DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Application
The Response to Non-Final Office Action filed October 2, 2025 is acknowledged.
Claims 11-12, 14-25 and new claims 26-29 are pending. Claims 11-12 and 14-25 are being examined on the merits. Claims 26-29 are newly withdrawn.
Response to Arguments
Applicant’s arguments filed October 2, 2025 have been fully considered.
The following rejections are MAINTAINED:
Prior art rejections
Double patenting
Response to arguments regarding prior art rejections
Applicant argues that the prior art rejections of independent claims 11 and 17, in particular, should be withdrawn for several reasons (Remarks, p. 5).
Specifically, Applicant argues the inconsistent positions that, first, the Office Action mailed April 10, 2025 “fails to address the feature of ‘discrete individual volumes’ as a whole”, and second, that the droplets of Ji, which were cited in the Office Action as the “discrete individual volumes”, are not equivalent to the instant “individual discrete volumes”. More specifically, Applicant argues that the droplets of Ji “are present only prior to the formation of any optically encoded particles, and are the precursors to the optically encoded particles” (Remarks, pp. 5-6; emphasis in original). Applicant additionally argues that, in the instant claims, “the optically encoded particles have already been made, and these particles are used to optically encode the discrete individual volumes” in contrast to the teachings of Ji (Remarks, p. 6). Finally, Applicant argues that the secondary references do not cure the deficiencies of Ji as to the “individual discrete volumes” issue (Remarks, p. 6).
As to the first argument, the Examiner disagrees. The limitation is addressed in the Office Action mailed April 10, 2025 as to claim 11 on p. 4, last para., and as to claim 17 on p. 8, para. 2.
As to the second argument, the Examiner also disagrees. As noted in the Office Action mailed April 10, 2025 and below, Ji teaches encapsulation of quantum dots (i.e., assigning … optically encoded particles) into volumes of alginate solution which are solidified into hydrogel microbeads (i.e., individual discrete volumes). The instant claims do not require that the “individual discrete volumes” and the “optically encoded particles” be created in some particular order (e.g., that the optically encoded particles “have been made already”). Further, Applicant’s argument seems to imply that the Ji hydrogel microbead can only be construed as being part of the “optically encoded particle” and cannot be construed as being the “individual discrete volume” itself. However, the Examiner disagrees that Ji should be read so narrowly. While the Ji composition of the hydrogel microbead plus quantum dot could be used downstream in a [second] “individual discrete volume”, the hydrogel microbead can itself be considered a [first] “individual discrete volume”. Stated differently, a quantum dot can be encapsulated in a first individual discrete volume of a hydrogel microbead and then that hydrogel microbead plus quantum dot composition could be added to a second individual discrete volume of a well in a microplate. The instant claims are not limited to the latter embodiments only.
These arguments are not persuasive. The rejections are maintained.
Double patenting rejection
Applicants did not file a terminal disclaimer or otherwise respond to the double patenting rejections. In addition, none of Applicant’s arguments as to prior art rejections are relevant to the double-patenting rejection (i.e., the rejection is not based on an issued patent in view of the teachings of a secondary reference cited as the basis of a prior art rejection). Accordingly, Applicant’s reply is non-responsive as to the double-patenting rejection. However, in view of MPEP 714.03 and in the interest in advancing examination, Applicant’s reply is considered a bona fide reply which is substantially complete, and is being examined accordingly.
The rejection is maintained.
Election/Restrictions
Newly submitted claims 26-29 are directed to an invention that is independent or distinct from the invention originally claimed for the following reasons: The subject matter of the group of claims 11-12 and 14-25 and the group of claims 26-29 are directed to related methods. The related inventions are distinct if: (1) the inventions as claimed are either not capable of use together or can have a materially different design, mode of operation, function, or effect; (2) the inventions do not overlap in scope, i.e., are mutually exclusive; and (3) the inventions as claimed are not obvious variants. See MPEP § 806.05(j). In the instant case, the inventions as claimed have a materially different design, mode or operation, function, or effect, in that the claim 11 group is directed to optically encoding discrete reaction volumes, while the claim 26 group is directed to identifying nucleic acid molecules in discrete reaction volumes. Furthermore, the inventions as claimed do not encompass overlapping subject matter and there is nothing of record to show them to be obvious variants. Thus, the invention of the claim 11 group is a complete and distinction invention, and applicant has received an action on the merits for that invention.
