- PTAB · May 15, 2025 · IPR2025-00028 · APJ Zhenyu Yang · IPR · Institution
The Board instituted IPR on claims 1–15 and 17–22 on all asserted obviousness grounds, finding a reasonable likelihood that Shapero and Delseny render claim 1 obvious.
RulingsInstitution decision- PTAB / AIA Trials › Discretionary denial › §325(d) same art / argumentsInstitution denied 325dDecided for petitioner
“To accord substantial weight to evidence of secondary considerations, it “must have a nexus to the claims, i.e., there must be a legally and factually sufficient connection between the evidence and the patented invention.” Quanergy Sys., Inc. v. Velodyne Lidar USA, Inc., 24 F.4th 1406, 1417 (Fed. Cir. 2022) (internal quotation marks omitted); see also In re Kao, 639 F.3d 1057, 1069 (Fed. Cir. 2011) (instructing that “the Board, in considering the evidence of unexpected results, should determine whether there is a nexus between the unexpected [results] and aspects of the claimed invention not already present in the prior art”). Moreover, “when unexpected results are used as evidence of nonobviousness, the results must be shown to be unexpected compared with the closest prior art.” In re Baxter Travenol Laboratories, 952 F.2d 388, 392 (Fed. Cir. 1991). On this record, it is unclear what Dr. Brooks considered to be the closest prior art when he alleged unexpected results. See Ex. 1002, 2013–17. We also find no persuasive evidence in either Brooks Declaration or the Examiner’s analysis on the requisite nexus. See id., 2055–56. As a result, we agree with Petitioner that “the Examiner erred in exclusively relying on Dr. Brooks’ declaration” to withdraw the obviousness rejection based on Jones and Tucker. See Pet. 58.” slip op. at 16
- Skill levelSkill level board ownDecided for petitioner
“We find Patent Owner’s proposed definition of the skill level insufficient. As Patent Owner recognizes, the challenged claims relate to sequencing methods using a next-generation sequencing (“NGS”) platform. See id. at 8; see also Ex. 1001, 35:56–57 (claim 1 reciting “sequencing the enriched nucleic acid sequence of interest on a massively parallel sequencing platform”). Also, as Patent Owner recognizes, [c]ompared to traditional, Pre-NGS sequencing methods, NGS sequencing utilized a new design that no longer relied upon disassembling and then piecing together a single original template DNA strand. Instead, NGS now allowed for hundreds of thousands of original template strands to be sequenced in the same reaction. With NGS, a user could perform massively parallel sequencing, allowing for elements of the genome to be sequenced in a fast, scalable manner. Prelim. Resp. 5 (internal citations omitted). As such, we disagree with Patent Owner that a POSA only need to have education “in a field related to molecular biology” or experience “in a molecular biology lab,” because an artisan having only experience with pre-NGS sequencing methods would not qualify as a POSA. Instead, for purposes of this Decision, we find a POSA would have had a Ph.D. in molecular biology, molecular genetics, bioinformatics, biochemistry, or a related field. Alternatively, a POSA would have had a B.S. or M.S. degree with three to five years of experience working in any of those fields. Additionally, the POSA would have had experience with NGS sequencing methods and a working knowledge of how those methods functioned. This definition of a POSA is consistent with the skill level reflected in the disclosures of the ’012 patent and prior art. We further note” slip op. at 18
- Claim Construction › Threshold & procedure › Whether a term needs construction (O2 Micro)No construction neededOther
“claim construction standard that would be used to construe the claim in a civil action under 35 U.S.C. [§] 282(b).” 37 C.F.R. § 42.100(b) (2020). Under that standard, the words of a claim “are generally given their ordinary and customary meaning,” which is “the meaning that the term would have to a person of ordinary skill in the art in question at the time of the invention, i.e., as of the effective filing date of the patent application.” Phillips v. AWH Corp., 415 F.3d 1303, 1312–13 (Fed. Cir. 2005) (en banc). Claim terms need only be construed to the extent necessary to resolve the controversy. Wellman, Inc. v. Eastman Chem. Co., 642 F.3d 1355, 1361 (Fed. Cir. 2011). On this record and for purposes of this Decision, we see no need to construe any claim term expressly.” slip op. at 19
- Obviousness (§103) › Motivation to combine / reasonable expectation of successMotivation foundReasonable expectation foundInstituted
“It is true that Delseny recognizes the limitations and challenges of NGS. Ex. 1007, 411, 417. But the language in Delseny that Patent Owner identifies does not amount to teaching away, which requires that prior art references “criticize, discredit, or otherwise discourage the solution claimed.” In re Fulton, 391 F.3d 1195, 1201 (Fed. Cir. 2004). Instead, Delseny notes the limitations of hybridization technology in genotyping. Ex. 1007, 417. According to Delseny, “[t]he ultimate resolution is at the base-pair level and NGSTs now open the possibility to genotype a line by sequencing it.” Id. In fact, Delseny specifically teaches that NGS “can substitute for the genotyping microarray strategy because of its higher resolution.” Id.” slip op. at 22
Claim construction§ 103 obviousnessDiscretionary denialcites PhillipsPatents in suitUS 10,036,012 - PTAB · May 14, 2025 · IPR2025-00027 · APJ Deborah Katz · IPR · Institution
The Board instituted IPR on claims 1–16 and all asserted grounds, finding a reasonable likelihood that at least one challenged claim is unpatentable.
