DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of Group III, flow cell, photoresist in the reply filed on 10/29/2025 is acknowledged.
Claims 1-12 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 10/29/2025.
Priority
The instant application was filed 07/24/2023 and claims priority from provisional application 63392076 , filed 07/25/2022.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 10/26/2023 is being considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Drawings
The drawings submitted 7/24/2023 are in color. Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
Specification
The disclosure is objected to because of the following informalities: The specification on page 49 has [0101], followed by [0065], [0066], then [0102] on page 50. The paragraph numbers should be in consecutive numbers. Applicant should review the entire application to ensure all paragraph numbers are sequential.
Appropriate correction is required.
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.
Claim(s) 13-17, 19 is/are rejected under 35 U.S.C. 102(a0(1)/102(a)(2) as being anticipated by Hunter (US20180187252).
Hunter teaches, “An example method includes reacting a first solution and a different, second solution on a flow cell by flowing the first solution over amplification sites on the flow cell and subsequently flowing the second solution over the amplification sites. The first solution includes target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates and replication enzymes. The target nucleic acids in the first solution transport to and bind to the amplification sites at a transport rate. The first reagent mixture amplifies the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from corresponding target nucleic acids. The amplicons are produced at an amplification rate that exceeds the transport rate. The second solution includes a second reagent mixture and lacks the target nucleic acids. The second solution is to increase a number of the amplicons at the amplification sites.” (abstract)
With regards to claims 13, 17 Hunter teaches, “[0009] In an example of this method, the flow cell includes a plurality of primers attached to the flow cell at the amplification sites, wherein the first solution reacts on the flow cell to bind the target nucleic acids and the amplicons to a first subset of the primers, and wherein the second solution reacts on the flow cell to produce additional amplicons and bind the additional amplicons to at least some of the primers in an exposed subset of the primers different than the first subset.” Hunter teaches, “[0012] In an example of this method, the flow cell includes a plurality of primers attached to the flow cell at the amplification sites, wherein at least some of the primers bind to the target nucleic acids in the first solution responsive to flowing the first solution over the array of amplification sites, and wherein subsequently flowing the second solution that lacks the target nucleic acids over the array of amplification sites results in no additional binding of the primers to the target nucleic acids.” Hunter teaches, “[0108] A more detailed example of kinetic exclusion via differential rates of amplicon formation follows. An amplification site can include three subpopulations of primers attached thereto. The first subpopulation of primers functions to capture a target nucleic acid (via a capture sequence) and as a primer for first amplicon formation. The first subpopulation of primers is reversibly blocked from extension, for example, via a dideoxy nucleotide at the 3′ end. The second subpopulation of primers can have a P5 primer sequence and the third population of primers can have a P7 primer sequence.” The primers of Hunter are nucleic acids and thus are cleavable. Thus Hunter teaches 3 different primer populations , attached to a solid support which have a common binding sequence within each population.
With regards to claim 14, Hunter teaches a flow cell. (abstract)
With regards to claim 15, Hunter teaches the flow cells have photoresist (0159).
With regards to claim 16, Hunter teaches, “[0093] In some examples, the features on the surface of an array substrate are non-contiguous, being separated by interstitial regions of the surface. Interstitial regions that have a substantially lower quantity or concentration of capture agents, compared to the features of the array, are advantageous. Interstitial regions that lack capture agents are particularly advantageous. For example, a relatively small amount or absence of capture moieties at the interstitial regions favors localization of target nucleic acids, and subsequently generated clusters, to desired features. In particular examples, the features can be concave features in a surface (e.g. wells) and the features can contain a gel material. The gel-containing features can be separated from each other by interstitial regions on the surface where the gel is at least substantially absent or, if present the gel is at least substantially incapable of supporting localization of nucleic acids. Methods and compositions for making and using substrates having gel containing features, such as wells, are set forth in U.S. Pat. No. 9,512,422, which is incorporated herein by reference in its entirety.” Thus Hunter teaches additional immobilized oligonucleotides at additional locations in flow cell.
With regards to claim 19, Hunter teaches, “[0111] An amplification reagent that is used in a method set forth herein is preferably capable of rapidly making copies of target nucleic acids at amplification sites. One or more amplification reagents used in a method of the present disclosure will include a polymerase and nucleoside triphosphates (NTPs). Any of a variety of polymerases known in the art can be used, but in some examples it may be desirable to use a polymerase that is exonuclease negative. The NTPs can be deoxyribonucleoside triphosphates (dNTPs) for examples where DNA copies are made. The four native species of dNTPs, including dATP, dTTP, dGTP and dCTP, may be present in a DNA amplification reagent; however, analogs can be used if desired. The NTPs can be ribonucleoside triphosphates (rNTPs) for examples where RNA copies are made. The four native species of rNTPs, including rATP, rUTP, rGTP and rCTP, may be present in a RNA amplification reagent; however, analogs can be used if desired.”
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.
Claim(s) 13-20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Hunter (US20180187252).
