DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
The claim set received 06 February 2026 has been entered into the application.
Claims 1, 18, 20, and 23 are amended.
Claims 4 and 21 are previously cancelled.
Claim(s) 1-3, 5-20, and 22-24 are pending.
Priority
Acknowledgment is made of the applicants claim to priority to U.S Provisional Application No. 62/716,406 received on 17 August 2018.
Information Disclosure Statement
The information disclosure statement (IDS) received 22 September 2025 has been considered and entered into the application.
It is noted that the references with lines through them were not received.
Claim Rejections - 35 USC § 102
The rejection of claim(s) 23 under 35 U.S.C. 102(a)(1) as being anticipated by Tan et al. (Cited in the Office Action mailed 26 April 2023) in the 06 November 2026 is withdrawn in view of the arguments and amendments received 06 February 2026.
Claim Rejections - 35 USC § 103
The instant rejection is maintained for reason for record in the Office Action mailed 06 November 2025 and modified in view of the amendments filed 06 February 2026. It is noted the amendments received 06 February 2026 are necessitated by new ground(s) of rejection.
The rejection of claim(s) 18-19 under 35 U.S.C. 103 as being unpatentable over Tan in view of Delley et al in view of Delley in view of Aghvanyan in the 06 November 2026 is withdrawn in view of the arguments and amendments received 06 February 2026.
The rejection of claim(s) 20 and 22 are rejected under 35 U.S.C. 103 as being unpatentable over Spetzler in view of Delley in view of Aghvanyan in the 06 November 2026 is withdrawn in view of the arguments and amendments received 06 February 2026.
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1-3 and 8-13 are rejected under 35 U.S.C. 103 as being unpatentable over Delley et al. (Scientific reports, 2018-02, Vol.8 (1), p.2919-8, Article 2919) in view of Tan et al. (Patent Pub US 2009/0208936, Pub Date 20 Aug 2009).
Claim 1 recites providing a plurality of samples, wherein each of the plurality of samples comprises 100 or more cells each comprising one or more cellular component targets. Claim 1 recites contacting each of the plurality of samples with a sample indexing composition of a plurality of sample indexing compositions, respectively. Claim 1 recites wherein the sample indexing composition comprises an aptamer composition comprising an aptamer and a sample indexing oligonucleotide. Claim 1 recites wherein the aptamer is capable of specifically binding to at least one of the one or more cellular component targets. Claim 1 recites wherein the sample indexing oligonucleotide comprises a sample indexing sequence, and wherein sample indexing sequences of at least two sample indexing compositions of the plurality of sample indexing compositions comprise different sequences. Claim 1 recites pooling the plurality of samples to form combined labeled samples. Claim 1 recites identifying sample origin of at least one cell 100 cells of the 100 or more cells based on the sample indexing sequence of at least one sample indexing oligonucleotide of the plurality of sample indexing compositions. Claim 1 recites wherein identifying the sample origin of a cell of the at least one cell 100 cells comprise identifying the presence or absence of the sample indexing sequence of at least one sample indexing oligonucleotide of the plurality of sample indexing compositions.
Delley et al. (Delley) teach a method for differentiating distinct cell type based on aptamer surface binding and gene expression [abstract]. Delley teaches aiming for about 200 cells and performing limited Illumina sequencing. Delley teaches obtaining high quality transcriptome and aptamer data of 58 cells. [page 3 Apt-seq provides independent information from RNAseq for inferring cell type]. Delley teaches using about 2,000 beads corresponding to 100-200 cells [page 5 single cell experiment], as in claim 1 providing a plurality of samples, wherein each of the plurality of samples comprises 100 or more cells each comprising one or more cellular component targets.
Delley teaches “to label the cells with aptamers, the mixed aptamer library is incubated with a cell suspension, and unbound aptamers washed away (Fig. 1b).” [page 2 Results]. Delley teaches 3T3 and Ramos cells were resuspended in aptamer binding buffer [page 5 Aptamer staining], as in claim 1 contacting each of the plurality of samples with a sample indexing composition of a plurality of sample indexing compositions, respectively. Here, the aptamer staining inherently reads on contacting the aptamers with the cells.
Delley teaches getting aptamer data for 58 cells. Delley teaches using the aptamer TD05 whose target protein is the membrane bound IgM, L-selectin, and PKT7 [page 3 Polyadenylation does not repair aptamer function], as in claim 1 wherein the sample indexing composition comprises an aptamer composition comprising an aptamer and a sample indexing oligonucleotide and wherein the aptamer is capable of specifically binding to at least one of the one or more cellular component targets.
Delley teaches to label the cells with aptamers, the mixed aptamer library was incubated with cell suspension [Delley, page 2 results], as in claim 1 pooling the plurality of samples to form a combined labeled sample.
Delley teaches “we aim for about 200 cells and perform limited Illumina MiSeq sequencing collecting ~12 million paired-end reads.” Delley teaches obtaining high-quality aptamer data for 58 cells. Delley teaches Apt-seq that infers cell type. Delley teaches “Based on the qPCR results and because TD05 is a binder of the immunoglobulin heavy chain, we expect the first rectangular block to represent Ramos and the second 3T3 cells. Because these cells are from different species, cell type can be inferred by direct sequence analysis of cDNA sequencing of suspended Ramos and 3T3 cells.” Delley teaches “Based on transcript sequences, we confirm that the lower block corresponds to the human Ramos and the upper block to the mouse 3T3 cells” [page 3 Apt-seq provides independent information from RNAseq for inferring cell type], as in claim 1 identifying sample origin of at least one cell 100 cells of the 100 or more cells based on the sample indexing sequence of at least one sample indexing oligonucleotide of the plurality of sample indexing compositions and wherein identifying the sample origin of a cell of the at least one cell 100 cells comprise identifying the presence or absence of the sample indexing sequence of at least one sample indexing oligonucleotide of the plurality of sample indexing compositions.
Delley teaches TD05, sgc3b, and sgc8a have reported protein targets, the membrane bound IgM, L-selectin, and PKT7 [page 3 polyadenylation does not impair aptamer function], as in claim 2.
Delley teaches barcoding the cell with Drop-seq. Delley teaches “after barcoding, the nucleic acids of many cells are pooled and sequenced. We aim for about 200 cells and perform limited Illumina MiSeq sequencing collecting ~12 million paired-end reads.” Delley teaches Apt-seq that infers cell type. Delley teaches “Based on the qPCR results and because TD05 is a binder of the immunoglobulin heavy chain, we expect the first rectangular block to represent Ramos and the second 3T3 cells. Because these cells are from different species, cell type can be inferred by direct sequence analysis of cDNA sequencing of suspended Ramos and 3T3 cells.” Delley teaches “Based on transcript sequences, we confirm that the lower block corresponds to the human Ramos and the upper block to the mouse 3T3 cells” [page 3 Apt-seq provides independent information from RNAseq for inferring cell type], as in claim 3.
Delley does not teach wherein the sample indexing oligonucleotide comprises a sample indexing sequence, and wherein sample indexing sequences of at least two sample indexing compositions of the plurality of sample indexing compositions comprise different sequences of claim 1.
Delley does not teach claims 8-13.
Tan discloses Dye-labeled aptamers were obtained from Integrated DNA Technologies, Inc. (Coralville, Iowa) and the sequences of the 15mer and 27mer thrombin-aptamer are 5'-GGTTGGTGTGGTTGG-3' (SEQID NO 1), and 5'-ACCCGTGGTAGGGTAGGATGGGGTGGT-3' (SEQID NO 2) [disclosure page 17 paragraph [0204]]. Tan discloses a human alpha-thrombin has two aptamers, with only one able to inhibit enzymatic activity of thrombin. The 15mer (i.e., 15Ap) and 27mer (i.e., 27Ap) were linked with 18 atoms as a spacer. Eight units of each spacer were used to link the two aptamers to form DA-8S [Spec page 22 left col. 0258], as in instant claim 1 wherein the sample indexing oligonucleotide comprises a sample indexing sequence, and wherein sample indexing sequences of at least two sample indexing compositions of the plurality of sample indexing compositions comprise different sequences. Here, the DA-8S aptamer makes obvious the sample indexing oligonucleotide comprises a sample indexing sequence and sample indexing sequences of at least two sample index compositions of instant claim 1.
Tan teaches administering a prey molecule to a composition of aptamer bound to a target molecule [claim 20]. Tan teaches an aptamer linked with a linking molecule [claim 32]. Tan teaches the two aptamers specific for a protein target are linked [claim 33]. Tan teaches the aptamers were linked with a polyethylene glycol chain [claim 34], as in instant claims 8-9.
Tan teaches the aptamer is a nucleic acid molecule [claim 13]. Tan teaches selecting aptamer that bind to different epitopes [claim 32], as in instant claim 10.
Tan teaches where in the aptamer is labeled with donor molecules at the 5’-end and an acceptor molecule as the 3’-end [claim 13]. Tan teaches the donor molecule is a fluorophore [claim 15]. Tan teaches the acceptor molecule is a fluorophore quenching molecule [claim 16], as in instant claim 11.
