• Illumina, Inc. v. Molecular Loop Biosciences, Inc.No claims unpatentable
  PTAB · Apr 15, 2026 · IPR2024-01419 · APJ Susan L C Mitchell · IPR · Final written decision

  Claims 1–9 were not shown unpatentable because the asserted references failed to disclose the claimed correcting step, and Chee was not prior art to claims 1–3 and 9.

  RulingsFinal written decision

  • Novelty / Anticipation (§102) › Priority / effective filing date / continuation supportPriority date awardedReference not prior artDecided for patent owner

    “We have considered both parties’ arguments and evidence and determine that Patent Owner has presented sufficient evidence of reasonable the invention to practice every day during the critical period in order to demonstrate reasonable diligence. See Perfect Surgical Techniques, Inc. v. Olympus America, Inc., 841 F.3d 1004, 1009 (Fed. Cir. 2016). “[D]iligence need not be perfectly continuous—only reasonably continuous.” Arctic Cat Inc. v. GEP Power Prods., Inc., 919 F.3d 1320, 1331 (2019). The key question is whether, “in light of the evidence as a whole, the invention was not abandoned or unreasonably delayed.” Id. (internal quotations omitted). Applying this standard, we determine that Patent Owner sufficiently demonstrates reasonably continuous diligence throughout the critical period.” slip op. at 32

  • Claim Construction › Intrinsic evidence (Phillips canons) › Plain and ordinary meaning to a POSITATerm construed patent owner constructionDecided for patent owner

    “introduced during said workflow by collapsing target:differentiator tag combinations observed more than once into a single count.” Ex. 1001, 131:46–48 (emphasis added). The “determining step” of claim 2 recites “determining a consensus base call for the target nucleic acid molecule sequences,” but performs “collapsing all sequence reads comprising a same differentiator tag into a single read,” before the “determining step.” Id. at 131:49–53. Patent Owner proposes an interpretation of these “collapsing” and “determining” steps recited in claims 1 and 2 and asserts that they should be construed as distinct steps performed in a particular order in which the “collapsing step” is performed before the “determining step.” PO Resp. 42–45. We agree. First, Patent Owner asserts a person of ordinary skill in the art would have understood that the “collapsing step” of claim 1 is distinct from, and must occur before, the “determining step” of claim 2 based on the plain language of claims 1 and 2. PO Resp. 42–43. Patent Owner argues that the “collapsing step” and the “determining step” are distinct steps because claims 1 and 2 use different terms to describe these distinct steps that are performed sequentially according to the claim language. Id. (citing Ex. 1001, 131:47–54; Ex. 2023 ¶ 133; Ex. 2024, 57:11–58:22). More specifically, Patent Owner explains that claim 1 recites a “collapsing step,” followed by claim 2, which depends from claim 1 and refers to “collapsing” before “determining a consensus base call” such that “claim 2 describes determining a consensus base call from collapsed reads, not performing ‘collapsing’ by determining a consensus base call.” Id. at 42 (citing Ex. 1001, 131:47–54). collapsing corrects for skewing, an issue related to over- or under-amplification, which is a separate and distinct problem from the sequence errors that a consensus base call is designed to address.” Id. at 43 (citing Ex. 1001, 27:47–50, 32:29–34). Patent Owner contends further that “‘[c]ollapsing’ is a different step, performed separately from determining any consensus base call, to provide even greater accuracy when subsequently determining a consensus base call” such that “if one were to collapse by determining the consensus base call, errors from amplification bias could still be represented in the consensus base call generated.” Id. at 43–44 (emphasis omitted, citing Ex. 2023 ¶¶ 134–37). Second, Patent Owner argues a person of ordinary skill in the art would have understood that the “collapsing step” of claim 1 is distinct from the “determining step” based on the specification of the ’730 patent. PO Resp. 43–45. For example, Patent Owner explains that the specification states that “[f]or any target:differentiator tag combination observed more than once, all such reads are ‘collapsed’ into a single read before consensus basecalls are determined. This will cancel the effect of bias on consensus basecall accuracy.” Id. at 43 (emphasis omitted) (quoting Ex. 1001, 72:63– 73:5) (citing Ex. 2023 ¶¶ 133, 138–142).” slip op. at 11

  • Novelty / Anticipation (§102) › Anticipation standard (single reference, every element)Not shown unpatentableNot shown unpatentable

    “We have considered both parties’ arguments and evidence and agree with Patent Owner’s position. As discussed above, we agree with Patent Owner that the “collapsing step” recited in claim 1 and the “determining step” recited in claim 2 are two different steps required by the challenged claims such that “collapsing” does not mean determining a consensus base call or sequence, and must occur before any determining step. As a result, we determine Chee’s step of determining a consensus sequence does not disclose the “collapsing step” recited in claim 1 that requires collapsing “target:differentiator tag combinations.” We are also unpersuaded by Petitioner’s reliance on Chee’s process of correcting for amplification bias as disclosing the claimed collapsing step. As recognized by Patent Owner, the claim language of the “collapsing step” requires “collapsing target:differentiator tag combinations,” rather than collapsing only differentiator tags. In view of this requirement, Chee does not disclose the “collapsing step” because Chee teaches quantifying the starting nucleic acid molecules using their unique identifiers, rather than target:differentiator tag combinations. As Petitioner admits, “Chee’s technique for correcting amplification bias corrects quantitative errors without correcting sequencing errors” (Reply 15), whereas claim 1’s “collapsing step” corrects both quantitative errors and sequencing errors by using target:differentiator tag combinations. See Ex. 1001, 131:47–49 target:differentiator tag combinations).” slip op. at 41

  • Obviousness (§103) › Graham factors (scope of art, differences, level of skill)Not shown unpatentableNot shown unpatentable

    “Given this claim interpretation requiring collapsing target:differentiator tag combinations, it is undisputed that McCloskey, who uses unique barcodes alone, does not teach this limitation. Petitioner does not rely on Bignell as teaching this collapsing step. Accordingly, we conclude Petitioner has not shown that the combination of Bignell and McCloskey teaches the “collapsing step” recited in claim 1. Because claims 4 through 6 depend from claim 1, they also require the “collapsing step” of claim 1 that is not taught by the combination of Bignell and McCloskey.” slip op. at 54

  Patent outcomesUS 11,840,730 not shown unpatentable
  Claim construction§ 102 anticipation§ 103 obviousnesscites Graham
  Patents in suitUS 11,840,730
• Alamar Biosciences, Inc. v. Olink Proteomics ABNo claims unpatentable
  PTAB · Mar 4, 2026 · IPR2024-01353 · APJ Tawen Chang · IPR · Final written decision

  Claims 1–20 were not shown unpatentable: the asserted obviousness grounds failed, including because Kanan and Neri did not teach selecting the claimed cis-reactive cells.

