Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Claim status
No claim amendments have been filed. Original claims 1-19 filed 7/14/2022 are pending.
Election/Restriction
Applicant’s election without traverse of Group I in the reply filed on 4/16/2026 is acknowledged.
Upon initial search and consideration of both groups, it does not appear to be an undue burden to examine both methods as they differ only in the flow ordering permutation. Accordingly
Claims 1-19, drawn to a system for sequencing using phase protection flow order with various flow orders are currently under examination.
Priority
This application filed 7/14/2022 is a divisional of application 16/801,254 filed 2/26/2020, now US Patent 11,390920; which is a continuation of application 13/859360 filed 4/9/2013, now US Patent 10,597711 which is a continuation of 13/440849 filed 4/5/2012, now US Patent 9,428807; and four provisional applications the oldest being 61/473721 filed 4/8/2011; and
is related to application 15/236172 filed now US Patent 10,370708 (by virtue of claim to 13/440,849).
Examiner comment: In application 16/801254 the non-elected system claims were amended to be dependent on the method claims and provided the limitations of the system which was not elected into the method claims. With the limitations required of the system incorporated into the method, it does not appear that the claims would be restricted if first presented as amended after election. It is further noted that the amendments and cancellation of the system did not allow for this assessment to be made of record in the parent application.
Sequence Rules and Objection to the Specification
3. The specification is objected because of the following informalities:
This application contains sequence disclosures that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.821(a)(1) and (a)(2). However, this application fails to comply the requirements of 37 CFR 1.821 through 1.825. Specifically, the instant application/drawings illustrates sequences that are not identified by SEQ ID No. (see Figure 4Q and Fig 5 for example) recite a nucleic acid sequence / amino acid sequence with more than 10 nucleotides or 4 amino acids, which is not identified by SEQ ID NO.). review of the drawings and description of the figures does not appear to provide a SEQ ID for the sequences.
Appropriate correction is required.
Non-statutory Double Patenting
5. 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 §§ 706.02(l)(1) - 706.02(l)(3) 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 USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The 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/process/file/efs/guidance/eTD-info-I.jsp.
Claims 1-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of U.S. Patent No. 10,370172. Although the claims at issue are not identical, they are not patentably distinct from each other because each are directed to a system for sequencing where the flows are modified. In view of the specification paragraph [0089] teaches: ‘In various embodiments, a phase-protecting reagent flow ordering may be derived from a set of k-ary de Bruijn sequences B(k,n), where k denotes a size of an alphabet (e.g., k may be set to 4 for an alphabet comprising the nucleotide species A, C, G, and T), and where n denotes a length of subsequences in the alphabet.’ and provides for effectively any combination of flows.
A copy of the allowed claim 1 is provided for completeness and clarity of the record.
A system for nucleic acid sequencing, comprising:
a device configured to sequence nucleic acids; a non-transitory machine-readable memory; and
a processor configured to execute machine-readable instructions, which, when executed by the processor, cause the system to perform steps including:
exposing a plurality of template polynucleotide strands in a plurality of defined spaces disposed on a sensor array, at least some of the template polynucleotide strands having a sequencing primer and a polymerase operably bound therewith, to a series of flows of nucleotide species flowed according to a predetermined ordering; and
determining, for each of the series of flows of nucleotide species, how many nucleotide incorporations occurred for that particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands,
wherein the predetermined ordering (a) is not a series of consecutive repetitions of a 4-flow permutation of four different nucleotide species, (b) is not specifically tailored to a particular combination of a particular template polynucleotide strand to be sequenced and a particular sequencing primer to be used, and (c) comprises a phase-protecting flow ordering that comprises a de Bruijn sequence of nucleotide species A, C, G, and T such that: (i) every possible subsequence of two of the nucleotide species A, C, G, and T appears once as a sequence of consecutive nucleotide species in the de Bruijn sequence or (ii) every possible subsequence of three of the nucleotide species A, C, G, and T appears once as a sequence of consecutive nucleotide species in the de Bruijn sequence.
Claims 1-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of U.S. Patent No.US 9,605,308. Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims 1-19 drawn to a system comprising a machine-readable memory and a processor which when executed perform the steps which are within the scope of the claims 1-17 of the patent ‘308. The variation being in wording the claims in the patent ‘308, wherein the fluidic controller (processor) executes the steps as claimed in the instant claims and encompass the instant claims Thus the claims in the patent ‘308 encompass the instant claims and are coextensive in scope. Thus, the claims are rejected as being obviousness type of double patenting.
