DETAILED ACTION
Status of the Claims
Claims 1-22 are currently pending.
Claims 1, 9-10, and 17-20 are amended.
Claims 21-22 are new.
Claims 1-22 are the subject of this Office Action.
The following Office Action is in response to Applicant’s communication dated 02/26/2026. Rejection(s) and/or objection(s) not reiterated from previous office actions are hereby withdrawn.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.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Modified Claim Rejections – 35 U.S.C. 103(a)
Necessitated by Amendment
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.
Mitra et al.
Claims 1-10 and 13-22 are rejected under 35 U.S.C. 103 as being unpatentable over Mitra et al. (U.S. PGPub 2015/0160204 A1, cited in IDS of 06/30/2025, of record).
Regarding claim 1, Mitra discloses a method of characterizing polypeptides (e.g., “characterizing structural properties of a polypeptide using analytical laboratory methods” as per [0006]), comprising:
providing a plurality of polypeptides attached to a surface of a substrate, with individual polypeptide molecules of the plurality of polypeptides being attached at individually addressable locations on the substrate (e.g., such “methods comprise immobilizing, on a solid support, individual protein or polypeptide strands comprised by the sample, such that each polypeptide strand to be analyzed is separated by an optically resolvable distance from other protein or polypeptide strands comprised by the sample” as per [0016] and/or [0053]),
contacting the polypeptides on the array with at least one hundred different affinity reagents by sequentially applying solutions comprising at least one affinity reagent from the at least one hundred different affinity reagents to the plurality of polypeptides (e.g., contacting the binding pools with the immobilized polypeptides to gather binding data as per paragraphs [0012] and/or [0046] and/or Example 1),
where each of the at least one hundred different affinity reagents (e.g., “a panel of binding pools can comprise up to about 400 probes, up to about 200 probes up to about 100 probes, or up to about 50 probes” noting that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists) comprises a binding affinity for a different epitope that is present in more than one of the plurality of polypeptides (e.g., Mitra discusses this in several places, including that “each binding pool target can be a binding target for at least one probe comprised by a binding pool, and can comprises at least one amino acid up to about six amino acids”, as per para [0037], “in certain aspects, a probe can be degenerate, i.e., the probe can recognize [and] bind more than one structure” as per para [0010], “[e]ach probe of a binding pool can recognize and bind a binding target” as per para [0008], see also para [0033]-[0039]),
separately detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate, and
characterizing each of the plurality of polypeptides based upon the different affinity reagents that bind to each of the individual polypeptide molecules (e.g., “[i]n various configurations of the present teachings, presence or absence of a binding pool target in a protein or polypeptide to be identified can be considered binary property” as per [0014]).
Regarding claims 2-4, Mitra discloses the method above, wherein the plurality of polypeptides attached to the surface of the substrate comprises at least 50,000, or 1,000,000, or 100,000,000 individual polypeptides (e.g., Mitra at [0016] discloses quantifying polypeptides in a sample by immobilizing said polypeptides at optically resolvable distances, such as about 1 micron as per [0055], such that 100,000,000 resolvable positions would fit on a substrate sized 1 cm2).
Regarding claims 5-9, Mitra discloses the method above, wherein the individual polypeptide molecules of the plurality of polypeptides attached to the surface of the substrate comprise at least 100, 500, 1000, 10,000, or 20,000 different individual polypeptide molecules (e.g., ~30,000 different polypeptides as per [0035]).
Regarding claim 10, Mitra discloses the method above, wherein the individual polypeptide molecules are attached to the surface of the substrate through an intermediate (e.g., via a reactive moiety as per [0016]).
Regarding claim 13, Mitra discloses the method above, wherein the individual polypeptide molecules are attached to the surface of the substrate within a plurality of nanowells on the surface of the substrate (e.g., as per [0013]).
Regarding claim 14, Mitra discloses the method above, wherein the affinity reagents are selected from the group consisting of: antibodies, antibody fragments and aptamers (e.g., probes can be antibodies or aptamers as per [0010]).
Regarding claim 15, Mitra discloses the method above, wherein the separately detecting step comprises optically detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate (e.g., “Binding or absence of binding of each binding pool can be determined for each polypeptide to be identified and the identities of the proteins or polypeptides can be determined by reference to a database of proteins or polypeptides, as described herein” as per [0015]).
