Prosecution Insights
Last updated: April 19, 2026
Application No. 17/182,817

METHODS, MODELS, SYSTEMS, AND APPARATUS FOR IDENTIFYING TARGET SEQUENCES FOR CAS ENZYMES FOR CRISPR-CAS SYSTEMS FOR TARGET SEQUENCES AND CONVEYING RESULTS THEREOF

Final Rejection §101§103§112
Filed
Feb 23, 2021
Examiner
WOITACH, JOSEPH T
Art Unit
1687
Tech Center
1600 — Biotechnology & Organic Chemistry
Assignee
President and Fellows of Harvard College
OA Round
2 (Final)
49%
Grant Probability
Moderate
3-4
OA Rounds
4y 8m
To Grant
78%
With Interview

Examiner Intelligence

Grants 49% of resolved cases
49%
Career Allow Rate
187 granted / 381 resolved
-10.9% vs TC avg
Strong +28% interview lift
Without
With
+28.5%
Interview Lift
resolved cases with interview
Typical timeline
4y 8m
Avg Prosecution
71 currently pending
Career history
452
Total Applications
across all art units

Statute-Specific Performance

§101
35.0%
-5.0% vs TC avg
§103
18.7%
-21.3% vs TC avg
§102
4.2%
-35.8% vs TC avg
§112
25.4%
-14.6% vs TC avg
Black line = Tech Center average estimate • Based on career data from 381 resolved cases

