Integrated DNA Technologies Inc v. Tecan Group AG

1. Case Identification

• Case #: IPR2024-01506
• Patent #: 11,725,241
• Filed: September 30, 2024
• Petitioner(s): Integrated DNA Technologies, Inc.
• Patent Owner(s): Tecan Genomics, Inc.
• Challenged Claims: 1-16

2. Patent Overview

• Title: Method for Detecting Duplicate Sequencing Reads
• Brief Description: The ’241 patent relates to a method for identifying duplicate sequencing reads in Next-Generation Sequencing (NGS). The method involves appending an adaptor containing a unique identifier sequence, or molecular tag, to nucleic acid fragments prior to amplification, which allows for the subsequent identification of PCR-generated duplicates by finding reads that share identical identifier and target sequences.

3. Grounds for Unpatentability

Ground 1: Anticipation over Kivioja - Claims 1-16 are anticipated by Kivioja under 35 U.S.C. §102.

• Prior Art Relied Upon: Kivioja (a 2011 article in Nature Methods titled Counting absolute numbers of molecules using unique molecular identifiers).
• Core Argument for this Ground:
  • Prior Art Mapping: Petitioner argued that Kivioja disclosed every element of the challenged claims in its method for improving NGS accuracy. Kivioja taught labeling nucleic acid fragments with adaptors containing a random molecular tag (a "10-base-pair random label," or identifier site) before amplification. Following sequencing, Kivioja described collapsing sequence reads with the same label and mapped fragment position into a single "unique molecular identifier" (UMI) to count original molecules. Petitioner asserted this process inherently meets the limitations of claim 1 by obtaining amplicons with appended adaptors containing a unique identifier, sequencing them, and identifying reads with identical identifier and target sequences as duplicates. Petitioner also contended that Kivioja's specific examples met the limitations of dependent claims, including using a priming reaction for appending (claim 10), using a 10-nucleotide identifier (claim 9), and incorporating a sample index for multiplexing (claim 13).

Ground 2: Anticipation over Bielas - Claims 1-3 and 6-16 are anticipated by Bielas under 35 U.S.C. §102.

• Prior Art Relied Upon: Bielas (International Publication No. WO 2013/123442).

• Core Argument for this Ground:

  • Prior Art Mapping: Petitioner argued Bielas taught a method using random molecular tags called "Cyphers" to distinguish true mutations from PCR-generated "artifact mutations." Bielas described ligating adaptors containing Cyphers to genomic DNA fragments. After amplification and sequencing, Bielas taught "computationally deconvoluting" the data by grouping reads with identical Cypher pairs and their corresponding fragment sequences into "families" to create a consensus sequence. Petitioner contended this method of grouping and collapsing reads is equivalent to the claimed steps of identifying duplicates. Bielas’s adaptors were described as containing all the required elements, such as primer binding sites and sample indexes. The use of ligation for appending adaptors and genomic DNA as the sample material was argued to meet the limitations of claims 10 and 6, respectively.

• Additional Grounds: Petitioner asserted additional obviousness challenges based on Kivioja (Ground II) and Bielas (Ground IV), arguing that to the extent any claims were not fully anticipated, they represented obvious modifications of the teachings in the primary references. For example, applying Kivioja's molecular tag method to genomic DNA (claim 6) or placing the identifier at the junction with the fragment (claim 11) would have been obvious variations.

4. Key Claim Construction Positions

• "appended": Petitioner argued the plain and ordinary meaning of "appended" is simply "added" and does not imply any specific method of attachment. This construction was supported by the ’241 patent's specification, which explicitly mentions that appending can be achieved by a "ligation reaction or a priming reaction." This broad construction is critical to the anticipation argument over Kivioja, which used a priming-based template switch reaction to attach its adaptors.
• "identifier site" / "indexing site": Petitioner noted these terms were explicitly defined in the ’241 patent's specification and applied those definitions. An "identifier site" is a molecular tag used to identify duplicate reads, while an "indexing site" is a sample index used for multiplexing.

5. Arguments Regarding Discretionary Denial

• Petitioner argued that discretionary denial under 35 U.S.C. §325(d) is inappropriate because the primary references, Kivioja and Bielas, were not before the Examiner during prosecution. Petitioner asserted the Examiner materially erred by allowing the claims based on a finding that the prior art of record did not teach de-duplication using both an identifier and a fragment sequence, a teaching Petitioner claims is explicit in both Kivioja and Bielas.
• Petitioner also argued against discretionary denial under Fintiv, stating that the parallel district court trial is scheduled for June 22, 2026, well after the Board’s projected Final Written Decision (FWD) date. Further, the district court case is in early discovery, and Petitioner stipulated that, if the inter partes review (IPR) is instituted, it will not pursue any arguments in district court that were raised or reasonably could have been raised in the petition.

6. Relief Requested

• Petitioner requests institution of an inter partes review and cancellation of claims 1-16 of Patent 11,725,241 as unpatentable.