DETAILED ACTION
Status of the Claims
Claims 21-41 are currently pending.
Claims 33-41 have been withdrawn as being drawn to non-elected subject matter (see below).
Claims 21-32 are examined herein.
The following Office Action is in response to Applicant’s communication dated 01/12/2026. Rejection(s) and/or objection(s) not reiterated from previous office actions are hereby withdrawn. The following rejection(s) and/or objection(s) are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 01/12/2026 has been entered.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Terminal Disclaimer
The terminal disclaimer filed on 11/26/2024 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of any patent granted on Application Number 16/458,268 has been reviewed and is accepted. The terminal disclaimer has been recorded.
Response to Restriction Requirement
During a telephone conversation with John Iwanicki on 08/05/2024 a provisional election was made with traverse to prosecute the invention of Group I, claims 21-32.
Claim 33-41 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 11/26/2024.
Applicant's election with traverse of Group I, claims 21-32, in the reply filed on 11/26/2024 is acknowledged. The traversal is on the ground(s) that there would allegedly be no serious search burden on the examiner to examine both inventions. This is not found persuasive because the inventions as claimed have a materially different mode of operation and do not overlap in scope. Specifically, the method of invention I uses a single probe per location, which is extended using the target RNA as a template followed by ligation, whereas the method of invention II requires the introduction of a splint probe that also hybridizes to the target RNA and is directly ligated to the first probe, resulting in a circularized probe. The two methods would require differing enzyme(s) to accomplish the circularization, different reaction conditions, etc. Further, there is nothing of record to indicate that they are obvious variants of each other.
The requirement is still deemed proper and is therefore made FINAL.
Claim Objections
Claims 28 and 30 are objected to as being dependent upon a rejected base claim, but would be free from the prior art if rewritten in independent form including all of the limitations of the base claim and any intervening claims. Appropriate correction is required.
Claim Rejections – 35 U.S.C. 103(a)
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Bernitz et al. and Clarke et al.
Claims 21-27, 29, and 31-32 are rejected under 35 U.S.C. 103 as being unpatentable over Bernitz et al. (U.S. 8,551,710 B2, of record) in view of Clarke et al. (WO 2013/119827 A1, of record).
Regarding claim 21(in part), Bernitz discloses a method for in situ detection of a nucleic acid molecule in a cell or tissue, comprising:
(a) hybridizing a nucleic acid probe to a nucleic acid molecule in a cell or tissue, wherein said nucleic acid probe comprises a first domain that hybridizes to a first target sequence of said nucleic acid molecule and a second domain that hybridizes to a second target sequence of said nucleic acid molecule, and wherein said nucleic acid molecule comprises a third target sequence disposed between said first target sequence and said second target sequence (e.g., a padlock probe as per Fig. 1, wherein said padlock probe can comprise a gap to be filled as per the paragraph bridging col. 8-9 and/or col. 30);
(b) extending said nucleic acid probe using said third target sequence as a template to generate an extended polynucleotide probe comprising a gap-filled sequence complementary to said third target sequence (the gap can be filled by extending the 3’ end of the padlock probe as per col. 8 and/or 30);
(c) circularizing said extended polynucleotide probe to generate a circular nucleic acid molecule (e.g., as per col. 30);
(d) amplifying said circular nucleic acid molecule to generate an amplification product comprising a sequence complementary to said gap-filled sequence (e.g., rolling circle amplification as per col. 9 and/or 30); and
(e) in said cell or tissue, sequencing said sequence complementary to said gap-filled sequence to detect said nucleic acid molecule in said cell or tissue (e.g., “[m]ultiplexed detection can also be achieved by applying in situ Sequencing technologies such as sequencing by ligation, sequencing by Synthesis, or sequencing by hybridization” as per col. 32, lines 44-46).
However, it is noted that Bernitz is silent on the newly added limitation of hybridizing the probe molecule directly to the RNA, without a step of cDNA synthesis, as set forth in claim 21.
Clarke discloses direct capture of RNA molecules with molecular inversion probes as a means to bypass the need to generate an intervening cDNA molecule (e.g., as per the SUMMARY OF THE INVENTION section on pages 2-4).
