DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Rejections - 35 USC § 112
2. The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
3. Claims 55-71 and 73-76 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Amended step e of claim 55 recites the phrase “wherein substantially every compartment in the plurality of compartments comprises at least one STC” and new claim 76 recites the phrase “wherein each compartment in the plurality of compartments comprises at least one STC,” however applicant’s specification does not provide adequate written description of an embodiment wherein “substantially every compartment in the plurality of compartments comprises at least one STC.” The closest basis for this phrase appears to be on pg. 10 lines 1-20 of applicant’s specification, with the recitation of “one to a few nucleic acid targets with STCs are mixed with one barcode template in one droplet.” However, this only discusses a single droplet in a plurality of water-in-oil emulsion droplets, and applicant’s specification further goes on to state “In this way, almost every emulsion droplet with contain at least a barcode template, which will be available for barcode attachment to a nucleic acid target when the target is also present in the droplet.” Examples 1 and 2 of applicant’s specification specifically mention barcode to droplet ratios that enable “95% of droplets containing at least one barcode template” but no similar description is provided regarding the STCs. Applicant’s specification provides no further description or example regarding each compartment comprising at least one STC, therefore this amendment lacks proper written description and constitutes new matter.
Claims 56-71 and 73-75 are further rejected as being dependent on a previously rejected claim.
4. The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
5. Claims 55-71 and 73-76 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
A. The term “substantially” in claim 55 is a relative term which renders the claim indefinite. The term “substantially” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. On pg. 10 of applicant’s specification there is discussion regarding “almost every” droplet comprising a barcode template, and then Examples 1 and 2 of applicant’s specification discuss “95% of droplets containing at least one barcode template,” however there is no similar discussing regarding the degree to which droplets need to be filled in order to have “substantially every compartment comprises at least one STC.” Is substantially greater than 50% but less that 95% (i.e., almost every)? Is substantially relative to other techniques (e.g., 20-30% vs. 10%)? The metes and bounds regarding this limitation are unclear, and therefore the claim is indefinite.
B. Claims 56-71 and 73-76 are further rejected for being dependent on a previously rejected claim.
Claim Rejections - 35 USC § 103
6. 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.
7. 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.
8. Claims 55-60, 73 and 75-76 are rejected under 35 U.S.C. 103 as being unpatentable over Redin et al (Efficient whole genome haplotyping and high-throughput single molecule phasing with barcode-linked reads, BioRxiv 356121, doi: https://doi.org/10.1101/356121, published 2018-06-26) in view of McDermott et al (United States Patent Application No. US20190345636, effectively filed 13 May 2019).
Regarding claim 55, Redin teaches a method for barcoding long DNA fragments (i.e., a sample; pg 2 ¶ 2) comprising providing a collection of long gDNA molecules (i.e., a plurality of samples), each sample comprising a plurality of gDNA molecules. Redin teaches providing a plurality of unique barcode templates, each having a different barcode sequence (pg 4 ¶ 2). Redin teaches binding the plurality of gDNA molecules to tagmentation beads, each tagmentation bead comprising multiple transposomes and each transposome comprising at least one transposon and one transposase (FIG 1 and FIG S1; incubating the samples from (a) and the transposomes from (b) to form at least one strand transfer complex (STC)). Redin teaches the compartmentalization of the plurality of gDNA molecules bound to tagmentation beads with barcode molecules, with functional compartments comprising a single bead (with multiple bound gDNA molecules, i.e., comprises a single sample) and a single barcode molecule (FIG 1 and pg 4 ¶ 2). Redin also teaches the amplification of said barcode molecule within a compartment, and attaching the amplified barcode to the plurality of nucleic acids (FIGs 1 and S1). Redin teaches that the emulsions are broken and the collected library is sequenced and grouped by barcode (i.e., on a per sample basis FIG 1 and associated caption). It is noted that the emulsion PCR taught by Redin comprises a heating step that inherently releases the transposase from the STC and finalizes the breakage of the nucleic acids attached to the STC into tagmented nucleic acid fragments.
Redin does not specifically teach the limitation wherein substantially every compartment comprises at least one STC.
However, McDermott teaches a method wherein barcode beads are compartmentalized with cells using microfluidics, and that parameters are adjusted such that a majority of partitions are occupied allowing for only a small percentage of unoccupied partitions ([0068]).