Tan discloses Dye-labeled aptamers were obtained from Integrated DNA Technologies, Inc. (Coralville, Iowa) and the sequences of the 15mer and 27mer thrombin-aptamer are 5'-GGTTGGTGTGGTTGG-3' (SEQID NO 1), and 5'-ACCCGTGGTAGGGTAGGATGGGGTGGT-3' (SEQID NO 2) [disclosure page 17 paragraph [0204]]. Tan discloses a human alpha-thrombin has two aptamers, with only one able to inhibit enzymatic activity of thrombin. The 15mer (i.e., 15Ap) and 27mer (i.e., 27Ap) were linked with 18 atoms as a spacer. Eight units of each spacer were used to link the two aptamers to form DA-8S [Spec page 22 left col. 0258], as in instant claim 12.
Tan teaches the aptamers are about 65% homologous to any one of the SEQ ID No’s 1-6 [claims 5-9], as in instant claim 13.
It would be obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Delley in view of Tan because Tan teaches methods for using aptamer compositions for measuring changes in anisotropy to determine molecular interaction between target and prey molecules [claim 20]. One of ordinary skill in the art would be motivated to combine Delley in view of Tan because Tan discloses a method of labeling an aptamer with a fluorophore, providing a bait and prey molecule, allowing binding of the bait and prey molecules resulting in releasing the aptamer so that fluorescence can be quantified for identifying a cell or sample (i.e., cellular) identification. Here, the method could be used to contact aptamer compositions with a cell(s) in a sample to identify the cellular origin of the sample. Thus, there is a reasonable expectation of success to combine the aptamer analysis of Tan with the cell identification methods of Delley to yield a predictable method for sample identification.
Claim(s) 5, 15-17, and 24 are rejected under 35 U.S.C. 103 as being unpatentable over Delley in view of Tan, as applied to claims 1-3 and 8-13, and in further view of Heil et al. (Patent Pub US 2009/0208936, Pub Date 30 November 2017).
Delley in view of Tan teach claims 1-3 and 8-13.
Delley in view of Tan make obvious claims 1-3 and 8-13 because Delley and Tan teach a method drawn to identifying sample origin by contacting a sample with an aptamer composition and indexing oligonucleotides.
Delley in view of Tan do not teach claims 5, 15-17, and 24.
With respect to claim 5, the claim is rendered obvious because Tan discloses “Aptamers are selected in a 5 to 100 cycle procedure. In each cycle, oligomers are bound to the target molecule, purified by isolating the target to which they are bound, released from the target, and then replicated by 20 to 30 generations of PCR amplification [disclosure page 8 left col para. 0106]. However, Tan does not teach the obtaining sequencing data and identifying steps of claim 5.
Heil discloses “The aptamer affinity complex (or optional aptamer covalent complex) is then quantified using known techniques for the quantitative replication of polynucleotides [disclosure page 13 right col para. 0113] which also discloses a replicating step. Delley teaches barcoding the cell with Drop-seq. Delley teaches “after barcoding, the nucleic acids of many cells are pooled and sequenced. We aim for about 200 cells and perform limited Illumina MiSeq sequencing collecting ~12 million paired-end reads.” Delley teaches Apt-seq that infers cell type. Delley teaches “Based on the qPCR results and because TD05 is a binder of the immunoglobulin heavy chain, we expect the first rectangular block to represent Ramos and the second 3T3 cells. Because these cells are from different species, cell type can be inferred by direct sequence analysis of cDNA sequencing of suspended Ramos and 3T3 cells.” Delley teaches “Based on transcript sequences, we confirm that the lower block corresponds to the human Ramos and the upper block to the mouse 3T3 cells” [page 3 Apt-seq provides independent information from RNAseq for inferring cell type].
Heil teaches said tag comprises a first nucleotide sequence and said probe comprises a second nucleotide sequence, and wherein said first nucleotide sequence is complementary to said second nucleotide sequence [Heil, claim 24], as in instant claim 15.
With respect to claim 16, the claim is rendered obvious because Tan discloses “the capture reagent can be a biological molecule, such as a polypeptide or a nucleic acid, which captures other biomarkers in a specific manner [disclosure page 15 para. 0171]. Heil also discloses using capture probes the capture tag was synthesized and coupled to an amine-reactive slide surface [disclosure page 18 right col para. 0150]. Delley teaches pooling all beads after barcode fusion, sequencing their content in parallel, and deconvoluting aptamers and mRNAs, allows evaluation of epitope profiles in single cells [page 2 figure 1].
With respect to claim 17, the claim is rendered obvious because Delley teaches an aptamer than targets the membrane bound IgM, L-selectin, and PKT7 [page 3 Polyadenylation does not repair aptamer function]. Tan teaches the prey molecule is protein organic molecule or nucleic acid molecules [claim 31]. Heil teaches targeting VEGF [page 19 para. 0152].
Heil discloses using methanol [para 0149]. Heil discloses using proteinase K [para. 0011] as in claim 24. Here, Heil renders obvious adding methanol and proteinase K to a cell lysis buffer.
It would be obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Delley in view of Tan and in further view of Heil because Heil discloses multiplex analyses of test sample [disclosure title] by detecting a target molecule that may be present in a test sample by contacting samples with aptamers for detecting said target [Heil, claim 1]. One of ordinary skill in the art would be motivated to combine Delley in view of Tan and in further view of Heil because Heil discloses methods for using test samples comprising target molecules (i.e., proteins [Disclosure col 40 lines 50-60], biological sample such a cellular extract [Disclosure col 40 lines 50-60], stool, and PBMC’s [Disclosure col 41 lines 41 -65], and whole blood [Disclosure col 42 lines 10-22]). Here, there is a reasonable expectation of success to combine the identifying a sample of mouse 3T3 cells of Delley and the aptamer compositions and determining molecular interactions of Tan with the detecting a target molecule that may be present in a sample of Heil to yield a predictable using aptamers, capture probes, barcodes, and extending, contacting, hybridizing, replicating methods for identifying sample origin of cells to identify the sample.
Claim(s) 6 are rejected under 35 U.S.C. 103 as being unpatentable over Delley in view of Tan in view of Heil, as applied to claims 1-3, 5, 8-13, 15-17, and 24, and in further view of Spetzler et al. (U.S Patent No 9,939,443 Date 10 April 2018).
Delley in view of Tan in view of Heil teach claims 1-3, 5, 8-13, 15-17, and 24.
Delley, Tan, and Heil make obvious a method of sample identification by replicating an indexing oligonucleotide and contacting said oligonucleotide with a capture probe, as in claims 1 and 5.
Delley in view of Tan in view of Heil do not teach claim 6.
Spetzler et al. (Spetzler) discloses that aptamers were pooled after ligating barcodes and adapter sequences [col 112 lines 20-60 Example 3]. Spetzler discloses multiple rounds of positive selection were performed and before each rounds the recovered aptamers products are PCR amplified and strand separated using stand methods [col 112 Example 5]. Here, it is obvious that the aptamers with the ligated barcode and adapter are being used to further generate replicated barcoded sample indexing oligonucleotides because Spetzler discloses that a number of aptamers were selected based on affinity binding to their target moiety [col 112 lines 20-60 Example 3]. Spetzler discloses that “after each round of selection in the Example above, the recovered aptamer pool was amplified using PCR with standard protocols.” Spetzler discloses the PCR products were captured and strand separated using methodology presented in this Example which discloses pluralities of replicated barcoded oligonucleotides (i.e., aptamers) are been generated for further testing and screening analysis [col 114-115 Example 6].
It would be obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Delley in view of Tan in view of Heil and in further view of Spetzler because Spetzler discloses methods for ligating replicated adapters to produce aptamers than can bind to a target protein. One of ordinary skill in the art would be motivated to combine Delley in view of Tan in view of Heil and in further view of Spetzler because Spetzler discloses a method for using aptamers attached to micro-vesicles for identifying aptamer(s). Here, the methods of Spetzler can be utilized to identify specific aptamers that can associate with cancer cells’ intracellular and extracellular proteins, for example. As such, there is a reasonable expectation of success that combining the aptamer identifying methods of Spetzler with the aptamer composition of Tan, the sample identification method of Delley, and the kit for detecting one target molecule present in a sample of Heil would yield a predictable method for using aptamers to target cellular components expression and identifying a sample.
Claim(s) 7 are rejected under 35 U.S.C. 103 as being unpatentable over Delley in view of Tan in view of Heil, as applied to claims 1-3, 5, 8-13, 15-17, and 24, and in further view of Aghvanyan et al. (Patent Pub US 2017/0089892, Pub Date 30 March 2017).
Delley in view of Tan in view of Heil teach claims 1-3, 5, 8-13, 15-17, and 24.
Delley, Tan, and Heil make obvious a method a method of sample identification by replicating an indexing oligonucleotide and contacting said oligonucleotide with a capture probe, as in claims 1 and 5.
Delley in view of Tan in view of Heil do not teach claim 7.
Aghvanyan et al. (Aghvanyan) discloses using extension processes that requires a first and second probes to be in proximity, extending the second probe to form an extended sequence comprising an anchoring sequence complement that is complementary to the anchoring sequence [Aghvanyan, claims 1 and 49], as in claim 7.
It would be obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Delley in view of Tan in view of Heil, and in further view of Aghvanyan because Aghvanyan discloses improved assay methods [disclosure title] that detect an analyte of interest [claim 1]. One of ordinary skill in the art would be motivated to combine Delley in view of Tan in view of Heil, and in further view of Aghvanyan because Aghvanyan discloses methods for binding, capturing, extending, hybridizing, and measuring the amount of the extended sequence bound to the surface which discloses methods for using nucleic acid sequences for detecting analytes of interest (i.e., target protein or sample indexing oligonucleotides) in a sample. Here, there is a reasonable expectation of success that combining the extension processes of Aghvanyan with the aptamer composition and measuring molecular interaction of Tan, the identifying a sample of mouse 3T3 cells of Delley, and the kit for detecting one target molecule present in a sample of Heil would yield a predictable method for identifying a sample or identifying the origin of a sample and measuring cellular component expression.
