DETAILED ACTION
The Applicant’s response, received 09 December 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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.
Applicant's submission filed on 09 December 2025 has been entered.
Status of the Claims
Claims 18-29, 31-32, and 36 are pending.
Claims 18-29, 31-32, and 36 are rejected.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Claims 18-21, 29, 31, and 36 are given the benefit of Foreign Application No. EPO 19156086, filed 07 February 2019. Claims 22 and 23 are not given benefit because there is not support for aligning processed reads with a directed graph. Claim 24 is not given benefit because there is not support for collapsing the processed reads by sorting them. Claim 25 is not given benefit because there is not support for converting the obtained data into sub read graphs and/or read graphs. Claim 26 is not given benefit because there is not support for removing dead ends and/or loops. Claims 27 and 28 are not given benefit because there is not support for dynamically adapting sequencing. Claim 32 is not given benefit because there is not support for a sequencer adapted to receive feedback from the data processing system.
Claims 18-29, 31-32, and 36 are given the benefit of Foreign Application No. EPO 19190900, filed 08 August 2019.
Information Disclosure Statement
The information disclosure statement (IDS) received on 04 September 2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The Specification received 04 August 2021 contains an embedded hyperlink and/or other form of browser-executable code on page 42/49 at paragraph [204].
Claim Interpretation
Claims 18, 29, and 36 recite a sequencer “taking into account information contained in a database of fingerprint data strings for a biological sequence database” in lines three and four. This recitation is interpreted to mean that the sequencer machine has communication connectivity with a data processing system (i.e., computer hardware and software).
Claim 18, 29, and 36 recite the limitation “information contained in a database of fingerprint data strings for a biological sequence database” in lines three and four. This limitation is interpreted as reciting a product-by-process limitation with the product being the information (i.e., fingerprint data strings for a biological sequence) contained in a database, and further interpreted to not require the active steps of performing the process steps to produce the product.
Claims 31 and 32 recite the term “data processing system.” The broadest reasonable interpretation of this term is computer hardware and computer software.
Claims 18, 29, and 36 recite the term “biological sequence.” This term is interpreted to mean a 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, ¶ [57]).
Claims 18, 19, 21, 22, 29, and 36 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, ¶ [59]), and is one sequence unit shorter than a subsequence that is not found in any biological sequence database (Specification, ¶ [65]). This term is further interpreted to be synonymous with the term HYFT fingerprint (Specification, ¶¶ [66] & [60]).
Claims 18, 19, 21, 22, 29, and 36 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, ¶ [60]).
Claim 27 recites the limitation “dynamically adapting said sequencing” and claim 28 recites the limitation “wherein said dynamically adapting.” The limitation “dynamically adapting” is interpreted to mean adapting the sequencing process based on information obtained from processing the data of previously sequenced reads using a data processing system (Specification, ¶¶ [26] & [106]).
Claim Rejections - 35 USC § 112
The amendment received 09 December 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.
Claim 18-29, 31-32, and 36 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 claim 36 contains 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.
Independent claims 18, 29, and 36 are indefinite for reciting the limitation “(b2) rejecting the read…” because it is not clear as to whether “rejecting the read” means that the processor (i.e., analysis of read data) is rejecting the read in some manner (e.g., identifying the read and removing it from the data file being analyzed) or alternatively if the limitation “rejecting the read” means that the sequencer is physically removing a molecule from a pore based on a data analysis determination processed by the processor. The limitation “rejecting the read” is interpreted to mean a data analysis step of removing data of a read from the analysis, because the step (b2) in independent claims 18, 29, and 36 follows step (b) “the processor of the sequencer processing the read by…” and further interpreted to not mean that the sequencer is physically removing a molecule from a pore.
Claims 19-28 and 31-32 are indefinite for depending from either of independent claims 18, 29, or 36 and for failing to remedy the indefiniteness of the claim from which they depend.
Claim Rejections - 35 USC § 101
The Applicant’s amendment received 09 December 2025 has been fully considered, however after further consideration, the rejection of claims 18-29 and 31-33 under 35 U.S.C. 101 in the Office action mailed 09 July 2025 is maintained with modification in view of the amendment.
The rejection of claim 33 is withdrawn in view of this claim having been cancelled in the amendment.