  RulingsFinal written decision

  • Skill levelSkill level petitioner adoptedDecided for petitioner

    “Accordingly, for purposes of this decision we adopt Petitioner’s proposal of a person of ordinary skill in the art, with the following changes noted in italics below: A person with “an advanced degree, such as a Ph.D., in organic chemistry, molecular biology, biochemistry, or a related field; and about two years of experience in industry and/or laboratory experience relating to small molecules and proteins and would have been familiar with nucleic acid chemistry and conventional hybridization techniques; and (b) access to one or more team members having an advanced degree, such as a Ph.D., in organic chemistry, molecular biology, biochemistry, or a related field; and about two years of experience in industry and/or laboratory experience relating to high throughput screening techniques such as nucleic acid sequencing. A person could also have qualified as a POSA with less formal education and more technical or professional experience.11 We emphasize, however, that our decision would not change if we instead used Patent Owner’s proposed definition of a POSA.” slip op. at 13

  • Claim Construction › Intrinsic evidence (Phillips canons) › Plain and ordinary meaning to a POSITATerm construed patent owner constructionDecided for patent owner

    “Because the parties have placed the limitation “selecting all cis- reactive cells exhibiting the detectable trace” into controversy, we construe the term below, but only to the extent necessary to resolve the controversy. See Realtime Data, LLC v. Iancu, 912 F.3d 1368, 1375 (Fed. Cir. 2019) (“The Board is required to construe ‘only those terms . . . that are in controversy, and only to the extent necessary to resolve the controversy.’”) (quoting Vivid Techs., Inc. v. Am. Sci. & Eng’g, Inc., 200 F.3d 795, 803 (Fed. Cir. 1999)). For the reasons discussed below, we agree with Patent Owner that the plain and ordinary meaning of this phrase, in light of the language of the claims, the Specification, and the prosecution history of record, requires “selecting all of the [molecular complexes or structures] meeting the defined criteria for [cis-reactive cells (CRCs)] and exhibiting the detectable trace.” Sur-reply 8 (citing Ex. 2008 ¶¶ 94, 98–119). We further agree that cis-reactive cells should be construed to mean “an association of at least two interactor moieties, joined by an associated oligonucleotide.” (PO Resp. 9 (quoting Ex. 1001, 9:35-37)). Accordingly, we determine that, properly construed, the claims require that what is “selected” at step 1(d) — what is differentiated or set apart from other molecular complexes or structures in the reaction mixture at the conclusion of step 1(d) — to be “an association of at least two interactor moieties joined by an associated oligonucleotide” that exhibits the detectable trace.” slip op. at 16

  • Obviousness (§103) › Graham factors (scope of art, differences, level of skill)Not shown unpatentableNot shown unpatentable

    “We agree that Petitioner has not shown that the combination of Kanan and Neri teaches “selecting all cis-reactive cells exhibiting the detectable trace,” as we have construed that phrase above. In particular, we determine that, properly construed, the limitation requires the selection of “all associations of at least two interactor moieties joined by an associated oligonucleotide and exhibiting the detectable trace.” Instead, as described in Kanan, what is “selected” is the molecules of interest joined by bond formation, with only one of the molecules of interest coupled to a nucleic acid moiety. Thus, the selected molecular complex or structure does not comprise two interactors (i.e., two molecules of interest coupled to NAMs). Moreover, to the extent there are two interactors, they are joined by the bond between the molecules of interest rather than an associated oligonucleotide.” slip op. at 35

  • ExcludeMotion to exclude, deniedDenied

    “III. PATENT OWNER’S MOTION TO EXCLUDE EVIDENCE Patent Owner moved to exclude Exhibit 1008, on the ground that it contains settlement statements and that Rule 408 of the Federal Rule of Evidence prohibits Petitioner from using the statements to impeach or contradict Patent Owner. Mot. 5. Because we do not rely in our analysis on this exhibit, we dismiss the Motion to Exclude as moot.” slip op. at 43

  Patent outcomesUS 7,883,848 not shown unpatentable
  Claim construction§ 103 obviousnesscites Phillips · KSR · Graham
  Patents in suitUS 7,883,848
• Illumina Inc. v. Molecular Loop Innovations LLCNo claims unpatentable
  PTAB · Jan 13, 2026 · IPR2024-00964 · APJ Annette R Reimers · IPR · Final written decision

  Claims 1–8 were not shown unpatentable over either asserted §103 combination because the prior art did not teach the discarding step or establish a reasonable expectation of success.

  RulingsFinal written decision

  • Claim Construction › Intrinsic evidence (Phillips canons) › Plain and ordinary meaning to a POSITATerm construed patent owner constructionDecided for patent owner

    “specification to interpret the meaning of a claim and importing limitations from the specification into the claim can be a difficult one to apply in practice.” Phillips, 415 F.3d at 1323. “[T]he line between construing terms and importing limitations”, however, “can be discerned with reasonable certainty and predictability if [our] focus remains on understanding how a person of ordinary skill in the art would understand the claim terms.” Id. Ultimately, we construe claim terms to “capture the scope of the actual invention more accurately than either strictly limiting the scope of the claims to the embodiments disclosed in the specification or divorcing the claim language from the specification.” Id. at 1324. Here, we are tasked with resolving the dispute between the parties as to the scope of the source of the claimed cross-over error. See Sur-reply 2. Although claim 1 does not explicitly recite cross-over error is created during cluster amplification, the specification shows otherwise. It repeatedly, consistently, and exclusively describes cross-over errors as arising from the formation of chimeric molecules during the amplification step of the sequencing workflow. See Ex. 1001, Fig. 1, Fig. 2, 4:29–52 (describing “improper molecular overlap via formation of a heteroduplex between patient A’s nucleic acid template and patient B’s nucleic acid template” “[w]hen the amplification process begins”), 5:29–58 (the same), 6:25–44 (the same), 6:64–7:23 (the same).” slip op. at 15

  • Skill levelSkill level petitioner adoptedDecided for petitioner

    “Petitioner asserts that a person of skill in the art (“POSA”) “would have had (i) a Ph.D. in molecular biology, genetics, bioinformatics, or a related field and at least two years of experience in high-throughput sequencing technologies or (ii) a Master’s degree in one of the same fields with at least four years of experience in high-throughput sequencing technologies.” Pet. 17 (citing Ex. 1003 ¶¶ 19–20). Patent Owner states that it adopts Petitioner’s proposal for a POSA for purposes of this proceeding. PO Resp. 13 (citing Ex. 2001 ¶¶ 19–22). We adopt Petitioner’s proposed definition of the skill level as it is consistent with the prior art’s demonstration of the level of ordinary skill in the art at the time of the invention. We find both Dr. Spellman and Dr. Adalsteinsson are qualified to opine from the perspective of a POSA, because each has at least ordinary skill in the art. See Ex. 1003 ¶¶ 4–15; Ex. 2001 ¶¶ 4–9.” slip op. at 8

  • Obviousness (§103) › Motivation to combine / reasonable expectation of successNot shown unpatentableReasonable expectation not foundNot shown unpatentable

    “The reasonable expectation of success requirement refers to the likelihood of success in combining references to meet the limitations of the claimed invention.” Intelligent Bio-Sys., Inc. v. Illumina Cambridge Ltd., 9 Because, as explained below, we find Petitioner has not met its burden to show reasonable expectation of success, we do not need to address whether Petitioner has shown sufficient reason to combine the asserted references. 821 F.3d 1359, 1367 (Fed. Cir. 2016); see also Allergan, Inc. v. Apotex Inc., 754 F.3d 952, 966 (Fed. Cir. 2014) (stating that “failure to consider the appropriate scope of the . . . patent’s claimed invention in evaluating the reasonable expectation of success . . . constitutes a legal error”). Here, the claimed invention is a method for reducing template cross-over error. Thus, we must determine whether, in December 2010, an ordinarily skilled artisan would have reasonably expected that the combination of Parameswaran and Gloor would reduce template cross-over error. slip op. at 26

  • Obviousness (§103) › Graham factors (scope of art, differences, level of skill)Not shown unpatentableNot shown unpatentable

