DETAILED ACTION
The Applicant’s response, received 17 November 2025 has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 .
Status of the Claims
Claims 16, 17, 19-32, 35, 36, and 39 are pending.
Claims 16, 17, 19-32, 35, 36, and 39 are rejected.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
This application is a 371 of PCT/EP2020/053223, filed 07 February 2020.
Claims 16, 17, 19-32, 35, 36, and 39 are not given the benefit of Foreign Application No. EPO 19156085, filed 07 February 2019, because there is not support for the limitation “directed graph.” Claim 20 is further not given benefit because there is not support for a batch of reads. Claim 22 is further not given benefit because there is not support for aligning processed reads with a directed graph. Claim 24 is further not given benefit because there is not support for converting processed reads into sub read graphs and/or read graphs.
Claims 16, 17, 19-32, 35, 36, and 39 are not given the benefit of Foreign Application No. EPO 19156086, filed 07 February 2019, because there is not support for the limitation “directed graph.” Claim 22 is further not given benefit because there is not support for aligning processed reads with a directed graph. Claim 24 is further not given benefit because there is not support for converting processed reads into sub read graphs and/or read graphs.
Claims 16, 17, 19-32, 35, 36, and 39 are not given the benefit of Foreign Application No. BE2019/5077, filed 07 February 2019, because there is not support for the limitation “directed graph.” Claim 22 is further not given benefit because there is not support for aligning processed reads with a directed graph. Claim 24 is further not given benefit because there is not support for converting processed reads into sub read graphs and/or read graphs.
Claims 16, 17, 19-23, 25-32, 35, 36, and 39 are given the benefit of Foreign Application No. EPO 19190899, filed 08 August 2019. Claim 24 is not given benefit because there is not support for converting processed reads into sub read graphs and/or read graphs.
Claims 16, 17, 19-23, 25-32, 35, 36, and 39 are given the benefit of Foreign Application No. EPO 19190901, filed 08 August 2019.
Claims 16, 17, 19-23, 25-32, 35, 36, and 39 are given the benefit of Foreign Application No. EPO 19190900, filed 08 August 2019.
Therefore, the effective filing date of the claimed invention is 08 August 2019.
Information Disclosure Statement
The information disclosure statements (IDS) received 28 August 2025 (two sets) are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements have been considered by the examiner.
Claim Interpretation
Claim 16 is interpreted as reciting a product-by-process limitation at step (a) with the product being the database of fingerprint data strings, and further interpreted to not require the active steps of producing the product (i.e., the database of fingerprint data strings).
Claim 36 is interpreted as reciting a product-by-process limitation at step (a) with the product being the database of fingerprint data strings, and further interpreted to not require the active steps of producing the product (i.e., the database of fingerprint data strings).
Claim 39 is interpreted as reciting a product-by-process limitation at step (a) with the product being the database of fingerprint data strings, and further interpreted to not require the active steps of producing the product (i.e., the database of fingerprint data strings).
Claims 16, 17, 25, 27, 35, 36, and 39 recite the term “biological sequence(s).” This term is interpreted to mean a data sequence of a biopolymer defining at least the biopolymer’s primary structure, and can for example be a deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or a protein (Specification, page 8, ¶ [56]).
Claims 16, 17, 19, 22, 25, 36, and 39 recite the term “characteristic biological subsequence(s).” This term is interpreted to mean a portion of a biological sequence that is smaller than the full biological sequence (Specification, page 9, ¶ [58]), and is one sequence unit shorter than a subsequence that is not found in any biological sequence database (Specification, pages 10-11, ¶¶ [64] – [65]). This term is further interpreted to be synonymous with the term HYFT fingerprint (Specification, page 11, ¶ [65]; and page 9, ¶ [59]).
Claims 16, 17, 19, 21, 22, 25, 35, 36, and 39 recite the term “fingerprint data string(s).” This term is interpreted to mean a data string that is representative of one or more characteristic biological subsequences (HYFT fingerprints) (Specification, page 9, ¶ [59]).
Claims 16, 17, 25, 26, 35, 36, and 39 recite the terms “biological entity” or “biological entities.” These terms are interpreted to mean anything from a biological subsequence (e.g., a sequencing read) to an organism or species, as long as a representative HYFT can be associated with the entity, including but not limited to a protein, a protein active site or domain, a gene, a genome, a membrane, organelle, a cell, a bacteria, a virus, an organ, etc. (Specification, page 20, ¶ [93]).