Regarding claim 16, Mitra discloses the method above, wherein a plurality of the at least 100 different affinity reagents have a binding specificity to a different epitope of three, four or five consecutive amino acid residues (e.g., binds to one to six amino acids as per [0008]).
Regarding claim 17, Mitra discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the at least one hundred different affinity reagents bound to each of the individual polypeptide molecules in the plurality of polypeptides on the surface of the array to characterize each of the plurality of polypeptides on the surface of the substrate (e.g., “determining presence or absence in the protein or polypeptide to be identified, of each binding pool target of a plurality of binding pool targets, wherein each binding pool target comprises one or more binding targets for one or more probes comprised by a binding pool” as per para [0007]).
Regarding claim 18, Mitra discloses the method above, wherein the step of detecting the binding of each of the at least one hundred different affinity reagents bound to each of the individual polypeptide molecules on the substrate comprises optically detecting a location on the surface of the substrate having an individual polypeptide molecule attached thereto at which each of the affinity reagents binds (e.g., optical detection as per para [0055]-[0056] using, for example, a fluorophore as per para [0045]).
Regarding claim 19, Mitra discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on substrate comprises identifying each of the plurality of polypeptides on the surface of the substrate (e.g., “determining presence or absence in the protein or polypeptide to be identified, of each binding pool target of a plurality of binding pool targets, wherein each binding pool target comprises one or more binding targets for one or more probes comprised by a binding pool” as per para [0007]).
Regarding claim 20, Mitra discloses the method above, wherein the step of characterizing the plurality of polypeptides on the substrate comprises quantifying each different individual polypeptide molecule in the plurality of polypeptides on the surface of the substrate (e.g., “in some aspects, the protein or polypeptide strands in a sample comprising an identical profile of binding pool targets can be quantified by summing the protein or polypeptide strands comprising the same profile of binding pool targets” as per [0016]).
Regarding claims 21-22, Mitra discloses the method above, wherein characterizing each of the plurality of polypeptides comprises determining a probable identity of each individual polypeptide molecules of the plurality of polypeptides and further comprises determining a confidence level of the probable identity (e.g., as per paragraphs [0014], [0036], [0053], and/or Examples 4 and/or 6, which discuss use of the collected binding data to search a polypeptide database and qualitatively determining a match or the closest match(es) thereby calling the “correct call” or “incorrect call”). Note that paragraph [00118] of the specification states that “Given the information about the binding characteristic of each affinity reagent, a database of the proteins in the sample, and list of binding coordinates, the pattern of binding, the software tool assigns a probable identity to each coordinate as well as a confidence for that identity. In the extreme case of precise 1-1 mappings between affinity reagents and proteins, this can be accomplished with a simple lookup table.” Further, Fig. 4 shows a quantitative analysis of the correctly called signatures, reasonably providing information on confidence scoring.
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Response to Arguments
The 02/26/2026 remarks argue: not all elements are taught.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
RE: “Mitra does not teach or make obvious a process where each affinity reagent within the at least 100 affinity reagents has a binding affinity for a different epitope that is present in more than one of the polypeptides on the substrate” (as per page 6 of the remarks).
In response, it is noted that Mitra discusses this in several locations. For example, in the para [0008], the reference states that “[e]ach probe of a binding pool can recognize and bind a binding target” and that “the protein or polypeptide to be identified comprises at least one binding target recognized by a probe comprised by the binding pool”. Further, para [0017] states that “each probe comprised by a binding pool … binds to a binding pool target comprising at least one amino acid up to about six amino acids, a glycosyl moiety of a glycopeptide or glycoprotein, a GPI anchor, a disulfide linkage, a pyroglutamic acid, a nitrotyrosine or a combination thereof.”
RE: “In fact, using probes that each bound to more than one of the polypeptides would likely confound the results of Mitra, since the goal of Mitra's process is to generate a specific digital signature for each polypeptide, which would likely be complicated by the use of cross-reacting probes” (as per page 6 of the remarks).
