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 .
Examiner Comment
As indicated in the interview summary of 8/11/2026, a response to the action mailed 6/29/2026 was not necessary and provided below is a first action on the merits.
Claim Status
Original claims 1-20 filed 6/15/2021 are currently under examination.
Priority
This application filed 6/15/2021 is a continuation of application 16/899716 filed 6/12/2020 (allowance mailed 6/25/2026) is a continuation of 15/153953, filed 5/13/2016 now US Patent 10689696 which was a 371 National stage filing of PCT/US14/68409 filed 12/3/204 which claims benefit to US provisional applications 61/915426 filed 12/12/2013, 61/915455 filed 12/12/2013 and 61/911319 filed 12/302013; and is the parent of 17/348212 filed 6/15/2021.
Information Disclosure Statement
The seven information disclosure statements (IDS) submitted between 6/17/2021 to 11/20/2025 were provided in the action mailed 6/29/2026.
It was noted that several PCT written opinions for PCTs and applications filed in foreign countries have been cited (see IDS file 7/6/17/2021 for example) without providing the application or claims that were under review or that are relevant to the applications, or any indication of their importance to the present claims and it is unclear if the references cited in these reviews been provided. These citations have been acknowledged and considered for what is written but not in the context of the full prosecution they may represent.
Additionally, it is noted that the listing of references in the specification is not a proper information disclosure statement. See for example pages 14 and 17. 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 Objections
Claims 1, 5, 14, 16, 18 objected to because of the term ‘star5’ is withdrawn.
Review of the specification provides literal support and definition of the term (see page 13, line 9 of the specification providing: “used herein, "Start5" refers to a binary metric that captures the sample preparation fragmentation at the beginning of a read.”.
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.
Claims 1-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of U.S. Patent No. 10,689696 (application 15/153953 is in the chain as a continuation of the present application).
Although the claims at issue are not identical, they are not patentably distinct from each other because ‘696 sets forth a system and method which provides for broader claim limitations for each of the steps for evaluating sequence data generated from a platform where over-lapping signals representing nucleotide incorporation are assessed to determine the most likely base incorporation at each cycle. Both methods and a system to implement the methodology are present in the claim set of ‘696. Claim 1 of ‘696 for the method is provided as evidence for the method which is implemented.
A method comprising:
(a) performing a plurality of cycles of a sequencing by synthesis reaction such that, at each cycle, a signal is generated that is indicative of incorporation of a same nucleotide into a plurality of identical polynucleotides, whereby a portion of the signal is noise associated with phasing or pre-phasing;
(b) detecting the signal at each cycle in at least one channel, wherein the signal at each cycle includes an intensity value for each channel; and
(c) performing cycle-by-cycle phasing corrections by applying a new first order phasing correction at each cycle to the intensity value for each channel;
wherein the new first order phasing correction is calculated for each channel of each cycle, wherein the new first order phasing correction includes subtracting an intensity value of an immediately previous cycle fromcurrent cycle; and wherein the same nucleotide incorporated into the plurality of identical polynucleotides is identified for each cycle.
Claims 1-20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of copending Application No. 16/899716 (parent of instant application, RCE filed 9/17/2026).
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims set forth a system and method which provides for broader claim limitations for each of the steps of ‘716 for evaluating sequence data generated from a platform where over-lapping signals representing nucleotide incorporation are assessed to determine the most likely base incorporation at each cycle. Claim 1 of ‘716 for the system is provided as evidence for the system and the method which is implemented.
A system comprising:
at least one processor; and
a non-transitory computer readable medium comprising instructions that, when executed by the at least one processor, cause the system to:
determine a base call for a nucleotide base of a polynucleotide;
generate an online-overlap metric, a purity metric, a phasing metric, and a start5 metric for the base call;
determine a quality score for the base call based on the online-overlap metric, the purity metric, the phasing metric, and the start5 metric; and
generate output-base-calling data comprising the base call for the nucleotide base and the quality score.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented. It is noted that notice of allowance has been mailed, however the application has not yet gone to issuance.