Claim Objections
The objection to claims 16 and 37 in the Office action mailed 15 July 2025 is withdrawn in view of the amendment received 17 November 2025.
Claim Rejections - 35 USC § 112
The rejection of claims 19-24, 29, 30, 37, and 38 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, in the Office action mailed 15 July 2025 is withdrawn in view of the amendment received 17 November 2025.
The Applicant’s amendment received 17 November 2025 has been fully considered, however after further consideration, new grounds of rejection are raised under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, in view of the amendment.
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 16, 17, 19-32, 35, 36, and 39 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Independent claims 16, 25, 29, 30, 31, 32, 36, and 39 contain the trademark/trade name “HYFT”. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name.
In the present case, the trademark/trade name is used to identify/describe subsequences of data and, accordingly, the identification/description is indefinite.
Claims 17, 19-24, 26-28, and 35 are indefinite for depending from either of claims 16, 25, 29, 30, 31, 32, 36, or 39 and for failing to remedy the indefiniteness of the claim from which they depend.
Claim Rejections - 35 USC § 101
The Applicant’s amendment received 17 November 2025 has been fully considered, however after further consideration, the rejection of claims 16, 17, 19-32, and 35-38 under 35 U.S.C. 101 in the Office action mailed 15 July 2025 is maintained with modification in view of the amendment.
The rejection of claims 37 and 38 under 35 U.S.C. 101 in the Office action mailed 15 July 2025 is withdrawn in view of these claims having been cancelled in the amendment received 17 November 2025.
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 16, 17, 19-32, 35, 36, and 39 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mental processes, i.e., concepts performed in the human mind (e.g., observation, evaluation, judgement, opinion); (b) mathematical concepts (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (c) a law of nature (e.g., naturally occurring relationships).
Subject matter eligibility evaluation in accordance with MPEP 2106.
Eligibility Step 1: Claims 16, 17, 19-24, 35, and 39 are directed to a method (i.e., a process) for processing a sequence read corresponding to a biological entity; claims 25-28 are directed to a method (i.e., a process) for associating information with one or more fingerprint data strings; claims 29 and 30 are directed to a data processing system comprising a processor and a non-transitory computer-readable storage medium (i.e., a machine or manufacture); claims 31 and 32 are directed to a non-transitory computer-readable storage medium (i.e., a machine or manufacture); and claim 36 is directed to a method (i.e., a process) for obtaining information on a biological entity.
Therefore, these claims are encompassed by the categories of statutory subject matter, and thus, satisfy the subject matter eligibility requirements under Step 1.
[Step 1: YES]
Eligibility Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2A: Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes whether the claim recites a judicial exception, i.e., whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim.
Independent claim 16 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
at step (b) parsing the sequence read with the fingerprint data strings from the database of fingerprint data strings and aligning the parsed sequence read with one or more fingerprint data strings from the database of fingerprint data strings which are representative for the sequence read using a directed graph in order to reconstruct and store the sequence read as a HYFT graph comprising fingerprint data strings (i.e., mental processes and mathematical concepts);
at step (c) determining, from structural data, relational data, spatial data and directional data of the HYFT graph, one or more of a medical condition, a biological function, a spatial structure, combinatory information or relational information corresponding to the one or more representative fingerprint data strings (i.e., mental processes);
wherein the sequence units comprise amino acids or codons (i.e., mental processes).
Independent claim 25 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
the abstract ideas recited in independent claim 16, as noted above;
searching the biological sequences for equivalent characteristic biological subsequences (i.e., mental processes); and
associating the equivalent information with the fingerprint data strings representing the equivalent characteristic biological subsequences (i.e., mental processes).
Independent claim 29 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
the abstract ideas recited in independent claim 16, as noted above.
Independent claim 30 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
the abstract ideas recited in independent claim 25, as noted above.
Independent claim 31 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
the abstract ideas recited in independent claim 16, as noted above.
Independent claim 32 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
the abstract ideas recited in independent claim 25, as noted above.