In response, Mitra specifically discloses the use of cross-reacting probes, stating that “a probe can be degenerate, i.e., the probe can recognize [and] bind more than one structure” (e.g., as per para [0010]). Further, a “digital signature” as collected by Mitra does not equate to the use of specific probes which can only recognize a single protein, as implied by the remarks. Rather, the “digital signature” is merely a representation or notation of which probes and binding pools recognized an epitope on the immobilized proteins. The remarks (page 7) point to “a set of x affinity reagents specific to unique amino acid 3-mers” noting that as per Fig. 13, “98% of human proteins can be uniquely identified with 8000 affinity reagents, wherein each of the affinity reagents binds to a three-mer set of amino acids”. This parallels the teachings of Mitra, whose probes bind epitopes of one to six amino acids (and some post-translational modifications) and also discuss the relationship between the percent of proteins that can be identified with collections of probes, such as Fig. 2 of Mitra:
PNG
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550
638
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Greyscale
Mitra also discusses the relationship between polypeptide lengths and proteins with unique signatures (e.g., as per Fig. 3) as well as optimizing said pools, as per Fig. 5-6 and shown in in Example 5.
Mitra et al. and Drmanac et al.
Claims 1-22 are rejected under 35 U.S.C. 103 as being unpatentable over Mitra et al. (U.S. PGPub 2015/0160204 A1, cited in IDS of 06/30/2025, of record) in view of Drmanac er al. (U.S. PGPub 2011/0071053 A1, of record).
Mitra is relied on as above, however, the reference is silent on the limitation of the sample polypeptides being attached to the substrate via an intermediate, wherein the intermediate comprises a nanoparticle or a nucleic acid molecule, as set forth in claims 11-12.
Drmanac discloses methods of immobilizing biomolecules in an array by attachment to DNA nanoparticles (e.g., as per Fig. 1E and Fig. 1H) using conventional attachment chemistries including common homo- and heterobifunctional linkers (e.g., as per [0035]).
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 use the DNA nanoballs of Drmanac to attach the sample polypeptides of Mitra to a substrate. One of ordinary skill in the art would have been motivated to do so since
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 Drmanac discloses several common and commercially available homo- and heterobifunctional linkers (e.g., from Pierce Biotechnology as per [0035]) which are compatible with those proposed for polypeptide immobilization by Mitra (e.g., as per [0055]).
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Response to Arguments
Applicant does not offer further arguments regarding the above obviousness rejections beyond what was set forth with regard to the 35 U.S.C. § 102 rejection, above. To the extent that Applicant is merely repeating their previous argument, the Examiner contends that those issues were adequately addressed in the above sections, which are incorporated in their entireties herein by reference.
Maintained Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory obviousness-type double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); and In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the conflicting application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
U.S. 16/972,341
Claim 1-15 and 17-22 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 43-44, 47-52, 56-61, 63-64, and 67 of copending Application No. 16/972,341 (the ‘341 application). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding claim 1, the claims of the ‘341 application discloses a method of characterizing polypeptides, comprising providing a plurality of polypeptides attached to a surface of a substrate, with individual polypeptide molecules being attached at individually addressable locations on the substrate, contacting the polypeptides on the array with at least one hundred different affinity reagents by sequentially applying solutions comprising at least one affinity reagent from the at least one hundred different affinity reagents to the plurality of polypeptides, where each of the at least one hundred different affinity reagents comprises a binding affinity for a different epitope that is present in more than one of the plurality of polypeptides, separately detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate, and characterizing each of the plurality of polypeptide molecules based upon the different affinity reagents that bind to each of the polypeptide molecules (e.g., as per claim 43 of the ‘341 application). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claims 2-9, the claims of the ‘341 application discloses the method above, wherein the plurality of polypeptides attached to the surface of the substrate comprises at least 100,000,000 individual polypeptides (e.g., as per claim 52 of the ‘341 application). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claim 10, the claims of the ‘341 application discloses the method above, wherein the polypeptides are attached to the surface of the substrate through an intermediate (e.g., as per claims 47-48 of the ‘341 application).
Regarding claim 11, the claims of the ‘341 application discloses the method above, wherein the intermediate comprises a nanoparticle (e.g., as per claim 47 of the ‘341 application).
Regarding claim 12, the claims of the ‘341 application discloses the method above, wherein the intermediate comprises a nucleic acid molecule (e.g., as per claim 48 of the ‘341 application).
Regarding claim 14, the claims of the ‘341 application discloses the method above, wherein the affinity reagents are selected from the group consisting of: antibodies, antibody fragments and aptamers (e.g., as per claim 43 of the ‘341 application).