    “Thus, on this record, we are persuaded by Patent Owner’s argument that Parameswaran’s “unexpected perfect pairings of unmatched forward and reverse barcodes” are not cross-over error. PO Resp. 31 (citing Ex. 2001 ¶¶ 116–123). In addition, as Petitioner acknowledges, Parameswaran merely “distinguished,” but did not “discard” sequences with mismatches. Pet. 34. Parameswaran states that “[t]he low false-discovery rate for perfect matches strengthens the argument that any sequence with both 5’ and 3’ barcode motifs will be placed with reasonable accuracy into the correct bin.” Ex. 1004, 8. But, because Parameswaran achieved a “remarkably low misassignment rate,” it did not discard, but included any sequence with a matched barcode. Id. Indeed, Parameswaran explains that “[f]or our purposes, all sequences with a match to one of the two expected sequence motifs were considered as true members of the corresponding dataset.” Id. In its Reply, Petitioner emphasizes Parameswaran’s language “[f]or our purposes.” Reply 14 (citing Ex. 1004, 8). According to Petitioner, “[a] POSA would have understood from Parameswaran that chimeric sequences could be kept or discarded, depending on the sequencing ‘purpose.’” Id. (citing Ex. 1054 ¶¶ 79–82). Petitioner is asking us to deem unpatentable a claim based on its reading of “for our purposes,” a broad, undefined statement, to mean something specific—a suggestion to discard perfect unexpected pairings, which Parameswaran explicitly did not do. See Ex. 1004, 8. Petitioner has not presented sufficient evidence and persuasive argument for us to do so.” slip op. at 24

  Patent outcomesUS 11,041,852 not shown unpatentable
  Claim construction§ 103 obviousnesscites Phillips · KSR · Graham
  Patents in suitUS 11,041,852
• Cisco Systems, Inc. v. Umbra Technologies Ltd.No claims unpatentable
  PTAB · Aug 28, 2025 · IPR2024-00270 · APJ Gregg I Anderson · IPR · Final written decision

  Claims 15–20 were not shown unpatentable because Hankins did not teach limitation 15.3; claims 1–14 were disclaimed.

  RulingsFinal written decision

  • Skill levelSkill level petitioner adoptedDecided for petitioner

    “Patent Owner does not dispute Petitioner’s proposal of the level of ordinary skill in the art. PO Resp. 6. Petitioner’s proposal is supported by the Reddy Declaration and is consistent with the ’595 patent and the asserted prior art. Accordingly, we apply Petitioner’s articulation in our obviousness evaluation below.” slip op. at 14

  • Claim Construction › Threshold & procedure › Whether a term needs construction (O2 Micro)No construction neededOther

    “B. Claim Construction Beyond plain and ordinary meaning, Petitioner does not propose any term for claim construction. Pet. 13. Patent Owner does not argue any claim construction issue. See generally PO Resp. The argument and evidence provided by the parties regarding limitation 15.3 is dispositive. See Section II.E. below. Our analysis of limitation 15.3 does not turn on any claim construction question. Id. Accordingly, we do not need to construe any claim term. See Nidec Motor Corp. v. Zhongshan Broad Ocean Motor Co., 868 F.3d 1013, 1017 (Fed. Cir. 2017) (noting that “we need only construe terms ‘that are in controversy, and only to the extent necessary to resolve the controversy’” (quoting Vivid Techs., Inc. v. Am. Sci. & Eng’g, Inc., 200 F.3d 795, 803 (Fed. Cir. 1999))). We apply the plain and ordinary meaning of all claim terms, as would have been understood by a person of ordinary skill in the art, in the context of the ’595 patent.” slip op. at 14

  • Adverse judgmentAdverse judgmentOther

    “D. Claims 1–14 as Obvious Over Kommula As already noted, Patent Owner has disclaimed claims 1–14. Ex. 3001. We do not analyze claims 1–14 as the challenge is mooted by the filing of the Statutory Disclaimer.” slip op. at 15

  • BurdenNot shown unpatentable

    “350 receiving a request for a listing of “services” from a gateway device and provisioning one or more tunnel servers has not been shown to teach generating “a list of available servers.” There is no persuasive evidence to support Petitioner’s assertion. Petitioner relies on unsupported argument because, at best, Hankins discloses gateway devices 311 and 321, each of which is located in different logical broadcast domains, requesting services from one another. Ex. 1005, 12:9–16. This particular disclosure, however, does not appear to implicate the functionality of Hankins’s controller 350, much less result in controller 350 generating a list of available tunnel servers that would allow gateway devices 311 and 312 to exchange a listing of “services” therebetween. Petitioner’s reliance on Hankins’s controller 350 provisioning additional tunnel servers both to improve performance and without human intervention fares no better. Ex. 1005, 25:45–55. There is no indication in Hankins that this provisioning performed by controller 350 is done in response to receiving a request for a list of available tunnel servers from either gateway device 311 or 312.” slip op. at 20

  Patent outcomesUS 11,108,595 not shown unpatentable
  Claim construction§ 103 obviousnesscites KSR · Graham
  Patents in suitUS 11,108,595
• Sarepta Therapeutics, Inc. v. The Trustees Of The University Of PennsylvaniaNo claims unpatentable
  PTAB · Aug 20, 2025 · IPR2024-00580 · APJ Susan L C Mitchell · IPR · Final written decision

  The Board held claim 8 not shown unpatentable under each of three §103 grounds because Petitioner failed to establish motivation to combine the references with a reasonable expectation of success.

  RulingsFinal written decision

  • Skill levelSkill level petitioner adoptedDecided for petitioner

    “In addressing the level of ordinary skill in the art, Petitioner contends that a person of ordinary skill in the art (“POSA” or “POSITA”) would have had at least a Ph.D. in biochemistry, molecular biology, or a related field and between one and four years of post-doctoral experience in the field of gene therapy. Alternatively, a POSA would have had at least a Master’s or Bachelor’s Degree in biochemistry, molecular biology, or a related field, with a corresponding number of additional years of experience in the field of gene therapy. Pet. 12 (citing Ex. 1005 ¶¶ 111–115). Patent Owner states that it does not challenge Petitioner’s definition. PO Resp. 10. On this complete record, we accept Petitioner’s proposed definition, as it appears consistent with the level of skill in the art reflected in the prior art of record and the disclosure of the ’274 Patent. See Okajima v. Bourdeau, 261 F.3d 1350, 1355 (Fed. Cir. 2001) (“the prior art itself [may] reflect[] an appropriate level” as evidence of the ordinary level of skill in the art (quoting Litton Indus. Prods., Inc. v. Solid State Sys. Corp., 755 F.2d 158, 163 (Fed. Cir. 1985)).” slip op. at 11

  • Claim Construction › Threshold & procedure › Whether a term needs construction (O2 Micro)No construction neededOther

