, sequencing them to produce reads containing both the tag and target sequence, and then "collapsing" reads with identical tags and target sequences to remove duplicates.
  • Key Aspects: Petitioner contended Porreca’s disclosure of "collapsing" duplicate reads directly teaches the limitations of identifying duplicates (claim 1) and removing them (claim 2). Porreca also explicitly discusses applying its methods to various nucleic acids, including RNA, genomic DNA, and cDNA, thus anticipating claims 5 and 6.

Ground 2: Obviousness of Claims 1-3 and 5-10 under 35 U.S.C. §103

• Prior Art Relied Upon: Schmitt (WO 2013/142378) in view of McCloskey (Application # 2007/0020640).

• Core Argument:

  • Prior Art Mapping: Petitioner asserted that Schmitt teaches a method for identifying PCR duplicates using a "single molecule identifier (SMI)" ligated in an adaptor to each DNA fragment prior to amplification and sequencing. This SMI serves as the claimed "unique identifier." Schmitt discloses all elements of claim 1 except for an "indexing site unique to a subset of the adaptors" being part of the initial adaptor. McCloskey was argued to supply this limitation by teaching an adaptor that contains both a "random barcode" (a unique identifier) and a "batch-stamp" (an indexing site) to tag molecules and identify their sample origin, respectively, before amplification.
  • Motivation to Combine: A Person of Ordinary Skill in the Art (POSA) would combine Schmitt with McCloskey to improve Schmitt’s method. While Schmitt adds a multiplexing barcode later in its process, a POSA would have been motivated to incorporate McCloskey’s well-known "batch-stamp" into the initial adaptor to enable more efficient and less error-prone multiplexing from the outset. Petitioner noted both references address the same technical problem, and Schmitt cites a related paper by McCloskey, making the combination logical.
  • Expectation of Success: A POSA would have had a high expectation of success, as combining barcode and identifier sequences onto a single adaptor was a standard, predictable technique in molecular biology. Schmitt itself teaches that its adaptors can be modified to include various sequences, such as primer binding sites, demonstrating the modular nature of the technology.

• Additional Grounds: Petitioner asserted additional obviousness challenges for dependent claims 4 and 7. For claim 4 (sequencing the identifier separately), Petitioner argued a POSA would have been motivated to apply the well-known separate "index read" method from Illumina 2008 to the systems of Porreca or Schmitt/McCloskey to increase the read length and efficiency of target sequence analysis. For claim 7 (a universal primer binding site), Petitioner argued it would have been obvious to incorporate a universal site, as taught by Illumina 2008 and Metzker 2010, into the adaptors of Porreca or Schmitt/McCloskey to enable standard, high-throughput next-generation sequencing.

4. Key Claim Construction Positions

• Petitioner argued that the term "adaptor" should be construed broadly as "any oligonucleotide that is attached to the target sequence." This construction is based on the patent's specification, which states an adaptor's function is to enable the generation of amplification-ready products, a function any such oligonucleotide can perform. Petitioner noted that the examiner adopted this broad construction during prosecution, and it is critical for establishing that the prior art adaptors, which may be incorporated via ligation or priming, fall within the claim scope.

5. Arguments Regarding Discretionary Denial

• Petitioner argued against discretionary denial under 35 U.S.C. §325(d), asserting that the core prior art references—Porreca, Schmitt, and the McCloskey application—were never presented to or considered by the examiner during prosecution. Petitioner contended these references are materially different from the art of record and establish a strong case of unpatentability.
• Petitioner also argued against discretionary denial under Fintiv. It was noted that the parallel district court litigation is in its early stages, and the trial date (July 27, 2026) is scheduled to occur after the statutory deadline for a Final Written Decision (FWD) in this inter partes review (IPR) (approx. April 2026). Furthermore, Petitioner stipulated that it would not pursue in the district court any ground on which IPR is instituted, thus mitigating concerns of duplicative efforts.

6. Relief Requested

• Petitioner requests institution of an IPR and cancellation of claims 1-10 of Patent 11,098,357 as unpatentable.