RulingsInstitution decision- Skill levelSkill level patent owner adoptedDecided for patent owner
“On this preliminary record, having considered Dr. Metzker’s testimony and Patent Owner’s reasoning, we agree that one of ordinary skill in the art would have had experience with next generation sequencing, but are not persuaded that this would only be possible in the field of molecular biology. For the purposes of this Decision, we find a person of ordinary skill would have had a Ph.D. in the field of chemistry, molecular biology, or biochemistry or a B.S. or M.S. degree with three to five years of experience working in any of those fields. The person of ordinary skill would have had experience with next generation sequencing methods and a working knowledge of how those methods functioned. This definition of a person of ordinary skill is consistent with the skill level reflected in the disclosures of the ’241 patent and prior art. We further note that neither aspect of the dispute over the skill level affects our decision to institute review. C. Claim Construction” slip op. at 8
- Claim Construction › Intrinsic evidence (Phillips canons) › Plain and ordinary meaning to a POSITATerm construed petitioner constructionDecided for petitioner
“Petitioner argues that we should construe the claim term “adaptor” as “any oligonucleotide that is attached to the target sequence.” (See Pet. 10.) Petitioner cites the ’241 patent as referring to an “adaptor” as “an oligonucleotide sequence, the ligation of which to a target polynucleotide or a target polynucleotide strand of interest enables the generation of amplification-ready products of the target polynucleotide or the target polynucleotide strand of interest.” (Ex. 1001, 4:14–21; see Pet. 10.) According to Petitioner, this described function can be performed by any oligonucleotide. Petitioner also cites the Examiner’s reasoning during prosecution that “since any oligonucleotide can perform such function, any oligonucleotide is considered to anticipate this term.” (See Pet. 10 (citing Ex. 1013, 77).) Petitioner further cites the specification of the ’241 patent for its disclosure that “appending the adaptor to the nucleic acid fragments generated by methods described herein can be achieved using a ligation reaction or a priming reaction.” (Ex. 1001, 9:34–37; see Pet. 10.) Patent Owner does not dispute this construction at this stage, arguing only that the term need not be construed beyond its plain and ordinary meaning and reserving the right to propose constructions and identify terms needing construction later in the proceeding. (See Prelim. Resp. 9.) For the purposes of this decision, we adopt Petitioner’s construction of the term “adaptor,” although we note that it does not affect our decision to institute review. D. Ground I – Anticipation by McCloskey” slip op. at 9
- PTAB / AIA Trials › Discretionary denial › §325(d) same art / argumentsDecided for petitioner
“In summary, Petitioner presents evidence, which we find preliminarily persuasive, showing that McCloskey, Porreca, and Schmitt disclose aspects of the claims that were alleged in the prosecution to be missing in McCloskey 2007. For at least the reasons noted above, we determine that each of Porreca, McCloskey 2007, and Schmitt are not substantially the same as either McCloskey 2007 or Samuels. Accordingly, the first part of the framework of Advanced Bionics is not met and we are not persuaded there is a reason to exercise our discretion to deny institution of review at least on the basis of anticipation under 35 U.S.C. § 102(a) over Porreca, McCloskey, or Schmitt. Because we do not exercise discretion to deny institution of review on the basis of at least one ground of challenge raised by Petitioner, we institute trial on all claims and all grounds asserted in the Petition. See 35 U.S.C. § 314(a); SAS Inst., 584 U.S. at 362.” slip op. at 46
- PTAB / AIA Trials › Institution threshold (reasonable likelihood / more likely than not)InstitutedInstituted
“We are not persuaded at this point in the proceeding by Patent Owner’s arguments because Dr. Metzker testifies that McCloskey refers to the redundant hypermethylated and hypomethylated sequences, which one of ordinary skill in the art would have understood to mean both the identical target sequence and the identical barcode to be used to identify duplicates. (See Ex. 1003 ¶ 90.) At this point in the proceeding, in the absence of contradictory evidence, we are persuaded that Petitioner has provided sufficient evidence that McCloskey teaches “identifying sequence reads with identical identifier and target sequences as duplicates.”” slip op. at 15
Claim constructionDiscretionary denialcites Phillips · KSR · GrahamPatents in suitUS 11,725,241 - PTAB · May 14, 2025 · IPR2025-00026 · APJ Deborah Katz · IPR · Institution
Instituted IPR of claims 1–10 on all asserted grounds after finding a reasonable likelihood that claim 1 is unpatentable over Porreca and declining § 325(d) denial.