Hunter teaches, “An example method includes reacting a first solution and a different, second solution on a flow cell by flowing the first solution over amplification sites on the flow cell and subsequently flowing the second solution over the amplification sites. The first solution includes target nucleic acids and a first reagent mixture that comprises nucleoside triphosphates and replication enzymes. The target nucleic acids in the first solution transport to and bind to the amplification sites at a transport rate. The first reagent mixture amplifies the target nucleic acids that are bound to the amplification sites to produce clonal populations of amplicons originating from corresponding target nucleic acids. The amplicons are produced at an amplification rate that exceeds the transport rate. The second solution includes a second reagent mixture and lacks the target nucleic acids. The second solution is to increase a number of the amplicons at the amplification sites.” (abstract)
With regards to claims 13, 17 Hunter teaches, “[0009] In an example of this method, the flow cell includes a plurality of primers attached to the flow cell at the amplification sites, wherein the first solution reacts on the flow cell to bind the target nucleic acids and the amplicons to a first subset of the primers, and wherein the second solution reacts on the flow cell to produce additional amplicons and bind the additional amplicons to at least some of the primers in an exposed subset of the primers different than the first subset.” Hunter teaches, “[0012] In an example of this method, the flow cell includes a plurality of primers attached to the flow cell at the amplification sites, wherein at least some of the primers bind to the target nucleic acids in the first solution responsive to flowing the first solution over the array of amplification sites, and wherein subsequently flowing the second solution that lacks the target nucleic acids over the array of amplification sites results in no additional binding of the primers to the target nucleic acids.” Hunter teaches, “[0108] A more detailed example of kinetic exclusion via differential rates of amplicon formation follows. An amplification site can include three subpopulations of primers attached thereto. The first subpopulation of primers functions to capture a target nucleic acid (via a capture sequence) and as a primer for first amplicon formation. The first subpopulation of primers is reversibly blocked from extension, for example, via a dideoxy nucleotide at the 3′ end. The second subpopulation of primers can have a P5 primer sequence and the third population of primers can have a P7 primer sequence.” The primers of Hunter are nucleic acids and thus are cleavable. Thus Hunter teaches 3 different primer populations , attached to a solid support which have a common binding sequence within each population.
Hunter does not specifically teach further comprising a first oligonucleotide comprising a first platform primer binding sequence, a second oligonucleotide comprising a second platform primer binding sequence, and a third oligonucleotide comprising a third platform primer binding sequence; or wherein the first oligonucleotide further comprises a first sequencing primer binding sequence and optionally an index sequence, the second oligonucleotide further comprises a second sequencing primer binding sequence and optionally an index sequence, and the third oligonucleotide further comprises a second sequencing primer binding sequence and [[an]] optionally an index sequence.
However, Hunter teaches, “0078] As used herein, the term “universal sequence” refers to a region of sequence that is common to two or more nucleic acid molecules where the molecules also have regions of sequence that differ from each other. A universal sequence that is present in different members of a collection of molecules can allow capture of multiple different nucleic acids using a population of universal capture nucleic acids that are complementary to the universal sequence. Similarly, a universal sequence present in different members of a collection of molecules can allow the replication or amplification of multiple different nucleic acids using a population of universal primers that are complementary to the universal sequence. Thus, a universal capture nucleic acid or a universal primer includes a sequence that can hybridize specifically to a universal sequence. Target nucleic acid molecules may be modified to attach universal adapters, for example, at one or both ends of the different target sequences.”
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the invention the first , second and third subpopulations of primers to have the same or different universal sequences (platform primer binding sequences.) the artisan would be motivated as Hunter teaches the use of universal sequences to allow capture of different members of a collection of samples. The artisan would have a reasonable expectation of success as the artisan is merely using known reagents.
With regards to claim 14, Hunter teaches a flow cell. (abstract)
With regards to claim 15, Hunter teaches the flow cells have photoresist (0159).
With regards to claim 16, Hunter teaches, “[0093] In some examples, the features on the surface of an array substrate are non-contiguous, being separated by interstitial regions of the surface. Interstitial regions that have a substantially lower quantity or concentration of capture agents, compared to the features of the array, are advantageous. Interstitial regions that lack capture agents are particularly advantageous. For example, a relatively small amount or absence of capture moieties at the interstitial regions favors localization of target nucleic acids, and subsequently generated clusters, to desired features. In particular examples, the features can be concave features in a surface (e.g. wells) and the features can contain a gel material. The gel-containing features can be separated from each other by interstitial regions on the surface where the gel is at least substantially absent or, if present the gel is at least substantially incapable of supporting localization of nucleic acids. Methods and compositions for making and using substrates having gel containing features, such as wells, are set forth in U.S. Pat. No. 9,512,422, which is incorporated herein by reference in its entirety.” Thus Hunter teaches additional immobilized oligonucleotides at additional locations in flow cell.