Claim 36 is newly rejected in view of this claim having been newly added in the amendment
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 18-29, 31-32, and 36 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) mathematical concepts (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (b) mental processes, i.e., concepts performed in the human mind (e.g., observation, evaluation, judgement, opinion).
Subject matter eligibility evaluation in accordance with MPEP 2106.
Eligibility Step 1: Step 1 of the eligibility analysis asks: Is the claim to a process, machine, manufacture or composition of matter?
Claims 18-28 are directed to a method (i.e., a process) for sequencing a biopolymer or biopolymer fragment using a sequencer comprising a processor and a non-transitory computer readable storage medium; claims 29, 31, and 32 are directed to a sequencer comprising a processor and a non-transitory computer readable storage medium (i.e., a machine or manufacture) for sequencing a biopolymer or biopolymer fragment; and claim 36 is directed to a method (i.e., a process) for sequencing a biopolymer or biopolymer fragment using a sequencer comprising a processor and a non-transitory computer readable storage medium.
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 18 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
taking into account information of fingerprint data strings for a biological sequence (i.e., mental processes);
each fingerprint data string representing a characteristic biological subsequence made up of sequence units (i.e., mental processes);
each characteristic biological subsequence defined where a first subsequence does not appear in the biological sequence database and where removing a terminal sequence unit from the first subsequence forms a second subsequence that does appear in the biological sequence database, the second subsequence being the characteristic biological subsequence (i.e., mental processes);
wherein the sequence units comprise amino acids when the characteristic biological subsequence relates to a protein and codons when the characteristic biological subsequence relates to DNA or RNA (i.e., mental processes);
the characteristic biological subsequences having varying lengths of between 4 and 20 sequence units (i.e., mental processes);
step (b) processing the read (i.e., mental processes) by;
step (b1) searching the read for occurrences of one or more of the characteristic biological subsequences represented by the fingerprint data strings (i.e., mental processes);
step (b2) rejecting the read when a sequence unit consecutive to the characteristic biological subsequence does not conform with the database of finger print data strings (i.e., mental processes); and/or
step (b1’) 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 (b2’) predicting one or more consecutive sequence units to the read from the database of finger print data strings and appending said one or more consecutive sequence units to the read (i.e., mental processes).
Independent claim 29 recites a sequencer comprising a processor and a non-transitory computer readable storage medium configured to perform the abstract ideas recited by independent claim 18.
Independent claim 36 recites a sequencer comprising a processor and a non-transitory computer readable storage medium configured to perform the abstract ideas recited by independent claim 18, plus the additional limitation of:
step (c) constructing a processed biological sequence comprising a fingerprint marker associated with the fingerprint data string which represents the processed read, and constructing the processed biological sequence as a directional HYFT graph.
Dependent claims 19, 21-26, and 28 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 19 further recites:
a first fingerprint data string representing a first characteristic biological subsequence of a first length (i.e., mental processes);
a second fingerprint data string representing a second characteristic biological subsequence of a second length (i.e., mental processes); and
wherein the first and the second length differ from one another (i.e., mental processes and mathematical concepts).
Dependent claim 20 further recites:
step (b), i.e., processing the reads, is started prior to all reads for the biopolymer or biopolymer fragment having been obtained (i.e., mental processes).
Dependent claim 21 further recites:
wherein step (b2) and/or (b2') comprises the use of:
data related to a secondary and/or tertiary and/or quaternary structure of the characteristic biological subsequence when said characteristic biological subsequence is present in a biopolymer (i.e., mental processes);
data related to a relationship between the characteristic biological subsequence and one or more further characteristic biological subsequences (i.e., mental processes);
data related to an interdistance with respect to the fingerprint data strings (i.e., mental processes); and
data related to a direction of the fingerprint data strings (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); and
aligning, using the characteristic biological subsequences identified in step (b1) and/or (b1'), the processed reads with a directed graph (i.e., mental processes, and mathematical concepts).
Dependent claim 23 further recites:
wherein said aligning comprises identifying variations for a possible sequence (i.e., mental processes).
Dependent claim 24 further recites:
wherein the method further comprises collapsing the processed reads by sorting them (i.e., mental processes).
Dependent claim 25 further recites:
wherein the method further comprises converting the obtained data into sub read graphs and/or read graphs (i.e., mental processes, and mathematical concepts).
Dependent claim 26 further recites:
wherein the method further comprises any of removing dead ends and/or loops (i.e., mental processes).
