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 .
DETAILED ACTION
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office Action.
Status of Claims
Claims 1, 5 and 22-39 are currently pending. Claims 1 and 5 have been amended by Applicants’ amendment filed 08-13-2026. Claims 22-39 have been added by Applicants’ amendment filed 08-13-2026. Claims 2-4 and 6-21 have been canceled by Applicants’ amendment filed 08-13-2026.
Applicant's election of Group I, claims 1 and 5, directed to a method of preparing an immobilized library of tagged fragments from a sample comprising RNA and DNA; and the election of Species as follows:
Species (A): Applicant failed to elect one of (a) to (c) (claim 5), in the reply filed May 5, 2026 was previously acknowledged.
Claims 2-4 and 6-21 were previously withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, there being no allowable generic or linking claim.
The restriction requirement was deemed proper and was made FINAL.
The claims will be examined insofar as they read on the elected species.
A complete reply to the final rejection must include cancellation of nonelected claims or other appropriate action (37 CFR 1.144) See MPEP § 821.01.
Therefore, claims 1, 5 and 22-39 are under consideration to which the following grounds of rejection are applicable.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on July 8, 2026 has been considered. An initialed copy of the IDS accompanies this Office Action.
Priority
The present application filed February 2, 2023 is a CON of 35 U.S.C. 371 national stage filing of International Application PCT/US21/44715, filed August 5, 2021, which claims the benefit US Provisional Patent Applications 63219014, filed July 7, 2021; 63168802, filed March 31, 2021; 63165830, filed March 25, 2021; and 63061885, filed August 6, 2020.
Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 120 as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of the first paragraph of 35 U.S.C. 112. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application 63168802, filed March 31, 2021, fails to provide adequate support or enablement in the manner provided by the first paragraph of 35 U.S.C. 112 for one or more claims of this application. The specific method steps recited in independent claim 1 does not have support for; combining a sample comprising RNA and DNA with a first solid support” and “combining a sample with a second solid support for immobilizing cDNA”; and “immobilizing the cDNA”. Therefore, the priority date for the presently claimed invention is July 7, 2021, the filing date of US Provisional Patent Application 63219014.
Applicants are invited to specifically indicate the location of the cited phrase pertinent to claim 1 of the instant application.
Withdrawn Objections/Rejections
Applicants’ amendment and arguments filed August 13, 2026 are acknowledged and have been fully considered. The Examiner has re-weighed all the evidence of record. Any rejection and/or
objection not specifically addressed below are herein withdrawn.
Maintained Objections/Rejections
Claim Rejections - 35 USC § 112(b)
The rejection of claims 1 and 5 is maintained, and claims 22-39 are newly rejected, under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 1 is indefinite for the recitation of the term “the tagged fragments” such as recited in claim 1, line 11. There is insufficient antecedent basis for the terms “the tagged fragments” in the claim because claim 1, line 1 recites the term “an immobilized library of tagged fragments”.
Claim 1 is indefinite for the recitation of the term “separating the tagged fragments from the sample” such as recited in claim 1, lines 11-12 because it is unclear why “performing tagmentation” does not encompass the broadly recited step of “separating” given that binding the DNA or cDNA to a solid support during tagmentation will separate the tagged DNA from the sample and, thus, the metes and bounds of the claim cannot be determined.
Claims 1, 5 and 29 are indefinite for the recitation of the terms “the RNA-specific barcode” such as recited in claim 1, lines 20-21 because the term “RNA-specific barcode” is defined in the as-filed Specification as an index for identifying RNA BLTs (RNA bead-linked transposomes) (See, paragraph [00447]). However, instant claim 1 recites that the “the RNA-specific barcode” is bound to double-stranded cDNA, and claim 1 does not recite the presence of beads, such that instant claim 1 does not appear to prepare tagged fragments comprising an “RNA-specific barcode” in accordance with the as-filed Specification and, thus, the metes and bounds of the claim cannot be determined.
Claims 26, 27, 29, 30 and 35 are indefinite for the recitation of the term “comprising” such as recited in claim 26, line 1 because claims 26, 27, 29, 30 and 35 depend from instant claim 1, wherein claim 1 already recites what the method of claim 1 “comprises” (e.g., combining, immobilizing, performing, separating, etc.), such that dependent claims 26, 27, 29, 30 and 35 cannot recite that the method of claim 1 ‘comprises’ something different (e.g., partitioning, adding, etc.) and, thus, the metes and bounds of the claim cannot be determined. The Examiner suggests that Applicant amend the claim to recite, for example, “the method of claim 1, further comprising”.