Since applicant has received an action on the merits for the originally presented invention, this invention has been constructively elected by original presentation for prosecution on the merits. Accordingly, claims 26-29 are withdrawn from consideration as being directed to a non-elected invention. See 37 CFR 1.142(b) and MPEP § 821.03.
To preserve a right to petition, the reply to this action must distinctly and specifically point out supposed errors in the restriction requirement. Otherwise, the election shall be treated as a final election without traverse. Traversal must be timely. Failure to timely traverse the requirement will result in the loss of right to petition under 37 CFR 1.144. If claims are subsequently added, applicant must indicate which of the subsequently added claims are readable upon the elected invention.
Should applicant traverse on the ground that the inventions are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing the inventions to be obvious variants or clearly admit on the record that this is the case. In either instance, if the examiner finds one of the inventions unpatentable over the prior art, the evidence or admission may be used in a rejection under 35 U.S.C. 103 or pre-AIA 35 U.S.C. 103(a) of the other invention.
Claim Rejections - 35 USC § 103
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.
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.
Claims 11-12 and 14-15 are rejected under 35 U.S.C. 103 as being unpatentable over Ji1 (Integrated parallel microfluidic device for simultaneous preparation of multiplex optical-encoded microbeads with distinct quantum dot barcodes, J Mater Chem, 21, 13380-13387, 2011) in view of Han2 (Quantum-Dot-Tagged Microbeads for Multiplexed Optical Coding of Biomolecules, Nat Biotechnol, 19, 631-635, 2001).
Regarding independent claim 11, Ji teaches …
A method for optically encoding individual discrete volumes comprising: assigning a set
of optically encoded particles to individual discrete volumes (Fig. 6; abstract: “preparation of quantum dot-encoded microbeads with controllable barcodes … formation of corresponding droplets [i.e., discrete volumes]”; p. 13381, left col., para. 3 through right col., para. 1: “preparation of QD [quantum dot]-encoded microbeads with controllable barcodes … microbeads … are employed as matrix to encapsulate QDs for barcoding … single-colored encoding with a five-level stepwise gradient in concentrations of monochromatic QDs or two-colored encoding with five controllable ratios of two different-sized QDs”);
Ji also teaches that the set of optically encoded particles comprises distinct particles, and teaches that each distinct particle can be identified (Fig. 6d), but Ji does not teach that each distinct particle comprises at least one nucleic acid particle identifier that identifies that distinct particle within the set of optically encoded particles. However, Han teaches this limitation. Specifically, Han teaches an embodiment with three optically encoded particles, each with a unique target-specific probe attached to the particle (Figs. 5-6; probes 1-4). Each particle type can thus be distinguished based on the sequence identity of the probe. Consequently, then the limitation requiring that an observable pattern of the distinct particles (i.e., the probes) within the set of optically encoded particles in each discrete volume allows each discrete volume to be independently identified (Figs. 5-6; probes 1-4).
Finally, regarding the limitation requiring that the set of optically encoded particles comprises 2 to 500 distinct particles, it is noted that Ji teaches that the set of optically encoded particles comprises distinct particles, and teaches that each distinct particle can be identified (Fig. 6d; also see p. 13386, left col., para. 1: teaches two color barcoding with composite gradients of quantum dots, where the different quantum dots have fluorescent peaks that avoid spectral overlapping – thus Ji teaches at least two distinct particles).