Dependent claim 28 further recites:
the number of reads that need to be obtained (i.e., mental processes); and/or
reads to be disregarded as erroneous reads based on information obtained from said processing and/or aligning (i.e., mental processes);
wherein said method comprises backtracking towards or up to a read (i.e., mental processes).
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., searching the read for occurrences of one or more of the characteristic biological subsequences represented by the fingerprint data strings), 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 the processed biological sequence as a directional graph) are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind.
Therefore, claims 18-29, 31-32, and 36 recite an abstract idea.
[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.
Dependent claims 21-26 do not recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements in independent claims 18, 29, and 36 include:
sequencing a biopolymer or biopolymer fragment using a sequencer comprising a processor and a non-transitory computer readable storage medium (claims 18 and 36);
obtaining at least one read for said biopolymer or biopolymer fragment using the sequencer (claims 18 and 36);
a database (claims 18, 29, and 36);
a sequencer comprising a processor and a non-transitory computer readable storage medium, the sequencer configured for sequencing a biopolymer or biopolymer fragment (claim 29); and
perform at least one read for said biopolymer or biopolymer fragment (claim 29).
The additional elements in dependent claims 19, 20, 27, 28, 31, and 32 include:
a database (claim 19);
obtaining a plurality of reads for said biopolymer or biopolymer fragment (claim 20);
obtaining information (i.e., data) and dynamically adapting sequencing (claim 27);
providing (i.e., outputting) feedback (i.e., data) and dynamically adapting sequencing (claim 28);
a sequencer adapted to transmit data to a data processing system (claim 31); and
a sequencer adapted to receive data from a data processing system (claim 32).
The additional elements of a processor and a non-transitory computer readable storage medium (claims 18, 29, and 36); a data processing system (claims 31 and 32); and a database (claims 18, 19, 29, and 36); invoke a computer and/or computer-related components merely as tools for use in the claimed process, such that they amount to no more than mere instructions to apply the exceptions using a generic computer (MPEP 2106.05(f)), and therefore are not an improvement to computer functionality itself, or an improvement to any other technology or technical field (see MPEP 2106.04(d)(1)).
The additional elements of a sequencer (claims 18, 29, and 36); sequencing a biopolymer or biopolymer fragment using a sequencer (claims 18, 29, and 36); obtaining at least one read for said biopolymer or biopolymer fragment using the sequencer (claims 18 and 36); perform at least one read for said biopolymer or biopolymer fragment (claim 29); and obtaining a plurality of reads for said biopolymer or biopolymer fragment (claim 20); are merely pre-solution activities of gathering data for use in the claimed process – nominal additions to the claims that do not meaningfully limit the claims, and therefore do not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
The additional elements of obtaining information, i.e., data (claim 27); providing (i.e., outputting) feedback (i.e., communication) to a sequencer (claim 28); a sequencer adapted to transmit data to a data processing system (claim 31); and a sequencer adapted to receive data from a data processing system (claim 32); are merely pre-solution activities of gathering data for use in the claimed process – nominal additions to the claims that do not meaningfully limit the claims, and therefore do not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
The additional element of dynamically adapting sequencing (claims 27 and 28) does not amount to more than mere instructions to implement an abstract idea, because the claims fail to recite details (i.e., description of the mechanism for accomplishing the result) of how the physical process of genomic sequencing is adjusted/modified based on the information obtained from the processing and/or aligning.
Furthermore, the additional element of dynamically adapting sequencing (claims 27 and 28) based on data received from a data processing system, is merely a pre-solution activity that is part of the gathering of data for use in the claimed process – a nominal addition to the claims that does not meaningfully limit the claims, because the instant claims are directed to analyzing data collected from a sequencer machine, and not directed to a sequencer machine itself, 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 and/or computer-related components as a tool, and/or amount to insignificant extra-solution data gathering activity, and/or are mere instructions to apply an exception, and as such, when all limitations in claims 18-29, 31-32, and 36 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 18-29, 31-32, and 36 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.