Regarding claim 15, the claims of the ‘341 application discloses the method above, wherein the separately detecting step comprises optically detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate (e.g., as per claim 49 of the ‘341 application).
Regarding claim 17, the claims of the ‘341 application discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the array to characterize each of the plurality of polypeptides on the surface of the substrate (e.g., as per claim 43 of the ‘341 application).
Regarding claim 18, the claims of the ‘341 application discloses the method above, wherein the step of identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the substrate comprises optically detecting a location on the surface of the substrate having a polypeptide attached thereto at which each of the affinity reagents binds (e.g., as per claim 49 of the ‘341 application).
Regarding claim 19, the claims of the ‘341 application discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the plurality of polypeptides on the surface of the substrate (e.g., as per claim 43 of the ‘341 application).
Regarding claim 20, the claims of the ‘341 application discloses the method above, wherein the step of characterizing the plurality of polypeptides on the surface of the substrate comprises quantifying each different polypeptide in the plurality of polypeptides on the surface of the substrate (e.g., as per claim 43 of the ‘341 application).
Regarding claims 21-22, the claims of the ‘341 application discloses the method above, wherein characterizing each of the plurality of polypeptides comprises determining a probable identity of each individual polypeptide molecules of the plurality of polypeptides and further comprises determining a confidence level of the probable identity (e.g., as per claim 59 of the ‘341 application).
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Response to Arguments
The 02/26/2026 remarks argue: not all elements are taught.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
Specifically, the remarks argue that the amendments to claim 1 are not found in the claims of the reference patent application. In response, it is noted that the rejection has been modified to address said limitations.
U.S. 19/180,024
Claim 1-20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 192-226 of copending Application No. 19/180,026 (the ‘024 application). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding claim 1, the claims of the ‘024 application discloses a method of characterizing polypeptides, comprising providing a plurality of polypeptides attached to a surface of a substrate, with individual polypeptide molecules being attached at individually addressable locations on the substrate, contacting the polypeptides on the array with at least one hundred different affinity reagents by sequentially applying solutions comprising at least one affinity reagent from the at least one hundred different affinity reagents to the plurality of polypeptides, where each of the at least one hundred different affinity reagents comprises a binding affinity for a different epitope that is present in more than one of the plurality of polypeptides, separately detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate, and characterizing each of the plurality of polypeptide molecules based upon the different affinity reagents that bind to each of the polypeptide molecules (e.g., as per claim 192 of the ‘024 application). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claims 2-9, the claims of the ‘024 application discloses the method above, wherein the plurality of polypeptides attached to the surface of the substrate comprises at least 100,000,000 individual polypeptides (e.g., as per claims 208-209 of the ‘024 application). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claim 10, the claims of the ‘024 application discloses the method above, wherein the polypeptides are attached to the surface of the substrate through an intermediate (e.g., as per claims 47-48 of the ‘024 application).
Regarding claim 11, the claims of the ‘024 application discloses the method above, wherein the intermediate comprises a nanoparticle (e.g., as per claim 192 of the ‘024 application).
Regarding claim 12, the claims of the ‘024 application discloses the method above, wherein the intermediate comprises a nucleic acid molecule (e.g., as per claim 194 of the ‘024 application).
Regarding claim 13, the claims of the ‘024 application discloses the method above, wherein the individual polypeptide molecules are attached to the surface of the substrate within a plurality of nanowells on the surface of the substrate (e.g., as per claim 223 of the ‘024 application).
Regarding claim 14, the claims of the ‘024 application discloses the method above, wherein the affinity reagents are selected from the group consisting of: antibodies, antibody fragments and aptamers (e.g., as per claims 199-200 of the ‘024 application).
Regarding claim 15, the claims of the ‘024 application discloses the method above, wherein the separately detecting step comprises optically detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate (e.g., as per claims 212-214 of the ‘024 application).
Regarding claim 16, the claims of the ‘024 application discloses the method above, wherein a plurality of the at least 100 different affinity reagents have a binding specificity to a different epitope of three, four or five consecutive amino acid residues (e.g., as per claim 201 of the ‘024 application).