It would have been obvious to one having ordinary skill in the art to have simply substituted the shaking-based emulsion method taught by Redin with the microfluidic emulsion method taught by McDermott to arrive at the instantly claimed invention with a reasonable expectation of success. One having ordinary skill in the art would have been motivated to make this substitution in order to generate more sequencing data from each experiment, as Redin teaches that compartments comprising only the barcode template or the tagmentation bead will not yield coupled amplicons and that such products are removed from the library (i.e., not analyzed; pg. 4 ¶ 2). In addition, it would have been obvious to one of ordinary skill in the art the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the compartmentalization of nucleic acids for the preparation of sequencing libraries.
Regarding claim 56, Redin teaches a central barcode sequence that is flanked by two primer binding sites (FIG S1, domains H1 and H2 on the barcode oligonucleotide).
Regarding claim 57, Redin teaches that each compartment comprises a single copy of the barcode oligonucleotide (pg 4 ¶ 2).
Regarding claim 58, Redin teaches samples that comprise a plurality of nucleic acid molecules (i.e., targets FIGs 1 and S1).
Regarding claim 59, Redin teaches that the nucleic acid targets are captured and form strand transfer complexes bead-linked transposomes (i.e., transposases and transposons linked to beads) before the compartmentalization step (FIG S1a). Redin teaches that these beads are from Illumina’s Nextera DNA Flex Library Preparation kit (FIG S1 caption and pg 8 ¶ 4), which inherently comprise Tn transposases.
Regarding claim 60, Redin teaches that the nucleic acid target is double stranded gDNA (FIGs 1 and S1).
Regarding claim 73, Redin teaches that the samples and barcode oligonucleotides are compartmentalized in water-in-oil emulsions made with HFE-7500 and 5% 008-Fluorosurfactant as the oil phase (FIG 1 and pg 8-9 ¶ 5 and 1). Droplet sizes within the range of 10-30 µm are inherently formed under these conditions (see evidentiary reference Redin et al, Droplet Barcode Sequencing for target linked-read haplotyping of single DNA molecules, Nucleic Acids Research, 45(13), e125, published 2017-07-27).
Regarding claim 75, Redin teaches that the amplification step comprises PCR (FIGs 1 and S1).
Regarding claim 76, the combination of Redin and McDermott does not specifically teach that each of the plurality of compartments comprises at least one STC and at least one unique barcode template, however, McDermott teaches that microfluidic parameters are selected to ensure a given number of unoccupied partitions (i.e., zero) and/or less than a certain level of multiply occupied partitions (e.g., partitions are multiply occupied to ensure that there are no unoccupied partitions; [0068]).
9. Claims 61-67 and 69-71 are rejected under 35 U.S.C. 103 as being unpatentable over Redin et al (Efficient whole genome haplotyping and high-throughput single molecule phasing with barcode-linked reads, BioRxiv 356121, doi: https://doi.org/10.1101/356121, published 2018-06-26) in view of McDermott et al (United States Patent Application No. US20190345636, effectively filed 13 May 2019) as applied to claim 55 above, and further in view of Cao et al (Joint profiling of chromatin accessibility and gene expression in thousands of single cells, Science, 361, 1380-1385, 2018-09-28).
Regarding claim 61, the method of claim 55 is discussed fully above and incorporated here. Briefly, Redin teaches the capture of samples comprising gDNA targets onto transposase-linked beads, compartmentalizing the samples with barcode molecules, amplifying the barcode molecules in the compartments and attaching them to the sample nucleic acids, then breaking the emulsions and sequencing the resulting library.
Neither Redin nor McDermott teach that each sample comprises a cell or nucleus.
However, Cao teaches a method for the single cell profiling of chromatin accessibility and mRNA wherein nuclei are extracted from cells, mRNA are indexed in situ, and accessible gDNA is indexed by transposase tagmentation (pg 1, columns 1 and 2, ¶ 2-1).
It would have been obvious to one having ordinary skill in the art that the gDNA samples taught by Redin could have simply been substituted with the nuclei samples taught by Cao, to arrive at the instantly claimed invention with a reasonable expectation of success. One having ordinary skill in the art would have been motivated to make this combination because Redin explicitly suggests that low nucleic acid input samples, such as cells, are feasible as future targets for their sequencing technique (pg 7 ¶ 3). In addition, the combinatorial indexing approach taught by Cao is another method to correlate sequencing results to the cells they originated from (pg 1, column 2, ¶ 1), similar to the phasing method taught by Redin. It would have been obvious to the ordinary artisan that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the preparation of sequencing libraries comprising barcodes correlated to a single cell.