Independent claim 36 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
at step (b) determining one or more fingerprint data strings which are representative for the biological entity (i.e., mental processes);
at step (c) constructing a HYFT graph from the at least one biological sequence using the one or more fingerprint data strings which are representative for the biological entity (i.e., mental processes and mathematical concepts);
at step (d) aligning the HYFT graph with a directed graph to construct at least one aligned biological sequence therefrom (i.e., mental processes); and
wherein the sequence units comprise amino acids or codons (i.e., mental processes).
Independent claim 39 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
at step (b) parsing the sequence read using the fingerprint data strings from the database of fingerprint data strings (i.e., mental processes); constructing from the parsed read a HYFT graph comprising nodes that encode fingerprint data strings and edges with positional, directional, structural, and relational metadata (i.e., mental processes and mathematical concepts); and aligning the HYFT graph with a directed graph representing reference sequences (i.e., mental processes);
at step (c) determining from the HYFT graph's structural data, relational data, spatial data and directional data one or more of a medical condition, a biological function, a spatial structure, combinatory information or relational information corresponding to the one or more representative fingerprint data strings (i.e., mental processes); and
wherein the sequence units comprise amino acids or codons (i.e., mental processes).
Independent claims 16, 25, 29, 30, 31, 32, and 39, and those claims dependent therefrom, further recite a law of nature by associating genomic data (i.e., fingerprint data strings which are representative for a biological entity, e.g., a gene or genome) with a phenotype (a medical condition), i.e., a genotype-phenotype correlation (MPEP 2106.04(b)).
Dependent claims 17, 19-24, 26-28, and 35 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 17 further recites:
wherein the one or more of fingerprint data strings which are representative for the biological entity comprise
the fingerprint data string representing a longest characteristic biological subsequence found in the at least one biological sequence (i.e., mental processes); or
if more than one longest characteristic biological subsequence is found, a characteristic biological subsequence among the longest characteristic biological subsequences having a lowest combinatory number (i.e., mental processes).
Dependent claim 19 further recites:
processing a sequencing read of a biopolymer or biopolymer fragment taking into account information contained in the database of fingerprint data strings
wherein the information associated with the fingerprint data strings comprised in the database includes combinatory data representing the different sequence units that appear as a consecutive sequence unit of the corresponding characteristic biological subsequence (i.e., mental processes); and
wherein step (b) comprises searching the read for occurrences of one or more of the characteristic biological subsequences represented by the fingerprint data strings (i.e., mental processes) and
step (d) comprises validating or rejecting the read by, for each occurrence, determining whether or not a sequence unit consecutive to the characteristic biological subsequence conforms with the combinatory data in the database (i.e., mental processes), and/or
step (b) comprises searching a head and/or tail of the read for an occurrence of one of the characteristic biological subsequences represented by the fingerprint data strings (i.e., mental processes) and
step (d) comprises predicting a consecutive sequence unit from the combinatory data in the database (i.e., mental processes).
Dependent claim 20 further recites:
performing the method according to claim 19 on each read in a batch of reads (i.e., mental processes).
Dependent claim 21 further recites:
wherein the information associated with the fingerprint data strings comprised in the database further comprises one or more of structural data, relational data, spatial data and directional data (i.e., mental processes).
Dependent claim 22 further recites:
wherein the fingerprint data strings are inherently directed and comprise positional information (i.e., mental processes);
aligning, using the characteristic biological subsequences identified in step (b), the processed read with a directed graph (i.e., mental processes).
Dependent claim 23 further recites:
wherein said aligning comprises identifying variations (i.e., mental processes).
Dependent claim 24 further recites:
wherein the method further comprises converting a plurality of processed reads into sub read graphs and/or read graphs (i.e., mental processes and mathematical concepts).
Dependent claim 26 further recites:
the method of claim 25, further comprising a step (a’), before step (a), of
step (a’) searching a pool of data for biological entities sharing equivalent information (i.e., mental processes).
Dependent claim 27 further recites:
wherein the pool of data comprises sequencing data or biological sequences (i.e., mental processes).
Dependent claim 28 further recites:
wherein the equivalent information comprises one or more of a medical condition, a biological function, a spatial structure or combinatory information (i.e., mental processes).
