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 .
Request for Continued Examination (RCE)
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 4/9/26 has been entered.
Priority
This application is a DIV of 15/084,307 (03/29/2016, now US11535882),
15/084,307 has PRO 62/152,644 (04/24/2015),
15/084,307 has PRO 62/140,360 (03/30/2015).
Status
Claims 1, 5-20 are pending.
Rejections not reiterated in this action are withdrawn.
Claim Rejections - 35 USC § 102 over Seelig
Claims 1, 5-12, 14-20 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Seelig et al. (US20160138086, EFD 2014-11-14).
Seelig teaches “methods of uniquely labeling or barcoding molecules within a cell, a plurality of cells” (Abstract) for sequencing ([0052]-[0061]) as shown in Fig. 8:
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wherein the combined tags correspond to the component barcodes of the instant claims, the partitions comprise a single cell, the barcodes are unique, comprise a linker, and are combinations that identify the partitions ([0063]: “providing a plurality of nucleic acid tags to each of the at least two aliquots, wherein each barcode sequence of the plurality of nucleic acid tags introduced into a given aliquot is the same, and wherein a different barcode sequence is introduced into each aliquot”; Example 2; [0030]; [0038]: “linker strand that is configured to hold a nucleic acid tag together with an adjacent nucleic acid”; claims 7 and 24).
Regarding claim 5, Seelig teaches linker sequence between the barcodes thus requiring one less than the corresponding number of barcodes linked (i.e. Fig. 8).
Regarding claim 6, Seelig teaches hybridization to the sample (claims 7 and 24, Fig. 8).
Regarding claim 7, Seelig teaches extension of the hybridized target to produce an extension product comprising the barcode (claims 7 and 24, Fig. 8).
Regarding claim 8, Seelig teaches PCR amplification ([0098]).
Regarding claim 9, Seelig teaches pooling (Example 8; [0098]: “PCR tubes can be combined”).
Regarding claim 10, Seelig teaches pooling the products in multiplex PCR and sequencing (Example 8; [0102]).
Regarding claim 11, Seelig teaches grouping the reads using the barcodes ([0102]: “The products can be sequenced on an ILLUMINA® MISEQ™ using paired end sequencing. The sequencing primers can be the standard TRUSEQ™ multiplex primers. Read 1 can sequence the cDNA sequence, while read 2 can cover the unique molecular identifier as well as the 3 barcode sequences (8 nucleotides each). Index read 1 can be used to sequence sample barcodes, so multiple samples may be sequenced together.”).
Regarding claim 12, Seelig teaches using the assembled sequences in identifying markers and haplotyping ([0045] gene specific primer).
Regarding claim 14, Seelig teaches single cell sequencing using the method as per claim 1 detailed above applied to single cell sequencing (Example 2 and 8; [0083]-[0087]: 96 first-round barcodes).
Regarding claim 15, Seelig teaches extension of the hybridized target to produce an extension product comprising the barcode (Example 8).
Regarding claim 16-17, Seelig teaches pooling the products in multiplex PCR and sequencing (Example 8; [0102]).
Regarding claim 18, Seelig teaches grouping the reads using the barcodes ([0102]: “The products can be sequenced on an ILLUMINA® MISEQ™ using paired end sequencing. The sequencing primers can be the standard TRUSEQ™ multiplex primers. Read 1 can sequence the cDNA sequence, while read 2 can cover the unique molecular identifier as well as the 3 barcode sequences (8 nucleotides each). Index read 1 can be used to sequence sample barcodes, so multiple samples may be sequenced together.”).
Regarding claim 19, Seelig teaches the target is an mRNA ([0043]-[0044]).
Regarding claim 20, Seelig teaches the first primer is oligo-dT ([0043]-[0044]).
Response to Remarks - 35 USC § 102 over Seelig
Applicant argues that amended claim 1 requires introducing into each partition m component barcodes and a sample comprising a single cell, and connecting, in each partition, the m component barcodes to generate a combinatorial barcode, and thus is materially different.
Giving the claims their broadest reasonable interpretation, m can equal 1, and thus Seelig anticipates the claimed invention because each of the steps of the claimed invention are taught therein, particularly because the claims are to a method comprising … introducing, … and connecting … to generate a combinatorial barcode. Thus, Applicant’s argument is not persuasive and the rejection maintained.
Claim Rejections - 35 USC § 102 over Nolan
Claims 1, 5-12, 14-19 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Nolan et al. (WO2012106385; cited in 2025-11-13 IDS).