Claims 26, 29, 38 and 39 are indefinite for the recitation of the term “the immobilized tagged fragments” and/or “immobilized tagged fragments” such as recited in claim 26, lines 1-2. There is insufficient antecedent basis for the terms “the immobilized tagged fragments” and “immobilized tagged fragments” in the claim because claim 1, line 1 recites the term “tagged fragments”.
Claim 28 is indefinite for the recitation of the term “performed by template switching” such as recited in claim 28, line 2 because claim 28 depends from instant claim 1, wherein claim 1 does not recite that preparing double-stranded cDNA is “performed” and, thus, the metes and bounds of the claim cannot be determined. The Examiner suggests that Applicant amend claim 28 to recite, for example, wherein preparing double-stranded cDNA from the RNA comprises template switching”.
Claim 32 is indefinite for the recitation of the term “a single reaction vessel” such as recited in claim 32, lines 1-2 because claim 32 depends from instant claim 1, wherein claim 1 does not recite “performing the method”, and/or the presence of one or more reaction vessels including “a single reaction vessel” and, thus, the metes and bounds of the claim cannot be determined.
Claim 34 is indefinite for the recitation of the term “performed with a uracil-intolerant DNA polymerase” such as recited in claim 34, lines 1-2 because claim 34 depends from instant claims 1 and 5, wherein claims 1 and 5 do not recite that the step of “amplifying” is “performed” and/or that amplifying comprises an enzyme or a DNA polymerase and, thus, the metes and bounds of the claim cannot be determined.
Claim 34 is indefinite for the recitation of the term “uracil-intolerant” in claim 34, lines 1-2 because the term “uracil-intolerant” is a relative term that renders the claim indefinite. The term “uracil-intolerant” is not defined by the claim, and the Specification does not provide a standard for ascertaining the requisite amount of ‘intolerance’ or sensitivity the enzyme has as compared to some other value that qualifies it to be “uracil-intolerant” polymerase, such that one of ordinary skill in the art would not be reasonably appraised of the scope of the invention.
Claims 38 and 39 are indefinite for the recitation of the term “the immobilized tagged fragments” such as recited in claim 38, line 1. There is insufficient antecedent basis for the term “the immobilized tagged fragments” in the claim because claim 38 and 39 depend from instant claim 1, wherein claim 1 recites “an immobilized library of tagged fragments”.
Claims 38 and 39 are indefinite for the recitation of the terms “decreasing” and “increasing” such as recited in claim 38, line 2 because the terms “decreasing” and “increasing” are relative terms that render the claim indefinite. The terms “decreasing” and “increasing” are not defined by the claim, and the Specification does not provide a standard for ascertaining the requisite density of transposomes complexes as compared to some other value that qualifies as “decreasing” and/or “increasing” density, such that one of ordinary skill in the art would not be reasonably appraised of the scope of the invention. Moreover, claims 38 and 39 depend from instant claim 1, wherein claim 1 does not recite any specific density of transposome complexes and, thus, the metes and bounds of the claim cannot be determined.
Claims 22-25, 31, 33, 36 and 37 are indefinite insofar as they ultimately depend from instant claim 1.
Claim Rejections - 35 USC § 102
Please note: the references have been modified slightly in view of Applicant’s amendments and arguments, filed August 13, 2026.
The rejection of claims 1 and 5 is maintained, and claims 22-27, 29-33 and 35-39 are newly rejected, under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Gormley et al. (hereinafter “Gormley”) (US Patent Application Publication No. 20140194324, published July 10, 2014; of record) as evidenced by Ishino et al. (hereinafter “Ishino”) (Frontiers in Microbiology, 2014, 5(465), 1-8).