Dependent claim 35 further recites:
wherein the at least one biological sequence of the biological entity is 80% covered by the fingerprint data strings (i.e., mental processes and mathematical concepts).
Dependent claim 28 further recites a law of nature by associating genomic data (i.e., fingerprint data strings which are representative for a biological entity, e.g., a gene or genome) with a phenotype (a medical condition), i.e., a genotype-phenotype correlation (MPEP 2106.04(b)).
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pen and paper (e.g., parsing the sequence read with the fingerprint data strings from the database of fingerprint data strings and aligning the parsed sequence read with one or more fingerprint data strings from the database of fingerprint data strings which are representative for the sequence read), and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas (e.g., constructing from the parsed read a HYFT graph comprising nodes that encode fingerprint data strings and edges with positional, directional, structural, and relational metadata) are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind. Furthermore, a law of nature correlating a genotype-phenotype relationship is identified at Eligibility Step 2A Prong One.
Therefore, claims 16, 17, 19-32, 35, 36, and 39 recite an abstract idea and a law of nature.
[Step 2A Prong One: YES]
Eligibility Step 2A: Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A Prong One are not integrated into a practical application because of the reasons noted below.
The additional elements in independent claims 16, 25, 29, 30, 31, 32, 36, and 39 include:
a computer (claims 16, 25, 29, 30, 31, 32, 36, and 39);
providing (e.g., receiving or accessing) a database of fingerprint data strings (claims 16, 36, and 39);
providing biological sequences of biological entities (i.e., data) (claim 25);
outputting, one or more of a medical condition, a biological function, a spatial structure, combinatory information or relational information corresponding to the one or more representative fingerprint data strings (i.e., data) (claims 16 and 39);
outputting the at least one aligned biological sequence (i.e., data) (claim 36);
a data processing system comprising a processor and a non-transitory computer-readable storage medium (claims 29 and 30); and
a non-transitory computer-readable storage medium (claims 31 and 32).
The additional elements in dependent claims 17, 19-24, 26-28, and 35 include:
a computer (claims 17, 19-24, 26-28, and 35); and
a database (claims 19, 21, and 27).
The additional elements of a computer (claims 16, 17, 19-32, 35, 36, and 39); a data processing system comprising a processor and a non-transitory computer-readable storage medium (claims 29 and 30); and a non-transitory computer readable storage medium (claims 31 and 32); invoke a computer and/or computer-related components merely as tools for use in the claimed process, and therefore are not an improvement to computer functionality itself, or an improvement to any other technology or technical field, and thus, do not integrate the judicial exceptions into a practical application (MPEP 2106.04(d)(1)).
The additional elements of providing a database (claims 16, 36, and 39) and/or accessing a database (claims 19, 21, and 27) and/or providing data (claim 25) are merely a pre-solution activity that is part of gathering data for use in the claimed process – a nominal addition to the claims that does not meaningfully limit the claims, and therefore does not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
The additional element of outputting data (claims 16, 36, and 39) is merely a post-solution activity that is used in the claimed process – a nominal addition to the claims that does not meaningfully limit the claims, and therefore does not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
Thus, the additionally recited elements merely invoke a computer as a tool, and/or amount to insignificant extra-solution activities, and as such, when all limitations in claims 16, 17, 19-32, 35, 36, and 39 have been considered as a whole, the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 16, 17, 19-32, 35, 36, and 39 are directed to an abstract idea (MPEP 2106.04(d)).
[Step 2A Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they amount to significantly more than the judicial exception (MPEP 2106.05A i-vi).
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below.
The additional elements recited in independent claims 16, 25, 29, 30, 31, 32, 36, and 39 and dependent claims 17, 19-24, 26-28, and 35 are identified above, and carried over from Step 2A: Prong Two along with their conclusions for analysis at Step 2B. Any additional element or combination of elements that was considered to be insignificant extra-solution activity at Step 2A: Prong Two was re-evaluated at Step 2B, because if such re-evaluation finds that the element is unconventional or otherwise more than what is well-understood, routine, conventional activity in the field, this finding may indicate that the additional element is no longer considered to be insignificant; and all additional elements and combination of elements were evaluated to determine whether any additional elements or combination of elements are other than what is well-understood, routine, conventional activity in the field, or simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, per MPEP 2106.05(d).
