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 .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-11, 14, 17, 20, 34, 38-39, 44, and 50 in the reply filed on April 20th, 2026 is acknowledged.
Claim 66 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on April 20th, 2026.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on July 29th, 2022, October 2nd, 2025, April 20th, 2026, and April 21st, 2026 are acknowledged. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Status
Claims 1-11, 14, 17, 20, 34, 38-39, 44, 50, and 66 are pending. Claim 66 is withdrawn from consideration as being withdrawn to a non-elected invention. Claims 12-13, 15-16, 18-19, 21-33, 35-37, 40-43, 45-49, 51-65, and 67-88 have been canceled. Claims 1-11, 14, 17, 20, 34, 38-39, 44, and 50 are under examination and discussed in this Office Action.
Claim Objections
Claims 1, 6, and 11 are objected to because of the following informalities:
In line 8 of claim 1, the word “target binding” should instead read “target-binding”. The claim inconsistently hyphenates the term throughout its limitation.
In line 6 of claim 6 is the word “acid” is missing between the word “nucleic” and “molecules”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 34 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 34 recites “the oligonucleotide barcode comprises an identical sample label, and/or an identical cell label.” The use of “and/or” is unclear which of the following distinct scopes the claim is intended to cover: a) an oligonucleotide barcode comprising an identical sample label only; b) an oligonucleotide barcode comprising an identical label only; or c) an oligonucleotide barcode comprising both an identical sample label and an identical cell label.
Claim 34 is further rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite. The term “identical” is used as a modifier for both “sample label” and “cell label” but the claim does not establish any reference point to which these labels are identical. The claim does not specify whether “identical” means: a) identical across all oligonucleotide barcodes in the plurality; b) identical within the oligonucleotide barcodes on a single synthetic particle or bead; or c) identical to some other unspecified reference sequence. Claim 9, from which claim 34 depends, introduces “a plurality of oligonucleotide barcodes” but does not establish any reference against which the sample label or cell label could be identical.
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 1-11, 14, 17, 20, 34, 38-39, 44, and 50 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of copending Application No. 11365409 in view of Shiroguchi et al (Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes, Proc. Natl. Acad. Sci. U.S.A. 109 (4) 1347-1352, https://doi.org/10.1073/pnas.1118018109 (2012)), Kurihara et al (US 10155942 B2; published December 18th, 2018), and Hindson (WO2014210353A2; published December 31st, 2014).
Although the claims at issue are not identical, they are not patentably distinct from each other because both the ‘409 and the instant application claim a method for analyzing or determining the number of a nucleic acid target in a sample comprising barcoding copies of the nucleic acid target using a plurality of oligonucleotide barcodes each comprising a molecular label and a target-binding region; attaching an oligonucleotide comprising a complement of the target-binding region to the barcoded nucleic acid molecules; intramolecularly hybridizing the target-binding region and the complement of the target-binding region within each of the barcoded nucleic acid molecules; extending the 3’-ends of the hybridized barcoded nucleic acid molecules to generate extended barcoded nucleic acid molecules each comprising the molecular label and a complement of the molecular label; and determining the number of the nucleic acid target based on distinct molecular label sequences associated with the extended barcoded nucleic acid molecules.
Instant claims 1 and 9 does not recite the limitation “wherein at least 10 of the plurality of oligonucleotide barcodes comprise different molecular label sequences” which is required in claim 1 and 8 of the ‘409 application. This difference makes instant claims 1 and 9 broader in scope than claims 1 and 8 of the ‘409 application.
Instant claims 1 and 9 specifies that attaching the oligonucleotide comprising the complement of the target-binding region to the barcoded nucleic acid molecules comprises ligating that oligonucleotide to the barcode nucleic acid molecules. Claims 1 and 8 of the ‘409 application recites only “attaching” without specifying the attachment method. This difference does not create patentable distinction. Shiroguchi teaches barcoded Y-shaped adapters were randomly ligated to both ends of phosphorylated Cdna fragments prior to PCR amplification and sequencing (Fig. 1; p. 1348, left column, para 3). A person of ordinary skill in the art would have found it obvious to perform the “attaching” step of claims 1 and 8 of the ‘409 application via ligation as taught by Shiroguchi, since ligation is the standard means for covalent attachment of oligonucleotides to nucleic acid molecules in this field and no unexpected results would arise from its use.