Regarding claim 1, Gormley teaches that the step of applying a target DNA comprises adding a biological sample to a solid support, wherein the biological sample can be any type that comprises DNA and which can be deposited onto the solid surface for tagmentation, wherein the biological sample comprises a mixture of DNA, protein, other nucleic acid species, other cellular components and/or any other contaminant present in approximately the same proportion as found in vivo (interpreted as combining a sample comprising DNA and RNA with a solid support, claim 1a) (paragraph [0062], lines 1-5 and 11-13). Gormley teaches methods and compositions useful for generating libraries of tagged DNA fragments for use, such as in next generation sequencing methods, and the like, wherein the invention relates to preparation of linear ssDNA fragments on a solid support from target DNA comprising any dsDNA of interest (including double-stranded cDNA prepared from RNA), from any source, for genomic, sub genomic, transcriptomic, or meta genomic analysis, or analysis of RNA expression (interpreted as preparing libraries of tagged fragments; sample comprising DNA and RNA; and preparing cDNA from RNA, claim 1) (paragraph [0004]). Gormley teaches that the method of preparing an immobilized library of tagged DNA fragments comprising: (a) providing a solid support having transposome complexes immobilized thereon (interpreted as a first and second solid support comprising transposome complexes immobilized thereon, claim 1a,e), wherein the transposome complexes comprise a transposase bound to a first polynucleotide, the first polynucleotide comprising (i) a 3' portion comprising a transposon end sequence, and (ii) a first tag comprising a first tag domain; and (b) applying a target DNA to the solid support under conditions whereby the target DNA is fragmented by the transposome complexes, and the 3' transposon end sequence of the first polynucleotide is transferred to a 5' end of at least one strand of the fragments; thereby producing an immobilized library of double-stranded fragments wherein at least one strand is 5'-tagged with the first tag including wherein the transposome complexes comprise a second polynucleotide comprising a region complementary to said transposon end sequence; and that the methods can further comprise (c) providing transposome complexes in solution and contacting the transposome complexes with the immobilized fragments under conditions whereby the target DNA is fragmented by the transposome complexes in solution; thereby obtaining immobilized nucleic acid fragments having one end in solution, such that the transposome complexes in solution can comprise a second tag, such that the method generates immobilized nucleic acid fragments having a second tag, the second tag in solution, wherein the first and second tags can be different or the same (interpreted as combining a sample with a first solid support and a second solid support comprising transposome complexes; immobilizing DNA; immobilizing cDNA; and comprising a DNA-specific barcode and an RNA-specific barcode, claims 1b, 1e and 1f) (paragraph [0005]). Gormley teaches that the terms "tag" and "tag domain" as used herein refer to a portion or domain of a polynucleotide that exhibits a sequence for a desired intended purpose or application (interpreted as DNA and RNA barcodes, claim 1) (paragraph [0049], lines 1-3). Gormley teaches that the barcoding method comprises providing a population of microparticles having transposome complexes immobilized thereto, the transposome complexes comprising a transposase bound to a first polynucleotide and second polynucleotide, such that the first polynucleotide comprises an index domain associated with the microparticle, wherein the index domain can be unique to the microparticle; and/or the population of microparticles comprises at least a plurality of index domains (interpreted as DNA-specific barcodes and RNA-specific barcodes, claim 1) (paragraph [0113]). Gormley teaches that the barcoding methods presented further comprise applying a target DNA to the population of microparticles, thereby generating immobilized DNA fragments that are tagged with the index domain, wherein DNA can be efficiently contacted with surface bound transposomes using any suitable method for increasing the probability of contact as discussed hereinabove, as exemplified by the incorporated materials Of WO 2010/115122 (interpreted as DNA-specific barcodes and RNA-specific barcodes, claim 1) (paragraph [0114]). Gormley teaches that Figure 2a illustrates a tagmentation reaction, wherein addition of DNA to the flowcell results in tagmentation and coupling of the DNA to the transposomes (interpreted as performing a tagmentation reaction, claim 1c,f) (paragraphs [0017]; [0019]; and Figures 2a and 3a).