The additional elements of a computer (claims 16, 17, 19-32, 35, 36, and 39); a data processing system comprising a processor and a non-transitory computer-readable storage medium (claims 29 and 30); a non-transitory computer readable storage medium (claims 31 and 32); providing a database (claims 16, 36, and 39); accessing a database (claims 19, 21, and 27); providing data (claim 25); and outputting data (claims 16, 36, and 39); are conventional (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
Therefore, when taken alone, all additional elements in claims 16, 17, 19-32, 35, 36, and 39 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 16, 17, 19-32, 35, 36, and 39 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)).
[Step 2B: NO]
Response to Arguments
The Applicant’s arguments/remarks received 17 November 2025 have been fully considered, but are not persuasive.
The Applicant states on page 14/21 (para. 6) of the Remarks that as amended, independent claim 16 requires a computer-implemented method for processing a sequence read corresponding to a biological entity including parsing the sequence read with the fingerprint data strings from the database of fingerprint data strings and aligning the parsed sequence read with one or more fingerprint data strings from the database of fingerprint data strings which are representative for the sequence using a directed graph in order to reconstruct and store the sequence read as a HYFT graph comprising fingerprint data strings, and determining, from structural data, relational data, spatial data and directional data of the HYFT graph, one or more of a medical condition, a biological function, a spatial structure, combinatory information or relational information corresponding to the one or more representative fingerprint data strings. The Applicant further states (para. 7) that the amended claim requires a level of complexity that cannot practically be performed in the human mind and the claims cannot be directed to an abstract idea of a mental process, and that notably, the claim requires sequence units comprising amino acids, of which there are 20 possibilities, and (page 15/21, para. 1) codons, of which there are 64 possibilities, and then, with these sequence units, the characteristic biological subsequences are defined as having in the biological sequence database a combinatory number which is lower than the total number of different sequence units available thereto, the combinatory number of a biological subsequence being defined as the number of different sequence units that appear in the biological sequence database as a consecutive sequence unit of the biological subsequence.
These arguments are not persuasive, because first, the amount of data, in and of itself is not a limitation which takes a process out of the realm of the human mind. It is the process performed on that data which is the mental step. Although the amount of data may be considered to be significantly large and take considerable time and effort to process manually, the use of a general-purpose computer to perform the claimed method at a rate and accuracy that can far outstrip the mental performance of a skilled artisan does not change the nature of the activity being performed (i.e., an abstract idea), and therefore does not materially alter the patent eligibility of the claimed subject matter. Second, the claims are directed to processing sequence read data by parsing a sequence read, aligning a sequence read using a directed graph, and determining from the aligned sequence read, e.g., whether a medical condition can be associated with the sequence read data, which are all steps that comprise the judicial exceptions identified at Step 2A Prong One of the eligibility analysis.
The Applicant states on page 15/21 (para. 2) of the Remarks that under Step 2A, Prong Two, claim 16 integrates any alleged abstract ideas into a practical application, and in particular, claim 16 does not merely “receive/compare/output” on a generic computer, but recites a particular technical pipeline that (i) parses a sequence read using fingerprint data strings; (ii) constructs and stores a HYFT graph with positional, directional, structural, and relational fields; and (iii) employs the HYFT graph to drive downstream operations. The Applicant points to the Specification (at paras. [06], [111], [152] and [158]) and further states that the Specification explains that this graph-based approach reduces complexity relative to existing techniques and avoids dynamic-programming heuristics that accumulate errors and supports concurrency and auto-completion of subgraphs at high confidence thresholds, and that the same HYFT-graph information may be used to control sequencing by validating/rejecting provisional reads and predicting next base(s) so that a sequencer may skip physical steps. The Applicant further states (para. 3) that these features clearly provide an improvement to a technical field and control of a particular machine, and so the claim integrates any abstract idea into a practical application at Prong Two, and further states that notably, the Office action’s suggestion that the improvements are “in the abstract idea itself” conflates the analysis, as Prong Two expressly considers improvements to “another technology or technical field.”