Nolan teaches barcoding for multiplex detection of cells (Abstract) as shown in Fig. 4:
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Nolan teaches the method in claims 113-255, including the use of component barcodes, comprising a unique barcode, linker, and that identifies the origin partition. Nolan teaches sequencing to identify the assembled barcodes (claim 154, 174; [0075]; [0190]-[0206]) wherein the target it mRNA ([0059]). Thus, the claims are anticipated.
Response to Remarks - 35 USC § 102 over Nolan
Applicant argues that Nolan teaches a repeated split/pool workflow while amended claim 1 requires introducing into each partition m component barcodes and a sample comprising a single cell, and connecting, in each partition, the m component barcodes to generate a combinatorial barcode, and thus is materially different. Applicant further argues that Nolan does not disclose the same-partition single-cell workflow of the claimed invention.
Giving the claims their broadest reasonable interpretation, m can equal 1, and thus Nolan anticipates the claimed invention because each of the steps of the claimed invention are taught therein, particularly because the claims are to a method comprising … introducing, … and connecting … to generate a combinatorial barcode. Thus, Applicant’s argument is not persuasive and the rejection maintained.
Claim Rejections - 35 USC § 103 over Seelig and Lausted
Claims 1, 5-20 are rejected under 35 U.S.C. 103 as being unpatentable over Seelig et al. (US20160138086, EFD 2014-11-14) in view of Lausted et al. (Genome Biology 2004, 5:R58, 17 pages).
Seelig teaches as detailed in the 35 USC 102 rejection supra and incorporated herein. Seelig also renders these claims obvious because the level of skill in the art is very high and multiplex nucleic acid analysis of single cells using barcoded arrays was well-known in the art.
Regarding claim 13, Seelig does not teach an inkjet printer for introducing component barcodes into the partitions.
Lausted teaches an “oligonucleotide synthesizer and microarrayer” (title) for delivering oligonucleotides to a microarray (abstract). One of ordinary skill in the art would have readily considered using Lausted’s tool in implementing Seelig’s technique as they are in the same field of endeavor and was well within their technical grasp.
The level of skill in the art is very high such that one of ordinary skill in the art would consider routine the combination of elements from the teaching of the art in the same field of endeavor. One of ordinary skill in the art would have recognized that the results of the combination would be predictable due to the well-known nature and optimizations routinely performed in the art. Thus, one of ordinary skill in the art would have arrived at the invention as claimed with a reasonable expectation of success.
Response to Remarks - 35 USC § 103 over Seelig and Lausted
Applicant argues Seelig does not disclose the amended claim 1 requirement of introducing, into each partition, m component barcodes and a sample comprising a single cell, and connecting, in each partition, the m component barcodes to generate a combinatorial barcode.
This argument is not persuasive for the same reasons as in the 35 USC 102 rejection supra. And further giving the claims their broadest reasonable interpretation, m can equal 1, and thus Seelig anticipates the claimed invention because each of the steps of the claimed invention are taught therein, particularly because the claims are to a method comprising … introducing, … and connecting … to generate a combinatorial barcode. Thus, Applicant’s argument is not persuasive and the rejection maintained.
Double Patenting
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 12188010 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 12157913 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-26 of U.S. Patent No. 12084712 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13 of U.S. Patent No. 12071617 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5-20 of U.S. Patent No. 11932849 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 11932901 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-29 of U.S. Patent No. 11773436 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 13-17 of U.S. Patent No. 11661631 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-19 of U.S. Patent No. 11639517 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-23 of U.S. Patent No. 11390914 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-17 of U.S. Patent No. 10927419 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-29 of U.S. Patent No. 10676779 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-28 of U.S. Patent No. 9567645 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 17-26 of U.S. Patent No. 9637799 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 10151003 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Claims 1, 5-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 10253375 in view of Seelig et al. (US20160138086, EFD 2014-11-14) and Lausted et al. (Genome Biology 2004, 5:R58, 17 pages) as detailed in the 35 USC 103 rejection supra and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because they are to an equivalent method of barcoding a sample using oligonucleotides in a substantially similar manner such that in view of the secondary references renders the claims obvious.
Response to Remarks - Double Patenting
Applicant requests the rejections be held in abeyance until the application is in condition for allowance.
Applicant did not substantively argue the rejection, thus, the rejection is maintained.
Conclusion
No claims allowed.
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/ROBERT H HAVLIN/Primary Patent Examiner, Art Unit 1626
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