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to modify the Ji method to incorporate the unique nucleic acid particle identifiers of Han. Ji teaches that optical barcoding using fluorescence-encoded beads is useful for highly multiplexed detection of nucleic acids (e.g., gene expression). The ordinary artisan would have been motivated to incorporate unique nucleic acid particle identifiers into the Ji method in order to achieve the expected advantage of being able to incorporate an additional unique identifier into the assay which would improve the combinatorial coding and analysis capability even further. The ordinary artisan would have had an expectation of success as the design and optimization of nucleic acid detection assays is well-known in the art.
Regarding dependent claims 12 and 14-15, Ji additionally teaches that the optically encoded particles are a microsphere/microbead, a quantum dot or a hydrogel bead (p. 13381, left col., para. 3 through right col., para. 1), as recited in claim 12, Ji further teaches optically detecting a combination of optically-encoded particles delivered to each discrete volume, specifically capturing one or more images in one or more channels corresponding to the optically encoded particles (Figs. 4c, 6b, 6d), as recited in claims 14 and 15, respectively.
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Ji (Integrated parallel microfluidic device for simultaneous preparation of multiplex optical-encoded microbeads with distinct quantum dot barcodes, J Mater Chem, 21, 13380-13387, 2011) in view of Han (Quantum-Dot-Tagged Microbeads for Multiplexed Optical Coding of Biomolecules, Nat Biotechnol, 19, 631-635, 2001) as applied to claim 11 above, and further in view of Bharadwaj3 (US Patent App. Pub. No. 2015/0292988).
Regarding dependent claim 16, Han teaches distributing a nucleic acid containing
specimen to the individual discrete volume, and hybridizing one or more oligonucleotides (specifically, a probe) to one or more target sequences in the nucleic acid containing specimen (Fig. 5). Bharadwaj teaches that the oligonucleotide is a primer (para. 33).
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to further modify the modified Ji method, discussed above, to incorporate the target sequence and primer of Han and Bharadwaj. Ji teaches that optical barcoding using fluorescence-encoded beads is useful for highly multiplexed detection of nucleic acids (e.g., gene expression). The ordinary artisan would have been motivated to incorporate the target nucleic acid into the Ji method to achieve the expected advantage of creating a high throughput and efficient method for detecting nucleic acids. The ordinary artisan would have been additionally motivated to incorporate a primer into this method in order to achieve the expected advantage of being able to incorporate an additional sequence into the target nucleic acid amplicon (e.g., using a primer comprising a barcode to incorporate a barcode into the amplicon) which would improve the combinatorial coding and analysis capability even further. The ordinary artisan would have had an expectation of success as the design and optimization of nucleic acid detection assays is well-known in the art.
Claims 17-25 are rejected under 35 U.S.C. 103 as being unpatentable over Ji (Integrated parallel microfluidic device for simultaneous preparation of multiplex optical-encoded microbeads with distinct quantum dot barcodes, J Mater Chem, 21, 13380-13387, 2011) in view of Han (Quantum-Dot-Tagged Microbeads for Multiplexed Optical Coding of Biomolecules, Nat Biotechnol, 19, 631-635, 2001).
Regarding independent claim 17, Ji teaches …
A method for optically encoding individual discrete volumes comprising: incorporating
particles into optically encoded particles, and distributing a set of the optically encoded particles to individual discrete volumes (Fig. 6; abstract: “preparation of quantum dot-encoded microbeads with controllable barcodes … formation of corresponding droplets [i.e., discrete volumes]”; p. 13381, left col., para. 3 through right col., para. 1: “preparation of QD [quantum dot]-encoded microbeads with controllable barcodes … microbeads … are employed as matrix to encapsulate QDs for barcoding … single-colored encoding with a five-level stepwise gradient in concentrations of monochromatic QDs or two-colored encoding with five controllable ratios of two different-sized QDs”).
