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 I, claims 1-10 in the reply filed on 11/26/2025 is acknowledged.
Claims 11-25 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 11/26/2025.
Priority
The instant application was filed 12/08/2022 Claims Priority from Provisional Application 63288213 , filed 12/10/2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 4/28/2023, 5/19/2023, 7/14/2023, 8/10/2023 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.
Claim Rejections - 35 USC § 112
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.
Claims 1-10 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.
Claim 1 recites, “providing a substrate comprising a plurality of the template polynucleotides in a cluster.” The metes and bounds are vague and unclear if the step is an active step which is missing elements as to how a cluster is provided or if the claim merely requires providing a template.
Claim 1 recites, “generating light to stimulate fluorescent emissions from the cluster.” This is vague and confusing and the claim provides no limitations which require the cluster is labeled to provide for fluorescent emissions. Thus the metes and bounds are unclear what is required of this step.
Claim 1 continues by reciting, “receiving a first signal emitted at a first intensity from a first plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a first site; receiving a second signal emitted at a second intensity from a second plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a second site.” The metes and bounds are unclear as the claim fails to provide any active in which anything is hybridized to the plurality of template nucleic acids. Thus it is unclear where and/or how hybridization occurs. Further as the claim encompasses single nucleotide analogs it is unclear how hybridization occurs or is specific to allow for the identifying step.
Claim 1 concludes with, “ identifying the nucleobases hybridized at the first and second sites of the template polynucleotide based on a combination of the first and second signals.” The claim is vague unclear and incomplete how this is done.
Claim 3 recites, “comprising identifying the nucleobases in the template polynucleotide based on the difference between the first intensity and the second intensity of the first and second signals.” The claim is vague unclear and incomplete how this is done.
The claims recite,”index primer,” “read primer,” “barcode index” and “non-barcode index.” Review and searching of the specification did not reveal limiting definitions of these terms. Thus the metes and bounds are unclear what is encompassed or excluded by the recitations, so that one of skill in the art can avoid infringement.
Claim 6 recites, “wherein identifying the nucleobases comprises comparing the first signal at the first intensity from the nucleotide analogs on the index primers with the second signal at the second intensity from nucleotide analogs on the read primers.” The claim is vague unclear and incomplete how this is done.
Claim 10 recites, “further comprising substantially simultaneously identifying nucleobases in an additional polynucleotide complementary to the template polynucleotide.” The claim is vague unclear and incomplete how this is done. Further Substantially simultaneously suggests there is less than substantially simultaneously. The specification and claims fail to provide a standard to differentiate the two. Thus the metes and bounds are unclear.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-10 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a mental step/abstract idea without significantly more. The claim(s) recite(s) the abstract idea or mental step of identifying the nucleobases hybridized at the first and second sites of the template polynucleotide based on a combination of the first and second signals.. This judicial exception is not integrated into a practical application because no steps depend from or otherwise integrate the judicial exception. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims provide no specific reagents.
Claim analysis
The instant claim 1 is directed towards method of identifying nucleobases in a template polynucleotide, the method comprising: providing a substrate comprising a plurality of the template polynucleotides in a cluster; generating light to stimulate fluorescent emissions from the cluster; receiving a first signal emitted at a first intensity from a first plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a first site; receiving a second signal emitted at a second intensity from a second plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a second site; and identifying the nucleobases hybridized at the first and second sites of the template polynucleotide based on a combination of the first and second signals.. The identifying step is a mental step or abstract idea.
The providing, generating and receiving are considered to be an active step requiring the analysis of a sample.
Dependent claims set forth further limitations to about nucleic acid analog and how they are provided.
According to the 2019 Patent Eligibility Guidance an initial two step analysis is required for determining statutory eligibility.
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter? In the instant case the Step 1 requirement is satisfied as the claims are directed towards a process.
Step 2A Prong one. Does the claim recite a law of nature, a natural phenomenon or an abstract idea? Yes, abstract idea/mental step.
