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 .
Priority
This application is a 371 of PCT/US2022/020028 filed 03/11/2022 which claims the benefit of U.S. Serial Application No. 63/160,576 filed 03/12/2021.
Status of the Applications, Amendments and/or Claims
This action is written in response to applicant's correspondence(s) submitted on 03/05/2026. In the paper of 03/05/2026, Applicant amended claims 1, 4-5, 8, 11, 25, 27, 29-31 and canceled claims 3, 6, 10, 14, 17, 19-23, 26 and 33-66. Accordingly, claims 1-2, 4-5, 7-9, 11-13, 15-16, 18, 24-25 and 27-32 are pending.
Election/Restrictions
Applicant’s election without traverse of group II (claims 11-13, 15-16, 18 and 24-25) in the reply filed on 03/05/2026 is acknowledged.
Claims 1-2, 4-5, 7-9 and 27-32 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention(s), there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 03/05/2026.
Status of the claims
Claims 1-2, 4-5, 7-9, 11-13, 15-16, 18, 24-25 and 27-32 are pending.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 11-12, 15-16, 18 and 24-25 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Church et al. (pub. 04/19/2007, US2007/0087362A1).
Regarding claim 11, Church et al. teach a polony gel for single cell RNA sequencing, the polony gel comprising:
a hydrogel comprising crosslinked polyacrylamide (PAA);
a first polony on a surface of the hydrogel, the first polony comprising a first template that comprises a first capture sequence and a first index sequence; and
a second polony on the surface of the hydrogel, the second polony bordering the first polony and comprising a second template that comprises a second capture sequence and a second index sequence (see para [0007] and [0014]: Church et al. teach an array having a plurality of beads immobilized in a semi-solid medium, in which a population of substantially identical nucleic acid sequences are attached to the beads. Church et al. further discloses claims 1-2, 4, 6, 8, 10 and 12 that are directed to an array comprising of a plurality of beads, wherein an individual bead has a population of substantially identical nucleic acid sequences attached thereto that differs in sequence from the population of substantially identical nucleic acid sequences attached to other individual beads, and wherein the plurality of beads is immobilized in a semi-solid medium to form an array, wherein the semi-solid medium is attached to a solid support, wherein the individual beads comprise two, three or four different populations of substantially identical nucleic acid sequences attached thereto, wherein the beads are immobilized as a monolayer, wherein the semi-sold medium has top and bottom surfaces and the plurality of beads is immobilized near the top surface, wherein the semi-solid medium is composed of polyacrylamide).
Regarding claims 1 and 12, the semi-solid medium of Church et al. composed of polyacrylamide comprised crosslinked polyacrylamide (PAA) (see para [0129]: wherein Church et al. teach preparation of crosslinked PAA by mixing of 3.0 µl beads, 5.0 µl H2O and 1.5 µl of 38% acrylamide, 2% bis-acrylamide, and 1.20 µl of 5% TEMED and 1.8 µl of 0.5% ammonium persulfate solution: Accordingly, Church et al. teach a hydrogel comprising of 3-20% acrylamide/bis, 0.01-1% ammonium persulfate, and 0.01-1% N,N,N',N'- tetramethylethylenediamine (TEMED)).
Concerning the instant capture and index sequences of claim 11, Church et al. teach bead with primer oligonucleotide having a sequence identical to the `reverse` PCR primer sequence (PR1-R) i.e. the biotin-modified `capture primer` PR1-R-BioXL: Biotin-5'-cgtaccccgcttggtctttctcccgtaccccgcttggtctttctccCTGCCCCGGGTTCCTCA- TTCTCT (SEQ ID NO:4) and that sequence complementary to the reverse PCR primer will only be present on strands of DNA that are the product of the PCR reaction, amplified beads selectively hybridized to these large capture beads, whereas empty beads did not hybridize to capture beads efficiently (para [0123]-[0124] and also para [0125]-[0126]). This primer oligonucleotide is construed as having capture and index sequence(s).
Regarding claim 15, Church et al. teach primer e immobilized to polymeric matrix via acrydite modification (para [0230]-[0231]).
Regarding claim 16, Church et al. teach first polony comprises 100- 1,000,000 copies of the first template, and wherein the second polony comprises 100-1,000,000 copies of the second template (para [0038], para [0067]).
Regarding claim 18, Church et al. teach first capture sequence specifically binds to a first RNA sequence, and second capture sequence specifically binds to a second RNA sequence (para [0032], [0040],[0246]).
Regarding claims 24-25, Church et al. teach width of the first polony is in a range of 0.1-1 µm, and wherein a width of the second polony is in a range of 0.1-1 µm and a distance between the first template and the second template is in a range of 0.1-1 µm (see para [0125]: wherein Church et al. teach enriched fraction of amplified one-micron beads for imbedding into surface of hydrogel).
Accordingly, the instant claims 11-12, 15-16,18 and 24-25 are anticipated by Church et al.