These arguments are not persuasive, because first, the claims are not directed to, nor require the use of a genomic sequencer machine. Second, regarding the Applicant’s assertion that “the Office action’s suggestion that the improvements are ‘in the abstract idea itself’ conflates the analysis, as Prong Two expressly considers improvements to “another technology or technical field” (e.g., see the Office action mailed 15 July 2025 at para. 101), it is noted that when the Eligibility analysis determines that the claims do not provide a practical application at Step 2A Prong Two when considered as a whole, and/or when the additional elements are determined to amount to significantly more than the judicial exceptions at Step 2B, then any assertion of a purported improvement therefore may be found in the limitations that comprise the judicial exceptions identified at Step 2A Prong One, as explained in the Office actions of record, and in the above rejection. Third, the steps asserted in the foregoing argument (i.e., elements (i), (ii), and (iii)) as providing the improvement are steps that comprise the recited judicial exceptions identified at Step 2A Prong One in the above rejection, and therefore any purported improvement is in the abstract idea itself, and not an improvement in the functioning of a computer, or an improvement to any other technology or technical field.
The Applicant points to the Specification (at paras. [129], [160-168], and [188-196]) and states on page 16/21 (para. 1) of the Remarks that embodiments of the current disclosure are directed to improvements in the functioning of the overall technological processes of “biological sequence design (e.g., protein) design,” “sequence similarity search,” and biological sequence alignment. The Applicant points to the MPEP at 2106.04(d)(1), and further states (para. 2) that the consideration of whether the claim as a whole includes an improvement to a computer or to a technical field requires an evaluation of the specification and the claim to ensure that a technical explanation of the asserted improvement is present in the specification, and that the claim reflects the asserted improvement, and further states that according to the background section of the current disclosure (Spec., paras. [05] & [08]), the cost of analyzing biological sequences, e.g., to identify a target for treating a certain pathology, has limited the effectiveness of biological sequencing. The Applicant further states (para. 3) that the current claims accordingly allow several technical improvements over known methods of biological sequence design, sequence similarity searching (Spec., para. [163]), and biological sequence alignment (Spec., paras. [165-166]), and that for example, para. [158] in the Specification indicates that according to the claimed methods, sequence “comparison can therefore be performed markedly faster and furthermore scales well with increasing complexity (e.g., increasing length of or number of biological sequences), even while requiring less computation power and storage space. The Applicant further states on page 17/21 (para. bottom) that these additional elements of claim 16 provide for improvements in the technical fields of biological sequence design, sequence similarity searching, and biological sequence alignment, and specifically, the recited steps provide for improved design using the information from the fingerprint data strings. The Applicant further states on page 18/21 (para. 1) that the claimed steps reflect the improvement described in the disclosure, and thus, claim 16, as a whole, integrates the judicial exception into a practical application such that the claim is not directed to the judicial exception.
These arguments are not persuasive, because first, and as noted and discussed in the above rejection, the claims do not recite any additional elements that apply, rely on, or use the judicial exceptions in a manner that imposes a meaningful limit on the judicial exception, and therefore the judicial exceptions are not integrated into a practical application (MPEP 2106(d)). Second, the purported technical improvements asserted in the foregoing argument comprise the limitations that are identified as judicial exceptions at Step 2A Prong One, e.g., biological sequence design, sequence similarity searching, and biological sequence alignment.
The Applicant states on page 18/21 (para. 2) of the Remarks that claim 16 recites significantly more than a generic computer, and that the recited nonconventional and non-generic arrangement of the claim limitations provide improvements to the underlying technology or technical field, as taught in at least the above cited portions of the disclosure, and further points to the MPEP at 2106.05(a) or alternatively, MPEP 2106.05(e), and further states that notably, the claimed limitations move from abstract scientific principle to specific application, and again points to MPEP 2106.05(e) (citing Classen).