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Delley in view of Tan in view of as applied to claims 1-3 and 8-13, and in further view of Ku et al. (Cited in the Office Action mailed 26 April 2023).
Delley in view of Tan teach claims 1-3 and 8-13.
Delley in view of Tan make obvious a method of sample identification by replicating an indexing oligonucleotide and contacting said oligonucleotide with a capture probe, as in claims 1 and 5.
Delley in view of Tan do not teach claim 14.
Ku et al. (Ku) teach using aptamer that have been conjugated with paramagnetic iron oxide nanoparticles which is similar to the metal nanomaterial step of claim 14 [page 16290], as in claim 14 step (a). Ku teaches using aptamer-nanomaterials comprising a labeled aptamer-hallow gold nanosphere w [page 16290], as in claim 14 step (b). Ku et al further shows a liposome vesicle aptamer-based conjugation which is similar to the lysosome, a micelle, a vesicle, a lipid membrane, a lipid bilayer, or a lipid monolayer [page 16290], as in claim 14 step (c).
It would have been further obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Delley in view of Tan in further view of Ku because Ku reviews general methods for using metal, gold, and lysosome as carriers with aptamers [page 16292 section 5.2]. One of ordinary skill in the art would be motivated to combine Delley in view of Tan in further view of Ku because Ku teaches using different nanoparticles which could be utilized as carriers of the aptamers [page 16292 section 5.2] such as gold [page 16293], liposomes [page 16292], and iron oxides [page16293]. Here, the carriers of Ku could be attached to the aptamers of Delley and Tan to yield aptamers associated with carriers such gold, liposomes, for example.
Claim(s) 18-19 are rejected under 35 U.S.C. 103 as being unpatentable over Tan in view of Delley et al in view of Fu et al. (US Patent Pub No.: US 2016/0257993, Patent Pub Date: 08 September 2016).
Claim 18 recites wherein each of the plurality of sample indexing compositions comprises an aptamer composition comprising a first cellular component-binding aptamer and a sample indexing oligonucleotide. Claims 18 recites wherein the cellular component-binding aptamer 1s capable of specifically binding to at least one cellular component target. Claim 18 recites wherein the sample indexing oligonucleotide comprises a sample indexing sequence for identifying sample origin of one or more cells of a sample. Claim 18 recites wherein sample indexing sequences of at least two sample indexing compositions of the plurality of sample indexing compositions comprise different sequences.
Claim 18 recites wherein a sample indexing composition comprises a second cellular component binding aptamer. Claim 18 recites wherein the cellular component-binding aptamer and the second cellular component-binding aptamer are capable of binding to different cellular component targets. Claim 18 recites wherein the second cellular component-binding aptamer is associated with a second sample indexing oligonucleotide comprising a second sample indexing sequence. Claim 18 recites wherein the sample indexing sequence and the second sample indexing sequence are identical
Tan et al. (Tan) teaches an aptamer composition for identifying molecular interactions comprising aptamers which specifically bind a target molecule [claim 1], as in instant claim 18 a plurality of sample indexing compositions.
Tan teaches measuring the fluorescence anisotropy of an aptamer bound to a target molecule and administering the prey molecule to a composition of aptamers bound to a target molecule [claim 20], as in instant claim 18 wherein each of the plurality of sample indexing compositions comprises an aptamer composition comprising a first cellular component-binding aptamer and a sample indexing oligonucleotide. Here, the aptamer bound to the target molecule makes obvious aptamer composition comprising a first cellular component-binding aptamer and a sample indexing oligonucleotide because the sample indexing comprises an aptamer comprising first cellular component (i.e., target molecule) and sample indexing oligonucleotide (i.e., aptamer).
Tan teaches producing aptamers specific for a target molecule, selecting aptamers that bind to different epitopes on the target molecule, and linking the selected aptamers with a linking molecule thereby, increasing the selectivity and affinity of the aptamers for a target molecule [claim 32], as in instant claim 18 wherein the cellular component-binding aptamers capable of specifically binding to at least one cellular component target. Here, producing aptamers specific to a target molecule a target molecule, selecting aptamers that bind to different epitopes on the target molecule, and linking the selected aptamers with a linking molecule makes obvious an aptamer specifically able to bind to at least one cellular component.
Tan teaches an aptamer composition for identifying molecular interactions comprising aptamers which specifically bind a target molecule [claim 1]. Tan discloses “diagnoses of diseases including cancers can be carried out by identify certain protein markers that are present in the cells. By developing aptamers for different cancer marker proteins, arrays can be constructed that have the capability of sensitive multiplex cancer marker detection. Based on our aptamer assay, the analysis of the cell content conducted highly efficiently. The fluorescence signals obtained from the array generate a pattern which shows the presence of different cancer related proteins. By comparing the patterns acquired from different cell samples, cancer diagnosis may be done with great ease and accuracy.” [page 2 para. 0017], as in instant claim 18 wherein the sample indexing oligonucleotide comprises a sample indexing sequence for identifying sample origin of one or more cells of a sample. Here, developing aptamers (i.e., aptamers that target different cancer marker proteins) to identify certain proteins markers that are present in cells can be used to detect cancer cells which makes obvious using aptamers for identifying the origin (i.e., cells causing cancer) of cells (i.e., mutated cell(s)) because identifying or diagnosing cancer requires identifying the origin of the cancerous cells and/or identifying which cell(s) is/are causing cancer.
Dependent claim(s): 19
Tan discloses Dye-labeled aptamers were obtained from Integrated DNA Technologies, Inc. (Coralville, Iowa) and the sequences of the 15mer and 27mer thrombin-aptamer are 5'-GGTTGGTGTGGTTGG-3' (SEQID NO 1), and 5'-ACCCGTGGTAGGGTAGGATGGGGTGGT-3' (SEQID NO 2) [disclosure page 17 paragraph [0204]]. Tan discloses a human alpha-thrombin has two aptamers, with only one able to inhibit enzymatic activity of thrombin. The 15mer (i.e., 15Ap) and 27mer (i.e., 27Ap) were linked with 18 atoms as a spacer. Eight units of each spacer were used to link the two aptamers to form DA-8S [Spec page 22 left col. 0258], as in instant claim 19.
Tan does not teach claim 18 wherein the sample indexing oligonucleotide comprises a sample indexing sequence for identifying sample origin of one or more cells of a sample of claim 18.
Tan does not teach claim 18 wherein a sample indexing composition comprises a second cellular component binding aptamer. Tan does not teach claim 18 wherein the cellular component-binding aptamer and the second cellular component-binding aptamer are capable of binding to different cellular component targets. Tan does not teach claim 18 wherein the second cellular component-binding aptamer is associated with a second sample indexing oligonucleotide comprising a second sample indexing sequence. Tan does not teach claim 18 wherein the sample indexing sequence and the second sample indexing sequence are identical
Delley teaches “we aim for about 200 cells and perform limited Illumina MiSeq sequencing collecting ~12 million paired-end reads.” Delley teaches obtaining high-quality aptamer data for 58 cells. Delley teaches Apt-seq that infers cell type. Delley teaches “Based on the qPCR results and because TD05 is a binder of the immunoglobulin heavy chain, we expect the first rectangular block to represent Ramos and the second 3T3 cells. Because these cells are from different species, cell type can be inferred by direct sequence analysis of cDNA sequencing of suspended Ramos and 3T3 cells.” Delley teaches “Based on transcript sequences, we confirm that the lower block corresponds to the human Ramos and the upper block to the mouse 3T3 cells” [page 3 Apt-seq provides independent information from RNAseq for inferring cell type]. Here, Delley teaches using the aptamer, TD05, for identifying mouse 3T3 cells which teaches an indexing sample oligonucleotide to identify one or more cells in a sample of claim 18.
Delley teaches aptamers that target membrane bound IgM, L-selectin, and PKT7 [Delley, page 3], as in instant claim 18 wherein a sample indexing composition comprises a second cellular component binding aptamer.
Delley teaches using a library of aptamers (i.e., TD05, sgc3b, and sgc8a) that is able to bind to TD05, sgc3b, and sgc8a have reported protein targets, the membrane bound IgM, L-selectin, and PKT7) [page 3 polyadenylation does not impair aptamer function], as instant claim 18 wherein the cellular component-binding aptamer and the second cellular component-binding aptamer are capable of binding to different cellular component targets.
Delley teaches using a library of aptamers (i.e., TD05, sgc3b, and sgc8a) that is able to bind to TD05, sgc3b, and sgc8a have reported protein targets, the membrane bound IgM, L-selectin, and PKT7) [page 3 polyadenylation does not impair aptamer function], as in instant claim 18 recites wherein the second cellular component-binding aptamer is associated with a second sample indexing oligonucleotide comprising a second sample indexing sequence. Here, it would be obvious that anyone of the aptamers (i.e., TD05, sgc3b, and sgc8a) could be utilized as second cellular component-binding aptamer is associated with a second sample indexing oligonucleotide.