Claims 11-12, 15-16, 18 and 24-25 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Shendure et al. (2011, Current Protocols in Molecular Biology, 96(1), pp.7-1.1 to 7.1.23) as evidenced by Shendure et al. (2005, Science, 309(5741), pp.1728-1732 and pp. 1-41 of Supplementary document of Shendure et al. (2005)) and Mitra et al. (2003, Analytical biochemistry, 320(1), pp.55-65).
Regarding claim 11, Shendure et al. (2011) teach Illumina’s sequencing platform generates polony sequencing which takes the following approach. Both forward and reverse PCR primers are immobilized to the two dimensional surface of a glass slide. The primers are designed to target universal adaptors that flank a complex library of sequencing templates. PCR is performed by standard thermal cycling of the slide, with all reagents present in aqueous phase except for the primers, which are only present in surface-bound form. Because all primers are immobilized, copies remain local, and the result of amplification of each single template molecule is a tight cluster of ∼1000 copies (pg 7.1.11, right col, last para). Shendure et al. (2011) cites Shendure et al. (2005) and Mitra et al. (2003) for disclosing the polony sequencing method performed on a polony gel.
Shendure et al. (2005) teach multiplex polony sequencing, wherein cell-free, mate-paired library provided single DNA molecules that were amplified in parallel to 1-micrometer beads by emulsion polymerase chain reaction. Millions of beads were immobilized in a polyacrylamide gel and subjected to automated cycles of sequencing by ligation and four-color imaging (see abstract).
More specifically, the Supplementary document of Shendure et al. teach 2 µl of beads were poured into 20% acrylamide, 0.25% bisacrylamide gels on standard polony slides. Gels were polymerized at 4°C to allow for monolayering of beads. Shendure et al. teach polony gel comprising polonies with beads having amplicons of length 102, 220, 328, 510, 1064, 1575, 2519, and 3497 base-pairs (see Supplementary pg 2, 2nd and 3rd para). Each of the amplicon comprise capture and index sequences (see Supplementary pg 3 for table with primer sequence(s) and pg 11, Supplementary Fig. 7a).
Regarding claims 16 and 24-25, Shendure et al. (2005) a width of the first polony is in a range of 0.1-1 µm, and wherein a width of the second polony is in a range of 0.1-1 µm and a distance between the first template and the second template is in a range of 0.1-1 µm (see pg 1729, left col., 2nd para: wherein Shendure discloses bead are sized at 1 µm: accordingly, best resolution of polonies should on the order of 0.1-1 µm. Shendure et al. (2005) further teach these enriched beads each bear thousand of copies). Highly efficient polony amplification, yielding an average 20,337 template copies per feature after 35 amplification cycles.
Regarding claim 11, Mitra et al. (2003) teach a polony gel for sequencing multiple polonies in parallel (abstract) Mitra et al. (2003) teach polony gel comprising:
a hydrogel comprising crosslinked polyacrylamide (PAA) (pg 56, right col., text of section entitled “Determining the efficiency of nucleotide extension” and pg 57, 1st para of left col.).
The polony gel of Mitra et al. (2003) comprises:
a first polony on a surface of the hydrogel, the first polony comprising a first template that comprises a first capture sequence and a first index sequence; and a second polony on the surface of the hydrogel, the second polony bordering the first polony and comprising a second template that comprises a second capture sequence and a second index sequence.
Regarding claim 12, Mitra et al. (2003) teach wherein the hydrogel comprises 3-20% acrylamide/bis, 0.01-1% ammonium persulfate, and 0.01-1% N,N,N',N'- tetramethylethylenediamine (TEMED) (pg 56, right col., text of section entitled “Determining the efficiency of nucleotide extension” and pg 57, 1st para of left col).
Regarding claim 15, Mitra et al. (2003) teach wherein the primers comprise an acrydite modification (pg 57, right col., 2nd para of section entitled “Overview”).
Regarding claim 16, Mitra et al. (2003) teach wherein the first polony comprises 100- 1,000,000 copies of the first template, and wherein the second polony comprises 100-1,000,000 copies of the second template.
Regarding claim 18, Mitra et al. (2003) teach wherein the first capture sequence specifically binds to a first RNA sequence, and wherein the second capture sequence specifically binds to a second RNA sequence (pg 56, right col., text of section entitled “Determining the efficiency of nucleotide extension” wherein Mitra et al. teach primer suitable for capturing RNA sequence(s); pg 57, right col., all text of section entitled “Results”; and pg 58, Fig. 1A).
Accordingly, the instant claims 11-12, 15-16, 18 and 24-25 are anticipated by Shendure et al. (2011) as evidenced by Shendure et al. (2005 and pp. 1-41 of Supplementary document of Shendure et al. (2005)) and Mitra et al. (2003).
Claims 11 and 18 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Daugharty et al. (WO2020/076976A1, pub April 16, 2020).
