Prosecution Insights
Last updated: April 19, 2026
Application No. 17/793,968

METHODS OF FUNCTIONALLY SCREENING BIOLOGICAL SEQUENCE FRAGMENTS

Non-Final OA §101§102§103§112
Filed
Jul 20, 2022
Examiner
SCHULTZHAUS, JANNA NICOLE
Art Unit
1685
Tech Center
1600 — Biotechnology & Organic Chemistry
Assignee
Massachusetts Institute Of Technology
OA Round
1 (Non-Final)
34%
Grant Probability
At Risk
1-2
OA Rounds
5y 0m
To Grant
74%
With Interview

Examiner Intelligence

Grants only 34% of cases
34%
Career Allow Rate
28 granted / 82 resolved
-25.9% vs TC avg
Strong +40% interview lift
Without
With
+39.5%
Interview Lift
resolved cases with interview
Typical timeline
5y 0m
Avg Prosecution
47 currently pending
Career history
129
Total Applications
across all art units

Statute-Specific Performance

§101
28.6%
-11.4% vs TC avg
§103
23.9%
-16.1% vs TC avg
§102
10.8%
-29.2% vs TC avg
§112
27.0%
-13.0% vs TC avg
Black line = Tech Center average estimate • Based on career data from 82 resolved cases

Office Action

§101 §102 §103 §112
DETAILED ACTION 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. 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. Claim Status Claims 1-6, 10, 14, 18, 20-21, 26-28, 35-36, 40, 51, and 64-65 are pending. Claims 7-9, 11-13, 15-17, 19, 22-25, 29-34, 37-39, 41-50, 52-63, and 66-70 are canceled. Claims 2 and 35 are objected to. Claims 1-6, 10, 14, 18, 20-21, 26-28, 35-36, 40, 51, and 64-65 are rejected. Priority The instant Application claims domestic benefit to US provisional application 62 / 965 , 138 , filed Jan 23 2020 . Applicant's claim for the benefit of a prior-filed application, PCT/US2021/014814 , filed Jan 23 2021 , is acknowledged. Accordingly, each of claims 1-6, 10, 14, 18, 20-21, 26-28, 35-36, 40, 51, and 64-65 are afforded the effective filing date of Jan 23 2020 . Information Disclosure Statement The information disclosure statements (IDS) filed on Feb 2 2023, Apr 23 2025, and Sep 12 2025 are in compliance with the provisions of 37 CFR 1.97 and have therefore been considered. Signed copies of the IDS documents are included with this Office Action. It is noted that the specification lists several references not cited on an IDS (see at least p. 11, lines 14-16). The listing of references in the specification is not a proper information disclosure statement. 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. Drawings The drawings are objected to for the following informalities: some text in FIG. 2 and 6 (example, the text above “Hashed order fragments” is not legible because it is too light or faint. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance. Nucleotide and/or Amino Acid Sequence Disclosures The sequence listing submitted Jul 20 2022 has been accepted. Specification The amendments to the specification submitted Jul 20 2022 are accepted. The disclosure is objected to for the following informalities. It is noted that for purposes of the instant Office Action, any reference to the s pecification pertains to the s pecification as originally filed on Jul 20 2022 . Abstract Applicant is reminded of the proper content of an abstract of the disclosure. A patent abstract is a concise statement of the technical disclosure of the patent and should include that which is new in the art to which the invention pertains. The abstract should not refer to purported merits or speculative applications of the invention and should not compare the invention with the prior art. If the patent is of a basic nature, the entire technical disclosure may be new in the art, and the abstract should be directed to the entire disclosure. If the patent is in the nature of an improvement in an old apparatus, process, product, or composition, the abstract should include the technical disclosure of the improvement. The abstract should also mention by way of example any preferred modifications or alternatives. Where applicable, the abstract should include the following: (1) if a machine or apparatus, its organization and operation; (2) if an article, its method of making; (3) if a chemical compound, its identity and use; (4) if a mixture, its ingredients; (5) if a process, the steps . Extensive mechanical and design details of an apparatus should not be included in the abstract. The abstract should be in narrative form and generally limited to a single paragraph within the range of 50 to 150 words in length. See MPEP § 608.01(b) for guidelines for the preparation of patent abstracts. The abstract of the disclosure is objected to because the abstract is not descriptive of the actual claimed invention. The abstract is only 19 words long and only describes generally what the invention relates to rather than the steps performed by the method. A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b). Appropriate correction for all objections to the specification is required. Claim Objections The claims are objected to for the following informalities: In claim 2 , the commas separating