Office Action

§101 §103 §112
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 amendment filed 9/30/2025 has been received and entered. Claims 1-3, 5, 6, 9 and 10 have been amended. Claims 1-15 are pending. Priority This application filed 2/23/2021 is a divisional of 14/738483 filed 6/12/2015, now US Patent 10930367, which is a CIP of PCT/US2013/074812 filed 12/12/2013 which claims benefit to numerous US provisional application where 61/736527 filed 12/12/2012 has the earliest priority date. Response to Applicants Comments Applicants assert that the instant claims are entitled to the December 12, 2012 of application 61/736527 noting Example 3 of the specification. In response, review of Example 3 and the specification as a whole do not appear to support the claims as amended. For example, a search of ‘527 for the term ‘unique’ the term is found 10 times, is not consistent with claims “determining average cutting frequency of a particular mismatch position for a particular Cas nuclease from a training data set as to the Cas nuclease,” as amended. Support appears to be consistent with sequences which are different than repeats in short elements, for example: “The CRISPR loci typically differ from other SSRs by the structure of the repeats, which have been termed short regularly spaced repeats (SRSRs) (Janssen et al., OMICS J. Integ. Biol., 6:23-33 [2002]; and Mojica et al., Mol. Microbiol., 36:244- 246 [2000]). In general, the repeats are short elements that occur in clusters that are regularly spaced by unique intervening sequences with a substantially constant length (Mojica et al., [2000], supra). Although the repeat sequences are highly conserved between strains, the number of interspersed repeats and the sequences of the spacer regions typically differ from strain to strain.”; and with several specific target genome sequences in S. pyogenes Cas9, for example: “Exemplary target sequences include those that are unique in the target genome. For example, for the S. pyogenes Cas9, a unique target sequence in a genome may include a Cas9 target site of the form MMMMMMMMNNNNNNNNNNNNXGG where NNNNNNNNNNNNXGG (Nis A, G, T, or C; and X can be anything) has a single occurrence in the genome.” None of specific examples, nor the guidance in general appear to support the combination of method steps required of the instant claims. In addition, review of 61/828130 in light of the amendments does not appear to support the instant claims. In addition to the support provided in ‘527, the specification appears to provide a hyperlink to a supplemental table (which does not appear to be provided) for unique sequences computationally identified not based on mismatch and cutting frequency as presently claimed, and specific sequences in human chromosome 12 provided in figure 48 and description in specification for example [0073]: “Figure 48 shows a UCSC Genome Browser track for identifying unique S. pyogenes Cas9 target sites. A list of unique sites for the human, mouse, rat, zebrafish, fruit fly, and C. elegans genomes have been computationally identified and converted into tracks that can be visualized using the UCSC genome browser. Unique sites are defined as those sites with seed sequences (3'-most 12 nucleotides of the spacer sequence plus the NGG PAM sequence) that are unique in the entire genome (Supplementary Methods). All tracks can be accessed using the hyperlinks listed in Supplementary Table 3 or through www.genome-engineering.org.”; and more specific types of specific targets “In general, the repeats are short elements that occur in clusters that are regularly spaced by unique intervening sequences with a substantially constant length (Mojica et al., [2000], supra).”; and “Applicants identify nucleotide sequences unique to the mutant HTT allele and use it to design guideRNA”. In view of the amendments and acknowledgement that the parent application is a CIP of the PCT, a review was performed, and support for the instant claims was identified in [0015] teaching: “Accordingly, as CRISPR motifs or PAN/I sequences may be recognized by a Cas enzyme in vitro, ex vivo or in vivo, in the in silico analysis, there is an analysis, e.g., comparison, of the sequence in interest against CRISPR motifs or PAM sequences to identify regions of the sequence in interest which may be recognized by a Cas enzyme in vitro, ex vivo or in vivo. When that analysis identifies a CRISPR motif or PAM sequence, the next analysis e.g., comparison is of the sequences upstream from the CRISPR motif or PAM sequence, e.g., analysis of the sequence10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 bp in length starting at the PA M or CRISPR motif and extending upstream therefrom. That analysis is to see if that upstream sequence is unique, i.e., if the upstream sequence does not appear to otherwise occur in a genome, it may be a unique target site. The selection for unique sites is the same as the filtering step: in both cases, you filter away all target sequences with associated CRISPR motif that occur more than once in the target genome.” Accordingly, in review of the instant amended claim limitations, it appears that claims are fully supported in PCT/US2013/074812 and accorded the priority data of 12/12/2013. However, in review of the provisional applications indicated in the priority claim, none of the provisional applications appear to fully supports the instant claims. Based on the analysis above, the effective filing date for determination of the priority date for the instant claims is 12/12/2013. Information Disclosure Statement The information disclosure statement (IDS) submitted 10/3/2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner. 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 1-15 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 for the limitation of ‘determining average cutting frequency of a particular mismatch’ is withdrawn. The amendments to the claims have made clear that there is a difference between the guide and the target is to be assessed, and the cutting of the CRISPR-CAS system is represented in the training set. Claim 5 is 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. Specifically, claim 5 requires determination of ‘effective free energy’ with a given relationship formula, however it is unclear what is being measured in claim 1 that is in the training data set. As amended in claim 1, the training data appears to provide relative cutting for a mismatch, but it does not appear that the training data set provides any information to practice claim 5. More clearly providing details of the training data set in claim 1 or for steps on how relative cutting is used in establishing effective free energy could address the basis of this rejection. 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 1-15 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. 