Regarding claim 11, Daugharty et al. teach a crosslinked hydrogel composed of crosslinked PAA and further comprising a first polony on a surface of the crosslinked hydrogel, the first polony comprising a first template that comprises a first capture sequence and a first index sequence; and comprising a second polony on the surface of the hydrogel crosslinked gel, the second polony bordering the first polony and comprising a second template that comprises a second capture sequence and a second index sequence (see para [00144], [00149], claim 66, [0012], [0075]-[0078], [0081], [0084] [0098]-[0099]).
Specifically, Daugharty et al. (WO2020/076976A1) teach a synthetic 3D matrix comprising crosslinked poly(acrylate-co-acrylic acid) (PAA) (para [0012], [0081], [0082] and Fig. 4B, para [0029]).
Daugharty et al. (WO2020/076976A1) teach the synthetic 3D matrix comprising a first polony/rolony and a second polony/rolony bordering the first polony (Fig. 4B and para [0029], [0037], [0098]), and teach the first polony as comprising a first template that comprises a first capture sequence and a first index sequence; and the second polony as comprising a second template that comprises a second capture sequence and a second index sequence (para [0098]-[0099]).
Regarding claim 18, Daugharty et al. teach wherein the first capture sequence specifically binds to a first RNA sequence, and wherein the second capture sequence specifically binds to a second RNA sequence (para [0085], para [0067]).
Concerning the instant capture and index sequences of claim 11, Daugharty et al. teach polony sequences that are embedded in 2D/3D polymer gel matrix as comprising UMI tag (para [0066], [0071], [0073], [0075]).
Accordingly, the instant claims 11 and 18 are anticipated by Daugharty et al.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
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 13 is rejected under 35 U.S.C. 103 as being unpatentable over Church et al. (pub. 04/19/2007, US2007/0087362A1) as applied to claim 11, and further in view of Rigatti et al. (pub. June 14, 2011, U.S. Patent No. 7,960,120).
The teachings of Church et al. as it relates to claim 11 is provided above.
Regarding claim 13, Church et al. do not teach the crosslinked hydrogel further comprises 1-50 mg/ml N-(5- bromoacetamidylpentyl) acrylamide (BRAPA).
Rigatti et al. teach that copolymerization of acrylamide and the hydrogel is formed by co-polymerisation of acrylamide and N-(5-bromoacetamidylpentyl) acrylamide (BRAPA), was already a matter of routine practice in the art (col 25, lines 32-38 and col. 27, lines 59-66 and col 28, lines 1-10).
It would have been prima facie obvious to an ordinary skilled artisan, before the effective filing date of the instant invention to modify the preparation of the polony gel of Church et al. by copolymerization of 1-50 mg/ml N-(5- bromoacetamidylpentyl) acrylamide (BRAPA) to form the crosslinked hydrogel based on the teachings of Rigatti et al. who teach copolymerization was suitable practice.
In view of the combined teachings of all of the cited reference(s), the instant claim 13 is prima facie obvious.
Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Shendure et al. (2011, Current Protocols in Molecular Biology, 96(1), pp.7-1.1 to 7.1.23) as evidenced by Shendure et al. (2005, Science, 309(5741), pp.1728-1732 and pp. 1-41 of Supplementary document of Shendure et al. (2005)) and Mitra et al. (2003, Analytical biochemistry, 320(1), pp.55-65) further in view of Rigatti et al. (pub. June 14, 2011, U.S. Patent No. 7,960,120).
Regarding claim 13, Shendure et al. (2011) as evidenced by Shendure et al. (2005) and pp. 1-41 of Supplementary document of Shendure et al. (2005) and Mitra et al. (2003) do not teach the crosslinked hydrogel further comprises 1-50 mg/ml N-(5- bromoacetamidylpentyl) acrylamide (BRAPA).
Rigatti et al. teach that copolymerization of acrylamide and the hydrogel is formed by co-polymerisation of acrylamide and N-(5-bromoacetamidylpentyl) acrylamide (BRAPA), was already a matter of routine practice in the art (col 25, lines 32-38 and col. 27, lines 59-66 and col 28, lines 1-10).
It would have been prima facie obvious to an ordinary skilled artisan, before the effective filing date of the instant invention to modify the preparation of the polony gel of Shendure et al. (2011) as evidenced by Shendure et al. (2005) and pp. 1-41 of Supplementary document of Shendure et al. (2005) and Mitra et al. (2003) by copolymerization of 1-50 mg/ml N-(5- bromoacetamidylpentyl) acrylamide (BRAPA), thereby form a copolymer crosslinked hydrogel based on the teachings of Rigatti et al. who teach copolymerization was suitable practice.
In view of the combined teachings of all of the cited reference(s), the instant claim 13 is prima facie obvious.
Conclusion
No claims are currently allowed.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to OLAYINKA A OYEYEMI whose telephone number is (571)270-5956. The examiner can normally be reached Monday -Thursday: 9:00 am - 5:00 pm, EST.
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OLAYINKA A. OYEYEMI
Examiner
Art Unit 1681
/OLAYINKA A OYEYEMI/Examiner, Art Unit 1681
/GARY BENZION/Supervisory Patent Examiner, Art Unit 1681
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