Regarding claim 62, Cao teaches that the nuclei are fixed (pg 1, column 1, ¶ 2).
Regarding claim 63, Cao teaches that an RNA-seq index is added in situ (i.e., in the nuclei) by reverse transcription (pg 1, column 1, ¶ 2).
Regarding claim 64, Cao teaches that the cDNA is based on the whole transcriptome by the use of a polyT primer (i.e., a primer that interacts with all polyA-tailed mRNA transcripts; pg 1, column 1, and ¶ 2 and in pg 1, column 3, ¶ 2).
Regarding claim 65, the combination of Redin, McDermott and Cao teaches that nuclei comprising tagged RNAs (i.e., the samples of claim 55 c.) are compartmentalized with barcode molecules and transposome beads in droplets. Cao further teaches that nuclei comprising tagged RNAs are sorted into plates by fluorescence-activated cell sorting (i.e., compartmentalized as they are in the combination of Redin and Cao), second strand synthesis is performed on the cDNA, the nuclei are lysed, and the cDNA is subjected to transposition by a Tn5 transposase (pg 1, column 2, ¶ 1). Transposition of the cDNA by the bead-linked transposases of Redin would inherently result in the formation of strand transfer complexes between the cDNA and the transposomes on the bead’s surface.
Regarding claim 66, Cao teaches that the reverse transcription primer comprises a UMI (pg 1, column 1, ¶ 2).
Regarding claim 67, the combination of Redin, McDermott and Cao teaches that nuclei are compartmentalized in droplets with barcode molecules and bead-linked transposomes. Cao further teaches an in situ transposition reaction that introduces an ATAC-seq index to the nuclear DNA using a Tn5 transposase (i.e., assesses transposase accessible chromatin; pg 1, columns 1 and 2, ¶ 2 and 1). In the combination of Redin and Cao, contacting the nuclei in droplets with the bead-labeled transposomes would inherently result in the formation of strand transfer complexes with the chromatin accessible DNA.
Regarding claim 69, Cao teaches that cells were pre-selected from either mouse or human cell lines (pg 1, column 3, ¶ 1), each cell line having recognizable transcriptome and chromatin accessibility markers (pg 1, column 3, ¶ 3).
Regarding claim 70, Cao teaches that these markers are identified by sequencing (sci-RNA-seq and sci-ATAC-seq; pg 1, column 3, ¶ 3).
Regarding claim 71, Cao teaches that the cell is a human cell (pg 1, columns 2 and 3, ¶ 2 and 1).
10. Claims 61, 62 and 68-71 are rejected under 35 U.S.C. 103 as being unpatentable over Redin et al (Efficient whole genome haplotyping and high-throughput single molecule phasing with barcode-linked reads, BioRxiv 356121, doi: https://doi.org/10.1101/356121, published 2018-06-26) in view of McDermott et al (United States Patent Application No. US20190345636, effectively filed 13 May 2019) as applied to claim 55 above, and further in view of Adey et al (US Patent Application No. US 20180023119 A1, published 2018-01-25).
Regarding claim 61, the method of claim 55 is discussed fully above and incorporated here. Briefly, Redin teaches the capture of samples comprising gDNA targets onto transposase-linked beads, compartmentalizing the samples with barcode molecules, amplifying the barcode molecules in the compartments and attaching them to the sample nucleic acids, then breaking the emulsions and sequencing the resulting library.
Neither Redin nor McDermott teach that the sample comprises a cell or nucleus.
However, Adey teaches a method of preparing a sequencing library comprising whole genome nucleic acids from nucleosome-depleted nuclei (abstract). Adey teaches that nucleosome-depleted nuclei are distributed into compartments and contacted with transposases in order to fragment and index the nucleic acids in preparation for sequencing ([0007]).