    “Petitioner asserts that the ’274 patent “does not specify a particular program or set of program parameters that should be used to align sequences and calculate percent identity for purposes of determining whether a particular test sequence falls within the scope of the claims.” Pet. 21. Petitioner asserts that it analyzed the percent identity claim elements, as Patent Owner did in the parallel District Court litigation, Penn-II, “using the Clustal program at default settings to generate amino acid sequence alignments and calculate percent identity values.” Id. at 21–22. Petitioner, however, does not ask for any particular construction of any claim term. See id. Patent Owner states that it “does not challenge Petitioner’s articulation of the lack of a need for claim construction.” PO Resp. 10. Having considered the record, we determine that no express claim construction of any claim term is necessary to reach our decision. See Realtime Data, LLC v. Iancu, 912 F.3d 1368, 1375 (Fed. Cir. 2019) (“The Board is required to construe ‘only those terms that . . . are in controversy, and only to the extent necessary to resolve the controversy.’”) (quoting Vivid Techs., Inc. v. Am. Sci. & Eng’g, Inc., 200 F.3d 795, 803 (Fed. Cir. 1999)); Nidec Motor Corp. v. Zhongshan Broad Ocean Motor Co. Ltd. v. Matal, 868 F.3d 1013, 1017 (Fed. Cir. 2017) (“[W]e need only construe terms ‘that are in controversy, and only to the extent necessary to resolve the controversy.’” (quoting Vivid Techs., 200 F.3d at 803)).” slip op. at 12

  • Expert testimonyPatent owner expert creditedDecided for patent owner

    “According to the import of the complete recitation of paragraph 250 of the ’772 Publication set forth above that Petitioner relies upon for the motivation to improve efficient gene transfer in liver, AAV8 already fulfills this need. See Tr. 28:15–18. We do not read the ’772 Publication as calling for a search for a more efficient variant to improve efficient gene transfer in liver. We credit Dr. Samulski’s testimony that supports this view of the teachings of the ’772 Publication. Dr. Samulski testifies: Additionally, when the inventors compared AAV8’s expression in the liver against new serotypes AAVrh2, AAVrh10, AAVrh13, and AAVrh21, they found that AAV8 remained superior: EX1007, ¶ 253. Notably, AAV8 was shown to have over fifty percent (50%) greater expression in liver than AAVrh10. As I discuss more below, a skilled artisan in 2005 would not have expected a single amino acid substitution to significantly alter tropism in order to target to a different tissue. Thus, in my opinion, in 2005, a skilled artisan with the goal of targeting the liver would have selected the best known vector for delivery to liver at that time—AAV8. Ex. 2027 ¶ 42. We also agree with Dr. Samulski’s opinion that a POSA would have selected the best vector for liver, AAV8, instead of modifying another vector to increase tropism to liver. Dr. Samulski testifies: In my opinion, a skilled artisan in 2005 would not have looked solely to modify a vector to try to improve tropism to a particular tissue. As discussed throughout this declaration, changing tropism is difficult to predict, and a skilled artisan would not have had a reasonable expectation that changes could be made to improve or alter tropism. A skilled artisan would also have been concerned that changes, even small ones, could negatively impact other properties of the capsid protein. Therefore, rather than seek to modify a vector, a skilled artisan” slip op. at 29

  • Obviousness (§103) › Motivation to combine / reasonable expectation of successNot shown unpatentableMotivation not foundNot shown unpatentable

    “The ’772 Publication, however, does not indicate as Petitioner asserts that a new variant is necessary to improve the efficiency of gene transfer to liver; the ’772 Publication indicates that AAV8 fulfills that need. See Ex. 1007 ¶ 250. In the paragraph that Petitioner relies upon for the alleged need to improve the efficiency of gene transfer to the liver, the ’772 Publication states in full: The tropism of each new vector is favorable for in vivo applications. AAV2/7 vectors appear to transduce skeletal muscle as efficiently as AAV2/1, which is the serotype that confers the highest level of transduction in skeletal muscle of the primate AAVs tested to date. Importantly, AAV2/8 provides a substantial advantage over the other serotypes in terms of efficiency of gene transfer to liver that until now has been relatively disappointing in terms of the numbers of hapatocytes stably transduced. AAV2/8 consistently achieved a 10 to 100-fold improvement in gene transfer efficiency as compared to the other vectors. The basis for the improved efficiency of AAV2/8 is unclear, although it presumably is due to uptake via a different receptor that is more active on the basolateral surface of hepatocytes. This improved efficiency will be quite useful in the development of liver-directed gene transfer where the number of transduced cells is critical, such as in urea cycle disorders and familial hypercholesterolemia. Id. (citations omitted) (emphasis added). According to the import of the complete recitation of paragraph 250 of the ’772 Publication set forth above that Petitioner relies upon for the motivation to improve efficient gene transfer in liver, AAV8 already fulfills this need. See Tr. 28:15–18. We do not read the ’772 Publication as calling for a search for a more efficient variant to improve efficient gene transfer in liver. We credit Dr. Samulski’s testimony that supports this view of the teachings of the ’772 Publication. Dr. Samulski testifies: Additionally, when the inventors compared AAV8’s expression in the liver against new serotypes AAVrh2, AAVrh10, AAVrh13, and AAVrh21, they found that AAV8 remained superior:” slip op. at 28

  Patent outcomesUS 11,680,274 not shown unpatentable
  Claim construction§ 103 obviousnesscites Phillips · KSR · Graham
  Patents in suitUS 11,680,274
• Gene Company Pty Ltd v. The Trustees Of Columbia University In The City Of New YorkNo claims unpatentable
  PTAB · Jun 23, 2025 · IPR2024-00313 · APJ Tawen Chang · IPR · Final written decision

  Claims 1–54 were not shown unpatentable because Petitioner failed to establish a reasonable expectation of success for the proposed combinations; objective indicia also supported non-obviousness.

  RulingsFinal written decision

  • Skill levelSkill level patent owner adoptedDecided for patent owner

    “As to the first issue, we agree with Patent Owner that defining the level of skill in view of the solution described in the patent risks improper hindsight. Okajima v. Bourdeau, 261 F.3d 1350, 1355 (Fed. Cir. 2001) 18 (“[T]he level of skill in the art is a . . . lens through which . . . the Board views the prior art and the claimed invention,” which “prevents . . . factfinders from using their own insight or . . . hindsight[] to gauge obviousness.”). We therefore do not include “practical knowledge about . . . the deuterium isotope effect, including the patents and publications discussed [in the Petition],” as part of our definition of a person of ordinary skill in the art.” slip op. at 18

  • Expert testimonyPetitioner expert creditedMixed

    “person of ordinary skill in the art would employ” in an obviousness analysis, we give some weight to Dr. Guengerich’s testimony. KSR, 550 U.S. at 418; Plantronics, Inc. v. Aliph, Inc., 724 F.3d 1343, 1354 (Fed. Cir. 2013) (explaining that “motivation to combine may be found. . . in . . . the background knowledge, creativity, and common sense of the person of ordinary skill”). Nevertheless, even if we were to agree that an ordinarily skilled artisan would have seen the 1,5-shift in NRPE in Mata’s A2E biosynthetic pathway as a particularly desirable location for intervention, we are not persuaded that such a person would have been motivated to substitute C20 deuterated vitamin A for the vitamin A in Ortho Pharma’s composition and method, because Petitioner has not shown, by a preponderance of evidence, that such an artisan would have reasonably expected the substitution to retard the accumulation of A2E or to treat macular degeneration.” slip op. at 42

  • Claim Construction › Intrinsic evidence (Phillips canons) › Preamble limiting or notPreamble limitingDecided for patent owner