Dependent claims 21-26 do not recite any elements in addition to the judicial exception(s). The additional elements recited in independent claims 18, 29, and 36 and dependent claims 19, 20, 27, 28, 31, and 32 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 processor and a non-transitory computer readable storage medium (claims 18, 29, and 36); a data processing system (claims 31 and 32); and a database (claims 18, 19, 29, and 36); are conventional (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
The additional elements of a sequencer (claims 18, 29, and 36); sequencing a biopolymer or biopolymer fragment using a sequencer (claims 18, 29, and 36); obtaining at least one read for said biopolymer or biopolymer fragment using the sequencer (claims 18 and 36); perform at least one read for said biopolymer or biopolymer fragment (claim 29); and obtaining a plurality of reads for said biopolymer or biopolymer fragment (claim 20); obtaining information (i.e., data) and dynamically adapting sequencing (claim 27); providing (i.e., outputting) feedback (i.e., communication) to a sequencer (claim 28); a sequencer adapted to transmit data to a data processing system (claim 31); and a sequencer adapted to receive data from a data processing system (claim 32); are conventional.
Evidence for the conventionality is shown by Plesivkova et al. (WIREs Forensic Science, 2019 (First published 27 December 2018), Vol. 1, Issue 1, pp. 1-12, as cited in the Office action mailed 07 November 2024). Plesivkova et al. reviews the MinION single-molecule sequencing system and shows that the user is able to stop sequencing when the sought-after information has been gathered (Abstract); the MinION sequencing device requires a laptop with a USB3.0 port, 1 terabyte of storage, 16 gigabytes of RAM, and a four core CPU (page 3, para. 2); software for the MinION sequencing device that performs core tasks such as assignments of run parameters, data acquisition, and feedback on how the experiment is progressing (page 3, para. 5); “live” base calling during the sequencing run (page 3, para. 6); using a MinION sequencer to identify the correct donor of DNA sample using SNPs in a process termed “sketching” using real-time sequence data analysis, where the correct identification of a sample from a database of 31,000 entries only required results from around 91 random SNPs and 3 minutes of “sketching” (page 5, para. 3); a ReadUntil feature that allows control over what is being sequenced by individual pores, where the signal measurements are aligned against the expected pattern for the target sequence and if the two patterns do not match, the voltage is reversed, and the strand is ejected from the pore (page 7, para. 5); and real-time base calling of selected sequences to generate relevant DNA sequence information, in theory within minutes of the beginning of sequencing (Ibid.).
Further evidence of conventionality is shown by Loose (“The potential impact of nanopore sequencing on human genetics,” Human Molecular Genetics, 2017, Vol. 26, No. R2, pp. R202-R207, newly cited). Loose reviews the nanopore sequencing platform (Title; and Abstract) and shows that nanopore technology is truly real time, because data are available for analysis the moment a read has traversed a nanopore, enabling the analysis to begin before an experiment (i.e., sequencing run) has completed (page R205, col. 1, para. 3). Loose further shows that by reversing the voltage over an individual channel (i.e., pore), a read can be rejected from a specific pore, and in this way, the amount of data sequenced from the individual regions of a genome can be controlled (page R205, col. 1, para. 4).
Therefore, when taken alone, all additional elements in claims 18-29, 31-32, and 36 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 18-29, 31-32, and 36 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 09 December 2025 have been fully considered, but are not persuasive.
The Applicant states on page 13/26 (para. 2) of the Remarks that the Applicant disagrees with both the characterization and the analytical approach of rejection of the instant claims. The Applicant further states (para. 3) that the focus of the claimed advance is not a disembodied mental calculation, but a concrete sequencing technique that uses a specific, non-generic fingerprint repository and particular processing steps implemented in a sequencer comprising a processor and a non-transitory computer-readable storage medium.
These arguments are not persuasive, because the eligibility analysis in the above rejection shows that the instant claims are directed to the analysis of sequence reads, in particular, steps of searching sequence read data for subsequences. The eligibility analysis further shows that the data used in the claimed process is generated, i.e., gathered, by using a genomic sequencer.
The Applicant states on page 13/26 (para. 4) of the Remarks that the identified steps are not “mental processes” as the term is used in the Guidance, and that mental processes are “concepts performed in the human mind (including an observation, evaluation, judgement, or opinion)” that can practically be carried out mentally. The Applicant further states that claim 18 requires use of a sequencer to obtain one or more reads for a biopolymer or biopolymer fragment, a fingerprint data base in which each fingerprint data string represents a characteristic biological subsequence defined with respect to the contents of an underlying biological sequence database, searching high-volume reads for occurrences of these characteristic subsequences, and rejecting reads or predicting and appending one or more consecutive sequence units based on the fingerprint database. The Applicant further states on page 14/26 (para. 1) that these operations cannot practically be performed “in the human mind” because they require processing of extremely large numbers of reads against a large repository of fingerprint data strings derived from biological sequence databases and performing real-time comparisons and predictions at sequencing speeds contemplated for high-throughput systems. The Applicant further states that the Specification (as explained at least at paras. [05-07]) expressly explains that existing mapping and assembly problems are NP-hard, and require dynamic programming and heuristics precisely because they cannot feasibly be solved manually.