Ji does not teach associating the particles with optically-labeled nucleic acids. However,
Han suggests this limitation, and specifically teaches that the nucleic acids are probes (Fig. 5). Specifically, Han teaches an embodiment with three optically encoded particles, each with a unique target-specific probe attached to the particle (Figs. 5-6; probes 1-4). Each particle type can thus be distinguished based on the sequence identity of the probe. Han also teaches labeling DNA molecules directly with a fluorescent dye (p. 634, right col., para. 1).
Finally, regarding the limitation requiring that the set of optically encoded particles comprises 2 to 500 distinct particles, it is noted that Ji teaches that the set of optically encoded particles comprises distinct particles, and teaches that each distinct particle can be identified (Fig. 6d; also see p. 13386, left col., para. 1: teaches two color barcoding with composite gradients of quantum dots, where the different quantum dots have fluorescent peaks that avoid spectral overlapping – thus Ji teaches at least two distinct particles).
Prior to the effective filing date of the instant invention, it would have been prima facie
obvious to modify the Ji method to incorporate the optically-labeled nucleic acids of Han. Ji teaches that optical barcoding using fluorescence-encoded beads is useful for highly multiplexed detection of nucleic acids (e.g., gene expression). The ordinary artisan would have been motivated to incorporate additional identifiers into the Ji method in order to achieve the expected advantage of being able to improve the combinatorial coding and analysis capability even further. The ordinary artisan would have had an expectation of success as the design and optimization of nucleic acid detection assays is well-known in the art.
Regarding dependent claims 18 and 22-23, Ji additionally teaches that the particles are a microsphere/microbead, a quantum dot or a hydrogel bead (p. 13381, left col., para. 3 through right col., para. 1), as recited in claim 18. Ji further teaches optically detecting a combination of optically-encoded particles delivered to each discrete volume, specifically capturing one or more images in one or more channels corresponding to the optically encoded particles (Figs. 4c, 6b, 6d), as recited in claims 22 and 23, respectively.
Regarding dependent claim 19, Ji also teaches that the set of optically encoded particles comprises distinct types of particles, and teaches that each distinct type of particle within the set can be uniquely identified (Fig. 6d), but Ji does not teach that each distinct type of particle within the set of optically encoded particles comprises at least one unique nucleic acid particle identifier that identifies that distinct particle type within the set of optically encoded particles. However, Han teaches this limitation. Specifically, Han teaches an embodiment with three optically encoded particles, each with a unique target-specific probe attached to the particle (Figs. 5-6; probes 1-4). Each particle type can thus be distinguished based on the sequence identity of the probe. Consequently, then the limitation requiring that the observable pattern of the one or more nucleic acid particle identifier of each distinct type of particle (i.e., the probes) within the set of optically encoded particles in each discrete volume allows each discrete volume to be independently identified (Figs. 5-6; probes 1-4).
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to further modify the modified Ji method, discussed above, to incorporate the unique nucleic acid particle identifiers of Han. Ji teaches that optical barcoding using fluorescence-encoded beads is useful for highly multiplexed detection of nucleic acids (e.g., gene expression). The ordinary artisan would have been motivated to incorporate unique nucleic acid particle identifiers into the Ji method in order to achieve the expected advantage of being able to incorporate an additional unique identifier into the assay which would improve the combinatorial coding and analysis capability even further. The ordinary artisan would have had an expectation of success as the design and optimization of nucleic acid detection assays is well-known in the art.
Regarding dependent claims 20-21 and 24, Han teaches or suggests mixing functionalized particles with optically-labeled nucleic acids, and annealing the mixture (Figs. 5-6; probes 1-4; p. 634, right col., para. 1), as recited in claim 20. Ji and Han both teach using distinct ratios of one or more optical labels (Ji: Figs. 5-6; p. 13382, right col., para. 2; p. 13386, left col., para. 1; Han: Figs. 5-6; abstract; p. 633, right col., para. 2), as recited in claim 21. Finally, Ji teaches that the particle is a hydrogel (p. 13381, left col., para. 3 through right col., para. 1), as recited in claim 24.