Regarding claim 17, the claims of the ‘024 application discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the array to characterize each of the plurality of polypeptides on the surface of the substrate (e.g., as per claim 207 of the ‘024 application).
Regarding claim 18, the claims of the ‘024 application discloses the method above, wherein the step of identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the substrate comprises optically detecting a location on the surface of the substrate having a polypeptide attached thereto at which each of the affinity reagents binds (e.g., as per claims 212-214 of the ‘024 application).
Regarding claim 19, the claims of the ‘024 application discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the plurality of polypeptides on the surface of the substrate (e.g., as per claim 207 of the ‘024 application).
Regarding claim 20, the claims of the ‘024 application discloses the method above, wherein the step of characterizing the plurality of polypeptides on the surface of the substrate comprises quantifying each different polypeptide in the plurality of polypeptides on the surface of the substrate (e.g., as per claim 207 of the ‘024 application).
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Response to Arguments
The 02/26/2026 remarks argue: not all elements are taught.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
Specifically, the remarks argue that the amendments to claim 1 are not found in the claims of the reference patent application. In response, it is noted that the rejection has been modified to address said limitations.
U.S. 19/391,598
Claim 1-15 and 17-20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 31-58 of copending Application No. 19/391,598 (the ‘598 application). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding claim 1, the claims of the ‘598 application discloses a method of characterizing polypeptides, comprising providing a plurality of polypeptides attached to a surface of a substrate, with individual polypeptide molecules being attached at individually addressable locations on the substrate, sequentially contacting the polypeptides on the array with a plurality (e.g., 2 or more) of different affinity reagents, where each of the at least one hundred different affinity reagents comprises a binding affinity for a different epitope that is present in more than one of the plurality of polypeptides, separately detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate, and characterizing each of the plurality of polypeptide molecules based upon the different affinity reagents that bind to each of the polypeptide molecules (e.g., as per claim 31 of the ‘598 application). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claims 2-9, the claims of the ‘598 application discloses the method above, with a plurality (i.e., 2 or more) of polypeptides attached to the surface of the substrate (e.g., as per claims 31 and 42 of the ‘598 application). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claim 10, the claims of the ‘598 application discloses the method above, wherein the polypeptides are attached to the surface of the substrate through an intermediate (e.g., as per claim 34 of the ‘598 application).
Regarding claim 11, the claims of the ‘598 application discloses the method above, wherein the intermediate comprises a nanoparticle (e.g., as per claim 35 of the ‘598 application).
Regarding claim 12, the claims of the ‘598 application discloses the method above, wherein the intermediate comprises a nucleic acid molecule (e.g., as per claim 36 of the ‘598 application).
Regarding claim 13, the claims of the ‘598 application discloses the method above, wherein the individual polypeptide molecules are attached to the surface of the substrate within a plurality of nanowells on the surface of the substrate (e.g., as per claim 31 of the ‘598 application).
Regarding claim 14, the claims of the ‘598 application discloses the method above, wherein the affinity reagents are selected from the group consisting of: antibodies, antibody fragments and aptamers (e.g., as per claim 38 of the ‘598 application).
Regarding claim 15, the claims of the ‘598 application discloses the method above, wherein the separately detecting step comprises optically detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate (e.g., as per claim 45 of the ‘598 application).
Regarding claim 17, the claims of the ‘598 application discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the array to characterize each of the plurality of polypeptides on the surface of the substrate (e.g., as per claim 31 of the ‘598 application).
Regarding claim 18, the claims of the ‘598 application discloses the method above, wherein the step of identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the substrate comprises optically detecting a location on the surface of the substrate having a polypeptide attached thereto at which each of the affinity reagents binds (e.g., as per claim 45 of the ‘598 application).
Regarding claim 19, the claims of the ‘598 application discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the plurality of polypeptides on the surface of the substrate (e.g., as per claim 31 of the ‘598 application).
Regarding claim 20, the claims of the ‘598 application discloses the method above, wherein the step of characterizing the plurality of polypeptides on the surface of the substrate comprises quantifying each different polypeptide in the plurality of polypeptides on the surface of the substrate (e.g., as per claim 31 of the ‘598 application).
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Response to Arguments
The 02/26/2026 remarks argue: not all elements are taught.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
Specifically, the remarks argue that the amendments to claim 1 are not found in the claims of the reference patent application. In response, it is noted that the rejection has been modified to address said limitations.