Instant claims 1 and 9 further recites “intramolecularly hybridizing the target-binding region and the complement of the target-binding region within each of the plurality of barcoded nucleic acid molecules” without reciting the formation of a stem loop. Claims 1 and 8 of ‘409 application requires “hybridizing the target-binding region and the complement of the target-binding region within each of the plurality of barcoded nucleic acid molecules to form a stem loop” This difference does not create patentable distinction. Intramolecular hybridization between a target-binding region and its completement on the same nucleic acid molecule necessarily and inherently produces a step-loop structure. The outcome of the hybridization step is identical whether or not it is explicitly named. Kurihara teaches that coupling oligonucleotide adaptors comprising complementary inverted repeat sequences to nucleic acid molecules produces molecules that form stem-loop structures upon intramolecular hybridization to those complementary regions (claim 1; column 2, para 2; column 3, para 2). The omission of the words “stem loop” from instant claims 1 and 9 does not create a patentably distinct scope from claim 1 and 8 of the ‘409 application when the recited method steps produce the same result.
Instant claim 1 and 9 further recites “extending 3’-ends of the plurality of intramolecularly hybridized barcoded nucleic acid molecules to generate a plurality of extended barcoded nucleic acid molecules each comprising the molecular label and a complement of the molecular label” Claims 1 and 8 of the ‘409 application recites “extending 3’-ends of the plurality of barcoded nucleic acid molecules to extend the stem loop to generate a plurality of extended barcoded nucleic acid molecules each comprising the molecular label and a complement of the molecular label.” This difference does not create a patentable distinction. The 3’-end of an intramolecularly hybridized barcoded nucleic acid molecules is the 3’-end of the stem formed by hybridization of the target-binding region and its complement. Extension from the 3’-end is equivalent to extending the stem loop as recited in claims 1 and 8 of the ‘409 application. Kurihara teaches that extension from the 3’-end of a molecule comprising an intramolecular stem-loop structure via nick translation or strand displacement polymerization through the stem region generates a complement of the barcode sequence on the same molecule (claim 1; column 8, para 4). This directly establishes the equivalence of the extending step in instant claims 1 and 9 and the extending step in claims 1 and 8 of the ‘409 application.
Instant claim 2 and 3 depend from instant claim 1 and add the step of determining the number of the nucleic acid target based on the number of molecular labels with distinct sequences, complements thereof, or a combination thereof (claim 2), or based on the number of complements of complements of molecular labels with distinct sequences (claim 3). Claim 2 and 3 of the ‘409 application add the same limitations and depend from claim 1 of the ‘409 application. The claim language is substantively identical.
Instant claim 4 depends from instant claim 1 and adds the limitations that barcoding the copies comprises contacting copies of the nucleic acid target to the plurality of oligonucleotide barcodes wherein each barcode comprises the target-binding region capable of hybridizing to the nucleic acid target, and extending the copies of the nucleic acid target hybridized to the oligonucleotide barcodes to generate the plurality of barcoded nucleic acid molecules. Claim 4 of the ‘409 application adds the same limitation and depends from claim 1 of the ‘409 application. The claim language is substantively identical.
Instant claim 5 depends from instant claim 1 and adds the limitation that at least 10 of the plurality of oligonucleotide barcodes comprise different molecular label sequences. Claim 1 of the ‘409 application recites this limitation as part of the independent claim. When instant claim 5 is read together with instant claim 1 from which it depends, the combined scope of instant claims 1 and 5 is substantively the same as claim 1 of the ‘409 application.
Instant claim 6 depends from instant claim 1 and adds the steps of amplifying the plurality of barcoded nucleic acid molecules to generate a plurality of amplified barcoded nucleic acid molecules, wherein attaching the oligonucleotide comprising the complement of the target- binding region. Claim 5 of the ‘409 application adds the same limitations and depends from claim 1 of ‘409 application. The claim language is substantively identical.
Instant claim 7 depends from instant claim 2 and adds amplification of the extended barcoded nucleic acid molecules to generate a plurality of single-labeled nucleic acid molecules. Claim 6 of the ‘409 application adds the same limitations and depends from claim 2 of the ‘409 application. The claim language is substantively identical.
Instant claim 8 depends from instant claim 2 and adds amplification to generate copies of the plurality of extended barcoded nucleic acid molecules with determining based on the number complements of molecular labels with distinct sequences associated with those copies. Claim 7 of the ‘409 application adds the same limitations and depends from claim 2 of the ’409 application. The claim language is substantively identical.
Instant claim 10 depends from instant claim 9 and adds the limitation that the molecular label is hybridized to the complement of the molecular label after extending the 3’- ends of the plurality of barcoded nucleic acid molecules, with a denaturation step prior to amplifying to generate the single-labeled nucleic acid molecules. Claim 9 of the ‘409 application adds the same limitations and depends from claim 8 of the ‘409 application. The claim language is substantively identical.