These arguments are not persuasive, because first, with regard to the Applicant pointing to MPEP 2106.05(e) citing Classen, and stating that notably, the claimed limitations move from abstract scientific principle to specific application, it is noted the MPEP 2106.05(e) (Other Meaningful Limitations) shows that the phrase “meaningful limitations” is used to describe additional elements that provide an inventive concept to the claim as a whole. As noted in the rejection above, the additional elements of a computer (claims 16, 17, 19-32, 35, 36, and 39); a data processing system comprising a processor and a non-transitory computer-readable storage medium (claims 29 and 30); a non-transitory computer readable storage medium (claims 31 and 32); providing a database (claims 16, 36, and 39); accessing a database (claims 19, 21, and 27); providing data (claim 25); and outputting data (claims 16, 36, and 39); are conventional (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes). Therefore, when taken alone, all additional elements in claims 16, 17, 19-32, 35, 36, and 39 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 16, 17, 19-32, 35, 36, and 39 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)). Second, the MPEP at 2106.05(e) (Other Meaningful Limitations) shows that there was an additional element (i.e., an immunization step) in Classen that was meaningful because it integrated the results of the analysis (i.e., abstract idea) into a specific and tangible method that resulted in the method “moving from abstract scientific principle to specific application.” In contrast, the instant claims do not recite any additional elements that meaningfully limit the abstract ideas, because the additional elements are conventional at Eligibility Step 2B, as shown in the rejection above.
The Applicant states on page 18/21 (para. 3) of the Remarks that independent claim 16, when considered as a whole, recites an additional element of a HYFT graph framework according to paras. [138-140] and [199] of the disclosure that applies the alleged judicial exceptions in a manner that imposes a meaningful limit on the judicial exceptions, and therefore integrates the judicial exceptions into a practical application. The Applicant further states (para. 4) that the practical application is an improved sequence graph data structure representing fingerprint data strings at targeted locations, which provides a framework for realigning relevant sequence reads for faster and more accurate characterization of the sequence reads at a lower processing cost. The Applicant points to the MPEP at 2106.04(d)(1) and 2106.05(a) and further states (para. 5) that the additional elements, when considered in combination, integrate the abstract idea into a practical application because the claim improves the functioning of a computer or technical field, and further states that the claim reflects this improvement in the technical field of sequencing devices, and thus, the claim as a whole integrates the judicial exception into a practical application, such that the claim is not directed to the judicial exception.
These arguments are not persuasive, because first, the claims are not directed to, nor require the use of a genomic sequencer machine. Second, the limitation reciting a HYFT graph framework is a limitation that is identified as a judicial exception at Step 2A Prong One (and accordingly, is not identified as an additional element at Step 2A Prong Two) and therefore is a limitation that cannot provide the practical application at Step 2A Prong Two or amount to significantly more than the judicial exceptions at Step 2B of the eligibility analysis. Third, and as noted and discussed in the above rejection, the claims do not recite any additional elements that apply, rely on, or use the judicial exceptions in a manner that imposes a meaningful limit on the judicial exceptions, and therefore the claims are not integrated into a practical application at Step 2A Prong Two (MPEP 2106.04(d)). Fourth, a purported improvement to the analysis of data is not an improvement to computer functionality itself, or an improvement to another technology or technical field.
The Applicant states on page 19/21 (para. 2) of the Remarks that the claims are not directed to an abstract idea but recite an improvement in computer technology as in Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1336, 118 USPQ2d 1684, 1689 (Fed. Cir. 2016), and further states that at least paras. [05-9] of the current disclosure describe challenges in accessing, analyzing, or employing sequence information in a meaningful way, and that these challenges are overcome by unconventional additional element of a HYFT graph sequence structure representing the sequence read, addressing the need for a solution to accessing, analyzing or employing sequence information in a meaningful way as described with respect to the improvements in at least paras. [14-21], [23-25], [126], [132], [152], [158], [163], and [166] of the disclosure (e.g., lossless compression, reduced computational requirements, increased flexibility/scalability, etc.). The Applicant further states (para. 3) that as expressly stated in the disclosure, the focus of the current claims is the specifically recited computer-related devices and operations that result in the technical advantages of reducing storage space requirements, reducing computational requirements, providing lossless processing, enabling flexibility and scalability, avoiding the accumulation of errors that result from prior art methods, and further resulting in an improved relational database, NoSQL database, or the like, and as such, the claims recite an improvement in computer technology as in Enfish, LLC v. Microsoft Corp., 822 F.3d 1327, 1336, 118 USPQ2d 1684, 1689 (Fed. Cir. 2016), and that taken together (para. 4) all of these foregoing features are clearly more than limitations that the courts have recognized, or those in the art would recognize, as elements that are well-understood, routine, and conventional. The Applicant further states (page 20/21, para. 1) that the recited nonconventional and non-generic arrangement of the claim limitations provide improvements to the underlying technology or technical field, as taught in at least the above cited portions of the disclosure and points to MPEP 2106.05(a) or, alternatively, MPEP 2106.05(e). The Applicant further states that notably, the claimed limitations move from abstract scientific principle to specific application, and points to MPEP 2106.05(e) citing Classen.