RulingsInstitution decision- PTAB / AIA Trials › Institution threshold (reasonable likelihood / more likely than not)InstitutedInstituted
“Director determines that the information presented in the petition filed under section 311 and any response filed under section 313 shows that there is a reasonable likelihood that the petitioner would prevail with respect to at least 1 of the claims challenged in the petition.” 35 U.S.C. § 314(a). We determine whether to institute inter partes review on behalf of the Director. See 37 C.F.R. § 42.4(a).” slip op. at 2
- PTAB / AIA Trials › Discretionary denial › §325(d) same art / argumentsInstitution denied 325dDenied
“(1) whether the same or substantially the same art previously was presented to the Office or whether the same or substantially the same arguments previously were presented to the Office; and (2) if either condition of first part of the framework is satisfied, whether the petitioner has demonstrated that the Office erred in a manner material to the patentability of challenged claims.” slip op. at 42
- Skill levelSkill level board ownOther
“Patent Owner asserts that Petitioner’s definition requiring a Ph.D. or a Master’s degree and several years of experience indicates higher than ordinary skill because by 2008 next generation sequencing was performed in laboratories according to published protocols and would have been accessible to experienced laboratory technicians and graduate students. (Prelim. Resp. 8.) Patent Owner proposes that, instead, the appropriate level of ordinary skill in the art was a Ph.D. in a field related to molecular biology, or a B.S. or M.S. degree with three to five years of experience working in a molecular biology lab. (See id.) On this preliminary record, having considered Dr. Metzker’s testimony and Patent Owner’s reasoning, we agree that one of ordinary skill in the art would have had experience with next generation sequencing, but are not persuaded that this would only be possible in the field of molecular biology. For the purposes of this Decision, we find a person of ordinary skill would have had a Ph.D. in the field of chemistry, molecular biology, or biochemistry or a B.S. or M.S. degree with three to five years of experience working in any of those fields. The person of ordinary skill would have had experience with next generation sequencing methods and a working knowledge of how those methods functioned. This definition of a person of ordinary skill is consistent with the skill level reflected in the disclosures of the ’357 patent and prior art. We further note that neither aspect of the dispute over the skill level affects our decision to institute review. C. Claim Construction” slip op. at 8
- Claim Construction › Intrinsic evidence (Phillips canons) › Plain and ordinary meaning to a POSITATerm construed petitioner constructionDecided for petitioner
“Petitioner argues that we should construe the claim term “adaptor” as “any oligonucleotide that is attached to the target sequence.” (See Pet. 9.) Petitioner cites the ’357 patent as referring to an “adaptor” as “an oligonucleotide sequence, the ligation of which to a target polynucleotide or a target polynucleotide strand of interest enables the generation of amplification-ready products of the target polynucleotide or the target polynucleotide strand of interest.” (Ex. 1002, 4:20-25; see Pet. 9–10.) According to Petitioner, this described function can be performed by any oligonucleotide. (See Pet. 10.) Petitioner also cites the Examiner’s reasoning during prosecution that “since any oligonucleotide can perform such function, any oligonucleotide is considered to anticipate this term.” (See Pet. 10 (citing Ex. 1013, 77).) Petitioner further cites the specification of the ’357 patent and claims of the ’241 patent, which is a continuation of the ’357 patent, in support of this construction. (See Pet. 9–10 (citing Ex. 1002, 9:43–46 (“appending the adaptor to the nucleic acid fragments generated by methods described herein can be achieved using a ligation reaction or a priming reaction.”) (emphasis omitted); Ex. 1001, claim 10).) Patent Owner does not dispute this construction at this stage, arguing only that the term need not be construed beyond its plain and ordinary meaning and reserving the right to propose constructions and identify terms needing construction later in the proceeding. (See Prelim. Resp. 9.) For the purposes of this decision, we adopt Petitioner’s construction of the term “adaptor,” although we note that it does not affect our decision to institute review. D. Ground I – Anticipation by Porreca” slip op. at 9
Claim construction§ 102 anticipation§ 103 obviousnessDiscretionary denialcites Phillips · KSR · GrahamPatents in suitUS 11,098,357 - PTAB · Apr 25, 2025 · IPR2024-01419 · APJ Susan L C Mitchell · IPR · Institution
The Board instituted IPR of claims 1–9 on all asserted grounds, finding a reasonable likelihood that claim 1 is anticipated by Chee.
RulingsInstitution decision- PTAB / AIA Trials › Institution threshold (reasonable likelihood / more likely than not)InstitutedInstituted
“We analyze the asserted grounds of unpatentability in accordance with these principles to determine whether Petitioner has met its burden to establish a reasonable likelihood of success at trial.” slip op. at 13
- BurdenDecided for petitioner
“Having considered the parties’ positions and evidence of record, summarized above, we determine that the information presented in the Petition establishes that Petitioner has shown sufficiently a reasonable likelihood of succeeding with respect to at least claim 1 challenged in Ground I. Petitioner provides sufficient support on the record before us to provide a reasonable likelihood of succeeding in showing that claim 1 is anticipated by Chee.” slip op. at 18
- Claim Construction › Threshold & procedure › Whether a term needs construction (O2 Micro)Term construed petitioner constructionNo construction neededDecided for petitioner
“tags,” and “locus of origin” need be addressed at this stage of the proceeding. We determine that no express construction of “consensus base call” is necessary to determine whether to institute inter partes review. Nidec Motor Corp. v. Zhongshan Broad Ocean Motor Co., 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., Inc. v. Am. Sci. & Eng’g, Inc., 200 F.3d 795, 803 (Fed. Cir. 1999))). 1. “Set of [Unique] Differentiator Tags” Petitioner asserts that both “set of differentiator tags” as used in claim 1 and “set of unique differentiator tags” as used in claim 9 should be given the same construction—“set of prepared tags where each tag includes a unique sequence as compared to the other tags.” See Pet. 16 (citing Ex. 1005 ¶ 89; Ex. 1001, 28:25–29, 28:53–57). Petitioner further asserts that “[t]hese unique differentiator tags are associated with target nucleic acids so that each nucleic acid is uniquely identifiable.” Pet. 16. Petitioner also points to the prosecution history of the ’730 patent in which Petitioner asserts the Patent Owner argued and the Board acknowledged that each differentiator tag is unique. Id. at 16–17. Petitioner concludes that “[a]n interpretation of ‘differentiator tags’ to include non-unique tags is not possible, and if it were, Applicant disclaimed any interpretation that would allow non-unique tags.” Id. at 17.” slip op. at 7
- Novelty / Anticipation (§102) › Anticipation standard (single reference, every element)Instituted
“Having considered the parties’ positions and evidence of record, summarized above, we determine that the information presented in the Petition establishes that Petitioner has shown sufficiently a reasonable likelihood of succeeding with respect to at least claim 1 challenged in Ground I. Petitioner provides sufficient support on the record before us to provide a reasonable likelihood of succeeding in showing that claim 1 is anticipated by Chee.” slip op. at 18
Claim construction§ 102 anticipation§ 103 obviousnesscites GrahamPatents in suitUS 11,840,730 - PTAB · Apr 25, 2025 · IPR2025-00016 · APJ Zhenyu Yang · IPR · Institution
The Board instituted review of claims 1–3, 5–12, and 14–19 on all asserted grounds, finding a reasonable likelihood that Meyer anticipates claim 1.