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Claim analysis
Claim 1 is directed to a system comprising a processor and readable medium with instructions to determine a base call using the steps of generating an ’on-line metric, a priority metric, a phasing metric and start5 metric’, using these metrics to provide a quality score and providing the base score and quality score. Given the guidance of the specification each of the metric are defined and provide specifically:
-"online overlap" refers to a measurement of the separation between the foreground called intensities and the background intensities which can be a statistic measuring the signal to noise of the read;
-"purity" refers to a measurement that captures how reliable a base call is likely to be based only on the current cycle, and measures how significant the called base is when compared to the other three bases;
-"phasing" refers to a measurement of the noise carried over from the previous and the next cycles; and
"Start5" refers to a binary metric that captures the sample preparation fragmentation at the beginning of a read.
Each of these are defined, however there is no specific means for assessing each of these require of the definitions or guidance of the specification. Further for claim 1, there is no specific requirement on how they are generated or used to determine a quality score for the method steps. Claim 1 does not set forth any specific type of data that is inputted or analyzed by the system, but given the art appears to be an assessment of a ‘determining a base call’ from a sequencing reaction, though not strictly required, and for example for ‘purity’ appears to imply a type of data which can be interpreted as separate and different bases, and in consecutive incorporations with respect to ‘phasing’; and broadly provides for assessing a chromatogram produced during a sequencing reaction. Dependent claims provide that the instructions ‘cause the system to determine’ which appears to indicate that the analysis is performed when the data is provided, and evaluations like “Phred algorithm’ (claim 7) can be used for the quality score. Independent claim 10 is directed to only the medium which is part of the system claim, and provides instructions for the analysis method consistent with claims 1-9. Independent claim 16 is the analysis method simply providing the instructions which would be stored on the medium or implemented with the processor on the system. No specific platform nor data to be analyzed is recited nor required of the method or set forth in the system, however in view of the specification and art of record sequencing methods that produce values associated with nucleotide base incorporation using known sequencing platforms, such as chromatograms produced for ATG and C incorporations where ‘base calls’ are usually made.
For step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a product and a process.
For step 2A of the 101 analysis, the judicial exception of the claims are the steps of analyzing base call data and providing the determined base call and quality. No specific means of making the base call is required, and the quality is based on four metrics of overlap, purity, phasing and start5 specification defined parameters. This applied to any data on which a base call could be made, but given the guidance and art of record would most likely be applied to sequencing data resulting from known platforms which also provide relative quality of the data in Phred analysis (claim 7). The judicial exception is a set of instructions for analysis of sequence data, which is a Mental Processes, that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion) because of the broad generic nature of the claims required for ‘determine’ and ‘generate’ which appear to encompass observation of intensity values or representation of multiple values on a graph after the data was obtained from the sequencing platform as no specific requirements to the metric are required and can be objectively or subjectively provided by observing a chromatogram of ATG and C incorporations, and also can be interpreted to be directed to mathematical concepts as the ‘metrics’ could be calculations if the relevant sequence data is provided as values and not images, that is to the extent that the claims encompass analysis of intensity data over time representing the incorporation of nucleotide bases of the sequence data generated on a given platform.
Recent guidance from the office requires that the judicial exception be evaluated under a second prong to determine whether the judicial exception is practically applied. In this case, the method are simply instructions, the media simply contains the instructions, and for the system the media with the instructions only provides analysis of the data when the data is provided and does not affect the function of the system (or particular processor which the media provides the instructions to).
The breadth of ‘determine’ and ‘generate’ are not physical steps but given the guidance of the specification encompasses non-transformative visual assessment of sequence data, and importantly must be coupled in part with prior knowledge of the correlation of what each intensity represents or correlates to for proper interpretation of the sequencing intensity value data that is first provided for base call analysis. This breadth does not impose a meaningful limit on the claim scope, such that all others are not precluded from using observation or mathematical assessment of values. The limitations required of the claim do not appear to integrate a judicial exception into a practical application; for example, merely including instructions to implement an abstract idea on a computer, or merely using a computer as a tool to perform an abstract idea, as discussed in MPEP § 2106.05(f). Computing, constructing datasets and using statistical models was well understood, conventional, and routinely performed in the art at the time the application was filed. Furthermore, the limitation of ‘selecting’ in the analysis nor the process of obtaining the data and does not change the steps to be performed. See MPEP § 2106.05(g) for a discussion on adding insignificant extra-solution (both pre-solution and post-solution) activity to the judicial exception. See also MPEP § 2106.05(h) for a discussion on generally linking the use of a judicial exception to a particular technological environment or field of use, here possible the field of sequence analysis.