It would have been obvious to one having ordinary skill in the art to have simply substituted the gDNA samples taught by Redin with the nucleosome-depleted nuclei taught by Adey to arrive at the instantly claim invention with a reasonable expectation of success. One having ordinary skill in the art would have been motivated to make this combination because Redin explicitly suggests that low nucleic acid in samples, such as cells, are feasible as future targets for their sequencing technique (pg 7 ¶ 3). In addition, the combinatorial indexing technique taught by Adey is another method to correlate sequencing results with cell the originated from ([0005]), similar to the phasing method taught by Redin. It would have therefore been obvious to the ordinary artisan that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the preparation of libraries for single cell sequencing.
Regarding claim 62, Adey teaches that nuclei are cross-linked (i.e., fixed) before nucleosome depletion ([0179], [0180-0184], and [0193]). The combination of Redin and Adey teaches that the nucleosome-depleted nuclei are compartmentalized by the methods taught by Redin, therefore the nuclei are cross-linked before compartmentalization.
Regarding claim 68, the combination of Redin, McDermott and Adey teaches that nucleosome-depleted nuclei (i.e., nuclei comprising whole genomic DNA) are contacted with bead-linked transposomes, each bead comprising a least one transposon and at least one transposase (Redin, FIG S1), prior to compartmentalization. This interaction inherently results in the formation of strand transfer complexes on the beads (Redin, FIG S1), and Redin teaches that these beads are from Illumina’s Nextera DNA Flex Library Preparation kit (FIG S1 caption and pg 8 ¶ 4), which inherently comprises Tn transposases.
Regarding claim 69, Adey teaches that nuclei were pre-selected from human cell lines having recognizable genetic markers ([0253]).
Regarding claim 70, Adey teaches that sequencing reads were processed and aligned to a reference genome (i.e., the markers were identified by sequencing [0253]).
Regarding claim 71, Adey teaches that the nuclei were isolated from human cells ([0253]).
11. Claim 74 is rejected under 35 U.S.C. 103 as being unpatentable over Redin et al (Efficient whole genome haplotyping and high-throughput single molecule phasing with barcode-linked reads, BioRxiv 356121, doi: https://doi.org/10.1101/356121, published 2018-06-26) in view of McDermott et al (United States Patent Application No. US20190345636, effectively filed 13 May 2019) as applied to claim 55 above, and further in view of Fan et al (Combinatorial labeling of single cells for gene expression cytometry, Science, 347, 1258367, published 2015-02-06).
Regarding claim 74, the method of claim 55 is discussed fully above and incorporated here. Briefly, Redin teaches the capture of samples comprising gDNA targets onto transposase-linked beads, compartmentalizing the samples with barcode molecules, amplifying the barcode molecules in the compartments and attaching them to the sample nucleic acids, then breaking the emulsions and sequencing the resulting library.
Neither Redin nor McDermott teach that the compartmentalization step comprises physical compartmentalization with a microwell, a microarray or a microtiter plate.
However, Fan teaches a method wherein cells are lysed in microwells and processed for the preparation of single-cell sequencing libraries (FIG 1).
It would have been obvious to one having ordinary skill in the art that the emulsion-based compartmentalization taught by Redin could simply be substituted for the microwell compartmentalization taught by Fan to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this combination because microwell arrays are reproducible (Fan; pg 6, column 3, ¶ 2 and pg 7, column 1, ¶ 1) and microwell arrays do not impose restrictions on cell sizes (i.e., input sample heterogeneity) allowing for the direct analysis of complex samples such as PBMCs (Fan; pg 5, column 3, ¶ 1). In addition, it would have been obvious to one having ordinary skill in the art that the known techniques of the cited references could have been combined with predictable results, because the known techniques of the cited references predictably result in the compartmentalization of samples for the formation of single cell sequencing libraries.
Double Patenting
12. 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.
13. Claims 55, 58-68, 74 and 76 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16, 23-24, 29 and 32 of copending Application No. 17/904,394 in view of McDermott et al (United States Patent Application No. US20190345636, effectively filed 13 May 2019).
Claims 1 and 32 of the copending application teach a method which has steps that include all of the limitations of instant claim 55, wherein the “plurality of cells” from copending claim 1 represents the “plurality of samples” from instant claim 55, except the limitations of amended step e.
However, McDermott teaches these limitations as discussed fully above and incorporated here.
