Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Applicant’s amendment
Applicant’s preliminary amendment filed 4/21/2022 has been received and entered. Claims 1-135 have been cancelled, claims 136-148 have been added.
Claims 136-148 are pending and currently under examination.
Priority
This application filed 12/9/2021 is a continuation of 14/241874 filed 7/23/2014 (now abandoned), which is a national stage filing of PCT/IL2012//000326 filed 8/30/2012, which claims benefit to US provisional applications 61/530384 filed 9/1/2011, 61/565435 filed 11/30/2011, 61/594320 filed 2/2/2012, and 61/594323 filed 2/2/2012.
Information Disclosure Statement
The information disclosure statement (IDS) submitted 4/22/2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Several of the cited references are Office actions are from foreign offices, some translated and some providing a summary. Similarly, office actions from US applications have also been submitted. It is noted that for review of these, the pending claims that were reviewed in these actions were not provided, but for completeness and clarity of the record the cited references when provided in this prosecution were considered only relative to the instant claims. Also, the foreign statutes and comments of the reviewers were not clearly in context of the pending claims and were not considered for their logic nor factual accuracy of comments in actions from other foreign offices.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 136-148 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement.
It is noted that the preliminary amendment was filed after the initial filing of the application. Review for support of the amendments is provided.
The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention. Specifically, upon review of claim 1 and support in the present specification, while the terms of step e) recited appear to have literal support within the specification, the specification does not appear to support the specific combination where modified sequences of harmful gene expression products are contemplated. A search of the specification does provide identification of ‘harmful’ sequences, however it fails to teach or suggest how they would be modified. The specification provides generically for harmful sequences and broad examples of possible sources and that they could be in a database, but there is no guidance that they should be changed (there appears to be support that they are reported). Support for change and modification appears to be directed to CpG or codon optimization, and does not support that the nucleic acid sequence does not encode the harmful expression product as presently claimed. It is noted that claim 126 recites that the design uses a ‘list of design rules’, however the specification provides only generically for this embodiment, and does not provide for any specific rules of design, in particular linked to harmful sequences. Dependent claims are included in the basis of the rejection because they fail to address the basis of the rejection and are subject to the same issue. Review of the specification provides a teaching at paragraphs 39-41 of:
[0039] It is a further object of the present invention to disclose the system as defined above, wherein said debugging module provides output with alternative alteration of said designed nucleic acid construct. [0040] It is a further object of the present invention to disclose the system as defined above, wherein said alteration is configured to fix a determined error in said designed nucleic acid construct. [0041] It is a further object of the present invention to disclose the system as defined above, wherein said alteration is configured to be automatically accepted by said system and updated said nucleic acid construct.
which provides the general high level guidance for making alterations, fixing errors in a design and the general idea of modification of a construct, but does not appear to provide any guidance for the claimed combination, nor any of the necessary guidance for modifying a toxic or harmful sequence for synthesis as required in the amended claims. It is noted that at Example 2 of the specification, examples of what databases one could use and general guidance that sequences could be aligned to detect harmful or toxic sequences are provided, and while providing an ‘alert’ it appears to be consistent with flagging for ‘a price increase’ not any guidance for changing the sequence, nor any specific definition or guidance as to any context to what is considered toxic or harmful as would be necessary to practice the claimed limitation. Additionally, Example 6 supports limitations for optimizing synthesis, however like in Example 2 appears consistent for cost effectiveness without any guidance for changing a toxic or harmful sequence. Review of the guidance noted by Applicants and the specification as a whole does not appear to provide for the combination nor the necessary guidance to support the claims as amended.
Providing specific support present in the instant specification or amending the claims to be consistent with the disclosure would address the basis of the rejection.
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 136-148 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter because the claimed invention is not directed to patent eligible subject matter.
Claim analysis
Claim 136 is generally directed to a method for synthesizing and designing nucleic acids comprising visualizing biological information in an interface, designing sequences wherein harmful sequences are identified, sending the design instructions to a synthesizer and synthesizing the nucleic acid. In review of the specification there is no specific list or definition of ‘harmful' nucleic acids, and the general broad guidance provides by example sequences which encode portions of toxins, viruses, bacteria and/or pathogens, and would include any variety of sequences that for a given context would be considered harmful. It is noted that based on the art of record, ‘harmful’ sequences is a broad term and can only be interpreted in a specific contest which would make possibly any given sequence harmful (harmful to humans if expressed, harmful for expression in cell system,…). The dependent claims require that the design and data of harmful sequences be specific types of genetic elements. For dependent claim 138, given the guidance of the specification, the editing is generic as required of the claim, but encompasses removing the harmful sequences. Claim 148 providing the instructions for the method is intended to be implemented by the system or synthesizer is one where harmful sequences are stored in a database, and used to assess a nucleic acid design for the presence of harmful sequences and to provide a warning and alternate design instructions to the use so that a harmful sequences is not encoded, then a final step for synthesizing a nucleic acid.