With regards to claim 1, the claim recites, “identifying the nucleobases hybridized at the first and second sites of the template polynucleotide based on a combination of the first and second signals.” This is an abstract idea or mental step.
Step 2A prong two. Does the claim recite additional elements that integrate the judicial exception into a practical application? The answer is no as no additional steps depend from or otherwise integrate the judicial exception.
Step 2B. Does the claim recite additional elements that are significantly more than the judicial exceptions? No, the claims provide no steps or limitations which provide for significantly more.
With regards to claim 1 the claim the specification in paragraph 0045 appears to suggest the claims encompass sequencing by synthesis, which is routine and conventional. Further Kozarewa (NATURE METHODS | VOL.6 NO.4 | APRIL 2009 | 291-295), Moorthie (HUGO J (2011) 5:1–12) and Busby (WO2009/086353) demonstrate the limitations of the claims that can be understood are routine and conventional.
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) 1-8, 10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kozarewa (NATURE METHODS | VOL.6 NO.4 | APRIL 2009 | 291-295), Moorthie (HUGO J (2011) 5:1–12).
This rejection is set forth in view of the breadth of the claims as detailed in the 112 rejections.
With regards to claim 1, Kozarewa teaches, “th base compositions at the extremes of high or low G+C content. Here we present an amplification-free method of library preparation, in which the cluster amplification step, rather than the PCR, enriches for fully ligated template strands, reducing the incidence of duplicate sequences, improving read mapping and single nucleotide polymorphism calling and aiding de novo assembly.” (abstract). Kozarewa teaches, “Unlike the standard Illumina adapters, no-PCR adapters contain additional sequences that allow hybridization of templates directly to the flowcell surface. Incompletely ligated fragments are inert in the cluster amplification step. Thus it is not necessary to retain the PCR step to enrich for properly ligated fragments, but to obtain an optimal clusterdensity, it is necessary to accurately quantify only those template fragments with an adaptor at either end. We achieve this by quantitative PCR, using primers that target the adaptor regions13.” (page 292, 1st column).
Kozarewa teaches following cluster amplification, the sequences were sequenced. Kozarewa does not specifically teach how sequencing was done.
However, Moorthie teaches
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Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims use cluster amplification of Kozarewa with second generation sequencing which encompasses sequencing by synthesis and detection of incorporated nucleotide analogs based on different emission emitted upon excitation of the nucleotide analogs by a light source. The artisan would be motivated as Kozarewa suggests sequencing and Moorthie teaches the sequencing by synthesis or NGS sequencing was known. The artisan would have a reasonable expectation success as the artisan is merely using known methods.
While claims 4-9 recite, “index primer” and “read primer” the claims and specification provide no definition to differentiate these. Thus the broadest reasonable interpretation is any primer sequences.
With regards to claim 2, 4-5Moorthie teaches,” Finally, DNA ‘barcode tags’ can be added to the ends of DNA fragments during initial preparation. These are sequenced along with the fragment during the run and serve to identify the source of each sequence read during analysis ((page 8, 1st column bottom).
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 to design the library to have a barcode (or index barcode) in the library. The artisan would be motivated to provide a barcode in the library to index or provide additional information about the nucleic acid template on sequencing. The artisan would have a reasonable expectation of success as the artisan is merely using known methods.
With regards to claim 3, 6-8 Moorthie teaches 4 color detection and thus 4 different intensities.
With regards to claim 5, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to design the library to have a barcode (or index barcode) in the library. The artisan would be motivated to provide a barcode in the library to index or provide additional information about the nucleic acid template on sequencing. The artisan would have a reasonable expectation of success as the artisan is merely using known methods.
With regards to claim 10, Moorthie teaches massively parallel sequencing (title).
Claim(s) 9 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kozarewa (NATURE METHODS | VOL.6 NO.4 | APRIL 2009 | 291-295), Moorthie (HUGO J (2011) 5:1–12) as applied to claims 1-8, 10 above, and further in view of
Busby (WO2009/086353)
The teachings of Kozarewa and Moothie are set forth above.