Instant claim 11 depends from instant claim 9 and adds the limitation that contacting copies of the nucleic acid target in the sample comprises contacting copies of a plurality of nucleic acid targets to a plurality of oligonucleotide barcodes, wherein extending the copies of the nucleic acid target comprises extending the copies of the plurality nucleic acid targets hybridized to the oligonucleotide barcodes to generate a plurality of barcoded nucleic acid molecules each comprising a sequence complementary to at least a portion of one of the plurality of nucleic acid targets, and wherein determining the number of the nucleic acid target comprises determining the number of each of the plurality of nucleic acid targets in the sample based on the number of the complements of the molecular labels with distinct sequences associated with single-labeled nucleic acid molecules of the plurality of single-labeled nucleic acid molecules comprising a sequence of the each of the plurality of nucleic acid targets. Claim 10 of the ‘409 application adds the same limitations and depends from claim 8 of the ‘409 application. The claim language is substantively identical.
Instant claim 14 depends from instant claim 9 and adds the limitation that at least 10 of the plurality of oligonucleotide barcodes comprise different molecular label sequences. Claim 8 of the ‘409 application recites this limitation as part of the independent claim. When instant claim 14 is read together with instant claim 9 from which it depends, the combined scope of instant claim 9 and 14 is substantively the same as claim 8 of the ‘409 application.
Instant claim 17 depends from instant claim 9 and that the extending step comprises 1) reverse transcribing to generate barcoded Cdna molecules, 2) extending the copies of the nucleic acid target hybridized to the oligonucleotide barcodes using a DNA polymerase lacking at least one of 5’ to 3’ exonuclease activity and 3’ to 5’ exonuclease activity, or both. Claim 12 of the ‘409 adds the same limitations and depends from claim 8 of the ‘409 application. The claim language is substantively identical.
Instant claim 20 depends from instant claim 9 and adds obtaining sequence information of the plurality of extended barcoded nucleic acid molecules. Claim 13 of the ‘409 application adds the same limitation and depends from claim 8 of the ‘409 application. The claim language is substantively identical.
Instant claim 34 depends from instant claim 9 and adds that the oligonucleotide barcode comprises an identical sample label, and/or an identical cell label. Claim 14 of the ‘409 application adds the same limitation and depends from claim 8 of the ‘409 patent. The claim language is substantively identical.
Instant claim 38 depends from claim 9 and adds that at least one of the plurality of barcoded nucleic acid molecules is associated with a solid support when intramolecularly hybridizing the target-binding region. Claim 15 of the ‘409 adds the same limitation except it recites “when hybridizing the target-binding region and the complement of the target-binding region within each of the plurality of barcoded nucleic acid molecules to form the stem loop” Instant claim 39 also depends from instant claim 9 and adds that at least one of the plurality of barcoded nucleic acid molecules dissociates from a solid support when intramolecularly hybridizing the target-binding region. Claim 16 of the ‘409 application adds the same limitation except it recites dissociation “when hybridizing…to form the stem loop.”
The difference between “intramolecularly hybridizing” in the instant claims and “hybridizing…to form the stem loop” in the ‘409 application claims does not create patentable distinction for the same reasons set forth above regarding instant claims 1 and 9. As established above with respect to Kurihara, intramolecular hybridization between complementary regions on the same molecule inherently produces a stem-loop structure (claim 1; column 2, para 2; column 3, para 2) and the omission of the words “stem loop” does not change the physical outcome of the hybridization step.
Instant claim 44 depends from instant claim 38 and adds that the solid support comprises a synthetic particle, wherein the synthetic particle comprises a material selected from the group recited in the claim. Claim 17 of ‘409 application depends from claim 16 and recites that the solid support comprises a synthetic particle. Claim 19 of the ‘409 application depends from claim 18 and recites the identical group of synthetic particle materials as instant claim 44. Therefore, the group of materials in instant claim 44 is directly disclosed in claim 19 of the ’409 application. Instant claim 44 is not patentably distinct from claim 17 and 19 of the ‘409 application because the synthetic particle martials recited are identical to those already claimed in the ‘409 application, and the use of those materials in the context of a solid support during intramolecular hybridization as recited in instant claim 38 would have been an obvious design choice to a person of ordinary skill in the art. Hindson teaches synthetic particles comprising these same materials for use in oligonucleotide barcode delivery and nucleic acid analysis application [00107].