the list of actions should be changed to semicolons. Claim 2 recites “wherein the acting in response to (d) comprises one of more of … DNA sequencing, DNA molecule design, polypeptide sequence determination, and further sequence identification steps ” . DNA sequencing, DNA molecule design, polypeptide sequence determination, and further sequence identification steps are each recitations of nouns and should be amended to recite verbs, such as, for example, “ performing DNA sequencing”. Claim 35 recites “(c)… the sequence fragments the preselected biological molecule ”, which should recite “(c)… the sequence fragments of the preselected biological molecule ”. Claim Interpretation Claim Terminology Contingent Claiming In the interest of compact prosecution, the instant claims are examined to consider all claim limitations. However, the claims contain recitations of intended use and contingent claim language that affect the scope of the claims, as listed below. The courts have stated that claims must be given their broadest reasonable interpretation (BRI) consistent with the specification (see MPEP § 2111). The instant claims include a recitation of contingent claim language. With respect to contingent claiming, said contingencies as claimed require that the claims are interpreted as provided for in the MPEP at 2111.04 (II), wherein: “the broadest reasonable interpretation of a method (or process) claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met). For example, assume a method claim requires step A, if a first condition happens and step B if a second condition happens. If the claimed invention may be practiced without either the first or second condition happening, then neither step A or B is required by the broadest reasonable interpretation of the claim. If the claimed invention requires the first condition to occur, then the broadest reasonable interpretation of the claim requires step A. If the claimed invention requires both the first and second conditions to occur, then the broadest reasonable interpretation of the claim requires both steps A and B”. In the instant claims, the following is a “contingent” recitation: Claim 4 : “wherein if the presence of a sequence match is detected in (d) the action comprises preventing synthesis of the test biological molecule”. With respect to the interpretations above, it is suggested that the claims be amended to recite alternative language so as to avoid interpretation of contingent claiming. These claims and the particular intended use and contingent recitations have been examined with respect to the prior art in the interest of compact prosecution. 35 U.S.C. 112(f) The following is a quotation of 35 U.S.C. 112(f): (f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof. The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked. As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph: (A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function; (B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and (C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function. Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function. Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function. Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. A. This application includes one or more claim limitations that use the word “means” or “step” but are nonetheless not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph because the claim limitation(s) recite(s) sufficient structure, materials, or acts to entirely perform the recited function. Such claim limitation(s) is/are: “ a means of preparing the testing sequence database ” in claim s 5 and 35 and “a means of the protecting ” in claim 27 . Because this/these claim limitation(s) is/are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are not being interpreted to cover only the corresponding structure, material, or acts described in the specification as performing the claimed function, and equivalents thereof. If applicant intends to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to remove the structure, materials, or acts that performs the claimed function; or (2) present a sufficient showing that the claim limitation(s) does/do not recite sufficient structure, materials, or acts to perform the claimed function. B. This application includes one or more claim limitations that use the word “means” which are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. Such claim limitation(s) is/are: “ a means for identifying the functional equivalents comprises a computational means ” in claim 21 . Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof. The specification as published sets forth that “ In some embodiments, a means for identifying the functional equivalents includes a computational means. In some embodiments, a means for identifying the functional equivalents includes an experimental means. In some embodiments, a computational means for selecting the functional equivalents included in the testing sequence database includes using a classifier based on experimental data to evaluate the accuracy of the computational means . ” at [0004]. Therefore, the specification does not disclose adequate acts for “ a means for identifying the functional equivalents ” or “computation means”. See below regarding issues under 112(a) and 112(b) arising from this claim interpretation. If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. Claim Rejections - 35 USC § 112 35 U.S.C. 112(a) 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. Claim 21 is 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. Claim 2 1 is rejected because, as outlined above under 35 USC 112(f), the disclosure does not contain adequate structure to perform the claimed function identifying the functional equivalents compris ing a computational means because the invention is not described with sufficient detail such that one of ordinary skill in the art can reasonably conclude that the inventor had possession of the claimed invention. The specification as published sets forth that “ In some embodiments, a means for identifying the functional equivalents includes a computational means. In some embodiments, a means for identifying the functional equivalents includes an experimental means. In some embodiments, a computational means for selecting the functional equivalents included in the testing sequence database includes using a classifier based on experimental data to evaluate the accuracy of the computational means .” at [0004]. Therefore, the specification does not disclose adequate acts for “ a means for identifying the functional equivalents ” or “computation means”, but does not disclose sufficient acts for performing the identification of the functional equivalents, or sufficient structure for “computational means”. 35 U.S.C. 112(b) 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. Claim s 4 and 65 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention. Claim 4 recites “ the action ”. There is insufficient antecedent basis for this limitation in the claim as there is no previous recitation of a n action . It is noted that claim 1 recites “ acting ”, and it is assumed that claim 4 should recite “the acting” rather than “the action”. Claim 65 recites “ A method of assessing a biological sequence using a testing sequence database of claim 64 ”. Claim 65 therefore attempts to claim a process without setting forth any steps involved in the process and therefore raises an issue of indefiniteness . The claim is indefinite because it merely recites a use without any active, positive steps delimiting how this use is actually practiced (see MPEP 2173.05(q)). Regarding the claim limitation that invokes 112(f) : Claim limitation “ a means for identifying the functional equivalents comprises a computational means ” in claim 21 invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. Therefore, the claim is indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. 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. A. Claim 64 is rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claim(s) does/do not fall within at least one of the four categories of patent eligible subject matter because claim 64 is directed to a testing sequence database . A database is interpreted as data per se which is information that does not have a physical or tangible form, and is therefore not directed to any of the statutory categories. B. Claims 1-6, 10, 14, 18, 20-21, 26-28, 35-36, 40, 51, and 65 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. MPEP 2106 organizes judicial exception analysis into Steps 1, 2A (Prongs One and Two) and 2B as follows below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials . Framework with which to Evaluate Subject Matter Eligibility : Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter; Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e . a law of nature, a natural phenomenon, or an abstract idea; Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept. Framework Analysis as Pertains to the Instant Claims: Step 1 With respect to Step 1 : yes, the claims are directed to methods , i.e. , a process, machine, or manufacture within the above 101 categories [ Step 1: YES ; See MPEP § 2106.03] . Step 2A, Prong One With respect to Step 2A, Prong One , the claims recite judicial exceptions in the form of abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as: mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations); certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information). With respect to the instant claims , under the Step 2A, Prong One evaluation, the claims are found to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing and organizing information) are as follows: Independent claim s 1 and 35 : (a) preselecting a biological molecule, wherein the biological molecule is capable of a function of interest; (b) preparing a testing sequence database