While, Kozarewa and Moothie teach next generation sequencing, they do not specially teach use of some primers which are blocked and other primers which are not blocked.
However, Busby teaches, “[0011] This invention provides a process to drive the yield of multiple reads much higher. The present invention utilizes an unblocked first primer in conjunction with one or more reversibly blocked primers. All of such primers can be efficiently hybridized to template nucleic acids before conducting sequencing by synthesis. The primers can then be individually deblocked to allow for the subsequent rounds of sequencing, without the need of the post-sequencing primer addition.”
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to use the blocked and unblocked primers of Busby in the methods of Kozarewa and Moorthie. The artisan would be motivated to use the blocked and unblocked primers as Busby teaches, “0009] The present invention provides a method of sequencing a nucleic acid molecule that contains two or more target regions to be sequenced (such as, for example, barcodes). The invention is advantageous for sequencing by synthesis two or more target regions whose combined lengths plus the length of any intermediate sequence exceeds the available read length on a given sequencing platform. This approach is suitable, for example, for reading nucleic acid barcodes. However, it may also be used for any other sequencing-by-synthesis application that requires sequencing any two or more non-contiguous regions (referred to herein as "target regions" or "target sequences") within the same nucleic acid template. By designing nucleic acid constructs in such a way as to have a different universal primer site for each target region, the need for the "melt-and-resequence" procedure is obviated, resulting in increased efficiency, accuracy, and/or speed of nucleic acid identification. One of the applications for which the present invention is suitable is a genomic signature sequencing (GSS™) assay.” The artisan would have a reasonable expectation of success as the artisan is merely using known methods of sequencing nucleic acid sequences.
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 1-10 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1, 5-10, 12-33 of copending Application No 18/190,809. 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 method of identifying nucleobases in a template polynucleotide, the method comprising: providing a substrate comprising a plurality of the template polynucleotides in a cluster; generating light to stimulate fluorescent emissions from the cluster; receiving a first signal emitted at a first intensity from a first plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a first site; receiving a second signal emitted at a second intensity from a second plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a second site; and identifying the nucleobases hybridized at the first and second sites of the template polynucleotide based on a combination of the first and second signals.
The claims of 809 are drawn to A method of sequencing clusters of labeled polynucleotides bound to a flowcell, comprising:exciting the clusters at a first excitation wavelength and detecting fluorescent emissions at a first detection wavelength from a first labeled nucleotide comprising a first fluorescent dye,exciting the clusters at a second excitation wavelength and detecting fluorescent emissions at a second detection wavelength from a second labeled nucleotide comprising a second fluorescent dye, wherein the first excitation wavelength and the second excitation wavelength are different, and wherein the first detection wavelength and the second detection wavelength are different,exciting the clusters at the first excitation wavelength and detecting fluorescent emissions at the second detection wavelength from a third labeled nucleotide comprising a third fluorescent dye, wherein the first fluorescent dye, the second fluorescent dye, and the third fluorescent dye are different,determining clusters that did not emit fluorescent emissions after excitation at the first or second excitation wavelengths to detect the presence of a fourth unlabeled nucleotide, anddetermining the nucleotide sequence of the polynucleotides based on the detected fluorescent emissions.
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 claims of 809 encompass the instant claims and are thus obvious variants.\
Claim 1-10 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-15, 20-22, 30, 33 of copending Application No 18/574,675. 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 method of identifying nucleobases in a template polynucleotide, the method comprising: providing a substrate comprising a plurality of the template polynucleotides in a cluster; generating light to stimulate fluorescent emissions from the cluster; receiving a first signal emitted at a first intensity from a first plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a first site; receiving a second signal emitted at a second intensity from a second plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a second site; and identifying the nucleobases hybridized at the first and second sites of the template polynucleotide based on a combination of the first and second signals.