Instant claim 50 depends from instant claim 9 and adds that the sample comprises a single cell, the method comprising associating a synthetic particle comprising the plurality of the oligonucleotide barcodes with the single cell in the sample. Claim 18 of the ‘409 patent adds the same limitations and depends from claim 8 of the ‘409 application. The claim language is substantively identical.
This is a provisional nonstatutory double patenting rejection.
Prior Art
The prior art made of record and not relied upon is considered pertinent to applicant’s disclosure.
Kivioja et al (Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods 9, 72–74 (2012)) teaches a method for quantifying individual RNA and DNA molecules using unique molecular identifiers (UMIs). Kivioja teaches that UMIs comprising random oligonucleotide label sequences are incorporated into nucleic acid molecules during reverse transcription using a labeled oligo(dT) adaptor primer, such that each molecule in the population in the population receives a distinct identifying sequence prior to PCR amplification (p. 72). Following amplification and sequencing, the original number of nucleic acid molecules in the sample is determined by counting the number of distinct UMI sequences rather than the total number of sequencing reads (p. 74, left column, para 1-2). Kivioja is pertinent because it teaches the concept of quantifying nucleic acid targets by counting distinct molecular label sequences associated with barcoded nucleic acid molecules, which is relevant to the quantification steps recited throughout the instant claims. However, Kivioja does not teach that attaching an oligonucleotide comprising a complement of the target-binding region to the barcoded nucleic acid molecules, intramolecular hybridization of the target-binding region and its complement, or extending the 3’-ends of the hybridized molecules to generate a complement of the molecular label.
Macosko et al (Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets Cell, 161, 1202-1214) teaches Drop-Seq, a method for single-cell transcriptome profiling in which individual cells are co-encapsulated with distinctly barcoded microparticles in nanoliter-scale droplets, the cell’s mRNAs are captured on bead-bound oligo(dT) primers comprising a cell barcode and a UMI, reverse-transcribed into cDNA and the resulting barcoded cDNA molecules are amplified and sequenced to determine gene expression at the single-cell level (summary; p. 1203-1204). Macosko is pertinent because it teaches associating a synthetic particle comprising a plurality of oligonucleotide barcodes with a single cell in a sample, with each barcode comprising a molecular label and a target-binding region capable of hybridizing to the nucleic acid target, which is relevant to the limitations of dependent claims of 34, 38-39, 44, and 50. However, Macosko does not teach attaching an oligonucleotide comprising a complement of the target-binding region to the barcoded nucleic acid molecules, intramolecular hybridization of the target-binding region and its complement, or extending the 3’-ends of the hybridized molecules to generate a complement of the molecular label.
Hindson (WO2014210353A2; published December 31st, 2014) teaches methods and compositions for barcoding sample materials using barcoded beads co-partitioned with sample components into droplets. Hindson teaches that each bead carries a plurality of oligonucleotides comprising a common barcode sequence and a variable domain, that the barcode sequences function as cell or sample identifiers, that the beads comprise synthetic particles made of materials including polystyrene, polyacrylamide, agarose, gelatine, silica, and ceramics, and that the barcoded beads are co-partitioned with the contents of single cells for single-cell nucleic acid analysis [claim 18; claim 89; claim 91; [107; 0425]). Hindson is pertinent because it teaches the limitations of dependent claims 34, 44, and 50 relating to identical cell and sample labels on the oligonucleotide barcodes, synthetic particle materials, and single-cell association with barcoded synthetic particles. However, Hindson does not teach attaching an oligonucleotide comprising a complement of the target-binding region to the barcoded nucleic acid molecules, intramolecular hybridization of the target-binding region and its complement, or 3’-end of the hybridized molecules to generate a complement of the molecular label.
Shiroguchi et al and Kurihara are relied upon in the nonstatutory double patenting rejection set forth above and are discussed therein.
The closest prior art to the subject matter in independent claims 1 and 9 is considered to be Fan et al (US9637799B2; published May 2nd, 2017), as identified during the Non-Final Office Action of parent, Application No. 11365409. Fan teaches a method for analyzing a nucleic acid target in a sample comprising barcoding and using molecular labels. However, Fan does not teach and none of the references of record, alone or in combination, teach the combination of: attaching an oligonucleotide comprising a complement of the target-binding region to the barcoded nucleic acid molecules, intramolecular hybridization of the target-binding region and its complement, and 3’-end of the hybridized molecules to generate a complement of the molecular label, as recited in independent claims 1 and 9.
Conclusion
All claims are rejected
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Nura Choudhury whose telephone number is (571)272-6148. The examiner can normally be reached M-F, 9-5 ET.
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/NURA M. CHOUDHURY/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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