Fu et al. (Fu) discloses stochastic barcode can refer to a polynucleotide sequence that can be used to stochastically label (e.g., barcode tag) a target. Fu discloses the stochastic barcode can comprise one or more labels. Fu discloses exemplary labels can include a universal label, a cellular label, a molecular label, a sample label, a plate label, a spatial label, and/or a pre-spatial label [Fu, pages 10-11 para 0090 right col]. Fu discloses that at least 60% of stochastic barcodes (i.e., index indexing sequence) on the same solid support may comprise the same cellular label (i.e., second sample indexing sequence). Fu discloses that at least 95% of stochastic barcodes on the same solid support may comprise the same cellular label [Fu, page 12 left col para 0099], as in instant claim 18 wherein the sample indexing sequence and the second sample indexing sequence are identical.
It would have been further obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Tan in view of Delley because Delley teaches identifying sample of using aptamers. One of ordinary skill in the art would be motivated to combine Tan in view of Delley because Delley teaches method for using the aptamer, TD05, for identifying a sample of mouse 3T3 cell. Here, there is a reasonable expectation of success that combining the aptamer compositions of Tan with the cell sample identification method of Delley would yield a sample indexing composition that can be utilized for sample identification.
It would be obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Spetzler in view of Delley in view of Fu because Fu discloses using different and identical labels and stochastic barcodes. One of ordinary skill in the art would recognize the labels and barcodes could be substituted as indexing sequences. One of ordinary skill in the art would be motivated to combine Tan in view of Delley in view of Fu because Fu discloses method for labeling targets (i.e., identifying the TCR alpha chain of T-cell [abstract]) and using universal labels such as (cellular label, molecular label [Fu, page 11, left col para 0090]) and barcodes that can be identical [Fu, page 11 right col para 0094]. Thus, there would be a reasonable expectation of success to combine the aptamers of Tan and Delley with the similar and identical barcodes and labels of Fu to yield predictable identical nucleic acid labels and barcodes that can utilized as a plurality of sample indexing compositions.
Claim(s) 20 and 22 are rejected under 35 U.S.C. 103 as being unpatentable over Spetzler in view of Delley in view of Aghvanyan and in view of Fu.
Claim 20 recites contacting a plurality of cellular component-binding aptamers with a plurality of cells comprising a plurality of cellular component targets. Claim 20 recites wherein each of the plurality of cellular component-binding aptamers comprises an aptamer specific oligonucleotide comprising a unique identifier sequence for the cellular component-binding aptamer. Claim 20 recites wherein the cellular component-binding aptamer is capable of specifically binding to at least one of the pluralities of cellular component targets.
Claim 20 recites wherein the cellular component binding aptamer comprises a poly(dA) region. Claim 20 recites wherein the aptamer specific oligonucleotide changes from a first conformation in which the poly(dA) region is inaccessible to a second conformation in which the poly(dA) region is accessible when the aptamer contacts the at least one of the cellular component targets.
Claim 20 recites partitioning the plurality of cells associated with the plurality of cellular component-binding aptamers to a plurality of partitions. Claim 20 recites wherein a partition of the plurality of partitions comprises a single cell from the plurality of cells associated with the cellular component-binding aptamers.
Claim 20 recites in the partition comprising the single cell, contacting a barcoding particle with the aptamer specific oligonucleotides. Claim 20 recites wherein the barcoding particle comprises a plurality of oligonucleotide probes each comprising a target binding region and a barcode sequence selected from a diverse set of unique barcode sequences.
Claim 20 recites extending oligonucleotide probes hybridized to the aptamer specific oligonucleotides to produce a plurality of labeled nucleic acids. Claim 20 recites wherein each of the labeled nucleic acid comprises a unique identifier sequence, or a complementary sequence thereof, and a barcode sequence.
Claim 20 recites obtaining sequence information of the plurality of labeled nucleic acids or a portion thereof to determine the quantity of one or more of the pluralities of cellular component targets in 100 or more cells of the plurality of cells. Claim 20 recites wherein the number of unique barcode sequences associated with the unique identifier sequence for the cellular component-binding aptamer capable of specifically binding to the at least one cellular component target in the sequencing information indicates the number of copies of the at least one cellular component target in one single cell of the plurality of cells.
Spetzler discloses contacting a sample with aptamer pool and a second sample with an aptamer pool to a micro vesicle [Spetzler, claim 1] with the first and second sample are separately contacted with the aptamer pools [Spetzler, claims 2-3]. Spetzler discloses the pools of candidate binding agents may comprise 10-1020 unique members [disclosure page 54 left col. para. 0184], as in claim 20 contacting a plurality of cellular component-binding aptamers with a plurality of cells comprising a plurality of cellular component targets, wherein each of the plurality of cellular component-binding aptamers comprises an aptamer specific oligonucleotide comprising a unique identifier sequence for the cellular component-binding aptamer, and wherein the cellular component-binding aptamer is capable of specifically binding to at least one of the pluralities of cellular component targets.
With respect to instant claim 20 partitioning the plurality of cells associated with the plurality of cellular component-binding aptamers to a plurality of partitions and wherein a partition of the plurality of partitions comprises a single cell from the plurality of cells associated with the cellular component-binding aptamers, in the partition comprising the single cell, contacting a barcoding particle with the aptamer specific oligonucleotides, and wherein the barcoding particle comprises a plurality of oligonucleotide probes each comprising a target binding region and a barcode sequence selected from a diverse set of unique barcode sequences, the claimed step is rendered obvious because Spetzler also discloses contacting targets molecule and aptamer composition [disclosure col 9 lines 50-55]. Spetzler teaches step-wise iteration of binding, partitioning, and amplification. Spetzler describes general steps for contacting target with nucleic acids with the target and partitioning unbound nucleic acids [col 9 lines 45-65]. Spetzler discloses that after partitioning, dissociation and amplification, a second nucleic acid mixture is generated, enriched for the higher binding affinity candidates [col 10 lines 5-15]. Spetzler discloses that the aptamer of the invention can be used to assess a single cell. Spetzler discloses the sample (i.e., cell) can be split into aliquots [col 21 lines 15-20], as in instant claim 20 partitioning the plurality of cells associated with the plurality of cellular component-binding aptamers to a plurality of partitions.
Spetzler discloses “The capture agent may bind a protein expressed on the surface of vesicles shed from diseased cells ("disease vesicle").” [disclosure col 6 lines 45-50]. Spetzler discloses “The detection agent, which may also be an aptamer or antibody, carries a detectable label, here a fluorescent signal.” [disclosure col 6 lines 55-60]. Spetzler discloses identifying step comprises sequencing the candidate that bound to a vesicle [Spetzler, claim 17], as in instant claim 22.
Spetzler does not disclose extending oligonucleotide probes hybridized to the aptamer specific oligonucleotides to produce a plurality of labeled nucleic acids and wherein each of the labeled nucleic acid comprises a unique identifier sequence, or a complementary sequence thereof, and a barcode sequence of instant claim 20. Spetzler does not disclose a portion thereof to determine the quantity of one or more of the pluralities of cellular component targets in 100 or more cells of the plurality of cells, wherein the number of unique barcode sequences associated with the unique identifier sequence for the cellular component-binding aptamer capable of specifically binding to the at least one cellular component target in the sequencing information indicates the number of copies of the at least one cellular component target in one single cell of the plurality of cells of instant claim 20. Spetzler does not discloses wherein the cellular component binding aptamer comprises a poly(dA) region of claim 20. Spetzler does not dicloses wherein the aptamer specific oligonucleotide changes from a first conformation in which the poly(dA) region is inaccessible to a second conformation in which the poly(dA) region is accessible when the aptamer contacts the at least one of the cellular component targets of claim 20.
With respect to claim 20 extending oligonucleotide probes hybridized to the aptamer specific oligonucleotides to produce a plurality of labeled nucleic acids and wherein each of the labeled nucleic acid comprises a unique identifier sequence, or a complementary sequence thereof, and a barcode sequence, the claims is rendered obvious because Aghvanyan discloses using extension processes that requires a first and second probes to be in proximity, extending the second probe to form an extended sequence comprising an anchoring sequence complement that is complementary to the anchoring sequence [claims 1 and 49]. Aghvanyan discloses the capture agent can be an aptamer [Aghvanyan, claims 2, 32-34, 53-54, 64-65]. Spetzler discloses aptamers were pooled after ligating barcodes and adaptor sequences [disclosure page 58 para. 0228-0229].