    “In our Institution Decision, we preliminarily construed the preamble of claim 28 as limiting. Inst. Dec. 30–31. Petitioner did not take issue with our construction, or dispute Patent Owner’s construction of the preambles of claims 1 and 29 as also limiting. After consideration of the full trial record, we maintain our construction of the preamble of claim 28 as limiting for the reasons set forth in our Institution Decision. For similar reasons and the reasons set forth in Patent Owner’s Response, we further construe the preambles of claims 1 and 29 as limiting. See PO Resp. 12–14. We further determine that we do not need to construe any other claim term in order to resolve the controversy between the parties. See Realtime Data, LLC v. Iancu, 912 F.3d 1368, 1375 (Fed. Cir. 2019) (“The Board is required to construe ‘only those terms . . . that are in controversy, and only to the extent necessary to resolve the controversy.’”) (quoting Vivid Techs., Inc. v. Am. Sci. & Eng’g, Inc., 200 F.3d 795, 803 (Fed. Cir. 1999)).” slip op. at 26

  • Claim Construction › Threshold & procedure › Whether a term needs construction (O2 Micro)No construction neededDecided for patent owner

    “415 F.3d 1303, 1312–19 (Fed. Cir. 2005) (en banc). Under this framework, claim terms are given their ordinary and customary meaning, as would be understood by a person of ordinary skill in the art, at the time of the invention, in light of the language of the claims, the specification, and the prosecution history of record. Id.” slip op. at 25

  Patent outcomesUS RE47,045 not shown unpatentable
  Claim construction§ 103 obviousnesscites Phillips · KSR · Graham
• Apple Inc. v. Fintiv, Inc.No claims unpatentable
  PTAB · May 23, 2024 · IPR2023-00398 · APJ George R Hoskins · IPR · Final written decision

  Claims 1–22 were not shown unpatentable as obvious over Dill, Vadhri, and Akashika because Dill was not shown to disclose the claimed Integration Tier Limitation.

  RulingsFinal written decision

  • Skill levelSkill level petitioner adoptedDecided for petitioner

    “We adopt Petitioner’s undisputed formulation of ordinary skill in the art as set forth above, because we are satisfied this formulation generally comports with the level of skill necessary to understand and implement the teachings of the ’196 patent and the asserted prior art. We do not adopt Patent Owner’s annotation to Petitioner’s formulation as requiring knowledge of “mobile wallets” specifically, because we determine knowledge of “mobile payment systems and techniques” per Petitioner’s formulation is tied sufficiently to the claims of the ’196 patent to reflect the level of ordinary skill in the pertinent art. At the same time, even if we were to include knowledge of “mobile wallets” in our formulation, it would not materially change our Decision as set forth below. That is, we would still determine Petitioner has not shown by a preponderance of the evidence that Dill discloses the Integration Tier Limitation.” slip op. at 10

  • Expert testimonyNot reached

    “We need not resolve the parties’ dispute as to whether Dr. Houh qualifies as an ordinarily skilled artisan. Even assuming that Dr. Houh possesses, at a minimum, ordinary skill in the art—as we have done in this Decision—we determine Petitioner still fails to show that any of the challenged claims are unpatentable.” slip op. at 12

  • Claim Construction › Threshold & procedure › Whether a term needs construction (O2 Micro)No construction neededDecided for patent owner

    “The Integration Tier Limitation requires no further construction for purposes of this proceeding. See Pet. Reply 7 (“[N]o specific construction is required.”). The claim clearly specifies that the claimed “web services communication mechanisms” must serve as an interface between the integration tier and (1) the claimed mobile wallet application and, separately, (2) “a plurality of different device types over a plurality of different communication channels.” For purposes of this Decision, we assume that this interface may be direct or indirect. See id. at 6 (asserting that “communication channels that interface, even indirectly, with the ‘web services communication mechanisms’ still interface with the ‘web services communication mechanisms’”).” slip op. at 28

  • Obviousness (§103) › Graham factors (scope of art, differences, level of skill)Not shown unpatentableNot shown unpatentable

    “However, we find that of those four channels (1)–(4), only the first channel (1) is associated with web interface 137 such that it qualifies as a “communication channel,” as required by claim 1. There is no indication in the Dill disclosures cited by Petitioner that any of the other three channels (2)–(4) are associated with web interface 137. For example, Figure 9 of Dill includes a double-headed arrow to illustrate communication between web interface 137 and transfer options module 145, but Figure 9 does not include any arrows to illustrate communication between web interface 137 and any one or more of IVR interface 136, other interfaces 138, agent system 135, or mobile network 115. See Ex. 1005, Fig. 9. In other words, Petitioner fails to show Dill teaches web interface 137 interfaces with any devices over any of channels (2)–(4), as would be required by Petitioner’s mapping. In the Petition, Petitioner never clearly (or persuasively) addresses this requirement of the claim. Petitioner does contend that transfer options module 145 is coupled to various devices via interfaces 136–138 and exchanges transaction information (see Pet. 25–26; see also Pet. Reply 10– 11), but that contention misses the mark. The salient question is whether Dill’s web interface 137 (i.e., the claimed “web services communication mechanisms”) interfaces with the different device types over the channels, not whether transfer options module 145 (i.e., the claimed “integration tier”) does so.” slip op. at 30

  Patent outcomesUS 10,438,196 not shown unpatentable
  Claim construction§ 103 obviousnesscites KSR · Graham
  Patents in suitUS 10,438,196
• Apple Inc. v. Fintiv, Inc.No claims unpatentable
  PTAB · May 23, 2024 · IPR2023-00399 · APJ Juliet Mitchell Dirba · IPR · Final written decision

  Claims 1–22 were not shown unpatentable under § 103 over Dill, Vadhri, and Akashika because Dill did not teach or render obvious the hardware SIM card and integration tier limitations.

  RulingsFinal written decision

  • Skill levelSkill level petitioner adoptedDecided for petitioner

    “In the Institution Decision, we determined that a person of ordinary skill in the art would have had “a bachelor’s degree in electrical engineering, computer science, or equivalent training, and approximately two years of work experience in software development with a basic knowledge of accounting” and “working knowledge of mobile payment systems and techniques,” as Petitioner proposes. Inst. Dec. 9 (quoting Pet. 3–4). We stated that “this definition generally comports with the level of skill necessary to understand and implement the teachings of the ’488 patent and the asserted prior art.” Id. (citing Ex. 1003 ¶ 22; Ex. 2001 ¶ 35).” slip op. at 10

  • Expert testimonyPetitioner expert discountedMixed

    “In addition, Petitioner’s reliance on Dr. Houh’s testimony (see Pet. 23–24) is unavailing. Although Dr. Houh agrees with the arguments in the Petition and includes quotes from the cited portions of Dill and Bykov (see Ex. 1002 ¶¶ 95–97), he provides no additional analysis or explanation beyond what was provided in the Petition. As a result, his testimony suffers the same deficiencies as the Petition. Also, we do not credit his conclusion that Dill includes the requisite disclosure (see id. ¶ 97) because he fails to provide sufficient supporting explanation or evidence (see 37 C.F.R. § 42.65(a)). Finally, we note that Petitioner misrepresents Dr. Shamos’s testimony by stating that Dr. Shamos “agrees that if a mobile device executes a mobile wallet over a cellular network, the mobile device has a SIM card for the mobile wallet.” Pet. Reply 22 (emphasis added) (citing Ex. 1022, 29:4–7, 40:9–10). In the cited testimony, Dr. Shamos agrees that mobile devices have SIM cards, but he does not address where a mobile wallet application would be installed. Ex. 1022, 29:4–7, 40:9–10. Thus, contrary to Petitioner’s argument, we determine that Dr. Shamos’s testimony does not support Petitioner’s position.” slip op. at 27

