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 .
Office Action: Notice
Any objection or rejection of record in the previous Office Action, mailed 12/22/2025, which is not addressed in this action has been withdrawn in light of Applicants' amendments and/or arguments. This action is FINAL.
Claim Status
Claims 2-20 are under examination (3/20/2026). Applicant amended claims 2 and 5 (3/20/2026). Claims 10-20 are withdrawn from consideration (10/21/2025).
Election/Restrictions
Applicant’s election with traverse of Group I in the reply filed on March 20, 2025 is acknowledged. Claims 10-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected Group 2, there being no allowable generic or linking claim.
Applicant’s species election in the reply filed on 10/21/2025 is acknowledged. Applicant’s species election was made with traverse of five species; (1) Contamination-resistant adapters (claims 6 and 19): Species 1: ACA1-A5 and (2) Contamination-resistant adapters basic arrangement (claims 9 and 20): Species 1: ACA1.
In response to the Applicant’s arguments against undue burden, the restriction is maintained because the elected Group 1. Applicant’s argument has been considered, but is not persuasive. As set forth in the Requirement for Restriction/Election (8/21/2025), Group 1 is directed to method claims for preparing a DNA library, whereas Group 2 is directed to composition claims reciting a DNA library capture kit, and the groups do not share a common technical feature that makes a contribution over the prior art. Accordingly, claims 10-20 do not overcome the lack of unity identified, and the restriction requirement between Groups 1 and 2 is maintained. Rejoinder will be considered if the elected composition claims are found allowable and the nonelected claims depend therefrom.
Priority
Claims 2-9 receive a priority date of 6/25/2019, the effective filing date of Chinese Provisional Patent CN201910555735.3.
Objections Withdrawn
Specification:
The objections to the specification due to the use of a trademark or tradenames are withdrawn in view of Applicant’s amendments.
The objection to the specification due to the absence of “Brief Description of Drawings” is withdrawn in view of Applicant’s amendments.
Rejections Withdrawn
Claim Rejections - 35 USC § 112(b)
The rejections of claims 2-9 under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, 2nd paragraph, are withdrawn in view of Applicant’s amendments of claims 2 and 5, to address antecedent basis issues.
Claim Rejections – 35 USC § 102
The 102 (a) (1) and 102 (a) (2) rejections of claims 2-3 and 5 are withdrawn in view of Applicant’s arguments and amendments (3/20/2026). Specifically, newly amended independent claim 2 clarifies that the recited 3’ extra bases are added to a first original adapter at its 3’ end and the recited 5’ extra bases are added to a second original adapter at the 5’ end. In view of the amendment, Shalek no longer expressly discloses each and every limitation of claim 2 arranged as claimed, and therefore the rejection under 35 USC 102 is withdrawn.
New Rejections
Claim Rejections - 35 USC § 103
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 (i.e., changing from AIA to pre-AIA ) 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.
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 text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
The factual inquiries 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.
Claims 2-9 are rejected under 35 U.S.C. 103 as being unpatentable over Shalek et al. (WO 2019/084058 A2; published 5/2/2019), in view of Seidman et al. (US PGPub 2014/0199284 A1; published 7/17/2014), Liu et al. (US PGPub 2014/0234289 A1; published 8/21/2014), Vogelstein et al. (US PGPub 2014/0227705 A1; published 8/14/2014) and Fan et al. (US PGPub 2018/0044724 A1; published 2/15/2018).
Regarding claims 2-3, Shalek teaches functionalized solid supports and methods of making functionalized solid supports, including methods for preparing a population of high quality functionalized solid supports for use in various nucleic acid analysis methods (Abstract). Further, Shalek teaches a drop-sequence method and apparatus providing a high-throughput single-cell RNA-Seq and/or targeted nucleic acid profiling (for example, sequencing, quantitative reverse transcription polymerase chain reaction, and the like) where the RNAs from different cells are tagged individually, allowing a single library to be created while retaining the cell identity of each read (Paragraph 200, lines 1-5). Further, Shalek teaches a plurality of nucleic acid molecules being sequenced is bound to a support (e.g., functionalized solid support described herein) in order to immobilize the nucleic acid on a support, a capture sequence/universal priming site can be added at the 3' and/or 5' end of the template where the nucleic acids may be bound to the support by hybridizing the capture sequence to a complementary sequence covalently attached to the support and the capture sequence (also referred to as a universal capture sequence) is a nucleic acid sequence complementary to a sequence attached to a support that may dually serve as a universal primer (Paragraph 195, lines 1-10). Specifically, Shalek teaches that RNA-Seq profiling of single cells may be performed on any number of cells, including tumor cells, associated infiltrating cells into a tumor, immune derived cells, microglia, astrocytes, CD4 cells, CD8 cells, most preferably Thl7 cells (Paragraph 227, lines 1-5). Further, Shalek teaches that the background template is most often inadvertent and it may be the result of carryover, or it may be due to the presence of nucleic acid contaminants sought to be purified away from the sample (Paragraph 171, lines 5-10). Shalek also teaches that nucleic acid tags can be sequentially ligated to create a sequence reflecting conditions and order of same. Alternatively, the tags can be added independently appended to solid support (Paragraph 219, lines 10-15).