93. With respect to claim 20 obtaining sequence information of the plurality of labeled nucleic acids or a portion thereof to determine the quantity of one or more of the pluralities of cellular component targets in 100 or more cells of the plurality of cells, wherein the number of unique barcode sequences associated with the unique identifier sequence for the cellular component-binding aptamer capable of specifically binding to the at least one cellular component target in the sequencing information indicates the number of copies of the at least one cellular component target in one single cell of the plurality of cells, the claimed step is render obvious because Delley teaches “we aim for about 200 cells and perform limited Illumina MiSeq sequencing collecting ~12 million paired-end reads.” Delley teaches obtaining high-quality aptamer data for 58 cells. Delley teaches Apt-seq that infers cell type. Additionally, Spetzler also discloses aptamer pools are sequenced using conventional sequencing protocols [claim 21 and disclosure page 58 para 0228-0238]. Delley teaches computationally grouping reads to single cells using barcodes and then to single molecules using unique molecular identifiers (UMI’s). Delley teaches “Based on the qPCR results and because TD05 is a binder of the immunoglobulin heavy chain, we expect the first rectangular block to represent Ramos and the second 3T3 cells. Because these cells are from different species, cell type can be inferred by direct sequence analysis of cDNA sequencing of suspended Ramos and 3T3 cells.” Delley teaches “Based on transcript sequences, we confirm that the lower block corresponds to the human Ramos and the upper block to the mouse 3T3 cells” [page 3 Apt-seq provides independent information from RNAseq for inferring cell type]. Here, Delley teaches using the aptamer, TD05, for identifying mouse 3T3 cells which teaches an indexing sample oligonucleotide to identify one or more cells in a sample [page 3 apt-seq provides independent information form RNAseq for inferring cell-type]. Delley teaches “a two-dimensional histogram of counts per aptamer per cell. The order of the cells is the same as in (a). (c) Two-dimensional histogram of the transcript counts for the 200 most variable transcript equivalence classes. The maximum read number is truncated at 100.” Delley teaches aptamer UMI count [page 4 figure 3]. Here, Delley teaches determining a quantity of specific aptamers for measuring aptamer TD05 which binds to IgM [page 3 Polyadenylation does not impair aptamer function]. Spetzler discloses the aptamers used to diagnosis proliferative disease such as cancer. Aghvanyan discloses the method can indicate the presence of a disease while the same techniques applied to the control cohort sample indicate the absence of a disease [pages 61-62 para. 0315-0320]. Here, Delley, Aghvanyan, and Spetzler would yield a step for obtaining sequence data for determining the quantity of cellular component targets for measuring cellular component expression.
Delley teaches aptamers with poly-A tails [Delley, page 2, figure 2]. Delley teaches a cell sample is incubated with a diverse aptamer library containing a poly-A sequence on its 3’ end [page 2 figure 1], as in instant claim 20 wherein the cellular component binding aptamer comprises a poly(dA) region.
Fu discloses a solid support can be a biological molecule. Fu discloses the biological molecule can be nucleic acid, a protein, an antibody, a histone, a cellular compartment, a lipid, a carbohydrate, and the like. Fu discloses solid supports can be amplified, translated, transcribed. Fu discloses the biomolecule can comprise a first confirmation when unmodified, but can change to a second confirmation when modified. Fu discloses the different conformations can expose stochastic barcodes of the disclosure to targets. Fu discloses a biological molecule can comprise stochastic barcodes that are inaccessible due to folding of the biological molecule. Fu discloses that modification of the biological molecule (e.g., acetylation), the biological molecule can change conformation to expose the stochastic labels. Fu discloses the timing of the modification can provide another time dimension to the method of stochastic barcoding of the disclosure [Fu, page 18 left col para 0138]. Delley teaches aptamers with poly-A tails [Delley, page 2, figure 2]. Delley teaches a cell sample is incubated with a diverse aptamer library containing a poly-A sequence on its 3’ end [page 2 figure 1], as in claim 20 wherein the aptamer specific oligonucleotide changes from a first conformation in which the poly(dA) region is inaccessible to a second conformation in which the poly(dA) region is accessible when the aptamer contacts the at least one of the cellular component targets. Here, Fu discloses a biomolecule that can comprise a nucleic acid, a protein, an antibody, a histone, a cellular compartment, a lipid, a carbohydrate, and the like and discloses the biomolecule can comprise a first confirmation when unmodified, but can change to a second confirmation when modified. Thus, it would be obvious to utilize the aptamers containing poly A tails (i.e., nucleic acid sequence/solid support) of Delley as biological molecule that can comprise stochastic barcodes (i.e., aptamer) that are inaccessible due to folding of the biological molecule [Fu, page 18 left col para 0138]. Therefore, using aptamers that can fold to hide and make accessible polyA tails upon contact with a cellular component is rendered obvious.
It would be obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Spetzler in view of Delley because Delley teaches determining the counts of the aptamer TD05 which is determined by sequencing. One of ordinary skill in the art would be motivated to combine Spetzler in view of Delley because Delley teaches measuring the counts of TD05 which targets IgM to determine sample identification of mouse 3T3 cells. Here, there is a reasonable expectation of success that combining the partitioning and contacting methods of Spetzler with the counting of UMI’s for detecting mouse 3T3 of Delley would yield predictable method steps for measuring cellular components expression in cells.
It would be obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Spetzler in view of Delley in view of Aghvanyan because Aghvanyan discloses improved assay methods by detecting an analyte of interest [Aghvanyan, claim 1]. One of ordinary skill in the art would be motivated to combine Spetzler in view of Delley in view of Aghvanyan because Aghvanyan discloses methods for binding, capturing, extending, hybridizing, and measuring the amount of the extended sequence bound to the surface which discloses methods for using nucleic acid sequences for detecting analytes of interest in a sample. Here, there is a reasonable expectation of success that combining the extension processes of Aghvanyan with the identifying at least one aptamer method of Spetzler and identifying a sample of mouse 3T3 cells of Delley would yield a predictable method for identifying a sample or identifying the origin of a sample and measuring cellular component expression.
It would be obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Spetzler in view of Delley in view of Aghvanyan in view of Fu because Fu discloses methods for labeling targets using solid biomolecules comprising nucleic acid, a protein, an antibody, a histone, a cellular compartment, a lipid, a carbohydrate, and the like and using biomolecules conformations which expose barcodes (i.e., nucleic acids) of the disclosure to targets. Here, although Fu does not explicitly disclose biological molecules (i.e., aptamer) that are inaccessible due to folding of the biological molecule and upon modification of the biological molecule (e.g., acetylation) the biological molecule can change conformation to expose the stochastic labels (i.e., nucleic acids), one of ordinary skill in the art would recognize that nucleic acids molecules/sequences can be substituted such that the stochastics barcode can be replaced by an aptamer. One of ordinary skill in the art would be motivated to utilize and substitute the nucleic acids of the aptamers of Tan and Delley for the stochastic barcodes and of Fu in order to construct a molecule that can hide a polyA tail and upon ligand/receptor interaction or modification the polyA tail can then be accessible. Thus, there would be a reasonable expectation of success to combine the aptamers of Tan and Delley and the improved assay method of Aghvanyan with the biomolecules of Fu to yield a predictable biomolecule that can change molecular conformations to make an aptamer inaccessible or accessible upon contact to cellular component target.
Claim(s) 23 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tan in view of Delley in view of Fu.
Claim 23 recites composition comprising: a plurality of cellular component-binding aptamers. Claim 23 recites wherein each of the plurality of cellular component-binding aptamers comprises an aptamer specific oligonucleotide comprising a unique identifier sequence for the cellular component-binding aptamer. Claim 23 recites wherein the cellular component-binding aptamer is capable of specifically binding to at least one of a plurality of cellular component targets. Claim 23 recites wherein the cellular component binding aptamer comprises a poly(dA) region. Claim 23 recites wherein the aptamer specific oligonucleotide changes from a first conformation in which the poly(dA) region is inaccessible to a second conformation in which the poly(dA) region is accessible when the aptamer contacts the at least one of the cellular component targets.
Tan teaches an aptamer composition for identifying molecular interactions comprising aptamers which specifically bind a target molecule [claim 1], as in instant claim 23 composition comprising a plurality of cellular component-binding aptamers.
Tan teaches producing aptamers specific for a target molecule, selecting aptamers that bind to different epitopes on the target molecule, and linking the selected aptamers with a linking molecule thereby, increasing the selectivity and affinity of the aptamers for a target molecule [claim 32]. Tan discloses a human alpha-thrombin has two aptamers, with only one able to inhibit enzymatic activity of thrombin. The 15mer (i.e., 15Ap) and 27mer (i.e., 27Ap) (i.e., unique identifier(s)) were linked with 18 atoms as a spacer. Eight units of each spacer were used to link the two aptamers to form DA-8S [Spec page 22 left col. 0258], as in instant claim 23 wherein each of the plurality of cellular component-binding aptamers comprises an aptamer specific oligonucleotide comprising a unique identifier sequence for the cellular component-binding aptamer and wherein the cellular component-binding aptamer is capable of specifically binding to at least one of a plurality of cellular component targets. Here, in light of the specification [Spec page 73 para. 0251], Tan makes obvious unique identifier sequence because Tan discloses a human alpha-thrombin has two aptamers, with only one able to inhibit enzymatic activity of thrombin. Tan teaches that a 15mer (i.e., 15Ap) and 27mer (i.e., 27Ap) (e.g., unique identifiers) were linked with 18 atoms as a spacer. Tan teaches that eight units of each spacer were used to link the two aptamers to form DA-8S [Spec page 22 left col. 0258].
Tan does not disclose claim 23 wherein the cellular component binding aptamer comprises a poly(dA) region. Tan does not disclose claim 23 wherein the aptamer specific oligonucleotide changes from a first conformation in which the poly(dA) region is inaccessible to a second conformation in which the poly(dA) region is accessible when the aptamer contacts the at least one of the cellular component targets.