For step 2B of the 101 analysis, each of the independent claim 1 recites additional elements and are found to be directed to a general purpose computer on which the instructions for analysis are stored or implemented using the processor. The media is a physical product but simply stores the instructions, and the method only recites instructions and has no additional elements associated with it. As such, the claims do not provide for any additional element to consider under step 2B beyond steps to obtain data which is subsequently and separately analyzed. While system claims require a processor and computer medium (note the method claims themselves do not require such limitations), it is noted that in explaining the Alice framework, the Court wrote that "[i]n cases involving software innovations, [the step one] inquiry often turns on whether the claims focus on the specific asserted improvement in computer capabilities or, instead, on a process that qualifies as an abstract idea for which computers are invoked merely as a tool." The Court further noted that "[s]ince Alice, we have found software inventions to be patent-eligible where they have made non-abstract improvements to existing technological processes and computer technology." Moreover, these improvements must be specific -- "[a]n improved result, without more stated in the claim, is not enough to confer eligibility to an otherwise abstract idea . . . [t]o be patent-eligible, the claims must recite a specific means or method that solves a problem in an existing technological process." As indicated in the summary of the judicial exception above and in view of the teachings of the specification, the steps are drawn to analysis of sequence data. While the instruction are stored on a medium and could be implemented on a computer, together the steps do not appear to result in significantly more than a means to compare sequences. The judicial exception of the method as claimed can be performed by hand and in light of the previous claims to a computer medium and in light of the teaching of the specification on a computer. In review of the instant specification the methods do not appear to require a special type of processor and can be performed on a general purpose computer. Dependent claims set forth additional steps which are more specifically define the considerations and steps of calculating, and comparing, and do not add additional elements which result in significantly more to the claimed method for the analysis.
In the instant case, the claims comprise steps of assessing sequence data and is considered the judicial exception. It is noted that while the claims set forth or imply information about the sequences being analyzed, this is only description of the data being analyzed and context and user defined. As such, the instant claims set forth an inventive concept that are drawn only to an abstract process that only manipulates data and, therefore, are not directed to statutory subject matter. No additional steps are recited in the instantly claimed invention that would amount to significantly more than the judicial exception than broad known means to analyze sequence data to make a base call. Furthermore, to the extent the data can be values, if a claim is directed essentially to a method of calculating, using a mathematical formula, even if the solution is for a specific purpose, the claimed method is non-statutory. In other words, patenting abstract idea (designing probes to a target sequence) cannot be circumvented by attempting to limit the use to a particular technological environment or purpose and desired result.
One way to overcome a rejection for non-patent-eligible subject matter is to persuasively argue that the claimed subject matter is not directed to a judicial exception. Another way for the applicants to overcome the rejection is to persuasively argue that the claims contain elements in addition to the judicial exception that either individually or as an ordered combination are not well understood, routine, or conventional. Another way for the applicants to overcome the rejection is to persuasively argue that the claims as a whole result in an improvement to a technology. Persuasive evidence for an improvement to a technology could be a comparison of results of the claimed subject matter with results of the prior art, or arguments based on scientific reasoning that the claimed subject matter inherently results an improvement over the prior art. The applicants should show why the claims require the improvement in all embodiments.
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 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.
Claims 1-20 rejected under 35 U.S.C. 103 as being unpatentable over Whiteford et al. and Garcia et al. (both of record) is withdrawn.
Upon review of the art, it is clear that sequencing system capable of recording light intensity or producing chromatograms of sequencing data were known and used to characterize sequences to make base calls, also providing analysis of the sequencing data relative to the quality such as phasing present in the separation or other elements of quality such as using Phred scores to assess the quality of the resulting read data, there is no teaching in the art to use a start5 metric in assessing quality of a base call.
Conclusion
No claim is allowed.
The art of record demonstrated that analyzing and making base calls and providing a relative quality of the base was known. For example, Whiteford teaches a method of generating a phasing-corrected intensity value and similarly Garcia teaches methods and systems for analysis of image data generated at multiple reference points, and particularly to image and sequence data generated during DNA sequencing which assesses a phasing-corrected intensity value.
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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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz R Skowronek can be reached at 571 272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Joseph Woitach/Primary Examiner, Art Unit 1687