These arguments are not persuasive, because first, the above rejection identifies elements of the claims that are hardware (e.g., a sequencer and/or a data processing system) as additional elements at Step 2A Prong Two, and not as mental processes. Second, regarding the Applicant’s argument that the claims “require processing of extremely large numbers of reads against a large repository of fingerprint data strings derived from biological sequence databases and performing real-time comparisons and predictions at sequencing speeds contemplated for high-throughput systems,” the amount of data and/or the amount of time to perform the process steps, in and of themselves 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, and mental steps identified in the claims do not have to be the fastest, most efficient, or require specialized computing elements (e.g., searching data strings, while tedious and time-consuming, is of the realm of the human mind). Thus, 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 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. Third, using heuristics, i.e., using “rules of thumb” to find a “good enough” solution, is within the realm of the human mind, and solving small instances of NP-Hard problems (e.g., small inputs such as N < 10 or 12) manually by so-called brute-forcing or systematic searching is possible, and therefore a claimed process using large inputs involving exponential time complexity does not take a process out of the realm of the human mind. Fourth, dynamic/adaptive sequencing is identified as additional element that is part of the data gathering process at Step 2A Prong Two and conventional at Step 2B, as noted and discussed in the above rejection.
The Applicant states on page 15/26 (para. 2) of the Remarks that the claims require particular data structures, e.g., fingerprint data strings that represent HYFT-type characteristic subsequences with strict directionality and constrained combinatory possibilities, tied to actual physical biopolymer fragments, and that these are not generic numbers or formulas, but instead provide specialized structures capturing intrinsic physical and chemical constraints of biopolymers, exploited to constrain and guide sequencing. The Applicant further states (para. 3) that the rejection treats definitional and structural recitations such as “wherein the sequence units comprise amino acids…and codons…” and “the characteristic biological subsequences having varying lengths of between 4 and 20 sequence units” as if they were mental thoughts, however in the claim, these recitations define the structure of the fingerprint repository and thereby the behavior of the sequencer, and further, that they are no more mental processes than the particular rule sets in McRO or the self-referential table in Enfish, which were held to be patent-eligible improvements to computer technology (Remarks, page 16/26, para. 1). Finally, the Applicant further states (para. 2) that as such, the claims are not directed to mental steps or mathematical concepts under Step 2A Prong 1, but instead to a specific, technological method of operating sequencing systems using a specially structured fingerprint repository.
These arguments are not persuasive, because first, genomic sequence data is inherently a particular data structure that is representative of various aspects of an organism’s DNA or RNA (e.g., the precise order of nucleotides), and further represents a comprehensive, digital blueprint detailing genetic variations, disease susceptibility, and evolutionary changes. Second, a so-called fingerprint data string is merely a data string that is representative of one or more characteristic biological subsequences, which are themselves subsequences of larger data strings. Third, adaptive/dynamic sequencing and the capability for ‘screening’ reads from regions of the genome (i.e., a type of targeted sequencing) is a feature of nanopore sequencing, and is conventional, as shown in the above rejection and in the Office actions of record. Fourth, the instant claimed invention does not recite any additional elements that could be considered as providing an improvement to either computer functionality itself, or sequencing technology, particularly nanopore sequencing technology. Fifth, regarding the Applicant’s attempt at analogizing the instant claims to Enfish, the instant claims are not analogous to the claims in Enfish, because the instant claims recite a data analysis process that is a purported improvement to the abstract idea itself (e.g., characterizing subsequences within biological sequence data, and using that data as a reference for searching within other sequences, matching and/or predicting the occurrence of a reference read within the read being searched (i.e., ‘screened’) and subsequently validating the read (or using nanopore sequencing technology to reject the screened read from the pore) and proceeding with the data gathering process and the data analysis), whereas in contrast, the improvement recited in Enfish is found 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. Sixth, with regard to the Applicant’s attempt at analogizing the instant claims with the eligibility determination in McRO, it is noted that in McRO, when looked at as a whole, claim 1 is directed to a patentable, technological improvement over the existing, manual 3-D animation techniques, i.e., the claim recited “a specific asserted improvement in computer animation” that was directed to the creation of something physical – namely, the display of lip synchronization and facial expressions of animated characters on screens for viewing by human eyes, and therefore was determined to not be directed to an unpatentable abstract idea at Eligibility Step 2A (i.e., Alice step one). Unlike the technological improvement found in McRO, the instant claimed advantage of using subsequences of sequence read data in a specific way to achieve the claimed improved technological result of finding and gathering sequence data for further analysis is a purported improvement to the abstract idea (data analysis), and not an improvement to computer functionality itself, or an improvement to another technology or technical field.