Delley teaches aptamers with poly-A tails [Delley, page 2, figure 2]. Delley teaches a cell sample is incubated with a diverse aptamer library containing a poly-A sequence on its 3’ end [page 2 figure 1]. Delley teaches aptamers with poly-A tails [Delley, page 2, figure 2]. Delley teaches a cell sample is incubated with a diverse aptamer library containing a poly-A sequence on its 3’ end [page 2 figure 1]. Delley also teaches unique identifiers such as computationally grouping reads to single cells using barcodes and then to single molecules using unique molecular identifiers (UMI’s). Here, Delley teaches using the aptamer, TD05, for identifying mouse 3T3 cells which teaches an indexing sample oligonucleotide to identify one or more cells in a sample [page 3 apt-seq provides independent information form RNAseq for inferring cell-type]. Delley teaches “a two-dimensional histogram of counts per aptamer per cell. The order of the cells is the same as in (a). (c) Two-dimensional histogram of the transcript counts for the 200 most variable transcript equivalence classes. The maximum read number is truncated at 100.” Delley teaches aptamer UMI count [page 4 figure 3], as in instant claim 23 wherein the cellular component binding aptamer comprises a poly(dA) region.
Fu discloses a solid support can be a biological molecule. Fu discloses the biological molecule can be nucleic acid, a protein, an antibody, a histone, a cellular compartment, a lipid, a carbohydrate, and the like. Fu discloses solid supports can be amplified, translated, transcribed. Fu discloses the biomolecule can comprise a first confirmation when unmodified, but can change to a second confirmation when modified. Fu discloses the different conformations can expose stochastic barcodes of the disclosure to targets. Fu discloses a biological molecule can comprise stochastic barcodes that are inaccessible due to folding of the biological molecule. Fu discloses that modification of the biological molecule (e.g., acetylation), the biological molecule can change conformation to expose the stochastic labels. Fu discloses the timing of the modification can provide another time dimension to the method of stochastic barcoding of the disclosure [Fu, page 18 left col para 0138], as in instant claim 20 wherein the aptamer specific oligonucleotide changes from a first conformation in which the poly(dA) region is inaccessible to a second conformation in which the poly(dA) region is accessible when the aptamer contacts the at least one of the cellular component targets. Here, Fu discloses a biomolecule that can comprise a nucleic acid, a protein, an antibody, a histone, a cellular compartment, a lipid, a carbohydrate, and the like and discloses the biomolecule can comprise a first confirmation when unmodified, but can change to a second confirmation when modified. Thus, it would be obvious to utilize the aptamers containing poly A tails (i.e., nucleic acid sequence/solid support) of Delley as biological molecule that can comprise stochastic barcodes (i.e., aptamer) that are inaccessible due to folding of the biological molecule [Fu, page 18 left col para 0138]. Therefore, using aptamers that can fold to hide and make accessible polyA tails upon contact with a cellular component is rendered obvious.
It would be obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Tan in view of Delley because Delley teaches a system using aptamers for cell-surface profiling [Delley, page 2 results]. One of ordinary skill in the art would be motivated to combine Tan in view of Delley because Delley teaches using libraries of aptamers for inferring cell type (i.e., using the method to profile Ramos and 3T3 cell). Here, there is a reasonable expectation of success to combine the aptamers with polyA tails of Delley with the aptamers of Tan construct a composition of aptamers. Therefore, combining the aptamers of Tan and Delley would yield a predictable composition of aptamers for cellular-binding. Here, the aptamers of Tan and Delley could be used to construct aptamer compositions to target the cell(s) in order identify the cellular origin/cell type profiling of the sample. Therefore, combining Tan in view of Delley would yield a predictable aptamer composition comprising cellular component-binding aptamers.
It would be obvious to one of ordinary skill in the art by the effective filing date of the claimed invention to modify Tan in view of Delley in view of Fu because Fu discloses methods for labeling targets using solid biomolecules comprising nucleic acid, a protein, an antibody, a histone, a cellular compartment, a lipid, a carbohydrate, and the like and using biomolecules conformations which expose barcodes (i.e., nucleic acids) of the disclosure to targets. Here, although Fu does not explicitly disclose biological molecules (i.e., aptamer) that are inaccessible due to folding of the biological molecule and upon modification of the biological molecule (e.g., acetylation) the biological molecule can change conformation to expose the stochastic labels (i.e., nucleic acids), one of ordinary skill in the art would recognize that nucleic acids molecules/sequences can be substituted such that the stochastics barcode can be replaced by an aptamer. One of ordinary skill in the art would be motivated to utilize and substitute the nucleic acids of the aptamers of Tan and Delley for the stochastic barcodes of Fu in order to construct a molecule that can hide a polyA tail and upon ligand/receptor interaction or modification of the polyA tail, the polyA tail can then be accessible. Thus, there would be a reasonable expectation of success to combine the aptamers of Tan and Delley with the solid biomolecules of Fu to yield a predictable biomolecule that can change molecular conformations to make an aptamer inaccessible or accessible upon contact to cellular component-binding target.
Response to Arguments
Applicant’s amendments, filed 06 February 2026, have been fully considered and the rejection is maintained. However, it is noted the amendments received 06 February 2026 necessitated new ground(s) of rejection. Here, Delley, Tan, Fu, Spetzler, Aghvanyan, Heil, and Ku address the amendments received 06 February 2026.
The Applicant disagrees with the rejection claims 18-19. The Applicant points to KSR for guidance. The Applicant states Tan and Delley, in combination and/or individually, do not teach or suggest the composition comprising the presently recited second cellular component-binding aptamer of claim 18. The Applicant points to the specification [0271] for guidance. The Applicant states claim 18 is patentable over Delley and Tan [remarks, pages 14-15].
In response, it is noted the specification [pages 83-84, para 0271] merely discloses how component-binding agents (i.e., antibody cocktails) increase labeling sensitivity, and the cocktail of cellular component-binding reagents can include two or more different types of cellular component binding reagents, for example, a wider range of cellular component binding reagents or antibodies. Additionally, it discloses the different component targets can be pooled together to create a cocktail of different labels for cell types of interests. Here, however, the specification does not distinctly disclose any particular second cellular component-binding aptamers. Thus, the aptamers of Tan, Delley, and Fu read of the second cellular component-binding aptamers of the instant claims. For example and as noted in the 103 rejection of claims 18-19, Delley teaches using a library of aptamers (i.e., TD05, sgc3b, and sgc8a) that is able to bind to TD05, sgc3b, and sgc8a have reported protein targets, the membrane bound IgM, L-selectin, and PKT7) [page 3 polyadenylation does not impair aptamer function].Furthermore, as note in the above 103 rejection of claims 18-19, Fu also discloses stochastic barcode can refer to a polynucleotide sequence that can be used to stochastically label (e.g., barcode tag) a target. Fu discloses the stochastic barcode can comprise one or more labels. Fu discloses exemplary labels can include a universal label, a cellular label, a molecular label, a sample label, a plate label, a spatial label, and/or a pre-spatial label [Fu, pages 10-11 para 0090 right col].
Therefore, in light of the specification [pages 83-84, para 0271], Tan, Delley, and Fu teach variations of compositions that encompasses cellular component-binding aptamers, such asTD05, sgc3b, and sgc8a that can target membrane bound IgM, L-selectin, and PKT7) which reads on the second cellular component-binding aptamers of claims 18-19.
It is noted that the arguments received 06 February 2026 are also in reference to the newly filed amendments received 06 February 2026. As noted in the above 103 rejection, Delley, Tan, Fu, Spetzler, Aghvanyan, Heil, and Ku address the amendments received 06 February 2026.
Double Patenting
The instant rejection is maintained for reason for record in the Office Action mailed 06 November 2025 and modified in view of the amendments filed 06 February 2026. It is noted the amendments received 06 February 2026 are necessitated by new ground(s) of rejection.
The rejection of claim 23 on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5, 10, and 13 of U.S. Patent No. US 11,460,468 (‘468) in the Office Action mailed 06 November 2025 is withdrawn in view of the arguments and amendments received 06 February 2026.
The rejection of claims 20, 22, and 23 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4, 7, and 13 of U.S. Patent No. U.S 10,338,066 (‘066) in the Office Action mailed 06 November 2025 is withdrawn in view of the arguments and amendments received 06 February 2026.
The rejection of claims 18 and 23 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 12 of U.S. Patent No. US 11,397,882 (‘882) in the Office Action mailed 06 November 2025 is withdrawn in view of the arguments and amendments received 06 February 2026.
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.
US 11,460,468 (‘468)
Claim 18-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5, 10, and 13 of U.S. Patent No. US 11,460,468 (‘468).
Claim 18
Claim 18 recites wherein each of the plurality of sample indexing compositions comprises an aptamer composition comprising a first cellular component-binding aptamer and a sample indexing oligonucleotide. Claims 18 recites wherein the cellular component-binding aptamer 1s capable of specifically binding to at least one cellular component target. Claim 18 recites wherein the sample indexing oligonucleotide comprises a sample indexing sequence for identifying sample origin of one or more cells of a sample. Claim 18 recites wherein sample indexing sequences of at least two sample indexing compositions of the plurality of sample indexing compositions comprise different sequences.