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. Specifically, claim 1 has been amended to provide a new wherein clause that “the training data set represents data relative to cutting by the CRISPR-Cas system at the particular mismatch position in a nucleotide sequence” and review of the specification and evidence of record there does not appear to be a dataset that exists that meets this limitation. While it appears that one can assess for off-site cutting of specific guides and specific Cas enzymes in various cells/genomes, there does not appear to be adequate support for the enormous number of possible guides, any possible target sequence, any and all possible eukaryotic genome sequences and any of the possible Cas enzymes so that a training data set is adequately supported as required by the claims as amended. To be able to practice the analysis of determining cutting frequency, the knowledge of how any of the Cas behave and might tolerate the various possible mismatches present in a guide, then to any possible target/genome sequence must first be determined to provide a training data set for the breadth of the claims. While off-site CRISPR activity was known at the time of filing, the enormous amount of information required of a data set to identify a “unique target sequence” in any eukaryotic cell does not appear to be adequately supported by the present disclosure or the art of record as a whole. While it is acknowledged there is literal support for the term ‘training data’, the specification fails to provide what this specifically is where the artisan could use such data in determining any cutting frequency of any target and practice the claims as broadly amended. Dependent claims fail to remedy the issue and rely on the ability to first make the assessment of a Cas system functional ability in mismatch tolerance to assess off-site cutting, to finally arrive at sequences which could not be a target or more specifically would represent a sequence in a genome that is not subject to off site CRISPR nuclease activity for any possible guide that could be created. It is noted that claims provide for Cas9 and PAM sequence targets, however this does not appear sufficient to address the breadth of data required is disclosed or sufficiently well known in the art to demonstrate that Applicants were in possession of the necessary training data set to practice the claims. 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 1-15 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 The claims have been amended and still are generally drawn to a method of assessing a CRISPR system to provide for unique sequences in a genome. More specifically, the claims have been amended to provide for a training data set which provides the basis of assessing CRISPR-Cas systems ability to target and cut any given sequence which might be represented in a genome. The method is performed in silico and the determining is established based on the training data and ability of any and all specific combination of elements in a CRISPR-Cas system to recognize any given sequence only once to establish that the genome target sequence is unique. Generally, this appears to be based in part on the data for all the possible combinations of guides and Cas enzymes, and assessment of a genome for where all these combinations would cut as a ‘determining’ step. Once establishing all the possible targets which are not subject to off site nuclease activity, a site would be ranked as a unique site. Dependent claimshave been amended to more clearly indicate that one or more sites may be identified. In review of the specification the steps of ‘determining' and ‘obtaining a ranking’ are calculation steps based on assessing any specific combination of target genomes and CRISPR-Cas systems. For step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a process. For step 2A of the 101 analysis, the judicial exception of the claims are the steps of accessing sequence data of a guide and a target for similarities and differences or calculating the free energy of the two (claim 5). The claims provide for ‘creating’ training data however this appears to be information and an abstract step. To the extent ‘determining’ relies on homology comparison, the step of aligning and comparing sequence to arrive at the identification of sites which can be ‘cut’ and somehow deriving a cutting frequency from this appear to be instructional steps. The judicial exception is a set of instructions for analysis of sequence data in the context of a Cas system function and appear to fall into the category of Mathematical Concepts, that is mathematical relationships for assessing frequency or free energy calculations and also in the category of Mental Processes, that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion) since the is no specificity in how the steps are to be practice or the necessary outcome for determining or ranking and could be assessed by visually determining similarities and differences, or comparing known sequence cutting information with that of the same ‘unique’ target. The breadth of “determining”, “ranking”, and steps of mathematical assessment of features encompasses non-transformative visual assessment of sequence data. This breadth does not impose a meaningful limit on the claim scope, such that all others are not precluded from using the natural principle of visually comparing two sequences and ranking them based on similarity or differences. Although the claims recite “creating’ a training data set, 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). Here nothing appears to be physically created, and broadly providing additional data. 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. The claims appear to fall into the category of Mathematical Concepts, as it applies the use of statistics and mathematical relationships in analyzing probabilities or frequencies, 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 required of the claims to which the analysis is applied This judicial exception requires steps recited at high level of generality and if practiced using a computer would only be stored on a non-transitory media, 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 sequence data. As such, the claims do not provide for any additional element to consider under step 2B to which the judicial exception is applied. 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. 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 that starts at a deletion or insertion) 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 (assessing 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 a summary of the rejections and the 2019 guidance, and explain that the invention meaningfully limits to identifying and producing one or more unique target sequences in a eukaryotic cell, an environment which CRISPR does not occur naturally. It is argued that providing unique sequences provide greater efficiency and minimize off target cleavage. In response, the claims provide only data and do not produce any product beyond information about possible target and CRISPR-Cas system functions. While that information may provide further uses, the claims do not require any of the uses noted. Further, the claims broadly require having a data set which informs the possible activity of possible target and CRISPR-Cas system functions combinations, and appears to effectively tie up any observation of other researchers as it could be interpreted to be a data set, and possibly then any consequential application of the unique site that was observed. For Step 2B applicants argue that the claims as a whole are significantly more noting several federal circuit decisions. In response, the case law cited is inconsistent with the fact pattern, which here is only analyzing or assessing possible cleavage sites for CRISPR-Cas systems. Under step 2B there are no additional elements to consider, and to the extent the method could be practiced using a computer there is no evidence as a whole that the claims provide significantly more. Again, producing target sequences in eukaryotic cells is not a physical act or considered an additional element, and is simply a description of a sequence in a genome which may cleaved only once given some specific CRISPR-Cas system requirements. Applicants argue that as of 2012 the skilled artisan would not reasonably expect that CRISPR-Cas9 system would function in eukaryotic environment noting the PTAB and Federal Circuit decisions in Exhibit A and B. In response, the exhibits are noted however the idea of enablement or expectation of a skilled artisan does not appear to a consideration for 101. The 101 analysis is an assessment of what the claims require, here the claims require providing a data set and based on the data set assessing sequences consistent with the data, which is cleavage activity of CRISPR-Cas for a given nucleotide sequence. While a sequence could exist in a eukaryotic cell, the claims are simply an assessment of a sequence and do not require that the CRIPR system even work in a cell. 