Regarding claim 5, Gormley teaches that Figures 9-12 provide an illustration of transposomes assembled on the surface of paramagnetic beads, such that Figure 9 shows a bead surface with two different first polynucleotides immobilized thereto, wherein the first polynucleotides that are shown comprise a transposon end sequence (ME), such that one of the first polynucleotides shown in comprises a tag domain comprising an amplification primer sequence (P5) and a sequencing primer sequence (Read 1); and the other polynucleotide shown in Figure 9 comprises a different amplification primer sequence (P7) and a sequencing primer sequence (Read 2), wherein the first polynucleotides can also comprise an index tag, such that the index tag can be unique to the bead, or it can be shared with one or more other beads in the population, wherein a single bead can have only a single index tag immobilized thereto, or it can have a plurality of index tags immobilized thereto (interpreted as DNA-specific and RNA-specific barcodes; barcodes comprising different primer binding sequences; and amplifying tagged fragments using a primer that binds the primer binding sequence, claim 5) (paragraph [0102]; and Figures 9-12). Figure 9 is shown below:
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Gormley teaches that the methods, immobilizing comprises: (a) providing a solid support having amplification primers coupled thereto; (b) hybridizing a second polynucleotide to one of the amplification primers, the second oligonucleotide comprising a region complementary to a transposon end sequence and a region complementary to the first tag (interpreted as a barcode comprising a primer binding sequence); (c) extending the amplification primer using a polymerase to generate a duplex comprising the first polynucleotide hybridized to the second polynucleotide, the first polynucleotide immobilized directly to the solid support (interpreted as amplifying); and (d) contacting the solid support with transposase holoenzyme, thereby assembling a transposome complex on the solid support (interpreted as barcodes comprising different primer binding sequences; encompassing a uracil-intolerant polymerase, and amplifying tagged fragments using a primer that binds the primer binding sequence, claims 5 and 34) (paragraph [0008]), where it is known that Pfu polymerase from family B performs highly accurate PCR amplifications; and that archaeal family B DNA polymerases including Pfu DNA polymerase and KOD DNA polymerase are not suitable for carry-over prevention PCR as evidenced by Ishino (pg. 3, col 1, first full paragraph; and pg. 6, col 1, first full paragraph). Gormley teaches that any of the amplification methodologies described herein or generally known in the art can be utilized with universal or target-specific primers to amplify immobilized DNA fragments, wherein suitable methods for amplification include, but are not limited to, the polymerase chain reaction (PCR), strand displacement amplification (SDA), transcription mediated amplification (IMA) and nucleic acid sequence based amplification (NASBA) (interpreted as amplifying tagged fragments comprising the DNA-specific barcodes and/or RNA-specific barcodes, claim 5) (paragraph [0079], lines 1-8). Gormley teaches nucleic acid amplification methods such as Tagged PCR which uses a population of two-domain primers such as, for example, in Grothues et al. Nucleic Acids Res. 21(5):1321-2 (1993), incorporated herein by reference in its entirety (interpreted as a primer mixture comprising a primer that binds and DNA- or RNA-specific barcode, claim 5) (paragraph [0082], lines 3-7). Gormley teaches standard sample preparation methods, each template contains an adaptor at either end of the insert and often a number of steps are required to both modify the DNA or RNA and to purify the desired products of the modification reactions, wherein these steps are performed in solution prior to the addition of the adapted fragments to a flowcell (interpreted as separating tagged fragments comprising a DNA-specific barcode from the sample, claim 1) (paragraph [0038], lines 1-6). Gormley teaches that purified, partially purified or even unpurified intact DNA template can be loaded directly onto a flowcell for generation of clusters (interpreted as separating tagged fragments comprising a DNA-specific barcode from the sample, claim 1) (paragraph [0042], lines 3-6). Gormley teaches that DNA is physically linked to the surface of the flowcell so purification of reagents following further manipulation of the DNA can be achieved by flow-through buffer exchange in the flowcell channel (interpreted as separating tagged fragments comprising a DNA-specific barcode from the sample, claim 1) (paragraph [0042], lines 9-12). Gormley teaches assembling long reads using barcodes on immobilized transposomes comprising barcode-assisted assembly of DNA fragments enables isolation of individual long DNA molecules within a population of DNA molecules and conversion of each molecule into a uniquely barcoded sub-fragment library, such that when the entire population of sub-fragmented DNA molecules is sequenced, the sub-fragments can be assembled back into their original long molecule by reference to the barcodes they contain (interpreted as DNA-specific barcodes, claim 1) (paragraph [0110], lines 4-8).
Regarding claim 22, Gormley teaches that solid supports are comprised of an inert substrate or matrix (e.g. glass slides, polymer beads, etc.) which has been functionalized (interpreting the solid supports to include beads, claim 22) (paragraph [0051], lines 1-4). Gormley teaches that the solid support comprises microspheres or beads including small discrete particles (interpreting the solid supports to include beads, claim 22) (paragraph [0056], lines 1-6).
Regarding claim 23, Gormley teaches that the biological sample can comprise, for example, blood, plasma, serum, lymph, mucus, sputum, urine, semen, cerebrospinal fluid, bronchial aspirate, feces, and macerated tissue, or a lysate thereof, or any other biological specimen comprising DNA (interpreting the sample to include blood, claim 22) (paragraph [0063], lines 1-5).
Regarding claims 24 and 25, Gormley teaches that the biological sample can comprise, for example, a crude cell lysate or whole cells (interpreting the sample to include cell lysate and crude cell lysate, claims 24 and 25) (paragraph [0062], lines 25-27).
Regarding claim 26, Gormley teaches that because the methods provided herein allow DNA to be bound to a solid support, other contaminants can be removed merely by washing the solid support after surface bound tagmentation occurs (interpreted as partitioning the immobilized DNA from the sample after tagmentation, claim 26) (paragraph [0062], lines 22-25).