It would have been prima facie obvious to a person of ordinary skill in the art prior to the effective filing date of the application to utilize the direct RNA capture as per Clarke in the in situ RNA detection and identification method of Bernitz. One of ordinary skill in the art would have been motivated to do so since Clarke discloses that “[t]his direct capture reduces the assay’s cost, time to result, and labor requirements” as per the paragraph bridging pages 11-12).
One of ordinary skill in the art would have had a reasonable expectation of success as of the application’s effective filing date in combining the teachings of the prior art references to arrive at the invention as presently claimed since Clarke discloses that their method of direct RNA capture can be used in many, many areas where molecular inversion probes are used, from gene expression profiling, RNA virus detection, human genetics, and several other (e.g., as per the Applications section on pages 9-11).
Regarding claims 22-24, Bernitz discloses the above, wherein said sequencing is sequencing by synthesis, sequencing by ligation, or sequencing by hybridization (e.g., “[m]ultiplexed detection can also be achieved by applying in situ Sequencing technologies such as sequencing by ligation, sequencing by Synthesis, or sequencing by hybridization” as per col. 32, lines 44-46).
Regarding claim 25, Bernitz discloses the above, wherein said nucleic acid probe comprises a sequencing primer domain (e.g., sequencing adapters as per Clarke at page 12 and/or Bernitz states “sequences may include binding sites for an RCA primer, hybridization probes, and/or amplification or sequencing primers” as per col. 10, lines 46-48).
Regarding claim 26, Bernitz discloses the above, further comprising identifying a sequence variation in said third target sequence of said RNA molecule (e.g., “the present method can meet this need, and that the ability it provides to visualize transcriptional variation directly in cells and tissues” as per col. 3, lines 1-3).
Regarding claims 27 and 29, Bernitz discloses the above, further comprising contacting said cell or tissue with a crowding agent that enhances a rate of hybridization between said nucleic acid probe and said RNA molecule, wherein said crowding agent comprises: (i) a polymer backbone; (ii) a hydrating group; and (iii) a cleavable linkage disposed between said polymer backbone and said hydrating group (e.g., cell interiors are known to be molecularly crowded, at least in part to the high concentrations of biomolecules, such as RNA, which is estimated to be 75-150 mg/mL as per Table 2 of Nakano et al. (Chem. Rev., 2014, 114:2733−2758, of record), which reasonably reads on the limitation of a crowding agent, RNA being a polyionic compound, and wherein RNA comprises a phosphodiester polymer backbone that reads on the polymer backbone, the hydrating group, and the cleavable linkage).
Regarding claim 31, Bernitz discloses the above, wherein said nucleic acid probe comprises a nucleic acid analog (e.g., LNA as per col. 7).
Regarding claim 32, Bernitz discloses the above, further comprising ligating a 5' end of said extended polynucleotide probe to a 3' end of said extended polynucleotide probe (e.g., as per Bernitz col. 30 and/or Clarke as per the Probes of the invention section at pages 6-9).
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Response to Arguments
The 01/12/2026 remarks argue: references teach away, no motivation to combine, and no reasonable expectation of success.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
RE: “Bernitz unambiguously states that ‘the high selectivity reported for padlock probes with in situ DNA detection and genotyping has not been reproduced with detection of RNA targets in situ... it is known that both the efficiency and the specificity of the ligation reaction are lower compared to ligation on a DNA template... The detection efficiency of direct mRNA detection with padlock probes has been estimated to be as low as 1%.’ Bernitz at column 2, lines 6-45 (emphasis added). As such, Bernitz does not ‘merely express[ ] a general preference for an alternative invention,’ or proffer a ‘somewhat inferior’ nonpreferred embodiment but unequivocally states that: ‘None of the methods for in situ detection of RNA presented thus far provide the possibility to detect sequence variation at the single nucleotide level and in particular to genotype transcripts.’ Bernitz at column 2 lines 39-42 (emphasis added). Based on this conclusion of Bernitz, the skilled artisan would be discouraged from further investigation into in situ detection of RNA, including via the claimed methods, and/or those the Office asserts are taught by Clarke. And, as such, Bernitz ‘lead[s] the skilled artisan in a direction divergent from’ direct RNA detection and instead to ‘converting an RNA target molecule into cDNA, [whereby] the reduction in padlock probe ligation efficiency and specificity is avoided and the excellent genotyping properties provided by padlock probes are preserved.’ Bernitz at column 2, lines 42- 45” and “Because Bernitz clearly and unambiguously ‘criticize[s], discredit[s], or otherwise discourage[s]’ the claimed solution of direct RNA detection, Bernitz teaches away from Applicant's claimed invention.”
