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 .
Applicants Amendment
Applicant’s amendment filed 8/21/024 has been received and entered. Claims 3, 5, 9 have been amended.
Claims 1-21 are pending.
Priority
This application filed 9/19/2023 is a National stage filing of PCT/US2022/020949 filed 3/18/2022, which claim benefit to US Provisional application 63/165507 filed 3/24/2021.
Information Disclosure Statement
The two information disclosure statements (IDS) submitted on 3/13/2025 and 8/21/2024 are 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. 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 not considered in light of the instant claims. 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 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 1-21 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 is unclear and appears incomplete in what is required of claim with respect to ‘obtain’ and how for each step this is performed. It is unclear if for example a fixed point number exists related to claimed method, or if some more in depth steps are required to obtain such a number. While generally, in computing a fixed-point is a method of representing fractional (non-integer) numbers by storing a fixed number of digits of their fractional part, and more generally, the term may refer to representing fractional values as integer multiples of some fixed small unit, e.g., a fractional amount of hours as an integer multiple of ten-minute intervals, it is unclear what must be performed to ‘obtain’ it relative to the claims, in particular since it appears relative to determining codeword size in the final forming step. Further, while generically one can obtain a library, it is unclear what structure the library has or how it was formed such the it represents or can be analyzed to provide informative information, or how it is related to the pre-amble of the claim for ‘writing information’ and how it is provided into the nucleic acid sequences that could be comprised within a library. It is unclear what a combinatorial space is relative to the library and what the nucleic acid sequences are within the library such that unique identifiers are found and ultimately can be analyzed various subsets as required of the claims. Further, the claims provide further steps of applying other types of operations such as AND, XOR, NOT or OR which are indicated to be ‘chemical’ and it is unclear what this is directed to relative to the library or the nucleic acid size or ratios. Additionally, the application of an undefined ‘chemical’ NIMPLY gate, which NIMPLY is generally known to be a binary digital logic gate that implements material nonimplication, as a chemical is undefined relative to what must occur. Dependent claims provide greater details of possible sizes or ratios, but fail to clarify the issues of claim 1.
More clearly providing details of how the steps are to be performed, or details about a library and how the sequences are designed or created such that they represent writing information 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 1-21 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 generally directed to encoding written information into nucleic acid sequences. More specifically, the method provides steps which in light of the specification appear to design for encoding and instructions of decoding based on size of a codeword. As part of the decoding, dependent claims provide for common operators that can be applied, and while not consistent with the preamble, the final steps provide subsets of identifiers nucleic acid molecules which size approximates a codeword.
For step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a method.
For step 2A of the 101 analysis, the judicial exception of the claims are each of the steps of assessing sequence data for what might be represented by the size of sequences which are relative to codewords. For example, paragraph [0005] provides that the invention and claims are directed to: “The present disclosure provides systems and methods for storing digital information into nucleic acid molecules in various ways to improve the efficiency of the retrieval and access of that digital information. For example, component nucleic acid molecules (e.g., components) are selected and concatenated to one another to form identifier nucleic acid molecules (e.g., identifiers), each of which corresponds to a particular symbol (e.g., bit or series of bits), or that symbol's position (e.g., rank or address), in a string of symbols (e.g., a bitstream). Those components may be organized in a structural manner, so as to provide an efficient scheme for representing digital data.” The judicial exception is a set of instructions for analysis of nucleic acid sequence data and appear to fall into the category of Mathematical Concepts, that is mathematical calculations relative to the need to provide ratios on observed sizes; an also Mental Processes, that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion) where here the broad generic steps appear to be instructions for evaluating the size of the nucleic acids in a library and correlating that to codewords representing written information. The breadth of “obtaining”, “identifying”, and “forming” encompasses non-transformative visual assessment of information. This breadth does not impose a meaningful limit on the claim scope beyond instructions of designing and encoding coded information into a nucleic acid.
As the steps of “obtaining”, “identifying”, and “forming” are very generally recited, and the combination of together can reasonably interpreted as mere data gathering and analysis. Computing, constructing datasets and using statistical models was well understood, conventional, and routinely performed in the art at the time the application was filed. The claims appear to fall into the category of Mathematical Concepts, as it applies the use of statistics and mathematical relationships in analyzing probabilities based on size, and also into the category of mental processes, as concepts performed in the human mind (including an observation, evaluation, judgment, opinion) because there is no apparent complexity to or amount of data that is collected and analyzed as presently claimed.
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 the instant case, the claims do not have an additional element to which the analysis is applied and appear to only provide steps for decoding information that may exist in a library. This judicial exception requires steps recited at high level of generality, and it is not found to be a practical application of the judicial exception as broadly set forth.
For step 2B of the 101 analysis, the claims fails to recite any additional elements and are found to be the steps of analyzing sequence data. As such, the claims do not provide for any additional element to consider under step 2B. To the extent the analysis can be performed using a computer, 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 could be 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 evaluate sequences for encoded information. The judicial exception of the method as claimed can be performed by observation of a sequence. 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. No additional steps are recited in the instantly claimed invention that would amount to significantly more than the judicial exception. Without additional limitations, a process that employs mathematical algorithms to manipulate existing information (identify a coded information) to generate additional information is not patent eligible. In other words, patenting abstract idea (designing codes into nucleic acid sequences) 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.
Conclusion
No claim is allowed.
At the time of filing, using DNA to store types of information was known, and there were many means of design of using the four bases, AGTC, to encode a variety of types of data. For example, Portney et al. (2008) demonstrate a means of using length to provide the basis of binary code. Review of the art of record provides examples of many designs, however fails to provide the basis of using a ratio of distinct identifier sequences of different subsets to represent a codeword based on size approximates as required of the claims.
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
Prosecution Insights