Regarding claim 27, Gormley teaches that the biological sample can be added to the flowcell and subsequent lysis and purification steps can all occur in the flowcell without further transfer or handling steps, simply by flowing the necessary reagents into the flowcell (interpreted as partitioning the immobilized fragments before tagmentation, claim 27) (paragraph [0062], lines 22-25). Gormley teaches that the plurality of target DNA molecules is flowed onto a flowcell comprising a plurality of nano-channels, the nano-channel having a plurality of transposome complexes immobilized thereto, wherein transposomes bound to the surface of a nano-channel tagment the DNA (interpreting flowing DNA through separate nanochannels as partitioning the immobilized DNA from the rest of the sample before tagmentation, claim 27) (paragraph [0074], lines 1-4 and 17-18).
Regarding claim 29, Gormley teaches that Figure 15 illustrates transfer of barcoded tagged molecules to a sequencing reaction, such that once the tagmentation is complete the DNA is transferred from the bead surface to solution so that individual fragments can be pooled and prepared for sequencing (interpreted as combining the solid supports after performing tagmentation, claim 29) (paragraph [0121], lines 1-5; and Figure 15).
Regarding claim 30, Gormley teaches that double stranded DNA is added to the solid support, the transposome complexes will tagment added DNA, thus generating ds fragments coupled at both ends to the surface (interpreted as adding dsDNA to the first solid support after tagmentation, claim 30) (paragraph [0059], lines 1-4).
Regarding claim 31, Gormley teaches that the immobilized double stranded fragments are further fragmented to liberate a free end (see FIG. 4a) prior to cluster generation, wherein cleaving bridged structures can be performed using any suitable methodology as is known in the art, as exemplified by the incorporated materials of WO 2012/025250, such that cleavage can occur by incorporation of a modified nucleotide, such as uracil as described in WO2012/025250, by incorporation of a restriction endonuclease site (interpreted as dsDNA comprising a uracil, claim 31) (paragraph [0073]).
Regarding claim 32, Gormley teaches that tagmentation and other downstream processing such as PCR amplification can all be performed in a single tube, vessel, droplet or other container (interpreted as performing tagmentation in a single reaction vessel, claim 32) (paragraph [0100], lines 29-32).
Regarding claim 33, Gormley teaches that the transposome complexes are present on the solid support at a density of at least 103, 104, 105, 106 complexes per mm2 (interpreted as encompassing a density of at least 103 complexes per mm2, claim 33) (paragraph [0012]).
Regarding claim 35, Gormley teaches that transposome adaptor sequences can contain sequences that enable subsequent cluster generation and sequencing (interpreted as sequencing, claim 35) (paragraph [0041], lines 11-13).
Regarding claim 36, Gormley teaches that the products of solid-phase amplification reactions such as those described in U.S. Pat. Nos. 7,985,565 and 7,115,400 are so-called "bridged" structures formed by annealing of pairs of immobilized polynucleotide strands and immobilized complementary strands, both strands being immobilized on the solid support at the 5' end via a covalent attachment (interpreted as bridge amplification, claim 36) (paragraph [0077]).
Regarding claim 37, Gormley teaches that the transposome complex comprises a hyperactive transposase, such as Tn5 transposase (interpreted as Tn5 transposase, claim 37) (paragraph [0012]).
Regarding claims 38 and 39, Gormley teaches that the length of bridged fragments can be varied by changing the density of the transposome complexes on the surface (interpreted as varying the length of the fragments by modulating the density, claims 38 and 39) (paragraph [0059], lines 4-6). Gormley teaches that the density of these surface bound transposomes can be modulated by varying the density of the grafted oligonucleotides containing the ME sequence or by the amount of transposase added to the solid support (interpreted as adjusting the density of transposomes on solid supports, claims 38 and 38) (paragraph [0058], lines 6-9; and Figure 1).
Gormley does not specifically exemplify template switching (claim 28); and (uracil-intolerant DNA polymerase (claim 34).
Gormley meets all the limitations of the claims and, therefore, anticipates the claimed invention.