comprising a plurality of sequence fragments of the preselected biological molecule, wherein the preselected sequence fragments are a predetermined length; (c) fragmenting the sequence of one or more test biological molecules into lengths equivalent to the predetermined length of the sequence fragments of the preselected biological molecule in the testing sequence database; (d) detecting a presence or absence of a sequence match between the sequence of at least one fragment of the fragmented test biological molecules and at least one of the plurality of sequence fragments of the preselected biological sequence . Independent claim 1 only : (e) acting in response to the detection in (d), wherein the detecting in (d) provides an assessment of the test biological molecule. Dependent claim 5 and i ndependent claim 35 : wherein a means of preparing the testing sequence database comprises: ( i ) screening the plurality of sequence fragments of the preselected biological sequence molecule against at least one control sequence database, wherein the control sequence database comprises a plurality of control sequence fragments of at least one molecule capable of a function of interest unrelated to the function of interest of the preselected biological molecule; (ii) identifying the presence of a match between a sequence fragment in the plurality of sequence fragments of the preselected biological molecule and a sequence fragment in the control sequence database that is a fragment of the biological molecule identified as capable of a function unrelated to the function of interest of the preselected biological molecule; and (iii) removing from the testing sequence database the sequence fragment of the preselected biological sequence identified as matching the sequence fragment of the biological sequence identified as capable of a function of interest unrelated to the function of interest of the molecule capable of the function of interest. Dependent c laim 3 : identifying in the testing sequence database one or more sequence fragments of the preselected biological sequence that match one or more sequence fragments, respectively, of a second biological molecule having a biological function unrelated to the biological function of interest of the preselected biological molecule, and removing the identified sequence fragments(s) from the testing sequence database. Claim 65 : assessing a biological sequence using a testing sequence database . Dependent claims 2, 6, 10, 14, 18, 20-21, 26-28, 36, 40, and 51 recite further steps that limit the judicial exceptions in independent claim s 1 and 35 and, as such, also are directed to those abstract ideas. For example, claim 2 further limits the acting of claim 1(e) to DNA molecule design and further sequence identification steps ; claim 4 further limits claim s 6 and 36 further limit the preselected biological molecule to a polynucleotide ; claims 10 and 40 further limit the preselected biological molecule to a polypeptide ; claim 14 further limits the control sequence database composition of claim 5; claims 18 and 20-21 further limit the testing sequence database composition; and claims 26-28 and 51 further limit the identities of all sequence fragments of one or both of the testing sequence database and the test biological molecule to being protected . The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined to each cover performance either in the mind and/or by mathematical operation because the method only requires a user to manually detect a sequence match between fragments of a preselected biological molecule and one or more test biological molecules, and then performing an action in response to the detection . Without further detail as to the methodology involved in “ preselecting”, “preparing”, “fragmenting”, “detecting”, and “acting ”, under the BRI, one may simply, for example, use pen and paper to preselect a biological molecule with a function of interest, fragment the sequence of the preselected biological molecule into predetermine d lengths to prepare a testing sequence database, screen those fragments against control sequences associated with an unrelated function of interest and remove any matches from the testing sequence database or add functionally equivalent sequences to the testing sequence database , fragment the sequence of one or more test biological molecules into predetermine lengths, detect whether or not there is match between the testing sequence database and the fragments of the test biological molecules, and perform an action in response to detecting step , where the action could be to design a DNA molecule or perform a further sequence identification step which could comprise a computational step able to be performed mentally . Therefore, claim s 1 and 35 and those claims dependent therefrom recite an abstract idea [ Step 2A, Prong 1: YES ; See MPEP § 2106.04 ]. Step 2A, Prong Two Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two , provides that the claims must be examined further to determine whether they integrate the judicial exception s into a practical application (MPEP 2106.04(d) ) . A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exception s are integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exception s, the claim is said to fail to integrate the judicial exception s into a practical application (MPEP 2106.04(d).III). Additional elements, Step 2A, Prong Two With respect to the instant recitations, the claims recite the following additional elements : D ependent claim 2 : wherein the acting in response to (d) comprises one of more of: preventing synthesis of the test biological molecule, permitting synthesis of the test biological molecule, sequencing one or more polynucleotide molecules, DNA sequencing, and polypeptide sequence determination . D ependent claim 4 : wherein if the presence of a sequence match is detected in (d) the action comprises preventing synthesis of the test biological molecule. Considerations under Step 2A, Prong Two With respect to Step 2A, Prong Two , the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to preventing synthesis of the test biological molecule, permitting synthesis of the test biological molecule, sequencing one or more polynucleotide molecules, DNA sequencing, and polypeptide sequence determination in response to (d), as in claim 2, are mere instructions to apply the judicial exception to a technical field (MPEP 2106.05( f )). Claim 2 recites the idea of a solution or outcome but fails to recite details of how a solution to a problem is accomplished in a general manner. Further, the acting is only performed in response to the performance of step (d), but does not link the actions to the outcome of step (d), i.e , whether a sequence match is detected or not. Claim 4 recites a contingent limitation which is not required to be performed and therefore cannot provide a practical application at Step 2A, Prong 2. It is noted that even if “preventing synthesis” were not recited contingently, such an action does not actually perform an action in the real world that would provide a practical application to the recited judicial exceptions. The specification as published discloses applications of the method in general at [ 0003 ], but does not provide a clear explanation for how the additional elements provide these improvements. Therefore, the additional elements do not clearly improve the functioning of a computer, or comprise an improvement to any other technical field. Further, the additional elements do not clearly affect a particular treatment; they do not clearly require or set forth a particular machine; they do not clearly effect a transformation of matter; nor do they clearly provide a nonconventional or unconventional step (MPEP2106.04(d)). Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to one or more judicial exception s [ Step 2A, Prong 2: NO ; See MPEP § 2106.04(d)]. Step 2B (MPEP 2106.05.A i -vi) According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s). With respect to the instant claims , the specification as published discloses that “ Various means of assessing DNA molecule design, sequencing of DNA and/or protein sequences are known in the art and can be applied as part of an action ” at [0044], indicating that synthesis of biological molecule s , sequencing one or more polynucleotide /DNA molecules, and polypeptide sequence determination are “apply it” additional element s that are routine, well-understood and conventional in the art. As such, the claims simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception (MPEP2106.05(d)). The data gathering steps as recited in the instant claims constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)). Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [ Step 2B: NO ; See MPEP § 2106.05]. Therefore, the instant claims are not drawn to eligible subject matter as they are directed to one or more judicial exception s without significantly more. For additional guidance, applicant is directed generally to the MPEP § 2106. Claim Rejections - 35 USC § 102 The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action: A person shall be entitled to a patent unless – (a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale , or otherwise available to the public before the effective filing date of the claimed invention. (a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention. A. Claims 1- 2 , 4, 6 , 20-21, 26-27, and 64-65 are rejected under 35 U.S.C. 102 (a)(1) as being anticipated by Esvelt (PLOS Pathogens, 2018, 14(1):e1007286, p. 1-7; cited on the Feb 2 2023 IDS) . Claim 1 discloses a method of assessing a biological sequence capable of a preselected function . The method of claim 1 comprise s : (a) preselecting a biological molecule, wherein the preselected biological molecule is capable of a function of interest; (b) preparing a testing sequence database comprising a plurality