Regarding dependent claim 25, Han teaches distributing a nucleic acid containing
species to the individual discrete volume, and hybridizing the labeled nucleic acids (specifically, a probe) to one or more target sequences in the nucleic acid containing species (Fig. 5).
Prior to the effective filing date of the instant invention, it would have been prima facie obvious to further modify the modified Ji method, discussed above, to incorporate the annealing steps, target sequence and unique probe of Han. Ji teaches that optical barcoding using fluorescence-encoded beads is useful for highly multiplexed detection of nucleic acids (e.g., gene expression). The ordinary artisan would have been motivated to incorporate the target nucleic acid into the Ji method to achieve the expected advantage of creating a high throughput and efficient method for detecting nucleic acids. The ordinary artisan would have been additionally motivated to incorporate a unique probe into this method in order to achieve the expected advantage of being able to incorporate an additional unique identifier into the assay which would improve the combinatorial coding and analysis capability even further. The ordinary artisan would have had an expectation of success as the design and optimization of nucleic acid detection assays is well-known in the art.
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 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); 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 nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 11-12, 14-19, 22-23 and 25 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2, 13 and 16 of U.S. Patent No. 11,421,270 (hereinafter, the ‘270 patent).
Although the claims at issue are not identical, they are not patentably distinct from each other because claims 1 and 16 of the ’270 patent teaches all of the limitations of instant claims 11 and 17, although in different embodiments. More specifically, claim 1 of the ’270 patent is directed to a method for multiplex screening of nucleic acid sequence variations comprising, in part, dispensing a solution comprising a set of optically-encoded particles to one or more discrete volumes, each of which also comprises a sample with target nucleic acids. The optically-encoded particles each have one or more primers of a same primer type associated with them. Each primer of the same primer type has a particle identifier that identifies the type of optically-encoded particle.
Instant independent claims 11 and 17 are directed to a method for optically encoding individual discrete volumes, using a set of optically-encoded particles, as with claim 1 of the ‘270 patent. Instant claim 11 also requires distinct types of optically-encoded particles where each comprises at least one unique nucleic acid particle identifier (e.g., a primer), where the pattern of the at least one unique identifier in each discrete volume allows that discrete volume to be independently identified. Thus, the instant claims 11 and 17 method of optically encoding individual discrete volumes are embodiments comprised within the “dispensing” clause of the ‘270 patent claim 1 method for multiplex screening of nucleic acid sequence variations.
In addition, claims 13, 1, 2, 1, 13, 1, 1, 2 and 1 of the ‘270 patent teach all of the limitations of instant claims 12, 14, 15, 16, 18, 19, 22, 23 and 25, respectively.
Modifying the ‘270 patent embodiments by re-arranging method steps to create different embodiments of the step of optically encoding individual discrete volumes would have been prima facie obvious to the ordinary artisan, as they would have been motivated to optimize the embodiment through routine experimentation to customize the embodiment as desired for a particular assay. The ordinary artisan would have had an expectation of success as nucleic acid assay design is well-known in the art. Thus, instant claims 12-16, 18, 19, 22-23 and 25 are not patentably distinct from claims 1-2 and 13 of the ‘270 patent.
Conclusion
Claims 11-12 and 14-25 are being examined, and are rejected. 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 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CAROLYN GREENE whose telephone number is (571)272-3240. The examiner can normally be reached M-Th 7:30-5:30 EST.
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/CAROLYN L GREENE/Examiner, Art Unit 1681 /GARY BENZION/Supervisory Patent Examiner, Art Unit 1681
1 Ji was cited in the PTO-892 Notice of References Cited mailed March 27, 2024.
2 Han was cited in the PTO-892 Notice of References Cited mailed March 27, 2024.
3 Bharadwaj was cited in the Information Disclosure Statement submitted November 30, 2022.