The Applicant states on page 16/26 (para. 3) of the Remarks that the claims as a whole integrate any alleged abstract idea into a practical application in the field of biological sequencing, and that the specification explains that the current claims provide methods and devices for sequencing biopolymers that reduce complexity, are deterministic, and improve sequencing (e.g., by decreasing errors and increasing speed) by relying on information contained in the repository of fingerprint data strings. The Applicant further states (para. 4) that these methods allow provisionally suggested sequences to be validated or rejected and reduce propagation of sequencing errors, and further speed sequencing by predicting next units or limiting the number of options for next units, and that these are concrete improvements in the operation of sequencing systems, and not improvements to an abstract idea itself.
These arguments are not persuasive, for the reasons given in response to the foregoing arguments and also in the above rejection, and in particular, because first, the claims do not recite any additional elements that would possibly provide an improvement to sequencing technology, particularly with regard to nanopore sequencing technology, and second, the use of adaptive/dynamic sequencing in combination with a data processor and a database of reference subsequences in the claimed process is a step of gathering data for analysis, and therefore does not provide a practical application of the recited judicial exceptions, and also does not provide an improvement to computer functionality itself, or an improvement to sequencing technology, or to any other technology or technical area.
The Applicant states on page 16/26 (para. 5) of the Remarks that the claimed steps are not merely “observing” or “evaluating” data, but using the fingerprint repository to actively control what reads are accepted, rejected, or supplemented, and how sequencing proceeds, and that this is analogous to cases in which specific rules or data structures are used to improve a technological process (e.g., McRO’s rule-based animation, Enfish’s table structure, and KPN’s specific error-checking scheme).
These arguments are not persuasive, because the claimed process is not analogous to either of Enfish or McRO for the reasons given in the foregoing responses to arguments, and not analogous to KPN for the reasons given in the Office actions of record, and further because in KPN the claims were found to be directed to an improved check data generating device that enables a data transmission error detection system to detect a specific type of error that prior art systems could not, whereas in contrast, the instant claimed process does not recite any additional elements that would possibly provide an improvement to sequencing technology, particularly with regard to nanopore sequencing technology, because the use of adaptive/dynamic sequencing in combination with a data processor and a database of reference subsequences in the instant claimed process is a step of gathering data for analysis, and therefore does not provide a practical application of the recited judicial exceptions, and also does not provide an improvement to computer functionality itself, or an improvement to sequencing technology, or to any other technology or technical area.
The Applicant states on page 17/26 (para. 1) of the Remarks that the Office action asserts that the purported improvement is in the abstract idea itself (i.e., analyzing sequence read data)” and that using a sequencer to generate read data is merely insignificant extra-solution data gathering. The Applicant further states that this mischaracterizes both the claims and the disclosure, because the claims do not simply analyze pre-existing data in the abstract, but specify how a sequencer is configured and operated, in real time, to generate sequence information by applying the fingerprint repository structure and the specific validation/prediction steps, and that the improvement is to the sequencing technology itself, including reducing errors, enabling deterministic control, and improving speed, not to an abstract mathematical concept in isolation.