It would have been obvious to one having ordinary skill in the art to have modified the copending claims with the microfluidic emulsion method taught by McDermott to arrive at the instantly claimed invention with a reasonable expectation of success. One having ordinary skill in the art would have been motivated to make this substitution in order to generate more sequencing data from each experiment, as McDermott teaches a method allowing for more functional droplets. In addition, it would have been obvious to one of ordinary skill in the art the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the compartmentalization of nucleic acids for the preparation of sequencing libraries.
The limitations of instant claims 58-68 and 74 are given in claims 1-16, 23-24, 29 and 32 of the copending application.
The copending claims do not teach a single claim that includes all of the limitations of claim 55+ in a single claim. However, it would have been prima facie obvious to one having ordinary skill in the art to have modified any one of the copending claims so as to have applied it to the compartmentalization and amplification of a barcode molecule before attaching it to a target, as this is a specific embodiment of the invention in claim 32 of the copending application. Since all the claims in the copending application are directed toward barcoding cellular nucleic acids for sequencing analysis, it would have been obvious to combine the methods of the copending claims to achieve the predictable outcome of uniquely barcoding nucleic acid targets from a single cell.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 56-57, 73 and 75 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16, 23-24, 29 and 32 of copending Application No. 17/904,394 McDermott et al (United States Patent Application No. US20190345636, effectively filed 13 May 2019) as applied to claim 55 above, and further in view of Redin et al (Efficient whole genome haplotyping and high-throughput single molecule phasing with barcode-linked reads, BioRxiv 356121, doi: https://doi.org/10.1101/356121, published 2018-06-26).
The limitations of claims 56-57, 73 and 75 are not disclosed in the copending application in view of McDermott.
However, Redin teaches a method of compartmentalizing barcode molecules and target nucleic acids, amplifying the barcode molecules, then attaching the barcode molecules to the target nucleic acids.
It would have been obvious to modify the claims of the copending application to include the limitations taught by Redin. An ordinary artisan would have been motivated to make these combinations because Redin’s teachings provide the additional advantage of performing the tagmentation reaction on beads, which helps preserve proximity information of tagmented molecules when they are separated into droplets (pg 4 ¶ 2). In addition, it would have been obvious to one of ordinary skill in the art that the known techniques of the cited reference could have been combined with the claims of the copending application with predictable results, because both techniques relate to the compartmentalization and modification of target nucleic acids with barcodes.
This is a provisional nonstatutory double patenting rejection.
Claims 69-71 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-16, 23-24, 29 and 32 of copending Application No. 17/904,394 McDermott et al (United States Patent Application No. US20190345636, effectively filed 13 May 2019) as applied to claim 55 above, and further in view of Cao et al (Joint profiling of chromatin accessibility and gene expression in thousands of single cells, Science, 361, 1380-1385, 2018-09-28).
The limitations of claims 69-71 are not disclosed in the copending application.
However, Cao teaches pre-selecting cells with one or more recognizable markers.
It would have been obvious to modify the claims of the copending application to include the limitations taught by Cao. An ordinary artisan would have been motivated to make these modifications because Cao’s teachings provide the additional advantage detecting transposase accessible DNA from the cells (pg 1, column 1, ¶ 1). In addition, it would have been obvious to one of ordinary skill in the art that the known techniques of the cited reference could have been combined with the known techniques of the copending application with predictable results, because both techniques relate to the preparation of single cell sequencing libraries.
This is a provisional nonstatutory double patenting rejection.
Response to Arguments
14. Any rejection not repeated in this Office Action has been overcome by amendments to the claims.
15. Applicant’s arguments, see pg. 7 ¶ 3 of applicant’s remarks, filed 11 August 2025, with respect to the rejection(s) of claim(s) 55-71 and 73-75 under 35 U.S.C. 102 and 103 have been fully considered and are persuasive. Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of Redin et al (Efficient whole genome haplotyping and high-throughput single molecule phasing with barcode-linked reads, BioRxiv 356121, doi: https://doi.org/10.1101/356121, published 2018-06-26) in view of McDermott et al (United States Patent Application No. US20190345636, effectively filed 13 May 2019).
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.
Conclusion
16. No claims are allowed.
17. Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN ELLIS YOUNG whose telephone number is (703)756-5397. The examiner can normally be reached M-F 0730 - 1700.
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/BRIAN ELLIS YOUNG/Examiner, Art Unit 1684
/JULIET C SWITZER/Primary Examiner, Art Unit 1682