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 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 negatived 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). Claim 1-15 stand rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Joseph et al. (May 2012-of record), Marraffini et al. (March 2010-of record), Ran FA, (November 2013-of record) and Cho et al. (March 2013-of record). Response to Applicants arguments Applicants argue the priority date is May 28, 2013 and that Ran does not qualify as prior art. In response, as noted above in the priority section, the support for the instant claims is found to be consistent with the disclosure of PCT/US2013/074812 and accorded the priority data of 12/12/2013, and none of the US provisional applications appear to support the instant amended claims. With this assessment, Ran is considered to qualify as prior art. Applicants argue that decisions by the PTAB and the Federal Circuit support that the skilled artisan did not expect CRISPR to be active in eukaryotic cells and that there is no reasonable expectation of success to practice the claims for eukaryotic cells. In response, the claims encompass analyzing sequence data not that information derived would necessarily be practice or work in eukaryotic cells. With respect to any function in eukaryotic cells Ran et al teach generally that targeted nucleases are powerful tools for mediating genome alteration with high precision, and specifically outline experiments using the RNA-guided Cas9 nuclease from the microbial clustered regularly interspaced short palindromic repeats (CRISPR) adaptive immune system can be used to facilitate efficient genome engineering in eukaryotic cells by simply specifying a 20-nt targeting sequence within its guide RNA. Ran et al provide evidence for a set of tools for Cas9-mediated genome editing via nonhomologous end joining (NHEJ) or homology-directed repair (HDR) in mammalian cells. Further, with respect to off site and more specific targeting to avoid off site affects, Ran et al teach that to minimize off-target cleavage a strategy using the Cas9 nickase mutant with paired guide RNAs for the selection of target sites and the evaluation of cleavage efficiency and analysis of off-target activity. This teaching appears to support an expectation of success as well as the recognition of off site cleavage and the need to assess based on observed activity specific targets which avoid the issue. The teachings of the other references are not specifically addressed in applicants arguments, and the basis of their teaching and reasoning of the 103 rejection is provided for completeness of the record. Joseph et al. provide detailed guidance for the thermodynamic assessment and basis of selecting guide target mismatch for RNA interference. With respect to claim 1, Joseph et al. teaches determining the amount location and nature of mismatches of candidate nucleic acids and when present for their contributions to hybridization free energy. For dependent claims, Joseph et al. provide detailed analysis and guidance for the local free energy using the equations provided in the instant claims. Joseph et al. provide the necessary guidance for assessing and correlating hybridization and the activity for molecules used in RNA interference, but fail to provide specific teaching for the use in analyzing CRISPR complexes. However, Marraffini et al. teach that CRISPR interference was a RNA-directed adaptive immunity in bacteria and archaea, and provide for description for the function of CRISPR. Further, the application of CRISPR was being used in genome engineering as evidenced by Ran et al. who teach using the CRISPR-Cas9 system for genome modifications, and Cho et al. who provide for CRISPR/CAS systems for genome engineering in human cells. In particular Cho et al. provide examples and experiments that demonstrate the importance of picking targets to avoid off target alterations when using CRISPR/CAS. While Joseph et al. provide detailed guidance for the thermodynamic assessment and basis of selecting guide target mismatch for RNA interference and not CRISPR, based on functioning components of the system that relies on hybridization and the effect of mismatches on function demonstrated by Cho et al., it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to design targeting sequences with analytical tools as provided by Joseph et al. to further analyze and explain the experimental results Cho et al. The use of CRISPR as a genome editing tool was known as provided in Marraffini et al. and greater use for genome editing is exemplified by Ran et al., and one having ordinary skill in the art would have been motivated to use the analysis tools of Joseph et al. to provide for better assessment and design of targeting molecules in experiments. There would have been a reasonable expectation of success given the results of Joseph et al. (May 2012-of record) for the application of hybridization analysis given the knowledge of the CRISPR/Cas system evidenced by Marraffini et al., Ran et al. and Cho et al. Thus, the claimed invention as a whole was clearly prima facie obvious. Conclusion No claim is allowed. In review of the art, Anderson et al. (Journal of Biotechnology Volume 211, 10 October 2015, Pages 56-65, Ava 17 July 2015) is noted for teaching the systematic analysis of CRISPR–Cas9 mismatch tolerance reveals low levels of off-target activity. In evaluating support for training data sets required of the instant claims, post filing art such as Anderson et al who performed a comprehensive evaluation of off-target potential of crRNAs containing mismatches with the target DNA, and which also cites other prior attempts of Fu et al. who evaluated transversion mutations at all possible single mis matches throughout 19 of the 20 nucleotides, their evaluation of double mismatches was limited to adjacent mismatches and a sub set of variably spaced ones, and Hsu et al. evaluated varying combinations of mismatches, both interspersed and concatenated, but they did not assess all possible mismatch combinations, likely due to the technical infeasible appear to support that comprehensive training data sets for assessing and defining ‘unique’ target sequences in eukaryotic cells did not exist. 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. Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. 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. Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /Joseph Woitach/Primary Examiner, Art Unit 1687
Read full office action