RulingsInstitution decision- PTAB / AIA Trials › Discretionary denial › §325(d) same art / argumentsDecided for petitioner
“During prosecution of the ’340 application, the Examiner specifically acknowledged that Jones 2005 “does not teach massively parallel sequencing as required by” the claim that issued as independent claim 1. Ex. 1017, 2421. Thus, contrary to Patent Owner’s assertion, the Examiner did not find Jones 2005 “discloses each limitation of claim 1 of the ’108 patent.” See Prelim. Resp. 39. In other words, the Examiner did not make “the same arguments with respect [to] Jones 2005 publication during the prosecution of the ’340 application.” Id. As a result, Petitioner’s anticipation challenge based on Meyer is not the same or substantially the same as the Examiner’s obviousness rejections based on Jones 2005.” slip op. at 8
- PTAB / AIA Trials › Institution threshold (reasonable likelihood / more likely than not)InstitutedInstituted
“it “never discloses increasing the percentage of the sequence of interest as compared to any other component of the sample.” Prelim. Resp. 25. But contrary to this assertion, Meyer specifically discloses that a single copy of the broken chain T-primer was found in “16% of the total” raw reads, “slightly more than the expectation (~10%).” Ex. 1006, 9. If the expected 3' end fragments are 10% of the total reads, the combined 5' end fragments and internal fragments would be 90%. By employing the broken chain T-primer, Meyer increased the percentage of the 3' end fragments to 16% of the total reads, which means the combined 5' end fragments and internal fragments would be decreased to 84%. In other words, Meyer discloses increasing the percentage of the 3' end fragments, which contains the broken chain T-primer sequence, as compared to the 5' end fragments and internal fragments. Patent Owner does not explain persuasively why, under such circumstances, enrichment is not met. Patent Owner emphasizes that Meyer “is directed toward improving the error rate of sequencing reads.” Prelim. Resp. 26 (citing Ex. 2021 ¶¶ 124–130); see also id. at 28 (“The ‘homopolymer problem’ that Meyer was trying to fix is an issue caused by the 454 sequencer.”). We agree with Patent Owner on this issue. Patent Owner, however, has not explained sufficiently why Meyer’s method of reducing read artifacts by increasing the proportion of 3' end fragments in the total read does not meet the claimed enrichment.” slip op. at 19
- Skill levelSkill level patent owner adoptedDecided for patent owner
“We do not see a material difference in the parties’ proposed levels of education and work experience. Indeed, although Petitioner asserts that a POSA “would have a PhD or equivalent training,” it allows more work experience to compensate for less education. Pet. 23 (stating that a POSA could have “commensurately less education and more work experience”). We, nevertheless, adopt Patent Owner’s proposal in this aspect because it specifies the years of experience needed. Patent Owner also disputes Petitioner’s proposal that a POSA would have had experience with “implementing and designing library preparation methods 454 and Illumina, the leading NGS platforms in 2012.” Id. at 15 (quoting Pet. 23, emphasis added by Patent Owner removed). According to Patent Owner, “[t]his level of skill inappropriately requires the POSA to be an inventor of library preparation methods.” Id. On this record, we agree with Patent Owner that “experience with implementing and designing library preparation methods 454 and Illumina” is above ordinary skill. We, however, find insufficient Patent Owner’s proposal that “the POSA would have had experience with DNA sequencing methods.” Id. at 15–16 (citing Ex. 2021 ¶¶ 65–68). The challenged claims relate to sequencing methods using a next-generation sequencing (“NGS”) platform. See Ex. 1002, 35:49–51 (claim 1 reciting “sequencing the amplified products comprising the enriched nucleic acid sequence of interest on a massively parallel sequencing platform”). As Patent Owner recognizes, [c]ompared to traditional, Pre-NGS sequencing methods, NGS sequencing utilized a new design that no longer relied upon disassembling and then piecing together a single original template DNA strand. Instead, NGS sequencing now allowed sequenced in the same reaction. With NGS, a user could perform massively parallel sequencing, allowing for elements of the genome to be sequenced in a fast, scalable manner. Prelim. Resp. 4. As such, we disagree with Patent Owner that a POSA only need to “have had experience with DNA sequencing methods” (id. at 15–16) because an artisan with experience with only pre-NGS sequencing methods would not qualify as a POSA. Instead, for purposes of this Decision, we find a POSA would have had a Ph.D. in the field of chemistry, molecular biology, or biochemistry. Alternatively, a POSA would have had a B.S. or M.S. degree with three to five years of experience working in any of those fields. Additionally, the POSA would have had experience with NGS sequencing methods and a working knowledge of how those methods functioned. This definition of a POSA is consistent with the skill level reflected in the disclosures of the ’108 patent and prior art. We further note that neither aspect of the dispute over the skill level affects our decision to institute review.” slip op. at 11
- Claim Construction › Threshold & procedure › Whether a term needs construction (O2 Micro)Term construed petitioner constructionNo construction neededOther
“Petitioner proposes that we construe the terms “sequence of interest” and “barcode.” Pet. 24–25. According to Petitioner, the ’108 patent defines nucleic acid sequence” and “target sequence,” as “a polynucleotide sequence of interest, for which enrichment is desired.” Id. at 24 (citing Ex. 1002, 21:3–5, 21:8–11). Patent Owner does not dispute Petitioner’s proposed construction of this term.8 See Prelim. Resp. 17. On this record, we adopt Petitioner’s proposed construction of the term “sequence of interest.” Petitioner also proposes that we construe the term “barcode.” Pet. 25. Patent Owner points out that the term “barcode” only appears in dependent claim 8 and argues that we do not need to construe this term. Prelim. Resp. 17. For purposes of this Decision, we agree with Patent Owner on this issue. Neither party proposes any special meaning for the term “enrich.” We see no reason to do so either. To the extent express construction of “enrich” is necessary, we adopt the plain and ordinary meaning of the term. See Ex. 3001 (entry e defining “enrich” to mean “to process so as to add or increase the proportion of a desirable ingredient”). Claim terms need only be construed to the extent necessary to resolve the controversy. Wellman, Inc. v. Eastman Chem. Co., 642 F.3d 1355, 1361 (Fed. Cir. 2011). On this record and for purposes of this Decision, we see no need to construe any other claim term expressly.” slip op. at 12
Claim construction§ 102 anticipationDiscretionary denialcites PhillipsPatents in suitUS 10,876,108 - PTAB · Apr 25, 2025 · IPR2025-00015 · APJ Zhenyu Yang · IPR · Institution
Instituted IPR of claims 1–3 and 5–22 on all asserted grounds; Meyer anticipation of claim 1 met the reasonable-likelihood threshold.