  • Claim Construction › Threshold & procedure › Whether a term needs construction (O2 Micro)No construction neededDecided for petitioner

    “for the term “hardware SIM card” because the important points are undisputed. In particular, the parties agree that a “hardware SIM card” is a SIM card implemented in hardware rather than software. See Pet. Reply 9 (citing Ex. 1021 ¶ 36); Tr. 40:25–41:2 (Patent Owner’s counsel explaining that the language in its proposed construction was “to differentiate it from a software SIM card”); see also PO Resp. 16, 19 (asserting that the term refers to a specific type of hardware, namely a “chip” or a “smart card”) (citing Ex. 2003 ¶¶ 32–33). The parties also agree that an ordinarily skilled artisan would have known that a “SIM card” is a component in a mobile device involved in identifying and authenticating a user to a mobile network. See Tr. 30:23–31:3 (Petitioner’s counsel stating “a SIM card, just as known in the art . . . would allow the user to be able to access the mobile network” 10 Each page in Exhibit 2021 includes at least two page numbers. For clarity, we refer to the page number of the exhibit (shown in the bottom right corner), and we have adjusted Patent Owner’s citation accordingly. given “the user’s identification information on it”), 39:24–40:2 (Patent Owner’s counsel stating that “I think everyone is in agreement that the critical aspect of what makes a SIM card a SIM card is that it can authenticate a mobile device to a wireless network”). The evidence supports the parties’ understanding. The word “SIM” is an acronym for “subscriber identity module” (see, e.g., Ex. 1001, 6:58–67; Ex. 2021, 5), and the record shows that a SIM is a specific component in a mobile device that is involved in identifying and authenticating a user to a mobile network (see Ex. 2003 ¶¶ 30–31; see also e.g., Ex. 2021, 7 (stating that a SIM’s “primary function” is “to authenticate the subscriber to the network”); Ex. 2025, 3 (describing the SIM)).11 Consequently, we determine that an ordinarily skilled artisan would have understood a “hardware SIM card” to be a hardware component in a mobile device that is involved in identifying and authenticating a user to a mobile network. We do not need to further construe the term, or determine whether the additional requirements proposed by Patent Owner are appropriate, because Petitioner fails to show that the prior art teaches or suggests the claimed “hardware SIM card,” as explained below. See infra § II.D.2.a (analyzing the parties’ substantive contentions).” slip op. at 13

  • BurdenNot shown unpatentable

    “Petitioner has not shown, by a preponderance of the evidence, that Dill discloses “a mobile wallet application installed on a hardware SIM card,” as required by element 1.3B. See Pet. 23–24. In particular, even assuming that Dill teaches installing a mobile wallet application somewhere on a mobile device (see Pet. 23),14 Dill does not teach installing it on a hardware SIM card,15 as specifically required by the claim. Petitioner relies upon paragraph 106 of Dill (see Pet. 23), but that paragraph does not disclose this claim limitation (see Ex. 1005 ¶ 106). In relevant part, that paragraph of Dill simply states: 14 Patent Owner disagrees with this premise, arguing that Dill does not disclose a mobile device that includes a mobile wallet application. See PO Resp. 52–56. We need not resolve that dispute because, even assuming Petitioner’s premise (as we have done in this Decision), Petitioner still fails to show that the claims are unpatentable. 15 As noted above, a “hardware SIM card” is a hardware component in a mobile device that is involved in identifying and authenticating a user to a mobile network. See supra § II.C.1 (addressing meaning of term). It should also be appreciated that the methods described above may be performed by hardware components or may be embodied in sequences of machine-executable instructions, which may be used to cause a machine such as a general-purpose or special-purpose processor or logic circuits programmed with the instructions to perform the methods. These machine-executable instructions may be stored on one or more machine readable mediums, such as CD-ROMs or other type of optical disks, floppy diskettes, ROMs, RAMs, EPROMs, EEPROMs, magnetic or optical cards, flash memory, or other types of machine-readable mediums suitable for storing electronic instructions. Alternatively, the methods may be performed by a combination of hardware and software. Ex. 1005 ¶ 106 (emphases added). This teaches storing instructions on “other types of machine-readable mediums,” but it fails to teach storing instructions on a hardware SIM card, much less storing Dill’s mobile wallet application there. In short, Dill is silent with respect to this issue, and silence is not disclosure. Notably, Petitioner does not contend (or show) that a mobile wallet application installed on a mobile device would necessarily be installed on a hardware SIM card. See Pet. 23–24; Ex. 1003 ¶¶ 95–97. Indeed, the record indicates that a mobile wallet application installed on a mobile device could instead be installed on a different component. See, e.g., Ex. 1001, 7:1–3, 9:33–35 (identifying device memory as alternate component); Ex. 2021, 5 (describing SIM as the “smaller of two computer chips inside a GSM mobile handset”); cf. Pet. Reply 9 (distinguishing between hardware SIM cards and software ones). Thus, Petitioner fails to show that this claim limitation is inherent in Dill. See PAR Pharm., Inc. v. TWI Pharms., Inc., 773 F.3d 1186, 1196 (Fed. Cir. 2014) (explaining that inherency requires a showing that “the limitation at issue necessarily must be present”).” slip op. at 22

  Patent outcomesUS 9,208,488 not shown unpatentable
  Claim construction§ 103 obviousnesscites Phillips · KSR · Graham
  Patents in suitUS 9,208,488
• Medivis, Inc. v. Novarad Corp.No claims unpatentable
  PTAB · Mar 6, 2024 · IPR2023-00042 · APJ Scott Raevsky · IPR · Final written decision

  Claims 1–6 and 11–20 were not shown unpatentable: Doo did not disclose the claimed volume, the Doo-Amira combination lacked a persuasive rationale, and the other references were not shown publicly accessible.

  RulingsFinal written decision

  • Skill levelSkill level board ownDecided for petitioner

    “We adopt Petitioner’s proposed level of skill, except that we excise part of Petitioner’s definition to produce the following modified version: a bachelor’s degree in computer science, electrical engineering, or a related field with several years of experience in the design, development, and study of augmented reality devices and . . . familiarity with conventional medical imaging data and visualization of data for medical procedures . . . . Our edit removes the alternative of “working with a team including someone with such familiarity” because one’s role in a team may be tangential to their personal experience with medical imaging. Regardless, had we adopted Petitioner’s original definition, our decision would not have changed.” slip op. at 7

  • Claim Construction › Threshold & procedure › Whether a term needs construction (O2 Micro)No construction neededNot reached

    “The parties propose constructions for the claim terms “three- dimensional (3D) data,” “inner layer(s) of the patient,” “confined within a virtual 3D shape,” and “being having.” Pet. 11–14; PO Resp. 11–18. We do not need to construe any of these claim terms in order to resolve the issues presented in this proceeding. See Realtime Data, LLC v. Iancu, 912 F.3d 1368 (Fed. Cir. 2019) (“The Board is required to construe ‘only those terms . . . that are in controversy, and only to the extent necessary to resolve the controversy.’” (quoting Vivid Techs., Inc. v. Am. Sci. & Eng’g, Inc., 200 F.3d 795, 803 (Fed. Cir. 1999)).” slip op. at 8

  • Novelty / Anticipation (§102) › Anticipation standard (single reference, every element)Not shown unpatentableNot shown unpatentable