Response to Arguments
Applicant’s arguments filed August 13, 2026 have been fully considered but they are not persuasive. Applicants essentially asserts: (a) Gromley does not disclose “a sample comprising RNA and DNA, wherein the tagged fragments comprise either a DNA-specific barcode or an RNA-specific barcode; and that independent claim 1 recites that the DNA specific barcode and the RNA-specific barcode serve to identify whether fragments originated from DNA or RNA within a sample comprising both DNA and RNA (Applicant Remarks, pg. 3, first full paragraph); (b) Gormley does not teach "combining a sample comprising RNA and DNA with a first solid support for immobilizing DNA," and/or the claimed workflow of performing tagmentation, separating, preparing, and combining (Applicant Remarks, pg. 3, last partial paragraph through pg. 4, first partial paragraph); and (c) Gormley is silent with respect to "(d) separating the tagged fragments comprising a DNA-specific barcode from the sample; and (e) preparing double-stranded cDNA from the RNA" (Applicant Remarks, pg. 4, first full paragraph).
Regarding (a), although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26USPQ2d 1057 (Fed. Cir. 1993). Moreover, as noted in MPEP 2112.01(I),
where the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990).
Applicant’s assertion that Gromley does not disclose “a sample comprising RNA and DNA, wherein the tagged fragments comprise either a DNA-specific barcode or an RNA-specific barcode; and that claim 1 recites that the DNA specific barcode and the RNA-specific barcode serve to identify whether fragments originated from DNA or RNA within a sample comprising both DNA and RNA, is not found persuasive. As an initial matter, instant claim 1 does not recite that the DNA specific barcode and the RNA-specific barcode serve to identify whether fragments originated from DNA or RNA within a sample. The Examiner respectfully requests that Applicant specifically point to this limitation in instant claim 1.
Moreover, the as-filed Specification defines the term “RNA-specific barcode” to refer to an index for identifying RNA bead linked transposomes (RNA BLTs); and the term “DNA-specific barcode” to refer to an index for identifying DNA BLTs (the Examiner notes, however, that instant claim 1 does not recite the presence of beads). Additionally, Gormley teaches:
Assembling long reads using barcodes on immobilized transposomes using barcode-assisted assembly of DNA fragments, wherein each molecule is uniquely barcoded sub-fragment library, such that when the entire population of sub-fragmented DNA molecules is sequences, the sub-fragments can be assembled back into their original long molecules (interpreted as DNA comprising DNA-specific barcodes, and RNA comprising RNA-specific barcodes, claim 1) (paragraph [0110]).
Target DNA comprising any dsDNA of interest (including double-stranded cDNA prepared from RNA), from any source, for genomic, sub-genomic, transcriptomic, or meta-genomic analysis, or analysis of RNA expression (interpreted as a sample comprising RNA, cDNA, and DNA) (paragraph [0004]).
Transposome complexes comprising a transposase bound to a first polynucleotide and a second polynucleotide (interpreted as an RNA polynucleotide and a DNA polynucleotide) (paragraphs [0005]; and [0009]).
A first polynucleotide comprises a first tag and a second polynucleotide comprises a second tag, wherein the first tag and the second tag can be different or the same (interpreted as RNA that comprises RNA-specific barcodes; and DNA that comprises DNA-specific barcodes) (paragraphs [0005]).
wherein the terms "tag" and "tag domain" as used herein refer to a portion or domain of a polynucleotide that exhibits a sequence for a desired intended purpose or application (interpreted as barcodes) (paragraph [0049], lines 1-3).
A first polynucleotide comprising an index domain associated with the microparticle and a second polynucleotide; applying a target DNA to the population of microparticles (interpreted as DNA comprising DNA-specific barcodes) (paragraph [0010]).
wherein the index tag can be unique to a bead (interpreting unique index tags on a bead as DNA comprising DNA-specific barcodes) (paragraph [0102], lines 11-12).
Gormley clearly teaches a sample comprising RNA and DNA; DNA-specific barcodes; and RNA-specific barcodes. Thus, the claims remain rejected.
Regarding (b), Applicant’s assertion that Gormley does not teach "combining a sample comprising RNA and DNA with a first solid support for immobilizing DNA," and/or the claimed workflow of performing tagmentation, separating, preparing, and combining, is not found persuasive. Regarding the claimed workflow, Applicant’s argument merely repeats the steps of the method without distinctly and specifically pointing out the supposed errors in the Examiner’s action as required by 37 CFR 1.111(b). Thus, the claims remain rejected for the reasons already of record. It is noted that the steps are not recited to occur in any particular order and/or with any specific timing.
For additional clarity, please see the discussion supra regarding DNA, RNA and specific-barcodes. Moreover, instant claim 1 uses the term “comprising”, which is open-ended and does not exclude additional, unrecited elements or method steps, including carrying out the steps of the method using a sample comprising both DNA and/or RNA. Regarding tagmentation, Gormley teaches:
Methods and compositions for nucleic acid sample preparation on a solid support, wherein a solid support can be a bead or particle (interpreted as combining a sample with a solid support) (paragraphs [0004], lines 1-2; and [0056], lines 3-6).