These arguments are not persuasive, for the reasons provided in the foregoing responses to arguments and in the above rejection, and further because the claims do not recite how a sequencer is configured with the exception that it is in communication with a computer processor and a storage medium (e.g., the claims do not recite any specific sequencer machine or technology, nor do the claims recite a configuration of a sequencer that reflects an improvement to the technology). Furthermore, genomic material (e.g., DNA) is sequenced using a sequencer to generate a data representation of the genomic material specifically for the purpose of data analysis (e.g., of the genome or regions of the genome) and therefore using a genomic sequencer to generate sequence read data is a step of gathering data for use in a claimed process, and therefore an insignificant extra-solution activity, as noted in the above rejection. Further, and as noted in the above rejection at Step 2B, dynamic/adaptive control is a feature of nanopore sequencing technology, and does not change the purpose of sequencing genomic material, i.e., gathering data for use in analytical processes.
The Applicant states on page 17/26 (para. 2) of the Remarks that under the 2019 Revised Guidance, claims integrate an abstract idea into a practical application when the apply it in a meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, and that here, the claims do far more than link a generic abstract idea to the environment of sequencing, rather the claims recite how the fingerprint data strings, their structural properties, and the particular searching/rejecting/predicting steps are used in a sequencer to solve specific technical problems identified in the art.
These arguments are not persuasive, for the reasons provided above in response to foregoing arguments, and in the above rejection, and further because the claims actually only recite a generic environment of a sequencer (e.g., the claims do not even recite a particular type of sequencer or which components of a sequencer are being improved) and further because the use of a sequencer to generate sequence read data is a step of gathering data for use in a claimed process, and therefore an insignificant extra-solution activity, as noted in the above rejection. Further, and as noted in the above rejection at Step 2B, dynamic/adaptive control is a feature of nanopore sequencing technology, and does not change the purpose of sequencing genomic material, i.e., gathering data for use in analytical processes.
The Applicant states on page 17/26 (para. 3) of the Remarks that even if it was maintained that the claims are directed to an abstract idea, the claims recite significantly more than any judicial exception, and the additional elements, particularly in combination, are not well-understood, routine, and conventional in the field. The Applicant further states (para. 4) that the current Office action concludes that the additional hardware elements are conventional computer components used as tools, however, the Step 2B inquiry focuses on whether the combination of these elements in the claimed arrangement, including the specific structure of the fingerprint repository and the specific processing operations (searching for characteristic subsequences, rejecting reads based on database non-conformance, and predicting/appending consecutive units), is well-understood, routine, and conventional. That Applicant further states on page 18/26 (para. 2) of the Remarks that the rejection cites Plesivkova et al. as evidence of conventionality, which shows that certain real-time sequencing and feedback capabilities exist, but does not disclose or suggest:
a repository of fingerprint data strings representing HYFT-type characteristic subsequences defined by the specific absence/presence rule in a biological sequence database;
constraining characteristic subsequences to lengths between 4 and 20 amino acids or codons;
a method of processing reads by searching for occurrences of these characteristic subsequences and, for each occurrence, evaluating whether a consecutive sequence unit conforms to a fingerprint database and thereby rejecting the read; or
predicting and appending one or more consecutive units to the read based on the fingerprint database as a deterministic, combinatorially constrained prediction mechanism.
The Applicant further states that at least these features provide the technical improvements described in the specification (e.g., reduced complexity, determinism, improved error detection and speed) and that (page 19/26, para. 1) there is no evidence of record that this particular combination of fingerprint structures and processing operations was routine or conventional in sequencing at the time of filing of the application.
These arguments are not persuasive, because first, at Step 2B, only the additional elements are carried over from Step 2A for further analysis, and of the features presented in the foregoing argument as providing the technical improvements described in the specification, it appears that the only limitation in the argument that is an additional element is a database (i.e., a repository), with the remainder of the limitations presented in the argument having been identified as abstract ideas at Step 2A Prong One (e.g., fingerprint data strings representing HYFT-type characteristic subsequences defined by specific absence/presence rule; constraining characteristic subsequences to lengths between 4 and 20 amino acids or codons; searching for occurrences of these characteristic subsequences and, for each occurrence, evaluating whether a consecutive sequence unit conforms to a fingerprint database; or predicting and appending one or more consecutive units to the read based on the fingerprint database as a deterministic, combinatorially constrained prediction mechanism).