The claims of 675 are drawn A method of base calling nucleobases of two or more polynucleotide sequence portions, the method comprising: (a) obtaining first intensity data comprising a combined intensity of a first signal obtained based upon a respective first nucleobase of at least one first polynucleotide sequence portion and a second signal obtained based upon a respective second nucleobase of at least one second polynucleotide sequence portion; (b) obtaining second intensity data comprising a combined intensity of a third signal obtained based upon the respective first nucleobase of the at least one first polynucleotide sequence portion and a fourth signal obtained based upon the respective second nucleobase of the at least one second polynucleotide sequence portion; (c) selecting one of a plurality of classifications based on the first and the second intensity data, wherein each classification represents a possible combination of respective first and second nucleobases; and (d) based on the selected classification, base calling the respective first and second nucleobases, wherein said polynucleotide sequence portions have been selectively processed such that an intensity of the signals obtained based upon the respective first nucleobase is greater than an intensity of the signals obtained based upon the respective second nucleobase..
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 claims of 675 encompass the instant claims and are thus obvious variants.\
Claim 1-10 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-15, 20-22, 30, 33 of copending Application No 18/573,965. 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 method of identifying nucleobases in a template polynucleotide, the method comprising: providing a substrate comprising a plurality of the template polynucleotides in a cluster; generating light to stimulate fluorescent emissions from the cluster; receiving a first signal emitted at a first intensity from a first plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a first site; receiving a second signal emitted at a second intensity from a second plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a second site; and identifying the nucleobases hybridized at the first and second sites of the template polynucleotide based on a combination of the first and second signals.
The claims of 965 are A method of determining sequence information from two or more polynucleotide sequence portions, the method comprising:(a) obtaining first intensity data comprising a combined intensity of a first signal obtained based upon a respective first nucleobase of at least one first polynucleotide sequence portion and a second signal obtained based upon a respective second nucleobase of at least one second polynucleotide sequence portion;(b) obtaining second intensity data comprising a combined intensity of a third signal obtained based upon the respective first nucleobase of the at least one first polynucleotide sequence portion and a fourth signal obtained based upon the respective second nucleobase of the at least one second polynucleotide sequence portion;(c) selecting one of a plurality of classifications based on the first and the second intensity data, wherein each classification of the plurality of classifications represents one or more possible combinations of respective first and second nucleobases, and wherein at least one classification of the plurality of classifications represents more than one possible combination of respective first and second nucleobases; and(d) based on the selected classification, determining sequence information from the at least one first polynucleotide sequence portion and the at least one second polynucleotide sequence portion...
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 claims of 965 encompass the instant claims and are thus obvious variants.\
Claim 1-10 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-43 of copending Application No 18/184,556. 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 method of identifying nucleobases in a template polynucleotide, the method comprising: providing a substrate comprising a plurality of the template polynucleotides in a cluster; generating light to stimulate fluorescent emissions from the cluster; receiving a first signal emitted at a first intensity from a first plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a first site; receiving a second signal emitted at a second intensity from a second plurality of nucleotide analogs hybridized to the plurality of template polynucleotides at a second site; and identifying the nucleobases hybridized at the first and second sites of the template polynucleotide based on a combination of the first and second signals.
The claims of 556 are A method of identifying nucleobases in a template polynucleotide, comprising: providing a substrate comprising a plurality of double stranded template polynucleotides in a cluster, wherein each double stranded template polynucleotide comprises a first strand and a second strand; contacting the plurality of double stranded template polynucleotides with first primers which bind to the first strand and second primers which bind to the second strand; extending the first primers and the second primers by contacting the cluster with labeled nucleobases to form first labeled primers and second labeled primers; stimulating light emissions from the first and second labeled primers, wherein an amplitude of the signal generated by the first labeled primers is greater than an amplitude of the signal generated by the second labeled primers; and identifying the labeled nucleobases added to the first primers and the second primers based on the amplitude of the signal generated by the labeled nucleobases....
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 claims of 556 encompass the instant claims and are thus obvious variants.
Summary
No claims are allowed.
Conclusion
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/Steven Pohnert/ Primary Examiner, Art Unit 1683
Prosecution Insights