Additionally, Shalek teaches that in order to immobilize the nucleic acid on a support, a capture sequence/universal priming site can be added at the 3' and/or 5' end of the template, where the nucleic acids may be bound to the support by hybridizing the capture sequence to a complementary sequence covalently attached to the support and the capture sequence (also referred to as a universal capture sequence) is a nucleic acid sequence complementary to a sequence attached to a support that may dually serve as a universal primer where the universal primer sequence is synthesized at the 3' end of the oligonucleotide sequences bound to the solid support to enable stoichiometric addition of diverse oligonucleotide capture sequences to mRNA capture beads (Paragraph 195, lines 1-10).
Shalek also teaches that a nucleic acid identifier can further include a unique molecular identifier and/or additional barcodes or bases specific to, for example, a common support to which one or more of the nucleic acid identifiers are attached and thus, a pool of target molecules can be added, for example, to a discrete volume containing multiple solid or semisolid supports (Paragraph 178, lines 1-5). Notably, Shalek teaches that the previously described purified composition is not intended to mean that some trace impurities may remain and purified refers to molecules, such as nucleic acid sequences, that are removed from their natural environment, isolated or separated, and are at least 60%> free, preferably 75% free, and more preferably 90% free from other components with which they are naturally associated (Paragraph 160, lines 10-20).
Regarding claim 5, Shalek teaches that the previously described method can be applied to include proteins with post translational modifications including but not limited to phosphorylation, methionine oxidation, deamidation, glycosylation, ubiquitination, carbamylation, s-carboxymethylation, acetylation, and methylation (Paragraph 217, lines 50-60). Further, Shalek teaches that during these oligonucleotide generation cycles, beads were removed from the synthesis column, pooled, and aliquoted into four equal portions by mass; these bead aliquots were then placed in a separate synthesis column and reacted with either dG, dC, dT, or dA phosphoramidite (Paragraph 218, lines 40-50). In other instances, dinucleotide, trinucleotides, or oligonucleotides that are greater in length are used, in other instances, the oligo-dT tail is replaced by gene specific oligonucleotides to prime specific targets (singular or plural), random sequences of any length for the capture of all or specific RNAs (Paragraph 218, lines 40-50; Figure 5K). Shalek also teaches that it is envisioned as to or in the practice of the invention provides that there can be a method for preparing uniquely barcoded mRNA capture microbeads, which has a unique barcode and diameter suitable for microfluidic devices which may comprise: 1) performing reverse phosphoramidite synthesis on the surface of the bead in a pool-and-split fashion, such that in each cycle of synthesis the beads are split into four reactions with one of the four canonical nucleotides (T, C, G, or A) or unique oligonucleotides of length two or more bases (Paragraph 207, lines 30-50).
As described above, and regarding claims 4 and 6-9, Shalek teaches functionalized solid supports and methods of making functionalized solid supports, including methods for preparing a population of high quality functionalized solid supports for use in various nucleic acid analysis methods (Abstract). Further, Shalek teaches a drop-sequence method and apparatus providing a high-throughput single-cell RNA-Seq and/or targeted nucleic acid profiling (for example, sequencing, quantitative reverse transcription polymerase chain reaction, and the like) where the RNAs from different cells are tagged individually, allowing a single library to be created while retaining the cell identity of each read (Paragraph 200, lines 1-5). Further, Shalek teaches a plurality of nucleic acid molecules being sequenced is bound to a support (e.g., functionalized solid support described herein) in order to immobilize the nucleic acid on a support, a capture sequence/universal priming site can be added at the 3' and/or 5' end of the template where the nucleic acids may be bound to the support by hybridizing the capture sequence to a complementary sequence covalently attached to the support and the capture sequence (also referred to as a universal capture sequence) is a nucleic acid sequence complementary to a sequence attached to a support that may dually serve as a universal primer (Paragraph 195, lines 1-10).