Claim 18 recites wherein a sample indexing composition comprises a second cellular component binding aptamer. Claim 18 recites wherein the cellular component-binding aptamer and the second cellular component-binding aptamer are capable of binding to different cellular component targets. Claim 18 recites wherein the second cellular component-binding aptamer is associated with a second sample indexing oligonucleotide comprising a second sample indexing sequence. Claim 18 recites wherein the sample indexing sequence and the second sample indexing sequence are identical
(‘468) discloses plurality of compositions, wherein the plurality of compositions comprises at least 100 protein-binding compositions each comprising a protein binding reagent associated with an oligonucleotide, wherein the oligonucleotide comprises a target region and a unique identifier sequence for the protein binding reagent that it is associated therewith, wherein the unique identifier sequence comprises a nucleotide sequence of less than 30 nucleotides in length, wherein the target region is at the 3' region of the oligonucleotide and the protein binding reagent is capable of specifically binding to a protein target [claims 1 and 10]. (‘468) discloses the composition can comprise an antibody, an aptamer, or a combination thereof [claim 5]. (‘468) discloses embodiments, the cell identification oligonucleotide comprises a barcode sequence, a binding site for a universal primer, or a combination thereof [disclosure col 25 lines 40-45]. (‘468) discloses the barcode sequences of at least two barcodes of the plurality of barcodes can comprise different sequences [disclosure col 10 15-20], as in instant claim 18 wherein each of the plurality of sample indexing compositions comprises an aptamer composition comprising a first cellular component-binding aptamer and a sample indexing oligonucleotide, wherein the cellular component-binding aptamer is capable of specifically binding to at least one cellular component target, wherein the sample indexing oligonucleotide comprises a sample indexing sequence for identifying sample origin of one or more cells of a sample.
(‘468) discloses 100 protein-binding compositions each comprising a protein binding reagent associated with an oligonucleotide [(‘468, claim 1]. (‘468) discloses the protein binding reagent can be an aptamer [(‘468), claim 1]. (‘468) discloses a protein binding reagent and second protein binding protein [(‘468), claim 1]. (‘468) discloses the protein target is a cell-surface protein, a cell marker, a B-cell receptor, a T-cell receptor, antibody [(‘468), claim 13]. (‘468) discloses the target nucleic acid sequence-bearing molecules may be modified to attach universal adapters (e.g., non-target nucleic acid sequences) to one or both ends of the different target nucleic acid sequences [(‘468), col 55 lines 55-59], as in instant claim 18 wherein a sample indexing composition comprises a second cellular component-binding aptamer, wherein the cellular component-binding aptamer and the second cellular component-binding aptamer are capable of binding to different cellular component targets, and wherein the second cellular component-binding aptamer is associated with a second sample indexing oligonucleotide comprising a second sample indexing sequence.
(‘468) discloses the protein binding reagent and second protein binding reagent. [(‘468), claim 1]. (‘468) discloses the cell identification composition of the plurality of cell identification compositions can comprise a second antigen binding reagent not conjugated with the cell identification oligonucleotide. (‘468) discloses the antigen binding reagent and the second antigen binding reagent can be identical [(‘468), col 27 lines 35-41]. (‘468) discloses the target nucleic acid sequence-bearing molecules may be modified to attach universal adapters (e.g., non-target nucleic acid sequences) to one or both ends of the different target nucleic acid sequences [(‘468), col 55 lines 55-59]. (‘468) discloses at least 100 protein-binding compositions each comprising a protein binding reagent associated with an oligonucleotide, wherein the oligonucleotide comprises a target region and a unique identifier sequence for the protein binding reagent that it is associated [(‘468), claim 1], as in instant claim 18 wherein the sample indexing sequence and the second sample indexing sequence are identical.
.
Dependent claim(s): 19
(‘468) discloses plurality of compositions, wherein the plurality of compositions comprises at least 100 protein-binding compositions each comprising a protein binding reagent associated with an oligonucleotide, wherein the oligonucleotide comprises a target region and a unique identifier sequence for the protein binding reagent that it is associated therewith, wherein the unique identifier sequence comprises a nucleotide sequence of less than 30 nucleotides in length, wherein the target region is at the 3' region of the oligonucleotide and the protein binding reagent is capable of specifically binding to a protein target [claims 1 and 10], as in instant claim 19.
Although the claims at issue are not identical, they are not patentably distinct from each other because then instant claims can be practiced with the claims of (‘468). Here, the both claim sets (i.e., (‘468) and the instant claims) provide compositions of protein binding agents that can comprise aptamers. Furthermore, and although the claims of (‘468) and the instant have minute differences, the limitations of the two claim sets are not patentably distinct, overlap, and have similar scope and/or breathe.
U.S 10,338,066 (‘066)
Claims 1 3, 7, and 15 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4, 7, and 13 of U.S. Patent No. U.S 10,338,066 (‘066).
Claim 1
Claim 1 recites providing a plurality of samples, wherein each of the plurality of samples comprises 100 or more cells each comprising one or more cellular component targets. Claim 1 recites contacting each of the plurality of samples with a sample indexing composition of a plurality of sample indexing compositions, respectively. Claim 1 recites wherein the sample indexing composition comprises an aptamer composition comprising an aptamer and a sample indexing oligonucleotide. Claim 1 recites wherein the aptamer is capable of specifically binding to at least one of the one or more cellular component targets. Claim 1 recites wherein the sample indexing oligonucleotide comprises a sample indexing sequence, and wherein sample indexing sequences of at least two sample indexing compositions of the plurality of sample indexing compositions comprise different sequences. Claim 1 recites pooling the plurality of samples to form a combined labeled sample. Claim 1 recites identifying sample origin of at least one cell 100 cells of the 100 or more cells based on the sample indexing sequence of at least one sample indexing oligonucleotide of the plurality of sample indexing compositions. Claim 1 recites wherein identifying the sample origin of a cell of the at least one cell 100 cells comprise identifying the presence or absence of the sample indexing sequence of at least one sample indexing oligonucleotide of the plurality of sample indexing compositions.
(‘066) discloses other technologies allow measurement of gene expression of 96 to 385 single cells [disclosure col 1 lines 40-45]. (‘066) discloses a plurality of cells and the second plurality of cells comprises single cells [disclosure col 26 lines 45-48]. (‘066) discloses “In some embodiments, identifying the sample origin of the at least one cell comprises identifying sample origin of the plurality of barcoded targets based on the cell identification sequence of the at least one barcoded cell identification oligonucleotide” [disclosure col 28 lines 35-43], as in instant claim 1 providing step.
(‘066) discloses a contacting a plurality of oligonucleotide-conjugated antibodies with a plurality of cells comprising protein targets wherein each of the plurality of oligonucleotide-conjugated antibodies comprises an antibody conjugated with an antibody specific oligonucleotide comprising a unique identifier for the antibody conjugated therewith and a poly(A) tail, and wherein the antibody is capable of specifically binding to at least one of the plurality of protein targets [claims 1 and 13], as in instant claim 1 contacting step.
(‘066) discloses the compositions can comprise antibodies, aptamers or combination thereof [disclosure col 2 lines 5-9]. (‘066) discloses “The cellular component binding reagent can comprise a cell surface binding reagent, an antibody, a tetramer, an aptamer, a protein scaffold, an invasion, or a combination thereof [disclosure col 21 lines 1-7]. (‘066) discloses “In some embodiments, the plurality of protein targets comprises a cell-surface protein, a cell marker, a B-cell receptor, a T-cell receptor, an antibody, a major histocompatibility complex, a tumor antigen, a receptor, or any combination thereof. In some embodiments, the plurality of protein targets can comprise intracellular proteins [claim 7], as in instant claim 1 wherein the sample indexing oligonucleotide comprises a sample step.
(‘066) discloses wherein the first control barcode sequence and the second control barcode sequence have different sequences [disclosure col 8 lines 24-28]. (‘066) discloses the compositions can comprise antibodies, aptamers or combination thereof [disclosure col 2 lines 5-9]. (‘066) discloses “the antigen binding reagent comprises an antibody, a tetramer, an aptamer, a protein scaffold, or a combination thereof. The cell identification oligonucleotide can be conjugated to the antigen binding reagent through a linker.” [disclosure col 26 lines 34-39], as in instant claim 1 wherein the sample indexing oligonucleotide comprises step.
(‘066) discloses other technologies allow measurement of gene expression of 96 to 385 single cells [disclosure col 1 lines 40-45]. (‘066) discloses a plurality of cells and the second plurality of cells comprises single cells [disclosure col 26 lines 45-48]. (‘066) discloses “In some embodiments, identifying the sample origin of the at least one cell comprises identifying sample origin of the plurality of barcoded targets based on the cell identification sequence of the at least one barcoded cell identification oligonucleotide” [disclosure col 28 lines 35-43]. (‘066) discloses the samples are pooled [fig 3]. (‘066) discloses the labeled targets are pooled. (‘066) discloses labeled targets from cells are pooled [(‘066), col 85 lines 50-67], as in instant claim 1 pooling step.
(‘066) discloses “In some embodiments, identifying the sample origin of the at least one cell comprises identifying sample origin of the plurality of barcoded targets based on the cell identification sequence of the at least one barcoded cell identification oligonucleotide” [disclosure col 28 lines 35-43]. (‘066) discloses other technologies allow measurement of gene expression of 96 to 385 single cells [disclosure col 1 lines 40-45]. (‘066) discloses a plurality of cells and the second plurality of cells comprises single cells [disclosure col 26 lines 45-48]. (‘066) discloses “In some embodiments, identifying the sample origin of the at least one cell comprises identifying sample origin of the plurality of barcoded targets based on the cell identification sequence of the at least one barcoded cell identification oligonucleotide” [disclosure col 28 lines 35-43], as in instant claim 1 identifying and wherein identifying steps.