RulingsInstitution decision- PTAB / AIA Trials › Discretionary denial › §325(d) same art / argumentsDecided for petitioner
“the ’785 application. See generally Ex. 1016. Also, the Examiner did not issue any anticipation rejection during prosecution of the ’785 application. Id. Instead, the Examiner rejected claims as obvious over Jones 2005 in combination with other prior art. Id. at 190–96. The Examiner specifically acknowledged that Jones 2005 “does not teach massively parallel sequencing as required by” the claim that issued as independent claim 1. Id. at 192. Thus, contrary to Patent Owner’s assertion, Jones 2005 could not have “disclosed the same elements that Petitioner claims Meyer discloses.” See Prelim. Resp. 40. As a result, Petitioner’s anticipation challenge based on Meyer is not the same or substantially the same as the Examiner’s obviousness rejections based on Jones 2005.” slip op. at 10
- PTAB / AIA Trials › Institution threshold (reasonable likelihood / more likely than not)InstitutedInstituted
“On this record and for purposes of institution, we find Petitioner has shown sufficiently that Meyer discloses enrichment of the 3′ end fragments, which include the broken chain T primer sequence.” slip op. at 29
- Skill levelSkill level patent owner adoptedDecided for patent owner
“We do not see a material difference in the parties’ proposed levels of education and work experience. Indeed, although Petitioner asserts that a POSA “would have a PhD or equivalent training,” it allows more work experience to compensate for less education. Pet. 25 (stating that a POSA could have “commensurately less education and more work experience”). We, nevertheless, adopt Patent Owner’s proposal in this aspect because it specifies the years of experience needed. Patent Owner also disputes Petitioner’s proposal that a POSA would have had experience with “implementing and designing library preparation methods 454 and Illumina, the leading NGS platforms in 2012.” Id. at 16 (quoting Pet. 25, emphasis added by Patent Owner removed). According to Patent Owner, “[t]his level of skill inappropriately requires the POSA to be an inventor of library preparation methods.” Id. On this record, we agree with Patent Owner that “experience with implementing and designing library preparation methods 454 and Illumina” is above ordinary skill. We, however, find insufficient Patent Owner’s proposal that “the POSA would have had experience with DNA sequencing methods.” Id. (citing Ex. 2021 ¶¶ 65–68). As Patent Owner recognizes, the challenged claims relate to sequencing methods using a next-generation sequencing (“NGS”) platform. See id. at 13; see also Ex. 1001, 35:56–57 (claim 1 reciting “sequencing the enriched nucleic acid sequence of interest on a massively parallel sequencing platform”). Also, as Patent Owner recognizes, [c]ompared to traditional, Pre-NGS sequencing methods, NGS sequencing utilized a new design that no longer relied upon disassembling and then piecing together a single original template DNA strand. Instead, NGS sequencing now allowed for hundreds of thousands of original template strands to be sequenced in the same reaction. With NGS, a user could perform massively parallel sequencing, allowing for elements of the genome to be sequenced in a fast, scalable manner. Prelim. Resp. 4. As such, we disagree with Patent Owner that a POSA only need to “have had experience with DNA sequencing methods” (id. at 16) because an artisan with experience with only pre-NGS sequencing methods would not qualify as a POSA. Instead, for purposes of this Decision, we find a POSA would have” slip op. at 13
- Claim Construction › Threshold & procedure › Whether a term needs construction (O2 Micro)Term construed petitioner constructionDecided for petitioner
“Petitioner proposes that we construe the terms “sequence of interest” and “barcode.” Pet. 26–27. According to Petitioner, the ’012 patent defines “sequence of interest,” which is used interchangeably with terms “target nucleic acid sequence” and “target sequence,” as “a polynucleotide sequence of interest, for which enrichment is desired.” Id. at 26 (citing Ex. 1001, 21:1–3, 21:6–9). Patent Owner does not dispute Petitioner’s proposed construction of this term.8 See Prelim. Resp. 17. On this record, we adopt Petitioner’s proposed construction of the term “sequence of interest.”” slip op. at 15
Claim construction§ 102 anticipationDiscretionary denialcites PhillipsPatents in suitUS 10,036,012 - PTAB · Apr 21, 2025 · IPR2024-01504 · APJ James A Worth · IPR · Institution
The Board instituted IPR on claims 1–4, 6, 7, 9, and 10 on all petitioned grounds, finding a reasonable likelihood that claim 1 is obvious over Iafrate and Kivioja.