Further, Shalek teaches that during these oligonucleotide generation cycles, beads were removed from the synthesis column, pooled, and aliquoted into four equal portions by mass; these bead aliquots were then placed in a separate synthesis column and reacted with either dG, dC, dT, or dA phosphoramidite (Paragraph 218, lines 40-50). Shalek also teaches that it is envisioned as to or in the practice of the invention provides that there can be a method for preparing uniquely barcoded mRNA capture microbeads, which has a unique barcode and diameter suitable for microfluidic devices which may comprise: 1) performing reverse phosphoramidite synthesis on the surface of the bead in a pool-and-split fashion, such that in each cycle of synthesis the beads are split into four reactions with one of the four canonical nucleotides (T, C, G, or A) or unique oligonucleotides of length two or more bases (Paragraph 207, lines 30-50).
Further, Shalek teaches mixtures for use in described technologies may comprise a plurality of solid support compositions, for example, microbeads, adorned with combinations of the following elements: bead-specific oligonucleotide barcodes; additional oligonucleotide barcode sequences which vary among the oligonucleotides on an individual bead and can therefore be used to differentiate or help identify those individual oligonucleotide molecules; additional oligonucleotide sequences that create substrates for downstream molecular-biological reactions, such as oligo-dT (for reverse transcription of mature mRNAs), specific sequences (for capturing specific portions of the transcriptome, or priming for DNA polymerases and similar enzymes), or random sequences (for priming throughout the transcriptome or genome) (Paragraph 211, lines 1-10). Shalek also teaches that in one example, each library element may comprise a different bead, wherein each bead is attached to a number of antibodies and the bead is encapsulated within a droplet that contains a different antibody in solution (Paragraph 224, lines 50-75).
Shalek does not teach or suggest the original adapters set forth in ADM-A5 and ADM-A7 as phosphorylation-based modifications, the contamination-resistant adapter ACA1-A5 or related basic arrangements, or the amplification primers Oligo PPS 1.1 or Oligo PPS 2.1.
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Seidman teaches diagnostic markers and methods for identifying a subject having an increased susceptibility for developing or having dilated cardiomyopathy, including determining if the subject has specified mutations (Abstract). Seidman further teaches SEQ ID NO: 684, a synthetic oligonucleotide, having 100% similarity as the sequence set forth in ADM-A5 and ACA1-A5 of the instant application, as shown below.
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Liu teaches an in vitro selection method that interrogates DNA sequences for their ability to be cleaved by active, dimeric nucleases, specifically engineered nucleases (zinc-finger) for genome manipulation (Abstract). Liu further teaches SEQ ID NO: 182, a synthetic oligonucleotide, having 100% similarity as the sequence set forth in ADM-A7 of the instant application, as shown below.
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Vogelstein teaches the identification of mutations that are present in a small fraction of DNA templates as progress for biomedical research, specifically through massively parallel sequencing instruments (Abstract). Further Vogelstein teaches SEQ ID NO: 81, an artificial primer or adaptor, with 100% similarity as the sequence set forth in Oligo PPS 1.1, as shown below.
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Fan teaches methods of DNA amplification mediated by DNA ligase, specifically a method of amplifying a target region at DNA level, which comprises repeating cycles of amplification (Abstract). Further, Fan teaches SEQ ID NO: 11, a synthetic sequence with 100% similarity match as the sequence set forth in Oligo PPS 2.1, as shown below.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine the teachings of Shalek with Seidman, Liu, Vogelstein and Fan. Specifically, Shalek teaches preparing sequencing libraries using functionalized solid supports and barcoded oligonucleotides for multiplexed nucleic acid analysis, while Vogelstein and Fan teach defined adapter and primer sequences for massively parallel sequencing and amplification, including sequences identical to those of the instant application. Seidman and Liu further teach synthetic oligonucleotides and adapter sequences used in nucleic acid amplification and sequencing workflows. One of ordinary skill in the art would have been motivated to combine these teachings to merely known and validated adapter and primer sequences within Shalek’s library preparation methods to achieve predictable amplification and sequencing results, including the incorporation of known two-base phosphorylation modifications as taught by Shalek. Because the cited references operate within the same technical field and utilized compatible nucleic acid chemistries, including ligation, phosphorylation, and primer-mediated amplification, a person of ordinary skill in the art would have had a reasonable expectation of success in making the combination. Therefore, combining these references together represents the use of known sequencing adapters and primers within an established library preparation framework, yielding predictable results, and would have been obvious at the time of the invention.