Claims 1-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of U.S. Patent No.US 11,390920. Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims 1-19 drawn to a system comprising a machine-readable memory and a processor which when executed perform the steps of the method and scope of the claims of the patent ‘920. As noted in the priority information, the claims directed to the method were amended to be dependent on the system and provide specific embodiments which make the method which requires providing flows on a system obvious over the system which is programed to provide the same method steps. The variation being in wording the claims in the patent ‘920 encompass the instant claims that are performed by the system. Thus, the claims are rejected as being obviousness type of double patenting.
Claims 1-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of U.S. Patent No.US 10,597711. Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims 1-19 drawn to a system comprising a machine-readable memory and a processor which when executed perform the steps of the method and scope of the claims of the patent ‘711. Patent ‘711 is parent to ‘920 as a continuation and is directed to a method which requires a system to provide the necessary flows of method. The method broadly encompasses the method and provide specific embodiments which make the method which requires providing flows on a system obvious over the system which is programed to provide the same method steps. The variation being in wording the claims in the patent ‘711 encompass the instant claims that are performed by the system. Thus, the claims are rejected as being obviousness type of double patenting.
Claims 1-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of U.S. Patent No.US 9418807. Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims 1-19 drawn to a system comprising a machine-readable memory and a processor which when executed perform the steps of the method and scope of the claims of the patent ‘807. Patent ‘807 is parent to ‘711 as a continuation and is directed to a method which requires a system to provide the necessary flows of method. The method broadly encompasses the method and provide specific embodiments which make the method which requires providing flows on a system obvious over the system which is programed to provide the same method steps. The variation being in wording the claims in the patent ‘711 encompass the instant claims that are performed by the system. Thus, the claims are rejected as being obviousness type of double patenting.
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 1-19 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Nobile et al. (US 2010/0300895 Al).
For claim 1, Nobile et al. teach a system comprising: a machine-readable memory and a processor configured to execute machine-readable instructions (see entire document, at least para 0047-0052, 0060), which when executed by the processor, cause the system to perform steps including: exposing a plurality of template polynucleotide strands, sequencing primers and polymerases in a plurality of defined spaces of a sensor array to a strands to a series of flows of nucleotide species flowed according to a predetermined ordering; determining for each of the series of flows of nucleotide species, a signal indicative of how many nucleotide incorporations occurred for a particular flow to determine a predicted sequence of nucleotides corresponding to the template polynucleotide strands, wherein the predetermined ordering (a) is not a series of consecutive repetitions of a 4-flow permutation of four different nucleotide species, (b) is not specifically tailored to a particular combination a particular template strand or a sequencing primer and (c) comprises a phase-protecting flow ordering (see entire document, at least para 0047-0052, 0060). For dependent claims, Nobile et al. teach that the phase-protecting flow ordering comprises a sequence of four predetermined nucleotides having a subsequence length parameter of two or three without any consecutive repeats of the same nucleotide species or a flow ordering that includes all possible distinct dimer pairs of four nucleotides or repeats of a 4-flow permutation (see page 9-10, para 0060, page 7, para 0052). Nobile et al. teach that the series further comprise a flow of N followed by a flow of X, further followed by a flow of Y, where X, Y and N represent different species of nucleotides and at least one nucleotide species flowed twice (see page 7, para 0052-0053). Nobile et al. teach that the predetermined ordering is selected based on assessing dephasing merit and efficacy of extension calculated for a plurality of candidate flow orderings using simulation sequencing data obtained for a plurality of random test sequences (see entire document, at least para 0065-0069). Nobile et al. teach that the sensor array is configured to detect hydrogen ions or inorganic pyrophosphatase released by incorporation of nucleotides (see entire document, at least para 0060-0070). For all the above, the claims are anticipated.
Nobile et al do not specifically teach that the flows are ‘phase-protecting’ but clearly provide for alternative flows than consecutive repeating flows which would be programed and could be interpreted based on observed incorporation into a template and would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to provide for various flows and interpretation to be run on a sequencing machine. One having ordinary skill in the art would have been motivated to substitute different flows for different templates and expected sequences to better interpret incorporations. The technology for sequencing systems is well known and no new machine is provided in the specification, and simply provides instructions for running these known systems, and in view of this it would have been a reasonable expectation of success to program a system to deliver any combination of flows as generally suggested by Nobile et al.
Thus, the claimed invention as a whole was clearly prima facie obvious.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Joseph T Woitach whose telephone number is (571)272-0739. The examiner can normally be reached Mon-Fri; 8:00-4:00.
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/Joseph Woitach/ Primary Examiner, Art Unit 1687
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