These arguments are not persuasive, because first, and as noted in the foregoing responses to arguments and in the above rejection, the claims do not recite any additional elements that apply, rely on, or use the judicial exceptions in a manner that imposes a meaningful limit on the judicial exceptions, and therefore the claims are not integrated into a practical application at Step 2A Prong Two (MPEP 2106.04(d)), and the claims do not recite any additional elements that amount to significantly more than the judicial exceptions when the additional elements are considered individually and in combination at Step 2B. Second, with regard to the Applicant pointing to MPEP 2106.05(e) citing Classen, and stating that notably, the claimed limitations move from abstract scientific principle to specific application, it is noted the MPEP 2106.05(e) (Other Meaningful Limitations) shows that the phrase “meaningful limitations” is used to describe additional elements that provide an inventive concept to the claim as a whole. As noted in the rejection above, the additional elements of a computer (claims 16, 17, 19-32, 35, 36, and 39); a data processing system comprising a processor and a non-transitory computer-readable storage medium (claims 29 and 30); a non-transitory computer readable storage medium (claims 31 and 32); providing a database (claims 16, 36, and 39); accessing a database (claims 19, 21, and 27); providing data (claim 25); and outputting data (claims 16, 36, and 39); are conventional (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes). Therefore, when taken alone, all additional elements in claims 16, 17, 19-32, 35, 36, and 39 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 16, 17, 19-32, 35, 36, and 39 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)). Third, the MPEP at 2106.05(e) (Other Meaningful Limitations) shows that there was an additional element (i.e., an immunization step) in Classen that was meaningful because it integrated the results of the analysis (i.e., abstract idea) into a specific and tangible method that resulted in the method “moving from abstract scientific principle to specific application.” In contrast, the instant claims do not recite any additional elements that meaningfully limit the abstract ideas, because the additional elements are conventional at Eligibility Step 2B, as shown in the rejection above. Fourth, with regard to the Applicant’s attempt to analogize the instant claims to Enfish, it is noted that the instant claims are analyzed for eligibility in accordance with their broadest reasonable interpretation, and are further analyzed based on the fact patterns set forth by the limitations recited in the claims. Thus, the eligibility analysis of the instant claims in the rejection above results in a different eligibility outcome than in Enfish, as pointed to by the Applicant in the argument above. Fifth, the fact pattern of the instant claims (i.e., biological information handling, e.g., manipulation of sequence read data) differs from Enfish (a data storage and retrieval system for computer memory). Sixth, the claims at issue in Enfish were found to not be directed to an abstract idea, but rather directed to a specific improvement to the way that computers operate, embodied in a data structure that corresponds to a storage and retrieval structure configured in a computer memory comprising a self-referential table that is designed to improve the way a computer stores and retrieves data in memory, and thus is an improvement to computer functionality itself. Stated a different way, the improvement was found in the structure of the table itself (e.g., relationships between rows and columns), irrespective of any particular data being stored or searched. In contrast, the eligibility analysis of the instant claims has determined, as shown in the rejection above, that the claims are directed to an abstract idea (i.e., sequence data manipulation) at Eligibility Step 2A for which computers are invoked merely as a tool. Seventh, since the eligibility analysis of the instant claims at Step 2A determined that the claims are directed to a judicial exception, the additional elements (which do not include the limitation of a directed graph, which is a judicial exception) recited by the claims are further evaluated at Step 2B to determine whether they amount to an inventive concept, i.e., amount to significantly more than the judicial exceptions. As noted in the rejection above, and in the foregoing responses to arguments, when all instantly claimed additional elements are analyzed at Step 2B, when taken alone, all additional elements in claims 6, 17, 19-32, 35, 36, and 39 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as a combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 6, 17, 19-32, 35, 36, and 39 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)).
Conclusion
No claims are allowed.
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.
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/S.W.B./Examiner, Art Unit 1687
/Joseph Woitach/Primary Examiner, Art Unit 1687