Further, it would have been obvious to one of ordinary skill in the art at the time of the invention to modify the library preparation methods of Shalek with the adapter and primer sequences taught by Seidman, Liu, Vogelstein, and Fan. Shalek teaches preparation of sequencing libraries utilizing oligonucleotide identifiers, barcodes, variable nucleotide additions, and pool-and-split synthesis techniques to generate populations of related oligonucleotide constructs differing by one or more nucleotides selected from the canonical bases. Specifically, the amended limitation (3/20/2026), requiring addition of two or three extra bases to an original adapter merely defines a particular implementation of the variable nucleotide additions taught by Shalek and would have represented no more than predictable use of known nucleotide modification techniques to generate distinguishable adapter variants. Specifically, selection of particular bases, numbers of bases, or proportions of bases from among the four canonical nucleotides constitutes optimization of a result-effective variable and would have been within the routine skill of the ordinary artisan seeking to generate a desired level of sequence diversity while maintaining sequencing combability.
Seidman and Liu teach adapter sequences corresponding to the claimed original adapters, while Vogelstein and Fan teach known amplification primer and adapter sequences used in sequencing workflows. A person of ordinary skill in the art would have recognized such terminal nucleotide additions as a routine design choice for generating distinguishable adapter variants suitable for multiplex sequencing applications. Further, one of ordinary skill in the art would have been motivated to incorporate such known adapter sequences into Shalek’s sequencing framework and modify the adapter termini through nucleotide additions as taught by Shalek in order to generate distinct adapter variants suitable for multiplexed sequencing and sample identification, with a reasonable expectation of success because the references employ compatible nucleic acid chemistries, adapter ligation techniques, phosphorylation modifications, and amplification methodologies.
Applicant’s Response: The Applicant argues that Shalek’s oligonucleotide sequences function as barcodes, capture probes, and universal primer sites rather than contamination-resistant adapters derived from original adapter pairs and therefore do not teach the claimed adapter architecture. Applicant further contends that the cited references fail to teach or suggest the claimed controlled adapter diversity, contamination-preventions strategy, bioinformation contamination-identification workflow, and specific contamination-resistant adapter arrangements disclosed in the application.
Examiner’s Response to Traversal: Applicant’s arguments have been carefully and fully considered and are found partially persuasive, as discussed below.
Although the Applicant contends that Shalek’s oligonucleotide sequences function as barcodes, capture probes, or universal primer sites rather than contamination-resistant adapters, claim 2 does not require any particular contamination-identification protocol, contamination-removal process, bioinformatic analysis, or specific use of the modified adapters. Rather, claim 2 broadly recites adding extra bases to original adapters at the 3’ and 5’ ends to generate modified adapter variants. Shalek teaches generating distinguishable oligonucleotide variants through the addition of nucleotides, including dinucleotides and trinucleotides, while the remaining references teach the claimed adapter and primer sequences. Thus, even assuming Shalek’s identifiers are characterized as barcodes rather than contamination-resistant adapters, it would have been obvious to apply Shalek’s nucleotide-addition techniques to the known adapter sequences taught by the secondary references to obtain the claimed modified adapter constructs. The amendment specifying that the extra bases are added to a fist original adapter at its 3’-end and to a second original adapter at its 5’-end merely identifies the location of the nucleotide additions on known adapter sequences and would have represented a predictable variation of the combined teachings. Further, the Applicant’s arguments regarding controlled diversity, contamination prevention, bioinformatic analysis, mutation identification, and cross-contamination detection are likewise not commensurate in scope with the pending claims, as such features are not positively recited.
Notably, the Applicant’s arguments regarding contamination-resistant adapter functionality are not commensurate in scope with the pending claims, which broadly recite the addition of extra bases to original adapters. The designation “contamination-resistant” utilized in independent claim 2 does not impart structural limitations beyond those positively recited in the claim, and patentability is determined based on the recited adapter structure and method steps, rather than the intended purpose or asserted advantage attributed to those adapters. To overcome this rejection, Applicant may amend the claims to recite the contamination-identification, contamination-tracking, or contamination-elimination features, workflows or analysis steps/arrangements relied upon in the arguments.
Conclusions
No claim is 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 ELIZABETH ROSE LAFAVE whose telephone number is (703)756-4747. The examiner can normally be reached Compressed Bi-Week: M-F 7:30-4:30.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at 571-272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ELIZABETH ROSE LAFAVE/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684
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