RulingsInstitution decision- Skill levelSkill level patent owner adoptedDecided for patent owner
“On this preliminary record, we agree with Patent Owner that Petitioner’s asserted level of ordinary skill in the art is higher than warranted when Petitioner argues that a person of ordinary skill “further would have had specific experience with implementing and designing library preparation methods.” Pet. 21–22. However, we disagree with Patent Owner that a POSA only need to “have had experience with DNA sequencing methods” (Prelim. Resp. 8) because an artisan with experience with only pre-NGS sequencing methods would not qualify as a person of ordinary skill. Instead, for purposes of this Decision, we find a person of ordinary skill would have had a Ph.D. in the field of chemistry, molecular biology, or biochemistry. Alternatively, a POSA would have had a B.S. or M.S. degree with three to five years of experience working in any of those fields. The person of ordinary skill would have had experience with NGS sequencing methods and a working knowledge of how those methods functioned. This definition of a person of ordinary skill is consistent with the skill level reflected in the disclosures of the ’357 patent and prior art. We further note that neither aspect of the dispute over the skill level affects our decision to institute review.” slip op. at 9
- Claim Construction › Intrinsic evidence (Phillips canons) › Lexicography (patentee as own lexicographer)Term construed petitioner constructionDecided for petitioner
“1. “indexing site” Petitioner argues that the ’357 patent defines “indexing site” as a sample index, specifically, “a nucleic acid sequence that acts as an index for multiple polynucleotide samples, thus allowing for the samples to be pooled together into a single sequencing run, which is known as multiplexing.” Pet. 23 (citing Ex. 1004, 4:40–44). Patent Owner does not disagree other than to argue that no claim requires construction. The ’357 patent states: An indexing site is a nucleic acid sequence that acts as an index for multiple polynucleotide samples, thus allowing for the samples to be pooled together into a single sequencing run, which is known as multiplexing. provide a definition for “indexing site,” and we construe the term in accordance therewith.” slip op. at 10
- Claim Construction › Threshold & procedure › Whether a term needs construction (O2 Micro)No construction neededOther
“3. “identifying sequence reads with identical identifier and target sequences as duplicates” Although the parties do not request construction of this limitation, we note that the parties may wish to address the construction of this limitation after institution. See Vivid Techs., Inc. v. Am. Sci. & Eng’g, Inc., 200 F.3d 795, 803 (Fed. Cir. 1999) (claims are construed only to the extent necessary the term “duplicates” means that the sequences are identical. We observe that the ’357 patent states: “A duplicate sequencing read can be a sequencing read with the same identifier site and target sequence as another sequencing read in the population of sequencing reads.” Ex. 1004, 4:12–15. The claim does not use the exact wording as the Specification.4” slip op. at 11
- Claim Construction › Intrinsic evidence (Phillips canons) › Plain and ordinary meaning to a POSITATerm construed board ownDecided for petitioner
“4. “comprising” The parties may address the meaning of the transitional phrase “comprising” and whether the prior art meets the claim if the prior art discloses a method of identifying as duplicates those sequence reads with identical labels and target fragments and, in addition also identifies other sequence reads as duplicates, including sequence reads with some mutations resulting from PCR or SBS error. See Ex. 1079 ¶ 117. On this preliminary record, we construe “comprising” as an open-ended transition that is not limited to the listed steps. See Vivid Techs., Inc., 200 F.3d at 811.” slip op. at 13
Claim construction§ 102 anticipation§ 103 obviousnessDiscretionary denialcites Phillips · GrahamPatents in suitUS 11,098,357 - PTAB · Apr 21, 2025 · IPR2024-01502 · APJ James A Worth · IPR · Institution
Instituted IPR of claims 1–3, 5–11, and 14–17 on all petitioned grounds; the Board found a reasonable likelihood that at least claim 1 was obvious over Iafrate and Kivioja.
RulingsInstitution decision- PTAB / AIA Trials › Institution threshold (reasonable likelihood / more likely than not)InstitutedInstituted
“On the record at this stage of the proceeding, we determine that Petitioner has made an adequate showing on claim 1’s preamble language.9 Kivioja discloses that “with the UMI method one can reproducibly detect the number of molecules after different numbers of PCR cycles without normalization.” Ex. 1012, 2–3. Dr. Sims opines that a person of ordinary skill would have understood that Kivioja’s method teaches a method of detecting and removing duplicate sequencing reads, i.e., that Kivioja’s method of counting unique sequences necessarily identifies duplicate reads. See Ex. 1079 ¶ 260. 8 We recognize that the burden remains with Petitioner to prove unpatentability of the challenged claims. See 35 U.S.C. § 316(e). 9 We do not need to decide for purpose of institution whether the preamble is limiting.” slip op. at 20
- Skill levelSkill level patent owner adoptedDecided for patent owner