of sequence fragments of the preselected biological molecule, wherein the preselected sequence fragments are a predetermined length; (c) fragmenting the sequence of one or more test biological molecules into lengths equivalent to the predetermined length of the sequence fragments the preselected biological molecule in the testing sequence database; and (d) detecting a presence or absence of a sequence match between the sequence of at least one fragment of the fragmented test biological molecules and at least one of the plurality of sequence fragments of the preselected biological sequence ; and (e) acting in response to the detection in (d), wherein the detecting in (d) provides an assessment of the test biological molecule. The prior art to Esvelt discloses a description of an upgrade the current system for screening synthesized DNA for hazardous sequences (abstract). Esvelt teaches that order fragments of approximately 40 bp ( i.e. , fragments of one or more test biological molecules in step (c) ) could be screened for exact matches ( i.e. , equivalent length to predetermined length of sequence fragments of preselected biological molecul e in step (c); detecting a match in step (d) ; to provide an assessment as in step (e) ) against a hashed database of hazardous sequences ( i.e. , testing sequence database of sequence fragments of a preselected biological molecule of interest capable of a function of interest in steps (a)-(b) ) by a cooperative international network of servers (Fig. 1; p. 2, par. 3). Esvelt teaches cleared sequences can be synthesized ( i.e. , acting in response in step (e) ) (Fig. 1) . Regarding claim 2 , Esvelt teaches claim 1 as described above. Claim 2 further adds that the acting in response to (d) comprises one of more of: preventing synthesis of the test biological molecule, permitting synthesis of the test biological molecule, sequencing one or more polynucleotide molecules, DNA sequencing, DNA molecule design, polypeptide sequence determination, and further sequence identification steps. Esvelt teaches clearing orders for DNA synthesis after screening ( i.e. , permitting synthesis of the test biological molecule ) (Fig. 1) and universal DNA synthesis screening for hazardous prior to DNA synthesis ( i.e. , preventing synthesis of the test biological molecule ). Regarding claim 4 , Esvelt teaches claim 1 as described above. Claim 4 further adds that if the presence of a sequence match is detected in (d) the action comprises preventing synthesis of the test biological molecule. Esvelt teaches clearing orders for DNA synthesis after screening ( i.e. , permitting synthesis of the test biological molecule ) (Fig. 1) and universal DNA synthesis screening for hazardous sequences prior to DNA synthesis ( i.e. , preventing synthesis of the test biological molecule ). Regarding claim 6 , Esvelt teaches claim 1 as described above. Claim 6 further adds that the preselected biological molecule is a polynucleotide. Esvelt teaches screening DNA ( i.e. , a polynucleotide ) synthesis orders (Fig. 1). Regarding claim 20-21 , Esvelt teaches claim 1 as described above. Claim 20 further adds that the testing sequence database further comprises sequences that are functional equivalents of the plurality of sequence fragments of the preselected biological molecule. Claim 21 further adds a means for identifying the functional equivalents comprises a computational means. Esvelt teaches that hazardous sequences could be filtered ( i.e. , a computational means ) from crowdsourced suggestions ( i.e. , functional equivalents ) by an international team of experts (Fig. 1). Regarding claim 26-27 , Esvelt in view of Diggans teaches claim 1 as described above . Claim 2 6 further adds that the identities of all sequence fragments of one or both of the testing sequence database and the test biological molecule are protected. Claim 27 further adds a means of the protecting comprises application of a cryptographic hash function, wherein the cryptographic hash function deterministically maps the sequence data to a bit string of fixed size using a one-way function. Esvelt teaches performing local one-way encryption ( i.e. , protection ) to produce hashed DNA synthesis orders which are screened against a hashed database (Fig. 1). Regarding claim 64 , Esvelt teaches claim 1 as described above. Claim 64 further adds a testing sequence database prepared by a method of claim 1. Esvelt teaches claim 1 as described above. Esvelt teaches a database for screening DNA synthesis orders (Fig. 1). Regarding claim 65 , Esvelt teaches claims 1 and 64 as described above. Claim 65 further adds a method of assessing a biological sequence using a testing sequence database of claim 64 . Esvelt teaches a database for screening DNA synthesis orders ( i.e. , assessing ) (Fig. 1). B. Claim 28 is rejected under 35 U.S.C. 102 (a)(1) as being anticipated by Esvelt , as applied to claims 1 and 26-27 above , and as evidenced by