10,473,654 B2
Claims 1-10 and 15-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-25 of U.S. Patent No. 10,473,654 B2 (the ‘654 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 1, the claims of the ‘654 patent discloses a method of characterizing polypeptides, comprising providing a plurality of polypeptides attached to a surface of a substrate, with individual polypeptide molecules being attached at individually addressable locations on the substrate, sequentially contacting the polypeptides on the array with a plurality (e.g., 2 or more) of different affinity reagents, where each of the at least one hundred different affinity reagents comprises a binding affinity for a different epitope that is present in more than one of the plurality of polypeptides, separately detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate, and characterizing each of the plurality of polypeptide molecules based upon the different affinity reagents that bind to each of the polypeptide molecules (e.g., as per claims 1 and 8 of the ‘654 patent). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claims 2-9, the claims of the ‘654 patent discloses the method above, with a plurality (i.e., 2 or more) of polypeptides attached to the surface of the substrate. (e.g., as per claim 1 of the ‘654 patent). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claim 10, the claims of the ‘654 patent discloses the method above, wherein the polypeptides are attached to the surface of the substrate through an intermediate (e.g., as per claim 13 of the ‘654 patent).
Regarding claim 15, the claims of the ‘654 patent discloses the method above, wherein the separately detecting step comprises optically detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate (e.g., as per claims 1 and 15 of the ‘654 patent).
Regarding claim 16, the claims of the ‘654 patent discloses the method above, wherein a plurality of the at least 100 different affinity reagents have a binding specificity to a different epitope of three, four or five consecutive amino acid residues (e.g., as per claim 6 of the ‘654 patent).
Regarding claim 17, the claims of the ‘654 patent discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the array to characterize each of the plurality of polypeptides on the surface of the substrate (e.g., as per claims 1-6 of the ‘654 patent).
Regarding claim 18, the claims of the ‘654 patent discloses the method above, wherein the step of identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the substrate comprises optically detecting a location on the surface of the substrate having a polypeptide attached thereto at which each of the affinity reagents binds (e.g., as per claims 1-6 of the ‘654 patent).
Regarding claim 19, the claims of the ‘654 patent discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the plurality of polypeptides on the surface of the substrate (e.g., as per claims 1-6 of the ‘654 patent).
Regarding claim 20, the claims of the ‘654 patent discloses the method above, wherein the step of characterizing the plurality of polypeptides on the surface of the substrate comprises quantifying each different polypeptide in the plurality of polypeptides on the surface of the substrate (e.g., as per claims 1-6 of the ‘654 patent).
***
Response to Arguments
The 02/26/2026 remarks argue: not all elements are taught.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
Specifically, the remarks argue that the amendments to claim 1 are not found in the claims of the reference patent. In response, it is noted that the rejection has been modified to address said limitations.
11,579,144 B2
Claims 1-10 and 15-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-25 of U.S. Patent No. 11,579,144 B2 (the ‘144 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 1, the claims of the ‘144 patent discloses a method of characterizing polypeptides, comprising providing a plurality of polypeptides attached to a surface of a substrate, with individual polypeptide molecules being attached at individually addressable locations on the substrate, sequentially contacting the polypeptides on the array with a plurality (e.g., 2 or more) of different affinity reagents, where each of the at least one hundred different affinity reagents comprises a binding affinity for a different epitope that is present in more than one of the plurality of polypeptides, separately detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate, and characterizing each of the plurality of polypeptide molecules based upon the different affinity reagents that bind to each of the polypeptide molecules (e.g., as per claims 1 and 8 of the ‘144 patent). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claims 2-9, the claims of the ‘144 patent discloses the method above, with a plurality (i.e., 2 or more) of polypeptides attached to the surface of the substrate. (e.g., as per claim 1 of the ‘144 patent). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claim 10, the claims of the ‘144 patent discloses the method above, wherein the polypeptides are attached to the surface of the substrate through an intermediate (e.g., as per claim 7 of the ‘144 patent).
Regarding claim 15, the claims of the ‘144 patent discloses the method above, wherein the separately detecting step comprises optically detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate (e.g., as per claim 8 of the ‘144 patent).