“On this preliminary record, we agree with Patent Owner that Petitioner’s asserted level of ordinary skill in the art is higher than warranted when Petitioner argues that a person of ordinary skill “further would have had specific experience with implementing and designing library preparation methods.” Pet. 23. However, we disagree with Patent Owner that a POSA only need to “have had experience with DNA sequencing methods” (Prelim. Resp. 8) because an artisan with experience with only pre-NGS sequencing methods would not qualify as a person of ordinary skill. skill would have had a Ph.D. in the field of chemistry, molecular biology, or biochemistry. Alternatively, a POSA would have had a B.S. or M.S. degree with three to five years of experience working in any of those fields. The person of ordinary skill would have had experience with NGS sequencing methods and a working knowledge of how those methods functioned. This definition of a person of ordinary skill is consistent with the skill level reflected in the disclosures of the ’399 patent and prior art. We further note that neither aspect of the dispute over the skill level affects our decision to institute review.” slip op. at 9
- Claim Construction › Intrinsic evidence (Phillips canons) › Lexicography (patentee as own lexicographer)Term construed petitioner constructionDecided for petitioner
“1. “indexing site” Petitioner argues that the ’399 patent defines “indexing site” as a sample index, specifically, “a nucleic acid sequence that acts as an index for multiple polynucleotide samples, thus allowing for the samples to be pooled together into a single sequencing run, which is known as multiplexing.” Pet. 24 (citing Ex. 1003, 4:34–38). Patent Owner does not disagree other than to argue that no claim term requires construction. The ’399 patent states: An indexing site is a nucleic acid sequence that acts as an index for multiple polynucleotide samples, thus allowing for the samples to be pooled together into a single sequencing run, which is known as multiplexing. Ex. 1003, 4:34–38. We understand this passage of the ’399 patent to provide a definition for “indexing site,” and we construe the term in accordance therewith. 2. “indexing primer binding site” Petitioner argues that the ’399 patent defines “indexing primer binding site” as the binding site for a primer used to read the indexing site/sample index, specifically, “a nucleotide sequence for binding a primer for an indexing site.” Pet. 24 (citing Ex. 1003, 4:33–34). Patent Owner does not disagree other than to argue that no claim term requires construction. The ’399 patent states: “An indexing primer binding site is a nucleotide sequence for binding a primer for an indexing site.” Ex. 1003, definition for “indexing primer binding site,” and we construe the term in accordance therewith. 3. “identifier site” Petitioner argues that the ’399 patent defines “identifier site” as a molecular tag attached to fragments prior to amplification, specifically, “a nucleic acid sequence that comprises random bases and is used to identify duplicate sequencing reads.” Pet. 25 (citing Ex. 1003, 4:43-45). Petitioner argues that an “identifier site” “can be designed as a set of sequences, or it can be semi-random, or it can be completely random.” Id. (citing Ex. 1003, 4:49–51). Petitioner argues that an “identifier site” can also “be a fixed length, or it can be a variable length.” Id. (citing Ex. 1003, 4:51–54). Patent Owner does not disagree other than to argue that no claim term requires construction. The ’399 patent states: “An identifier site is a nucleic acid sequence that comprises random bases and is used to identify duplicate sequencing reads.” Ex. 1003, 4:43–45. We understand this passage of the ’399 patent to provide a definition for “identifier site,” and we construe the term in accordance therewith. 4. “target sequence primer binding site” Petitioner argues that the ’399 patent defines “target sequence primer binding site” as a binding site for a primer used to read the fragment sequence, specifically, a “nucleotide sequence for binding a primer for a target sequence.” Pet. 25 (citing Ex. 1003, 4:62–65). Petitioner also argues that the ’399 patent expressly discloses that this site can be a standard Illumina sequence compatible with an Illumina primer for an SBS reaction to read the DNA fragment. Id. (citing Ex. 1003, 16:48–51 & SEQ ID No. 3). requires construction. The ’399 patent states: “A target sequence primer binding site nucleotide sequence for binding a primer for a target sequence.” Ex. 1003, 4:62–63. The ’399 patent appears to have a typographical error at this juncture in the Specification because the quoted text is missing a verb (e.g., “is”) and is therefore an incomplete sentence. Based on the context of the surrounding parts of the Specification, we infer that the ’399 patent intended to define “target sequence primer binding site” as a “nucleotide sequence for binding a primer for a target sequence.”” slip op. at 11
- Claim Construction › Threshold & procedure › Whether a term needs construction (O2 Micro)No construction neededOther
“5. “identifying a duplicate sequencing read as the sequencing read comprising the same identifier site and nucleic acid fragment as another sequencing read in the population of sequencing reads” Although the parties do not request construction of this limitation, we note that the parties may wish to address the construction of this limitation after institution. See Vivid Techs., Inc. v. Am. Sci. & Eng’g, Inc., 200 F.3d 795, 803 (Fed. Cir. 1999) (claims are construed only to the extent necessary to resolve a dispute). For example, the parties may wish to address whether the “same identifier and nucleic acid fragment” means that the sequences are identical. We observe that the ’399 patent states: “A duplicate sequencing read can be a sequencing read with the same identifier site and target sequence as another sequencing read in the population of sequencing reads.” Ex. 1003, 4:8–11. The claim does not use the exact wording as the Specification.5” slip op. at 13
Claim construction§ 103 obviousnessDiscretionary denialcites Phillips · GrahamPatents in suitUS 9,546,399 - PTAB · Apr 21, 2025 · IPR2024-01506 · APJ Georgianna W Braden · IPR · Institution
The Board instituted IPR of claims 1–16 on all asserted challenges, finding a reasonable likelihood that Kivioja anticipates at least one challenged claim.
