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 2/27/2026 has been received and entered. Claim 1 and 21 have been amended.
Claim 1-21 are pending
Priority
This application filed 4/27/2022 is a 371 national stage filing of PCT/KR2020/016965 filed 11/26/2020; and claim benefit to foreign application KR10-2019-0157540 filed 11/29/2019.
Receipt is acknowledged of a certified copy of foreign application KR10-2019-0157540 filed 11/29/2019, however the present application does not properly claim priority to the submitted foreign application. If this copy is being filed to obtain priority to the foreign filing date under 35 U.S.C. 119(a)-(d) or (f), 365(a) or (b), or 386(a), applicant must also file a claim for such priority as required by 35 U.S.C. 119(b) or 365(b), and 37 CFR 1.55. If the application was filed before September 16, 2012, the priority claim must be made in either the oath or declaration or in an application data sheet; if the application was filed on or after September 16, 2012, the claim for foreign priority must be presented in an application data sheet.
If the application being examined is an original application filed under 35 U.S.C. 111(a) (other than a design application), the claim for priority must be presented during the pendency of the application, and within the later of four months from the actual filing date of the application or sixteen months from the filing date of the prior foreign application. See 37 CFR 1.55(d)(1). If the application being examined is a national stage application under 35 U.S.C. 371, the claim for priority must be made within the time limit set forth in the PCT and Regulations under the PCT. See 37 CFR 1.55(d)(2). Any claim for priority under 35 U.S.C. 119(a)-(d) or (f), 365(a) or (b), or 386(a) not presented within the time period set forth in 37 CFR 1.55 is considered to have been waived. If a claim for foreign priority is presented after the time period set forth in 37 CFR 1.55, the claim may be accepted if the claim properly identifies the prior foreign application and is accompanied by a grantable petition under 37 CFR 1.55(e) to accept an unintentionally delayed claim for priority and the applicable petition fee under 37 CFR 1.17(m)(1) or (m)(2).
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 2/27/2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
It is noted that the IDS contain office actions related to foreign applications, but do not provide a context or specific claims or references that are discussed in the actions (see for example #s 5 and 6 in NPL list of IDS). These have been reviewed for what is provided within them, but the relevant application material such as specification, claims and cited references have not been used for the review.
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 stand 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
The method in claim 1 has been amended and still is generally directed to identifying diamer pairs in primers for the use in detecting sequences. Specifically, the claim has been amended to be ‘computer-implemented’ in the preamble with no changes to the active steps required. The method broadly comprises any form of implementation, but in light of claim 21 directed to a product that is a medium that contains the instructions of the analysis, the specification and the art as a whole the sequence analysis can be performed using a computer. More specifically, the claims are directed to a method where two sequences are evaluated and if there is homology which would result in a diamer formation, the pair are discarded and new set are evaluated until there is not diamerization. This is performed until two sets of primer pairs are obtained. Dependent claims set forth the analysis for homology is using Watson-Crick base pairing and additional instructions as to what to do when a diamer is observed, and that when a diamer pair is observed indicating that it is a diamer link and needs to be replaced as part of the process.
For step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a method stored on a non-transitory medium.
For step 2A of the 101 analysis, the judicial exception of the claims are the steps of accessing sequence data for whether two sequences have homology and could form a diamer pair. The step of aligning and comparing sequence to arrive at the identification of a pair of sequences based on homology are instructional steps. When using a computer, the claim requires computing similarity scores based on homology of the two sequence. The judicial exception is a set of instructions for analysis of sequence data and appear to be directed to a Mental Processes, that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion). The breadth of “providing” and “replacing” encompasses non-transformative visual assessment of individual sequences for any homology. This breadth does not impose a meaningful limit on the claim scope, such that all others are not precluded from using the natural principle that two sequences that share homology may hybridize and form a diamer. Although the claims provide the instructions are on a medium and could be performed using a computer, the courts have also identified limitations that did not 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). The steps required of the claims are very generally recited, the combination of each together reasonably interpreted as mere data gathering and analysis of short primer sequences for homology. The claims appear to fall 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 or judicial exception is applied. This judicial exception requires steps recited at high level of generality and are only stored on a non-transitory, and is not found to be a practical application of the judicial exception as broadly set forth.
For step 2B of the 101 analysis, each of the independent claims recites additional elements and are found to be the steps of obtaining and evaluating sequence data for possible homology. As such, the claims do not provide for any additional element to consider under step 2B. To the extent the claims encompass 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 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.
Therefore, the result of Step 2A analysis is that the claims are directed towards a judicial exception, i.e. an abstract idea. The second part, Step 2B of the two step analysis is to determine whether any element or combination of elements, in the claim is sufficient to ensure that the claim as a whole amounts to significantly more than the judicial exception. 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 (aligning sequences) to manipulate existing information (identify a probe which forms or does not form a diamer) to generate additional information is not patent eligible. Furthermore, 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.
Response to Applicants Arguments
Applicants provide an overview that the analysis can improve the multiplex PCR and guidance in the specification, and argue that the method provides for analysis times that are faster than other programs, such as that disclosed in Vallone et al (of record).
In response, the difference in computer implementation is not the basis of the analysis, but rather what analysis steps are required. As noted above in reference to the fact pattern of the Alice decision, a claim is not necessarily patent eligible if simply implemented using a computer. The instant claims require ‘a pool of oligonucleotide sets’ which given the breadth can comprise two sets to make up such a pool. The analysis steps that follow can easily be performed on such a’ pool’. Moreover, even if the set of oligos were to grow, the analysis require does not change, only the number of comparisons, so does not appear to move the analysis method out of the category of abstract concepts and steps that can be performed by observation. While it is acknowledged that some methods will perform an analysis very quickly when performed on a computer, this is not the basis of patentability. Further, the problem of choosing primer pairs while part of the scope of the use of the analysis, is not limiting on what is performed and the analysis itself still provides abstract instructional steps as a solution to designing and choosing primer pairs, and again is all relevant to what ‘pool’ is provided as input data-which is not specifically required of the claims.
Therefore, for the reasons above and of record, the rejection is maintained.
As noted previously, 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 (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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-21 rejected under 35 U.S.C. 103 as being unpatentable over Vallone et al. and Cheng-Chung et al. is withdrawn.
Upon review, while the art provides for comparison of primers, ie diamers, it fails to provide all the recited analysis steps of the claims. While it is relevant to the input data, the references do not require that all candidate combination are generated based on ‘all primer pairs for potential cross-reactivity’ nor relacing one oligo with the data source.
Accordingly, the rejection is withdrawn.
Conclusion
No claim is allowed.
Based on the teachings of the specification, the claimed method encompass steps in identifying diamer pairs in sets of potential primers for the use in detecting sequences. The method broadly comprises and form of assessment for diamer formation, but generally relies on homology between the two potential primer sequences, where dependent claim state that the homology is based on the common Watson-Crick base pairing. The method can be done by any form of implementation, but in light of claim 21 directed to a product that is a medium that contains the instructions of the analysis and the specification as a whole the sequence analysis can be performed using a computer. Potential issues with primer design, in particular diamer formation was well known and there were several programs which would evaluate a target sequence and provide primers to a sequence of interest where the primers would not form diamers. For example, Peter M. Vallone & John M. Butler provide a program called AutoDimer which provides a method for screening tool for primer-dimer and hairpin structures. More generally, Cheng-Chung e al. provide guidance for optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression and for the use of multiple primer probes, and optimization between all the possible existing pairs. Neither reference specifically state that random oligos to a target are first provided, then compared, the kept or discarded based on the ability to form a diamer.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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
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