In response, it is noted that Bernitz does point out the difficulties and limitations that were known in the art at the time. Bernitz states that “While RNA molecules can also serve as templates for the ligation of padlock probes … RNA detection with padlock probes in situ has so far proven more difficult than DNA detection and is subject to limitations” (e.g., as per col. 2, lines 6-9). Bernitz then speculates that “This is possibly due to problems with ligation of DNA molecules on an RNA template, since it is known that both the efficiency and the specificity of the ligation reaction are lower compared to ligation on a DNA template” (e.g., as per col. 2, lines 13-16).
The Clark reference, with an effective filing date of about 1 year after Bernitz, acknowledges these issues, recites that “Direct capture of RNA molecules, in the absence of generating an intermediate cDNA, for, e.g., sequencing or quantifying particular species (molecules/ transcripts) is technically challenging, but is scientifically important” (e.g., as per page 1, lines 12-14), and that “Ligation of DNA to DNA when hybridized to an RNA template is poorly catalysed by known DNA ligases” (e.g., as per page 5, lines 31-32). Clark addresses these known limitations by having “Identified RNase H negative RTs to preserve RNA integrity and enable multiple cycles of interrogation”, “Identified non-strand displacing RT mutant that does not displace 5' binding arm”, “optimized the reaction conditions to enable highest affinity molecular inversion probe circularization”, and “developed a protocol that uses Mg2+ dependent reverse transcriptase to enable use of lower concentrations of Mg2+ for the combined gap-filling and ligation step” (e.g., as per pages 5-6).
Thus, while Bernitz rightly noted the known problems and limitations associated with probe circularization directly on RNA without reverse transcription into cDNA, the later disclosure of Clark acknowledges such issues and offers solutions to overcome them, stating that their “invention provides, inter alia, easy methods of capturing sequences of target RNA molecules using molecular inversion probes (MIPs) in the absence of generating a full-length intervening cDNA molecule” (e.g., as per page 2, lines 13-15). When viewed together, there is no indication that one of ordinary skill in the art would conclude that the references together criticize, discredit, or otherwise discourage the solution claimed.
RE: “Applicant respectfully submits that the Office's alleged rationale for the skilled artisan to look to Clarke is not tenable” and “Applicant respectfully submits that the skilled artisan would not sacrifice 99% of detection efficiency (from the 1% figure from Bernitz) just to save a few hours of labor, cost, and/or time to result. Any savings in ‘cost, time to result, and labor’ asserted by Clarke is not at all beneficial, if the resulting method is essentially non-functional or significantly less reliable in the claimed in situ context as Berntiz suggests would be the case.”
This argument has been fully considered, but is not persuasive. Applicant’s assertion of a 1% efficiency based on Bernitz ignores the teachings of Clarke. The Clarke reference (which is post-Bernitz) acknowledges that “no previous disclosure has enabled the use of the technology on an RNA template” but that “[h]ere, Applicants describe two embodiments of the technology that enable capture directly from RNA templates without a cDNA intermediate” (e.g., as per p. 9 of Clarke). Therefore, in response to Applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
RE: “given that Bernitz teaches that ‘the detection efficiency of direct mRNA detection with padlock probes has been estimated to be as low as 1%,’ the reference does not provide any reasonable expectation of success, with the combination of any reference. If anything, with its low reported efficiency based on several results, Bernitz leads the skilled artisan to the conclusion that the RNA detection method of Bernitz, without the generation of cDNA, would not work for its intended purpose, nor with any reasonable expectation of success, even with the alleged teachings of Clarke and/or Christian.”
Here, Applicant alleges that Bernitz would not work for its intended purpose even with the teachings of Clarke, but does not offer any evidence or reasoning as to why. Therefore, the arguments are not persuasive and the rejection is properly maintained.
Conclusion
No claims are allowed.
All claims are identical to or patentably indistinct from, or have unity of invention with claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction (including a lack of unity of invention) would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684