Regarding claim 16, the claims of the ‘144 patent discloses the method above, wherein a plurality of the at least 100 different affinity reagents have a binding specificity to a different epitope of three, four or five consecutive amino acid residues (e.g., as per claims 18-19 of the ‘144 patent).
Regarding claim 17, the claims of the ‘144 patent discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the array to characterize each of the plurality of polypeptides on the surface of the substrate (e.g., as per claim 1 of the ‘144 patent).
Regarding claim 18, the claims of the ‘144 patent discloses the method above, wherein the step of identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the substrate comprises optically detecting a location on the surface of the substrate having a polypeptide attached thereto at which each of the affinity reagents binds (e.g., as per claim 8 of the ‘144 patent).
Regarding claim 19, the claims of the ‘144 patent discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the plurality of polypeptides on the surface of the substrate (e.g., as per claim 1 of the ‘144 patent).
Regarding claim 20, the claims of the ‘144 patent discloses the method above, wherein the step of characterizing the plurality of polypeptides on the surface of the substrate comprises quantifying each different polypeptide in the plurality of polypeptides on the surface of the substrate (e.g., as per claim 1 of the ‘144 patent).
***
Response to Arguments
The 02/26/2026 remarks argue: not all elements are taught.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
Specifically, the remarks argue that the amendments to claim 1 are not found in the claims of the reference patent. In response, it is noted that the rejection has been modified to address said limitations.
11,754,559 B2
Claims 1-12 and 14-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-23 of U.S. Patent No. 11,754,559 B2 (the ‘559 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 1, the claims of the ‘559 patent discloses a method of characterizing polypeptides, comprising providing a plurality of polypeptides attached to a surface of a substrate, with individual polypeptide molecules being attached at individually addressable locations on the substrate, sequentially contacting the polypeptides on the array with a plurality (e.g., 2 or more) of different affinity reagents, where each of the at least one hundred different affinity reagents comprises a binding affinity for a different epitope that is present in more than one of the plurality of polypeptides, separately detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate, and characterizing each of the plurality of polypeptide molecules based upon the different affinity reagents that bind to each of the polypeptide molecules (e.g., as per claim 1 of the ‘559 patent). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claims 2-9, the claims of the ‘559 patent discloses the method above, with a plurality (i.e., 2 or more) of polypeptides attached to the surface of the substrate. (e.g., as per claim 1 of the ‘559 patent). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claim 10, the claims of the ‘559 patent discloses the method above, wherein the polypeptides are attached to the surface of the substrate through an intermediate (e.g., as per claim 4 of the ‘559 patent).
Regarding claim 11, the claims of the ‘559 patent discloses the method above, wherein the intermediate comprises a nanoparticle (e.g., as per claim 6 of the ‘559 patent).
Regarding claim 12, the claims of the ‘559 patent discloses the method above, wherein the intermediate comprises a nucleic acid molecule (e.g., as per claim 5 of the ‘559 patent).
Regarding claim 14, the claims of the ‘559 patent discloses the method above, wherein the affinity reagents are selected from the group consisting of: antibodies, antibody fragments and aptamers (e.g., as per claims 12-14 of the ‘559 patent).
Regarding claim 15, the claims of the ‘559 patent discloses the method above, wherein the separately detecting step comprises optically detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate (e.g., as per claims 16-18 of the ‘559 patent).
Regarding claim 16, the claims of the ‘559 patent discloses the method above, wherein a plurality of the at least 100 different affinity reagents have a binding specificity to a different epitope of three, four or five consecutive amino acid residues (e.g., as per claim 15 of the ‘559 patent).
Regarding claim 17, the claims of the ‘559 patent discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the array to characterize each of the plurality of polypeptides on the surface of the substrate (e.g., as per claims 1, 19, and 23 of the ‘559 patent).
Regarding claim 18, the claims of the ‘559 patent discloses the method above, wherein the step of identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the substrate comprises optically detecting a location on the surface of the substrate having a polypeptide attached thereto at which each of the affinity reagents binds (e.g., as per claims 16-18 of the ‘559 patent).
Regarding claim 19, the claims of the ‘559 patent discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the plurality of polypeptides on the surface of the substrate (e.g., as per claims 1, 19, and 23 of the ‘559 patent).