El- Moursy et al. ( J. Softw . Eng. Intell . Syst, 2018, 3(1) : 67-82 ; newly cited). Regarding claim 28 , Esvelt teaches claims 1 and 26-27 as described above. Claim 28 further adds that the application of the cryptographic hash function cannot be reversed without a brute-force search of all possible sequence inputs into the testing sequence database, optionally, wherein the application of the cryptographic hash function further comprises use of one or more information keys that must be accessed to attempt the brute-force search . The claim is interpreted only serving to further limit the cryptographic hash function applied in claim 27 to one that cannot be reversed without a brute-force search , While Esvelt teaches hash functions to protect the DNA synthesis orders and the database (Fig. 1), Esvelt does not explicitly teach that the hash function can be reversed with a brute-force search of all possible sequence inputs into the testing sequence database . However, as evidenced by El- Mousry , the key element of breaking any encryption mechanism , including encryption of DNA sequences, is brute force attacks (p. 74, par. 2). Therefore it is considered that the hash function taught by Esvelt inherently teaches claim 28. Claim Rejections - 35 USC § 10 3 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. The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows: 1. Determining the scope and contents of the prior art. 2. Ascertaining the differences between the prior art and the claims at issue. 3. Resolving the level of ordinary skill in the pertinent art. 4. Considering objective evidence present in the application indicating obviousness or nonobviousness . 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. A. Claim s 3, 5 , 10, 14 , and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Esvelt , as applied to claim 1 in the above 35 USC 102 rejection, and in further view of Diggans (US 2017 / 0357 , 752 ; newly cited ) . Regarding claim s 3 and 5 , Esvelt teaches claim 1 as described above . Claim 3 further adds identifying in the testing sequence database one or more sequence fragments of the preselected biological sequence that match one or more sequence fragments, respectively, of a second biological molecule having a biological function unrelated to the biological function of interest of the preselected biological molecule, and removing the identified sequence fragments(s) from the testing sequence database. Claim 5 further adds a means of preparing the testing sequence database that comprises: ( i ) screening the plurality of sequence fragments of the preselected biological sequence molecule against at least one control sequence database, wherein the control sequence database comprises a plurality of control sequence fragments of at least one molecule capable of a function of interest unrelated to the function of interest of the preselected biological molecule; (ii) identifying the presence of a match between a sequence fragment in the plurality of sequence fragments of the preselected biological molecule and a sequence fragment in the control sequence database that is a fragment of the biological molecule identified as capable of a function unrelated to the function of interest of the preselected biological molecule; and (iii) removing from the testing sequence database the sequence fragment of the preselected biological sequence identified as matching the sequence fragment of the biological sequence identified as capable of a function of interest unrelated to the function of interest of the molecule capable of the function of interest. Esvelt teaches that the database contains hazardous sequences curated by experts (Fig. 1), which indicates that non-hazardous sequences ( i.e. , control sequences ) are not present in the database, but does not explicitly teach the limitations of steps ( i )-(iii). However, the prior art to Diggans discloses software tools for effective biosecurity based on community knowledge and participation (abstract). Diggans teaches database comprising a list of harmful biological sequences , receiving one or more design instructions for a plurality of biological sequences , and automatically determining whether the plurality of biological sequences corresponds to a threshold of the harmful biological sequence s in the database [0003]. Diggans teaches that the database pathogenic proteins to the database in an attempt to include most potentially regulated sequences or other sequences known to be harmful , and that t he system may curate an “unrestricted” list of NCBI GI identifiers corresponding to genes that may be considered harmless [0036]. Diggans teaches that sequences found to be on the restrictive list are further evaluated against an unrestricted list that comprises known false positives ( i.e. , steps ( a )-( b ) of claim 5 ) [0041]. It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, Esvelt and Diggans because both references disclose methods