For step 1 of the 101 analysis, the method is a statutory category as directed to process.
For step 2A of the 101 analysis, the judicial exception of the claim is found to be the instructions, and claim 148 instructions stored on the medium that compare input sequence data and the comparison of the input with sequences within an existing database and provide possible feedback to the user if a match is found as part of the designing process. The judicial exception is a set of instructions for analysis of sequence data and appear to fall into the category of mental process, that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion). While it can be acknowledged that the use of a computer and the necessary software speeds the analysis and comparison of a reference sequence and those present in a database, there is no necessary complexity nor amount of data that is required of the claims in the analysis, and appear that comparing two sequences to see if they share homology can be done in one’s mind or on paper, and results in providing a nucleic acid design without the ‘harmful’ sequence as part of the analysis and final instructions.
Recent guidance from the office requires the analysis of a second prong under 2A, and whether the recited judicial exception is practically applied. In review of the guidance of the specification, the high level of generality for providing any input and analysis of the input by homology search of a data set consisting of potentially harmful pathogenic sequences provides for a conditional step and the following steps are only implemented if a harmful sequence(s) detected (and must be present in the database also), and broadly providing steps to identify harmful sequences in a proposed construct and if and/or when identified do not synthesize the proposed sequence does not appear to be practical application to the steps of receiving data and synthesizing a nucleic acid as set forth in step d). To the extent that step d) is an additional element, as broadly set forth when practiced does not appear to be a practical application of the analysis and simply provides for a step to make what was broadly designed.
For step 2B of the 101 analysis, in review of the specification the method and medium with instruction for a system/synthesizer on a computer readable medium appear to be a general purpose computer for the purpose of the 101 analysis. It is noted that claim 136 recites and requires a final step to ‘synthesizing a nucleic acid’. As noted above, two interpretations of the limitation of step d) are possible, first simply as instructions to produce/synthesize a nucleic acid design or second as a physical step where it is physically produced. For the computer implemented aspect of the claims, 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." Here each of the instructional steps are to analyze a proposed construct for possible harmful sequences, and do not appear to provide for an improved result in the analysis or in the resulting construct if the sequence is removed.
To the extent that step d) can be an additional element, that is the step of physically producing a nucleic acid, it would be considered an additional element of the claim for 101 analysis. Synthesizing a designed nucleic acid sequence (for either useful or harmful sequences) is a conventional step, and does not appear by itself or within the claim as a whole to provide for significantly more than producing a sequence. Reviewing the art of record, Mulligan (Blueheron presentation 2006) provides evidence that commercial synthesis of sequences were known, and more specifically that software to analyze sequences for nefarious applications (see slides starting at slide 32, in particular slide 39 which teaches that all sequences should be screened).
What is left is the method implemented by the computer which is the judicial exception of the abstract instruction for designing/providing and detecting possible harmful sequences. In review of the specification, the harmful sequence is defined and provided by the user and/or intended use of the sequence and not inherent to the sequence itself. As broadly set forth, the steps require providing a sequence design and comparing it to possible ‘harmful’ reference sequences, where the most specific claim requires them to be in a database and that they are pathogenic in the context of a human. The step for analysis and comparing are considered abstract instructional steps to compare sequence data, and do not appear to be rooted or affect the system (here a general purpose computer) where the claim as a whole are found to be patent eligible. Dependent claims set forth limitations as to what the design of the nucleic acid is directed and general use and ‘functionality known in the art’ (see original) claim 70 for example).
Conclusion
No claim is allowed.
The closest art of record is Mulligan (Blueheron presentation 2006) who provides evidence that commercial synthesis of sequences were known, and more specifically that software to analyze sequences for nefarious applications should be used. More generally at the time of filing methods of identifying sequences in DNA constructs and/or artificially created sequences were well known; however the art does not teach to create a database where harmful sequences exist (in part this would be dependent on where and how they are used to make the context of why/how they are ‘harmful’) and where the database is associated with a system to automatically identify and provide design suggestions (design also would be dependent on the context and specifics of use as well) for DNA constructs.
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 on Mon-Fri; 9:00-5:00.
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/Joseph Woitach/ Primary Examiner, Art Unit 1631
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