Target DNA comprising any dsDNA of interest (including double-stranded cDNA prepared from RNA), from any source, for genomic, sub-genomic, transcriptomic, or meta-genomic analysis, or analysis of RNA expression (interpreted as a sample comprising RNA, cDNA, and/or DNA) (paragraph [0004]).
Figure 2a illustrates a tagmentation reaction, wherein addition of DNA to the flowcell results in tagmentation and coupling of the DNA to the transposomes (interpreted as performing a tagmentation reaction; and separating the tagged fragments from the sample, claim 1) (paragraphs [0017]; [0019]; and Figures 2a and 3a).
Gormley teaches all of the limitations in the claims. Thus, the claims remain rejected.
Regarding (c), please see the discussion supra regarding the Examiner’s response to Applicant’s arguments, and the teachings of Gormley including the use of the term “comprising”. Additionally, Gormley teaches:
Standard sample preparation methods, each template contains an adaptor at either end of the insert and often a number of steps are required to both modify the DNA or RNA and to purify the desired products of the modification reactions, wherein these steps are performed in solution prior to the addition of the adapted fragments to a flowcell (interpreted as separating tagged fragments comprising a DNA-specific barcode from the sample, claim 1) (paragraph [0038], lines 1-6).
Purified, partially purified or even unpurified intact DNA template can be loaded directly onto a flowcell for generation of clusters (interpreted as separating tagged fragments comprising a DNA-specific barcode from the sample, claim 1) (paragraph [0042], lines 3-6).
DNA is physically linked to the surface of the flowcell so purification of reagents following further manipulation of the DNA can be achieved by flow-through buffer exchange in the flowcell channel (interpreted as separating tagged fragments comprising a DNA-specific barcode from the sample, claim 1) (paragraph [0042], lines 9-12).
Gormley teaches all of the limitations in the claims. Thus, the claims remain rejected.
Claim Rejections - 35 USC § 103
Please note: the references have been modified slightly in view of Applicant’s amendments and arguments, filed August 13, 2026.
The rejection of claims 1 and 5 is maintained, and claims 22-39 are newly rejected, under 35 U.S.C. 103 as being unpatentable over Gormley et al. (hereinafter “Gormley”) (US Patent Application Publication No. 20140194324, published July 10, 2014; of record) in view of Reuter et. al. (hereinafter “Reuter”) (US patent Application Publication No. 20180080021, published March 22, 2018; of record) as evidenced by Ishino et al. (hereinafter “Ishino”) (Frontiers in Microbiology, 2014, 5(465), 1-8).
The teachings of Gormley as applied to claims 1, 5, 22-27, 29-33 and 35-39 are described supra.
Gormley does not specifically exemplify additional primer mixes (claim 5, in part); template switching (claim 28); and (uracil-intolerant DNA polymerase (claim 34).
Regarding claim 5 (in part), Reuter teaches methods, compositions, and kits for simultaneously generating RNA and DNA sequencing libraries are disclosed including methods that allow high-throughput amplification and sequencing of both RNA and DNA from a single sample source without the need to divide the sample to separate nucleic acids from each other, wherein all of the preparation steps from harvesting nucleic acids from cells or tissue to preparing RNA and DNA sequencing libraries can be performed with the RNA and DNA pooled together, such that this technology streamlines generation of DNA and RNA sequencing data in combination and makes possible comprehensive genomic and transcriptomic profiling of a cell population concurrently (interpreted as a sample comprising RNA and DNA, claim 1) (Abstract). Reuter teaches that index or barcode sequences can be added to amplicon products to identify whether an amplicon was derived from DNA or RNA and the sample source from which each amplified nucleic acid originated, wherein index/barcode sequences can be used to distinguish amplicons derived from genomic DNA from amplicons derived from RNA (i.e., cDNA) to allow pooling of DNA and RNA from the same sample for high-throughput amplification and sequencing, such as a "DNA index sequence" can be used to identify DNA sequences and an "RNA index sequence" can be used to identify RNA sequences (interpreted as DNA-specific barcodes or RNA-specific barcodes, claim 5) (paragraph [0086], lines 1-11). Reuter teaches that an index/barcode sequence can be added during amplification by carrying out PCR with a primer that contains a region comprising the index/barcode sequence and a region that is complementary to an oligonucleotide adapter sequence (e.g., RNA-specific adapter attached to RNA fragment by ligation or DNA-specific adapter attached to DNA fragment by tagmentation) already ligated to the nucleic acid such that the index/barcode sequence is incorporated into the final amplified nucleic acid product, wherein index/barcode sequences can be added at one or both ends of an amplicon (interpreted as DNA-specific barcodes or RNA-specific barcodes comprising a primer binding sequence, claim 5) (paragraph [0086], lines 23-33). Reuter teaches that oligonucleotides, particularly primer or probe oligonucleotides for amplification or sequencing, can be coupled to labels for detection, such that there are several means known for derivatizing oligonucleotides with reactive functionalities which permit the addition of a label (paragraph [0087], lines 1-5). Reuter teaches quantifying the presence of both DNA-seq and RNA-seq libraries in the pool using droplet digital PCR (ddPCR) (interpreted as amplifying tagged fragments, claim 5) (paragraph [0112], lines 4-6). Reuter teaches that DNA libraries were amplified using standard Nextera indexing primers (interpreted as a primer mix, claim 5) (paragraph[0138], lines 45-46). Reuter teaches PCR reaction to enrich cDNA using custom multiplex primers (interpreted as a primer mix, claim 5) (paragraph [0254]).