With regards to claim 19, Hunter teaches, “[0111] An amplification reagent that is used in a method set forth herein is preferably capable of rapidly making copies of target nucleic acids at amplification sites. One or more amplification reagents used in a method of the present disclosure will include a polymerase and nucleoside triphosphates (NTPs). Any of a variety of polymerases known in the art can be used, but in some examples it may be desirable to use a polymerase that is exonuclease negative. The NTPs can be deoxyribonucleoside triphosphates (dNTPs) for examples where DNA copies are made. The four native species of dNTPs, including dATP, dTTP, dGTP and dCTP, may be present in a DNA amplification reagent; however, analogs can be used if desired. The NTPs can be ribonucleoside triphosphates (rNTPs) for examples where RNA copies are made. The four native species of rNTPs, including rATP, rUTP, rGTP and rCTP, may be present in a RNA amplification reagent; however, analogs can be used if desired.”
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 13-18 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-14 of copending Application No. 18/364849. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
The instant claims are drawn to A solid support comprising a plurality of amplification sites, wherein each amplification site comprises a population of first platform primers, a population of second platform primers, and a population of third platform primers, wherein each of the third platform primers comprise a cleavable site, each of said populations have a different platform primer binding sequence relative to each population, and each of said different populations have a common platform primer binding sequence within each population.
The claims of 849 are drawn to A method of differentially amplifying a first plurality of polynucleotides relative to a second plurality of polynucleotides on a solid support, wherein said solid support comprises a first plurality of polynucleotides, wherein each polynucleotide in said first plurality of polynucleotides comprise a first platform primer sequence immobilized to a solid support, a first template sequence, and a second platform primer binding sequence; a second plurality of polynucleotides, wherein each polynucleotide in said second plurality of polynucleotides comprise the first platform primer sequence, a second template sequence, and a third platform primer binding sequence; a population of first platform primers, a population of second platform primers, and a population of third platform primers, wherein each of said first platform primers, said second platform primers, and said third platform primers are immobilized to said solid support; said method comprising: (i) contacting said solid support with a plurality of blocking elements thereby forming a plurality of blocked polynucleotide complexes, wherein each of said blocked polynucleotide complexes comprise a blocking element bound to one of said third platform primer binding sequences of said second polynucleotide; or (ii) contacting said solid support with a plurality of blocking elements thereby forming a plurality of blocked third platform primer complexes, wherein each of said blocked third platform primer complexes comprises a blocking element bound to one of said third platform primers; and amplifying said first plurality of polynucleotides; thereby differentially amplifying the first plurality of polynucleotides relative to a second plurality of polynucleotides on a solid support.
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the method renders obvious the instant products as the product is require to practice the claimed method.
Claim 13-18 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-30 US Patent 12,600,962 Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
The instant claims are drawn to A solid support comprising a plurality of amplification sites, wherein each amplification site comprises a population of first platform primers, a population of second platform primers, and a population of third platform primers, wherein each of the third platform primers comprise a cleavable site, each of said populations have a different platform primer binding sequence relative to each population, and each of said different populations have a common platform primer binding sequence within each population.
The claims of 962 are drawn to A method of sequencing an overlapping amplification cluster, said method comprising: contacting a solid support with a first polynucleotide comprising a first sequencing primer binding sequence, a second polynucleotide comprising a second sequencing primer binding sequence, and a third polynucleotide comprising a third sequencing primer binding sequence, wherein each of said polynucleotides and sequencing primer binding sequences are different and distinct; hybridizing an amplification primer binding sequence of the first polynucleotide to a first oligonucleotide sequence attached to the solid support; hybridizing an amplification primer binding sequence of the second polynucleotide to a second oligonucleotide sequence attached to the solid support; hybridizing an amplification primer binding sequence of the third polynucleotide to a third oligonucleotide sequence attached to the solid support; wherein each of said amplification primer binding sequences are the same, and each of said oligonucleotide sequences are different; amplifying the polynucleotides thereby forming an overlapping amplification cluster; and sequentially sequencing said overlapping amplification cluster by hybridizing a first sequencing primer to the first sequencing primer binding sequence, or a complement thereof, and generating a first sequencing read comprising 10 or more nucleotide bases; after generating the first sequencing read, hybridizing a second sequencing primer to the second sequencing primer binding sequence, or a complement thereof, and generating a second sequencing read comprising 10 or more nucleotide bases; after generating the second sequencing read, hybridizing an extendable third sequencing primer to the third sequencing primer binding sequence, or a complement thereof, and generating a third sequencing read comprising 10 or more nucleotide bases; wherein sequencing comprises contacting each hybridized sequencing primer with a sequencing solution comprising one or more modified nucleotides comprising a reversible terminator, and monitoring the sequential incorporation of said one or more modified nucleotides to generate a sequencing read, wherein the reversible terminator is removed prior to the introduction of the next modified nucleotide, and wherein the reversible terminator of each modified nucleotide is cleaved using the same cleaving agent cleaved by the same cleaving agent.
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims the method renders obvious the instant products as the product is require to practice the claimed method.
Summary
No claims are allowed
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEVEN C POHNERT PhD whose telephone number is (571)272-3803. The examiner can normally be reached Monday- Friday about 6:00 AM-5:00 PM, every second Friday off.
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/Steven Pohnert/Primary Examiner, Art Unit 1683
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