Regarding claim 20, the claims of the ‘559 patent discloses the method above, wherein the step of characterizing the plurality of polypeptides on the surface of the substrate comprises quantifying each different polypeptide in the plurality of polypeptides on the surface of the substrate (e.g., as per claims 1, 19, and 23 of the ‘559 patent).
***
Response to Arguments
The 02/26/2026 remarks argue: not all elements are taught.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
Specifically, the remarks argue that the amendments to claim 1 are not found in the claims of the reference patent. In response, it is noted that the rejection has been modified to address said limitations.
11,768,201 B2
Claims 1-12 and 14-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 11,768,201 B2 (the ‘201 patent). Although the claims at issue are not identical, they are not patentably distinct from each other because the rejected claims of the present invention would be anticipated and/or rendered obvious by the subject matter in the claims of the reference patent.
Regarding claim 1, the claims of the ‘201 patent discloses a method of characterizing polypeptides, comprising providing a plurality of polypeptides attached to a surface of a substrate, with individual polypeptide molecules being attached at individually addressable locations on the substrate, sequentially contacting the polypeptides on the array with at least one hundred different affinity reagents, where each of the at least one hundred different affinity reagents comprises a binding affinity for a different epitope that is present in more than one of the plurality of polypeptides, separately detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate, and characterizing each of the plurality of polypeptide molecules based upon the different affinity reagents that bind to each of the polypeptide molecules (e.g., as per claims 1 and 3 of the ‘201 patent). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claims 2-9, the claims of the ‘201 patent discloses the method above, wherein the plurality of polypeptides attached to the surface of the substrate comprises at least 100,000,000 individual polypeptides (e.g., as per claims 1 and 3-4 of the ‘201 patent). Note that in accordance with MPEP 2144.05(I), in the case where the claimed ranges “overlap or lie inside ranges disclosed by the prior art” a prima facie case of obviousness exists.
Regarding claim 10, the claims of the ‘201 patent discloses the method above, wherein the polypeptides are attached to the surface of the substrate through an intermediate.
Regarding claim 11, the claims of the ‘201 patent discloses the method above, wherein the intermediate comprises a nanoparticle (e.g., as per claim 7 of the ‘201 patent).
Regarding claim 12, the claims of the ‘201 patent discloses the method above, wherein the intermediate comprises a nucleic acid molecule (e.g., as per claim 7 of the ‘201 patent).
Regarding claim 14, the claims of the ‘201 patent discloses the method above, wherein the affinity reagents are selected from the group consisting of: antibodies, antibody fragments and aptamers (e.g., as per claims 9-11 of the ‘201 patent).
Regarding claim 15, the claims of the ‘201 patent discloses the method above, wherein the separately detecting step comprises optically detecting binding of each of the at least one hundred different affinity reagents to the individual polypeptide molecules on the substrate (e.g., as per claim 8 of the ‘201 patent).
Regarding claim 16, the claims of the ‘201 patent discloses the method above, wherein a plurality of the at least 100 different affinity reagents have a binding specificity to a different epitope of three, four or five consecutive amino acid residues (e.g., as per claim 1 of the ‘201 patent).
Regarding claim 17, the claims of the ‘201 patent discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the array to characterize each of the plurality of polypeptides on the surface of the substrate (e.g., as per claim 1 of the ‘201 patent).
Regarding claim 18, the claims of the ‘201 patent discloses the method above, wherein the step of identifying each of the at least one hundred different affinity reagents bound to each of the plurality of polypeptides on the surface of the substrate comprises optically detecting a location on the surface of the substrate having a polypeptide attached thereto at which each of the affinity reagents binds (e.g., as per claims 1 and 8 of the ‘201 patent).
Regarding claim 19, the claims of the ‘201 patent discloses the method above, wherein the step of characterizing each of the plurality of polypeptides on the surface of the substrate comprises identifying each of the plurality of polypeptides on the surface of the substrate (e.g., as per claim 1 of the ‘201 patent).
***
Response to Arguments
The 02/26/2026 remarks argue: not all elements are taught.
Applicant's arguments have been fully considered but they are not persuasive for at least the following reasons.
Specifically, the remarks argue that the amendments to claim 1 are not found in the claims of the reference patent. In response, it is noted that the rejection has been modified to address said limitations.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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 extension fee 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 date of this final action.
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/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684