RulingsInstitution decision- PTAB / AIA Trials › Discretionary denial › §325(d) same art / argumentsDenied
“framework set forth under Advanced Bionics, LLC v. Med-El Electromedizinische Geräte GmbH, IPR2019-01469, Paper 6 at 7 (PTAB Feb. 13, 2020) (precedential) (“Advanced Bionics” or “AB”). Under the first prong of that framework, we must determine whether the same or substantially the same art or arguments previously were presented to the Office. If so, we turn to the second prong which focuses on whether the petitioner has demonstrated that the Office erred in a manner material to the patentability of the challenged claims. Id. at 8. a. Advanced Bionics Prong One: whether “the same or substantially the same art or arguments previously were presented to the Office” In evaluating whether the same or substantially the same prior art or arguments were previously presented to the Office, the Board has identified several non-exclusive factors for consideration. Becton, Dickinson & Co. v. B. Braun Melsungen AG, Case IPR2017-01586, Paper 8 at 17–18 (PTAB Dec. 15, 2017) (Paper 8) (precedential § III.C.5, first para.) (“the Becton Dickinson factors”). Specifically, we must weigh the following non-exclusive factors: (a) the similarities and material differences between the asserted art and the prior art involved during examination; (b) the cumulative nature of the asserted art and the prior art evaluated during examination; (c) the extent to which the asserted art was evaluated during examination, the overlap between the arguments made during examination and the manner in which Petitioner relies on the prior art or Patent Owner distinguishes the prior art; (e) whether Petitioner has pointed out sufficiently how the Examiner erred in its evaluation of the asserted prior art; and (f) the extent to which additional evidence and facts presented in the Petition warrant reconsideration of prior art or arguments. Becton Dickinson, at 17–18. Thus, the Becton Dickinson factors are framed as comparing the art or arguments in a petition against what was before an examiner during prosecution.” slip op. at 9
- Claim Construction › Threshold & procedure › Whether a term needs construction (O2 Micro)No construction neededOther
“Construction is needed only for those terms “that are in controversy, and only to the extent necessary to resolve the controversy.” See Nidec Motor Corp. v. Zhongshan Broad Ocean Motor Co., 868 F.3d 1013, 1017 (Fed. Cir. 2017) (quoting Vivid Techs., Inc. v. Am. Sci. & Eng’g, Inc., 200 F.3d 795, 803 (Fed. Cir. 1999)). Although Petitioner provides us with constructions for “appended,” “identifier site” and “indexing site,” the meaning of these terms are not in controversy at this stage of the proceeding and their constructions will not aid in our analysis. We acknowledge, the ’241 patent. See Ex. 1005, 4:37–40, 4:45, 4:51–53.” slip op. at 13
- Claim Construction › Intrinsic evidence (Phillips canons) › Plain and ordinary meaning to a POSITAPlain and ordinary meaningOther
“2. “identifying sequence reads with identical identifier and target sequences as duplicates” The parties do not request construction of the limitation, “identifying sequence reads with identical identifier and target sequences as duplicates.” Nonetheless, we invite the parties to address the construction of this limitation after institution. See Vivid Techs., Inc. v. Am. Sci. & Eng’g, Inc., 200 F.3d 795, 803 (Fed. Cir. 1999) (claims are construed only to the extent necessary to resolve a dispute). Specifically, the parties may wish to address whether the “same identifier and nucleic acid fragment” means that the sequences actually are identical. The ’241 patent states: “A duplicate sequencing read can be a sequencing read with the same identifier site and target sequence as another sequencing read in the population of sequencing reads.” Ex. 1003, 4:10–13. Yet, the claim does not use the exact wording used in the Specification.4 The ’241 patent goes on to disclose “apparent duplicates” and “true” slip op. at 14
- Skill levelSkill level patent owner adoptedDecided for patent owner
“We do not see a material difference in the parties’ proposed levels of education and work experience. Indeed, although Petitioner asserts that a POSA “would have a PhD or equivalent training,” it allows more work experience to compensate for less education. Pet. 20 (stating that a POSA could have “commensurately less education and more work experience”). We, nevertheless, adopt Patent Owner’s proposal in this aspect because it specifies the years of experience needed. Patent Owner further disputes Petitioner’s proposal that a POSA would have had experience with “implementing and designing library preparation methods for Illumina, the leading NGS platforms in 2013.” Prelim. Resp. 7–8 (quoting Pet. 20, emphasis added by Patent Owner removed). According to Patent Owner, “[t]his level of skill inappropriately requires the POSA to be an inventor of library preparation methods.” Id. at 8. We agree with Patent Owner that “experience with implementing and designing library preparation methods for Illumina” is above ordinary skill. have had experience with DNA sequencing methods and a working knowledge of how these sequencing methods functioned.” Id. As Patent Owner recognizes, the challenged claims relate to obtaining amplicons with an amplified nucleic acid fragment and an appended adaptor and then sequencing the amplicon to generate sequence reads. See Ex. 1005, 25:33– 43. Accordingly, for purposes of this Decision, we find a person of ordinary skill in the art at the critical time would have had a Ph.D. in the field of chemistry, molecular biology, or biochemistry. Alternatively, a person of ordinary skill in the art would have had a B.S. or M.S. degree with three to five years of experience working in any of those fields. The person of ordinary skill in the art would have had experience with NGS sequencing methods and a working knowledge of how those methods functioned. This definition of a person of ordinary skill in the art is consistent with the skill level reflected in the disclosures of the ’241 patent and prior art. We further note that neither aspect of the dispute over the skill level affects our decision to institute review.” slip op. at 20
Claim construction§ 102 anticipation§ 103 obviousnessDiscretionary denialcites Phillips · KSR · GrahamPatents in suitUS 11,725,241 - Encube Ethicals PTV. Ltd. v. Dermavant Sciences GmbHAdverse judgmentPTAB · Mar 7, 2025 · IPR2024-00834 · APJ Tawen Chang · IPR · Adverse judgment
The Board entered adverse judgment against Patent Owner on all challenged claims, 1–4, 6–10, 16, 18, 21, and 22, following their disclaimer.
RulingsAdverse judgment- Adverse judgmentAdverse judgmentGranted
“Terminate Proceeding and Parties’ Joint Motion for Entry of Adverse Judgment (collectively “Motion”). The parties jointly request that the Board enter adverse judgment in light of the disclaimer filed by Patent Owner disclaiming all challenged claims. Mot. 1 (citing 37 C.F.R. § 42.73(b)(2)). The Motion attaches as an exhibit a disclaimer under 37 C.F.R. § 1.321(a), filed January 28, 2025, of claims 1–4, 6–10, 16, 18, 21, and 22 of the ’088 patent, which constitute all of the claims challenged in the inter partes review. Ex. 2001; Paper 1, 3.” slip op. at 2
- PTAB / AIA Trials › Other PTAB motions (exclude, strike, seal, additional discovery, rehearing)Denied
“Accordingly, we grant the Parties’ Joint Motion for Entry of Adverse Judgment. This Adverse Judgment is sufficient to dispose of this proceeding and Patent Owner’s Motion to Terminate is denied as moot.1” slip op. at 3
NonePatents in suitUS 11,590,088
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.