Prosecution Timeline

Feb 23, 2021
Application Filed
Aug 17, 2021
Response after Non-Final Action
Jun 26, 2025
Non-Final Rejection — §101, §103, §112
Sep 30, 2025
Response Filed
Feb 17, 2026
Final Rejection — §101, §103, §112 (current)

Precedent Cases

Applications granted by this same examiner with similar technology

Patent 12603152
METHODS AND APPLICATIONS OF GENE FUSION DETECTION IN CELL-FREE DNA ANALYSIS
2y 5m to grant Granted Apr 14, 2026
Patent 12525361
SYSTEMS AND METHODS FOR MODELLING PHYSIOLOGIC FUNCTION USING A COMBINATION OF MODELS OF VARYING DETAIL
2y 5m to grant Granted Jan 13, 2026
Patent 12522819
SYSTEMS AND METHODS FOR DETERMINING NUCLEIC ACIDS
2y 5m to grant Granted Jan 13, 2026
Patent 12522820
SYSTEMS AND METHODS FOR DETERMINING NUCLEIC ACIDS
2y 5m to grant Granted Jan 13, 2026
Patent 12516385
METHODS FOR USING MOSAICISM IN NUCLEIC ACIDS SAMPLED DISTAL TO THEIR ORIGIN
2y 5m to grant Granted Jan 06, 2026
Study what changed to get past this examiner. Based on 5 most recent grants.

AI Strategy Recommendation

Get an AI-powered prosecution strategy using examiner precedents, rejection analysis, and claim mapping.
Powered by AI — typically takes 5-10 seconds

Prosecution Projections

3-4
Expected OA Rounds
49%
Grant Probability
78%
With Interview (+28.5%)
4y 8m
Median Time to Grant
Moderate
PTA Risk
Based on 381 resolved cases by this examiner. Grant probability derived from career allow rate.

Sign in with your work email

Enter your email to receive a magic link. No password needed.

Personal email addresses (Gmail, Yahoo, etc.) are not accepted.

Free tier: 3 strategy analyses per month