Dependent claim(s): 3, 7, and 15
(‘066) discloses contacting a barcoded particle [claims 1 and 13 step (c)]. (‘066) discloses extending the oligonucleotide probes hybridized to the antibody specific oligonucleotides via the hybridization between the poly(A) tails of the antibody specific oligonucleotides and the poly(T) regions of the oligonucleotide probes to produce a plurality of labeled nucleic acids, wherein each of the labeled nucleic acid comprises a unique identifier, or a complementary sequence thereof, and a barcode sequence [claims 1 and 13 steps (d)]. (‘066) discloses obtaining sequence data [claims 1 and 13 steps (e)]. (‘066) discloses “In some embodiments, identifying the sample origin of the at least one cell comprises identifying sample origin of the plurality of barcoded targets based on the cell identification sequence of the at least one barcoded cell identification oligonucleotide” [disclosure col 28 lines 35-43]. (‘066) discloses other technologies allow measurement of gene expression of 96 to 385 single cells [disclosure col 1 lines 40-45]. (‘066) discloses a plurality of cells and the second plurality of cells comprises single cells [disclosure col 26 lines 45-48]. (‘066) discloses “In some embodiments, identifying the sample origin of the at least one cell comprises identifying sample origin of the plurality of barcoded targets based on the cell identification sequence of the at least one barcoded cell identification oligonucleotide” [disclosure col 28 lines 35-43], as in instant claim 3.
(‘066) discloses contacting oligonucleotides-conjugated antibodies with a plurality of cells [claims 1 and 13 steps (a)]. (‘066) discloses that a barcode can comprise a capture probe [disclosure col 67 lines 19-21]. (‘066) discloses extending the oligonucleotide probes hybridized to the antibody specific oligonucleotides via the hybridization between the poly(A) tails of the antibody specific oligonucleotides and the poly(T) regions of the oligonucleotide probes to produce a plurality of labeled nucleic acids, wherein each of the labeled nucleic acid comprises a unique identifier, or a complementary sequence thereof, and a barcode sequence [claims 1 and 13 steps (d)]. (‘066) discloses “For each single cell, the mRNA molecules were reverse transcribed and the antibody oligonucleotides were replicated using stochastic barcodes conjugated with a bead for the cell. The samples after reverse transcription and replication were PCR amplified for 15 cycles” [disclosure col 192 lines 30-37], as in instant claim 7. Here, it is obvious to replicate sample indexing oligonucleotides to generate replicated sample indexing oligonucleotides because it is known that before replicating barcode sequences or target sequences that first barcode must come into contact with the sample and the barcodes probes are extended and hybridized prior to replicating.
(‘066) discloses extending the oligonucleotide probes hybridized to the antibody specific oligonucleotides via the hybridization between the poly(A) tails of the antibody specific oligonucleotides and the poly(T) regions of the oligonucleotide probes to produce a plurality of labeled nucleic acids, wherein each of the labeled nucleic acid comprises a unique identifier, or a complementary sequence thereof, and a barcode sequence [claims 1 and 13 steps (d)], as in instant claim 15.
Although the claims at issue are not identical, they are not patentably distinct from each other because then instant claims can be practiced with the claims of (‘066). Here, the both claim sets (i.e., (‘066) and the instant claims) provide compositions of protein binding agents that can comprise aptamers. Furthermore, and although the claims of (‘066) and the instant have minute differences, the limitations of the two claim sets are not patentably distinct, they overlap, and they have similar scope and/or breathe.
US 11,397,882 (‘882)
Claims 1, 3, and 11 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 12 of U.S. Patent No. US 11,397,882 (‘882).
Claim 1
Claim 1 recites providing a plurality of samples, wherein each of the plurality of samples comprises 100 or more cells each comprising one or more cellular component targets. Claim 1 recites contacting each of the plurality of samples with a sample indexing composition of a plurality of sample indexing compositions, respectively. Claim 1 recites wherein the sample indexing composition comprises an aptamer composition comprising an aptamer and a sample indexing oligonucleotide. Claim 1 recites wherein the aptamer is capable of specifically binding to at least one of the one or more cellular component targets. Claim 1 recites wherein the sample indexing oligonucleotide comprises a sample indexing sequence, and wherein sample indexing sequences of at least two sample indexing compositions of the plurality of sample indexing compositions comprise different sequences. Claim 1 recites pooling the plurality of samples to form a combined labeled sample.Claim 1 recites identifying sample origin of at least one cell 100 cells of the 100 or more cells based on the sample indexing sequence of at least one sample indexing oligonucleotide of the plurality of sample indexing compositions. Claim 1 recites wherein identifying the sample origin of a cell of the at least one cell 100 cells comprise identifying the presence or absence of the sample indexing sequence of at least one sample indexing oligonucleotide of the plurality of sample indexing compositions.
(‘882) discloses for each cell of a plurality of cells in a sample, using a plurality of stochastic barcodes to stochastically barcode a plurality of nucleic acid targets and thereby generate a plurality of stochastically barcoded nucleic acid targets from RNA from the cell, wherein each stochastic barcode of the plurality of stochastic barcodes comprises a molecular label [claim 1 step (a)]. (‘882) discloses the sample can contain or more cells [disclosure col 81 lines 19-25], as in instant claim 20 providing step. (‘882) discloses the cleavable linker can be an aptamer [disclosure 48 lines 60-64]. (‘882) discloses the barcode can refer to polynucleotide sequence comprising labels and target-biding region [disclosure col 30 lines 5-15]. Here, it is obvious the sample contain 100 or more cells.
(‘882) discloses contacting a sample and a stochastic barcode or contacting sample (i.e., cells) to a substrate of the disclosure [disclosure col 43 lines 50-65], as in claim 1 contacting step.
(‘882) discloses for each cell of a plurality of cells in a sample, using a plurality of stochastic barcodes to stochastically barcode a plurality of nucleic acid targets and thereby generate a plurality of stochastically barcoded nucleic acid targets from RNA from the cell, wherein each stochastic barcode of the plurality of stochastic barcodes comprises a molecular label [claim 1 step (a)]. (‘882) discloses the sample can contain or more cells [disclosure col 81 lines 19-25]. (‘882) discloses the labeled targets can be and are pooled [(‘882), col 45 lines 50-59]. (‘882) discloses labeling targets [(‘882), claims 1-8], as in claim 1 pooling the plurality of samples to form a combined labeled sample
(‘882) discloses the one or more universal primers when the non - depleting reservoir is associated with a pool of attached to the target nucleic acid can be the same or different from each other [disclosure col 25 lines 50-56]. (‘882) discloses identifying a cell type of each of the plurality of cells based on the RNA expression profile by correlating the number of the nucleic acid target(s) estimated in (c) with the cell type [claims 1 and 12 steps (e)], as in claim 1 wherein the sample indexing oligonucleotide and wherein the sample origin step. Here, identifying the sample origin is obvious because identifying cell types encompasses identifying cellular origin which encompass identifying a sample cellular origin.
Dependent claims 3 and 11
(‘882) discloses the barcode can refer to polynucleotide sequence comprising labels and target-biding region [disclosure col 30 lines 5-15]. (‘882) discloses obtaining sequencing data [claims 1 and 12 step (b)]. (‘882) discloses “targets can be single or double stranded. In some embodiments targets can be proteins. In some embodiments targets are lipids.” [disclosure col 30 lines 30-33], as in instant claim 3.
(‘882) discloses using a plurality of stochastic barcoded nucleic acids comprising molecule label [claims 1 and 2 step (a)]. (‘882) discloses “targets can be single or double stranded. In some embodiments targets can be proteins. In some embodiments targets are lipids.” [disclosure col 30 lines 30-33]. (‘882) discloses “As used herein, the term "gene-specific stochastic barcode" can refer to a polynucleotide sequence comprising labels and a target-binding region that is gene-specific [disclosure col 30 lines 5-15], as in instant claim 11. Here, it is obvious to use a second aptamer and a second sample indexing oligonucleotide because the claims can target samples containing cell, tissues, organs, and organisms which requires using multiple aptamers and indexing nucleotides.
Although the claims at issue are not identical, they are not patentably distinct from each other because then instant claims can be practiced with the claims of (‘882). Here, the both claim sets (i.e., (‘882) and the instant claims) provide compositions of protein binding agents that can comprise aptamers. Furthermore, and although the claims of (‘882) and the instant have minute differences, the limitations of the two claim sets are not patentably distinct, the claims overlap, and the claims have similar scope and/or breathe.
Response to Arguments
Applicant's arguments filed 06 February 2026, have been fully considered and the rejections are maintained.
The Applicant disagrees with the double patenting rejections. The Applicant request the Examiner to hold the rejection in abeyance until the present application is otherwise in condition for allowance.
In response, the rejection in not held in abeyance because holding a rejection is not an appropriate response to a double patenting rejection. Furthermore, a request to hold a rejection in abeyance is not a proper response to a rejection. Rather, a request to hold a matter in abeyance may only be made in response to an OBJECTION or REQUIREMENTS AS TO FORM (see 37 CFR 1.111(b) and MPEP §714.02). Thus, the double patenting rejections of record have been maintained as no response to these rejections has been filled by applicant at this time.
Conclusion
Claim(s) 1-3, 5-20, and 22-24 are rejected.
No claims are allowed.
Finality
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.
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/J.C.P./ Examiner, Art Unit 1687
/Anna Skibinsky/
Primary Examiner, AU 1635
Prosecution Insights