    “First, neither the Petition nor Dr. Kazanzides explains how Doo’s curved plane teaches the claimed “volume.” See Pet. 36–37; Ex. 1012 ¶¶ 74–75 (essentially repeating the Petition). The Petition merely asserts that Doo’s image in Figure 7 “is confined within the volume of the virtual 3D shape illustrated in Figure 9,” without explaining how the shape of Figure 9 has a “volume.” Pet. 37. The Reply does no better, asserting that “Doo’s shape 532 in Figure 9 and shape 432 in Figure 7 are virtual 3D shapes.” Reply 18. This statement is conclusory and does not explain how Doo’s “false 3D” shapes have volume. Petitioner further attempts to establish that Doo’s disclosure of Figure 9’s shape 532 as “mimic[ing] the surface curvature of the patient’s body” is evidence that Doo discloses a 3D shape. Id. (citing Ex. 1008 ¶ 76). This argument, however, is unpersuasive because it takes Doo’s statement out of context. Doo explains that Figure 9’s warped “two-dimensional image 532 . . . mimic[s] the surface curvature of the patient’s body,” not that it has volume. See Ex. 1008 ¶ 76 (emphasis added). In other words, even though Doo’s shape 532 of Figure 9, when projected on a patient’s body (as in Figure 7) may appear to a surgeon like a 9 Our Institution Decision did not rely on Petitioner’s theory based on Doo Figures 7–9. We discuss our Institution Decision’s reasoning below under Petitioner’s second theory based on Doo Figures 6 and 11. half-cylinder shape having a volume, Doo’s technique avoids rendering a 3D shape like a half-cylinder (hence calling these “false 3D shapes”) because it instead simulates the body’s curvature with a mere curved two-dimensional plane. Second, we find that Doo’s curved plane does not, in fact, have a volume.10 Instead, Doo’s curved plane is a 2D plane merely “wrapped around an axis.” See Ex. 1008 ¶¶ 75–76. As Patent Owner persuasively argued at the hearing, Doo’s curved plane is not “half of a cylinder. It’s just a wrapped piece of paper.” Tr. 33:14–15. Just as curving a piece of paper would not give the curved paper a half cylinder’s volume, neither does curving Doo’s flat 2D plane create a half cylinder with volume. Viewed another way, curving a 2D plane does not impart volume to the plane any more than curving a 1D line into a parabola would impart area to the 1D line.” slip op. at 12

  • Obviousness (§103) › Motivation to combine / reasonable expectation of successMotivation not foundNot shown unpatentableNot shown unpatentable

    “The U.S. Supreme Court has emphasized that “rejections on obviousness grounds cannot be sustained by mere conclusory statements; instead, there must be some articulated reasoning with some rational underpinning to support the legal conclusion of obviousness.” KSR, 550 U.S. at 418 (quoting In re Kahn, 441 F.3d 977, 988 (Fed. Cir. 2006)). Petitioner’s argument fails this standard. Petitioner asserts a generic rationale that one of ordinary skill in the art would have applied Amira to Doo “to take advantage of the visualization technology disclosed in Amira (or any similar visualization software).” Pet. 41. But Petitioner’s assertion contains no explanation why one of ordinary skill would have taken advantage of Amira’s technology in the context of Doo. Petitioner’s rationale is so vague and broad that it could be applied to combine any two references because it merely asserts that one reference would “take advantage of the . . . technology disclosed in” another. See, e.g., In re Van Os, 844 F.3d 1359, 1361 (Fed. Cir. 2017) (explaining that “a finding that a combination of prior art would have been . . . ‘intuitive’ is no different than merely stating the combination ‘would have been obvious’”). This approach wholly misses KSR’s “articulated reasoning” standard. See KSR, 550 U.S. at 418. The Reply’s assertion that reducing a surgeon’s cognitive load in Doo “suggests an improvement on conventional medical imaging displays, such as disclosed in Amira,” fares no better. Reply 20. This assertion again fails to explain why one of ordinary skill in the art would have combined Amira with Doo. For instance, Petitioner provides no explanation as to how Amira’s display would further reduce cognitive load. See Reply 19–20 (only vaguely referring to Amira’s “[t]racking capabilities [that] allow for . . . interaction with the visualization” (Ex. 1005, 14, 26)). Not only that, but Doo itself presents a solution for the cognitive load problem. See Ex. 1008 ¶ 14 (“The present invention is particularly adapted to manage the multitude of medical images needed to be viewed by a surgeon during an operation so that a surgeon is not required to look away from the patient, so that the surgeon does not have to sustain heavy cognitive loading.”). Petitioner does not persuasively explain why one of ordinary skill in the art would turn to yet another reference (like Amira) for an additional solution, or even what that solution would be.” slip op. at 23

  Patent outcomesUS 11,004,271 not shown unpatentable
  Claim construction§ 102 anticipation§ 103 obviousnesscites Phillips · KSR
  Patents in suitUS 11,004,271
• Twinstrand Biosciences, Inc. v. Guardant Health, Inc.No claims unpatentable
  PTAB · Jan 26, 2024 · IPR2022-01400 · APJ Michael A Valek · IPR · Final written decision

  Claims 1–29 were not shown unpatentable over the asserted obviousness grounds because the prior-art combinations did not teach key limitations of claims 1, 17, and 29.

  RulingsFinal written decision

  • BurdenNot shown unpatentable

    “Having considered these arguments on the full trial record, we find Patent Owner has the better position because Petitioner’s showing that element 1(b) is taught by Schmitt is unpersuasive. We begin with Patent Owner’s argument concerning the distinction between the cfDNA molecules and the duplex tag comprising the molecular barcode found in the text of claim 1. Element 1(a) recites “a population of cell-free deoxyribonucleic acid (cfDNA) molecules.” Ex. 1001, 61:7–9. Element 1(b) recites “tagging a plurality of the cfDNA molecules in the population” of element 1(a) “with duplex tags comprising molecular barcodes to produce tagged parent polynucleotides . . . wherein the duplex tags are attached to both ends of a added). We agree with Patent Owner and credit the testimony of its declarant that this claim language distinguishes the duplex tags from the ends of the cfDNA molecule to which they are attached. Resp. 8; Ex. 2015 ¶¶ 38–39, 60, 61. That is, the duplex tag is not part of the cfDNA molecule itself, but rather is “attached to both the ends” of that molecule by “tagging” it as recited in element 1(b). We also agree with Patent Owner that given this distinction, claim 1 does not encompass Schmitt’s hybrid embodiment. Resp. 18–20. As Petitioner notes, “[i]n Schmitt’s hybrid-tag embodiment, the strands are grouped based on the combination of the short n-mer barcode and the end of the target DNA.” Pet. 11; see Resp. 17 (“[T]he combination of the endogenous shear sequence and exogenous 3-mer sequence together provide the SMI used for grouping and matching in Schmitt’s DCS process.”). Petitioner and its declarant illustrate the grouping in Schmitt’s hybrid embodiment with the following diagram. Pet. 12; Ex. 1002 ¶¶ 96–98. Petitioner’s diagram shows the PCR products produced from sequencing a “Target DNA” molecule that has been tagged with 3-mers X and Y according to Schmitt’s hybrid embodiment. See Ex. 1002 ¶ 98 (describing diagram). A portion of the endogenous sequence of the DNA molecule labeled L and R is used in combination with the 3-mer sequence to group the resulting strands into two families labeled the “X+L→R+Y Family” and the “R+Y→X+L Family.” Ex. 1002 ¶ 98; Ex. 2015 ¶ 62 (explaining that Petitioner’s diagram shows that “the relied upon hybrid SMI sequences of Schmitt include sequence from the sample DNA molecule not contained in the adapter or the duplex tags”). SMIs, differently label the strands and therefore are the recited “duplex tags.” See Pet. 27–28 (“duplex tags comprise both the fragment DNA end sequences and a shorter n-mer tag”) (emphasis added) (internal quotations omitted). However, we credit Dr. Quackenbush’s testimony that end sequences L and R are not “attached to both ends” of the cfDNA molecule by “tagging” it as recited in element 1(b). See Ex. 2015 ¶ 59–62 (explaining that Schmitt’s hybrid SMI sequences include a portion of the sample DNA molecule, which is “not contained in adapter molecules or duplex tags that are attached to the DNA molecules”). Rather, end sequences L and R are the pre-existing, endogenous ends of that molecule. Id. Thus, Petitioner’s theory of unpatentability does not account for the distinction the claim language draws between the cfDNA molecule and the duplex tags. Petitioner’s argument that the ’306 patent defines “duplex tag” as a” slip op. at 20