for screening biological sequences before sequencing. Although Diggans does not explicitly teach removing sequences found on both the restricted and unrestricted list, it would have been obvious to one or ordinary skill in the art to remove those sequences, because Diggans teaches that they are known to be false positives for identifying harmful sequences [0041]. Regarding claim 1 0 , Esvelt teaches claim 1 as described above . Claim 10 further adds that the preselected biological molecule comprises a polypeptide molecule , which Esvelt does not teach. However, Diggans teaches examining protein sequences of pathogens [0022]. Regarding claim 14 , Esvelt teaches claim 1 and, in view of Diggans , claim 5 as described above. Claim 14 further adds that the control sequence database comprises a plurality of control sequence fragments of at least one molecule capable of a function of interest unrelated to the function of interest of the preselected biological molecule , which Esvelt doesn’t teach. However, Diggans teaches an “unrestricted” list of NCBI GI identifiers corresponding to genes that may be considered harmless ( i.e. , a function of interest unrelated to the function of interest of the preselected biological molecule ) [0036]. Regarding claim 18 , Esvelt teaches claim 1 as described above. Claim 18 further adds that the testing sequence database comprises one or more sequence fragments randomly or pseudorandomly selected from sequences of molecules known to be capable of a function different from the preselected molecule's function of interest , which Esvelt does not teach. However, Diggans teaches an “unrestricted” list of NCBI GI identifiers corresponding to genes that may be considered harmless [0036], which reads on random or pseudorandom selected from sequences of molecules known to be capable of a function different from the preselected molecule's function of interest as instantly claimed. B . Claim s 35- 36, 40, and 51 are rejected under 35 U.S.C. 103 as being unpatentable over Esvelt (PLOS Pathogens, 2018, 14(1):e1007286, p. 1-7; cited on the Feb 2 2023 IDS) in view of Diggans ( US 2017 / 0357 , 752 ; newly cited ) . Claim 35 discloses a method of identifying a biological sequence capable of a preselected function . The method of claim 35 comprise s : (a) preselecting a biological molecule, wherein the preselected biological molecule is capable of a function of interest; (b) preparing a testing sequence database comprising a plurality of sequence fragments of the preselected biological molecule, wherein the preselected sequence fragments are a predetermined length; (c) fragmenting the sequence of one or more test biological molecules into lengths equivalent to the predetermined length of the sequence fragments the preselected biological molecule in the testing sequence database; and (d) detecting a presence or absence of a sequence match between the sequence of at least one fragment of the fragmented test biological molecules and at least one of the plurality of sequence fragments of the preselected biological sequence ; wherein a means of preparing the testing sequence database comprises: ( i ) screening the plurality of sequence fragments of the preselected biological sequence molecule against at least one control sequence database, wherein the control sequence database comprises a plurality of control sequence fragments of at least one molecule capable of a function of interest unrelated to the function of interest of the preselected biological molecule; (ii) identifying the presence of a match between a sequence fragment in the plurality of sequence fragments of the preselected biological molecule and a sequence fragment in the control sequence database that is a fragment of the biological molecule identified as
Read full office action

Prosecution Timeline

Jul 20, 2022
Application Filed
Mar 26, 2026
Non-Final Rejection — §101, §102, §103 (current)

Precedent Cases

Applications granted by this same examiner with similar technology

Patent 12603149
VALIDATION METHODS AND SYSTEMS FOR SEQUENCE VARIANT CALLS
2y 5m to grant Granted Apr 14, 2026
Patent 12580046
Computer Method and System of Identifying Genomic Mutations Using Graph-Based Local Assembly
2y 5m to grant Granted Mar 17, 2026
Patent 12548643
BRAIN NETWORK ACTIVITY ESTIMATION SYSTEM, METHOD OF ESTIMATING ACTIVITIES OF BRAIN NETWORK, BRAIN NETWORK ACTIVITY ESTIMATION PROGRAM, AND TRAINED BRAIN ACTIVITY ESTIMATION MODEL
2y 5m to grant Granted Feb 10, 2026
Patent 12537074
METHOD OF CHARACTERISING A DNA SAMPLE
2y 5m to grant Granted Jan 27, 2026
Patent 12512184
PARALLEL-PROCESSING SYSTEMS AND METHODS FOR HIGHLY SCALABLE ANALYSIS OF BIOLOGICAL SEQUENCE DATA
2y 5m to grant Granted Dec 30, 2025
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

1-2
Expected OA Rounds
34%
Grant Probability
74%
With Interview (+39.5%)
5y 0m
Median Time to Grant
Low
PTA Risk
Based on 82 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