Regarding claim 28, Reuter teaches that SIMUL-SEQ incorporates dual 5' and 3' indices specific for both DNA and RNA molecules, minimizing cross contamination due to spurious ligation and tagmentation or from template switching during pooled PCR (interpreted as preparing cDNA from RNA via template switching, claim 28) (paragraph [0109], lines 16-20).
Regarding claim 34, Reuter teaches that DNA and cDNA can be amplified prior to sequencing using any suitable polymerase chain reaction technique known in the art (interpreted as encompassing a uracil-intolerant polymerase, claim 34) (paragraph [0076], lines 1-3). Reuter teaches that polymerases include Thermococcus litoralis (Vent polymerase) (interpreted as encompassing a uracil-intolerant polymerase, claim 34) (paragraph [0078], lines 14-15).
It is prima facie obvious to combine prior art elements according to known methods to yield predictable results; the court held that, "…a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. KSR International Co. v. Teleflex Inc., 550 U.S. ___, ___, 82 USPQ2d 1385, 1395 (2007); Sakraida v. AG Pro, Inc., 425 U.S. 273, 282, 189 USPQ 449, 453 (1976); Anderson’s-Black Rock, Inc. v. Pavement Salvage Co., 396 U.S. 57, 62-63, 163 USPQ 673, 675 (1969); Great Atlantic & P. Tea Co. v. Supermarket Equipment Corp., 340 U.S. 147, 152, 87 USPQ 303, 306 (1950)”. Therefore, in view of the benefits of comprehensive genomic and transcriptomic profiling exemplified by Reuters, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of using immobilized transposase and a transposon end for generating an immobilized library of tagged double-stranded target fragments as disclosed by Gormley, to include methods for high-throughput amplification and sequencing as taught by Reuter with a reasonable expectation of success in simultaneously generating RNA and DNA sequencing libraries from the same sample; in generating 5’- and 3’-tagged fragments for massively parallel sequencing; and/or in using index/barcode sequences to quantify the presence of both DNA-seq and RNA-seq libraries in a mixture of nucleic acids.
Thus, in view of the foregoing, the claimed invention, as a whole, would have been obvious to one of ordinary skill in the art at the time the invention was made. Therefore, the claims are properly rejected under 35 USC §103(a) as obvious over the art.
Response to Arguments
Applicant’s arguments filed August 13, 2026 have been fully considered but they are not persuasive. Applicants essentially asserts: (a) Gormley fails to anticipate independent claim 1 as discussed above in the § 102 section, independent claim 1 is not rendered obvious over Gormley in view of Reuter; and Gormley fails to teach the features recited in claim 1 as indicated supra (Applicant Remarks, pg. 6, first and second full paragraphs).
Regarding (a), please see the discussion supra regarding Applicant’s assertions, the Examiner’s response to Applicant’s arguments, and the teachings of Gormley. Thus, the claims remain rejected.
New Objections/Rejections
Claim Objection
Claim 33 is objected to because of the following informalities: Claim 33 recites the term "mm2”, where an abbreviation should be spelled out in the first encounter of the claims.
Appropriate correction is required.
Conclusion
Claims 1, 5 and 22-39 are rejected.
THIS ACTION IS MADE FINAL. 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 AMY M BUNKER whose telephone number is (313) 446-4833. The examiner can normally be reached on Monday-Friday (6am-2:30pm).
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/AMY M BUNKER/Primary Examiner, Art Unit 1684