  • Obviousness (§103) › Motivation to combine / reasonable expectation of successNot shown unpatentableNot shown unpatentable

    “That is, although Meyer teaches that its particular protocol results in 40–60% tagging efficiency, Petitioner has not sufficiently explained why a person of ordinary skill in the art would have expected Meyer’s tagging efficiency to apply to Schmitt’s DCS method when used with Narayan’s sequencing of cfDNA. For example, the Petition does not address the differences between Meyer’s adapters and Schmitt’s adapters and how those differences affect the tagging efficiency. Meyer’s barcodes comprise “single self-hybridized palindromic oligonucleotides, carrying an Srf I restriction site in the middle (GCCCGGGC), a sequence tag at the 3’ end and the reverse complementary tag sequence at the 5’ end.” Ex. 1005, Fig. 1. Schmitt, on the other hand, teaches a “hybrid method” of tagging that uses a combination of the sheared ends of the DNA fragments and a “shorter n-mer tag (such as 1 or 2 or 3 or 4 or more degenerate or semi degenerate bases) in the adaptor.” Ex. 1083 ¶ 30. sticky-end adapter-DNA litigation to be even more efficient than Meyer’s blunt-end adapter-DNA ligation” is also unpersuasive. See Pet. 60–61. The KAPA data sheet discloses sticky-end adapter DNA ligation, but KAPA teaches that only 0.5 to 15% tagging efficiency is expected when the starting sample is 100 pg–100 ng of “high quality DNA.” Ex. 1015, 4. Thus, the KAPA data suggests that the use of sticky-end adapters, such as what Schmitt discloses, does not in and of itself teach or suggest the tagging efficiency limitations. Moreover, the record shows that tagging efficiency depends on a variety of other factors, including the quality of the input DNA. The KAPA data sheet states that tagging efficiency “can be significantly lower for DNA of lower quality.” Ex. 1015, 4. Fisher also explains that “the efficiency of adaptor ligation varies between samples, probably because of variation in input DNA quality.” Ex. 1031, 5–6. Petitioner’s argument that the DNA the KAPA data sheet refers to as “lower quality” is “from formalin-fixed, paraffin-embedded (‘FFPE’) samples (well known for having chemically damaged DNA)” is unavailing. See Reply 25–26 (citing Ex. 1098 ¶¶ 96–98). First, neither Petitioner, nor its declarant, address the similar teaching in Fisher. Second, even if the specific type of lower quality DNA in the KAPA data sheet is different, the salient point, i.e., that tagging efficiency depends on DNA quality, remains unrebutted. This is significant because Petitioner does not sufficiently address how the quality of the cfDNA of Narayan compares to the quality of the genomic DNA samples of Meyer and Schmitt or how that would affect the expected tagging efficiency. Petitioner’s assertion that “significant quantities of cfDNA could be isolated from blood samples” (see Reply 26), fact that a significant quantity of cfDNA could be obtained does not show that the quality of that DNA is similar such that a POSA using such would have expected to achieve a tagging efficiency similar to that in Meyer.” slip op. at 40

  • Strike new argumentNew argument disregardedDenied

    “We are not persuaded. First, this is an inappropriate new argument. The Petition presents a different mapping, alleging that the “duplex tag” comprises both the endogenous end sequence of the cfDNA molecule and the 3-mer barcode of Schmitt’s hybrid tag embodiment. Pet. 27 (“the duplex tags comprise both the fragment DNA end sequences and ‘a shorter n-mer tag’ to serve as ‘unique molecular identifiers’”) (quoting Ex. 1083 ¶ 30, Ex. 1002 ¶¶ 162–163); see also Tr. 62:13–63:19 (Petitioner’s counsel noting he was unaware of any explicit statement in the Petition that Schmitt’s duplex tag comprised just the 3-mer without the end sequence). Nor did Petitioner regarding element 1(b). See Reply 8–10. Rather, consistent with the mapping in the Petition, the Reply identifies “Schmitt’s hybrid tags,” i.e., the combination of the endogenous end sequence and the n-mer, as the duplex tags in element 1(b). See Reply 8 (urging that “duplex tags” are “tags that differently label the complementary strands,” which “is precisely what Schmitt’s hybrid tags do”). Because this argument was not previously presented, Patent Owner has not been afforded a sufficient opportunity to address it. Thus, Petitioner’s new argument excluding the end sequences in Schmitt’s hybrid tag embodiment from the alleged “duplex tags comprising molecular barcodes” has been waived. Second, even if we were to consider it on the merits, Petitioner’s new mapping for element 1(b) is inconsistent with Petitioner’s allegations for element 1(e). Element 1(e) recites “reducing or tracking redundancy” in sequence reads “using at least sequencing information from the molecular barcodes of the duplex tags to determine distinct cfDNA molecules.” Ex. 1001, 61:26–30. For these limitations, the Petition points to Schmitt’s grouping of reads into families based on their SMI and asserts that Schmitt determines distinct cfDNA molecules based on “the complementary nature of the SMI on the two strands of the duplex.” See Pet. 30–32 (internal quotations omitted). Thus, like Petition’s mapping for element 1(b), Petitioner’s allegations for element 1(e) rely on a duplex tag that includes both the 3-mer and the end sequence of the cfDNA molecule. Petitioner has not sufficiently explained, much less shown by a preponderance of the evidence, that Schmitt teaches or suggests the limitations in element 1(e) based on its new mapping of the 3-mer alone as duplex tags.” slip op. at 25

  • PTAB / AIA Trials › Other PTAB motions (exclude, strike, seal, additional discovery, rehearing)Motion to exclude, deniedDenied

    “We do not rely on any of these exhibits in rendering our decision on Petitioner’s grounds. Therefore, we dismiss as moot Petitioner’s motion to exclude Exhibits 1069, 1074, 1078, 1079, and 1085–1088.” slip op. at 46

  Patent outcomesUS 11,149,306 not shown unpatentable
  § 103 obviousnesscites Phillips · KSR · Graham
  Patents in suitUS 11,149,306

Holdings, summaries, rulings, issues, outcomes, winners and claim constructions shown for a decision were generated by a large language model reading the opinion. They are a guide to the decision, not the decision. Confirm every one against the court's own text before relying on it. Outcomes read from the patent owner’s side. Party names are extracted from the decision and are missing on about 900 short Director denials and scans, which carry the trial number instead.