The Applicant states on page 19/26 (para. 2) of the Remarks that whether claim elements are well-understood, routine, and conventional, is a factual determination that must be supported by evidence when, as here, the elements are not indisputably conventional. The Applicant further states that the current Office action relies on essentially high-level statements (e.g., generic computer components are conventional) and a reference that does not disclose the HYFT-based fingerprint repository or the claimed processing steps, and further that this is insufficient to show that the ordered combination of claim elements is merely well-understood, routine, and conventional. The Applicant further states (para. 3) that indeed, the specification itself characterizes the HYFT-based approach as addressing limitations of existing k-mer and heuristic methods, which suffer from error accumulation and lack of specificity, and that the disclosed methods and devices are presented as solving technical problems for which “no efficient method is currently known to validate directly whether a (fragment) sequence is correct or whether it contains one or more sequence errors” and that the Office action has not pointed to any contrary evidence. The Applicant further states (para. 4) that accordingly, under Step 2B, the claims recite an inventive concept in the form of a non-conventional, non-generic arrangement of a sequencer, data processing system, and a specially structured fingerprint repository, configured to perform specific search, validation, rejection, and prediction operations that improve the technological process of sequencing.
These arguments are not persuasive, for the reasons already provided in the foregoing responses to arguments and in the above rejection, and further because the references used at Step 2B to show conventionality are used to show conventionality of claim limitations that have been identified as additional elements (i.e., the identified judicial exceptions are not considered in the analysis under Step 2B), and thus the cited references do not necessarily show a database (i.e., having been previously shown to be a conventional computer and/or computer-related component or function in the rejection) and in particular, the cited references at Step 2B would not necessarily show limitations that have been identified as judicial exceptions at Step 2A Prong One (e.g., fingerprint data strings and/or data processing steps). Furthermore, and as noted in the above rejection, even when all of the recited additional elements are evaluated as a combination, those additional elements fail to transform the exception(s) into a patent-eligible application of that exception, and thus, are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s).
The Applicant states on page 19/26 (para. 5) of the Remarks that it is noted that in the previous response, arguments were submitted analogizing the claims to those deemed patent-eligible in Koninklijke KPN N.V. v. Gemalto M2M GmbH, which concerned a specific technique for error checking in data transmission systems, and that in response, the Office action distinguishes KPN on factual grounds, noting that KPN involved data transmission and that the instant claims involve generating biological sequence information. The Applicant further states on page 20/26 (para. 2) of the Remarks that however, while the subject-matter context differs, the principle is the same, and that in both cases, the claims recite a specific technical solution (in KPN, modifying the permutation used to generate check data, and the current case, using a specially defined fingerprint repository and particular search/validation/prediction steps) to improve the functioning of a technological process (error detection in data transmission vs. error detection and predictive sequencing in biological sequencing). The Applicant further states that the fact that the problem domain is sequencing rather than network transmission does not render the improvement non-technical.
These arguments are not persuasive, for the reasons already provided in the foregoing responses to arguments and also in the above rejection, and further because the Applicant’s attempt at analogizing the instant claimed process with KPN is conflicted with the fact pattern of the instant claims, in that the instant claimed process compares sequencing reads to previously generated and stored subsequences of larger sequences, and validates the reads being sequenced by searching the read for occurrences of one or more of the reference subsequences (i.e., step (b1) of the instant independent claims) (i.e., matching reads being sequenced to a corresponding matched read in the database). In contrast, however, KPN recognizes that matching check data is not always a reliable indicator of accurate data transmission, because certain generating functions coincidentally produce the same check data for a corrupted data block as well as for an uncorrupted data block, and that when this happens, the check data is functionally defective, because the system will mistakenly believe that there were no errors in the data transmission, and further that the problem of defective check data is aggravated for a particular type of persistent error, i.e., “systemic error,” that repeats across data blocks in the same way. The improvement in KPN solves this problem by varying the way check data is generated by varying the permutation applied to different data blocks, and that varying the permutation for each data block reduces the chances that the same systematic error will produce the same defective check data across different blocks, and thus KPN replaces the prior art check data generator with an improved, dynamic check generator that enables increased detection of systematic errors that recur across a series of transmitted data blocks (page 3, bottom, and page 4, top). Further still, the Applicant’s attempt at analogizing the instant claimed process with KPN is conflicted with the fact pattern of the instant claims, in that the instant claimed step of using a genomic sequencer is a step of gathering data (e.g., generating a data representation of DNA molecules) and therefore an insignificant extra-solution activity, whereas the claims in KPN are directed to an improved check data generating device that enables a data transmission error detection system to detect a specific type of error that prior art systems could not.
The Applicant states on page 20/26 (bottom) of the Remarks that new independent claim 36 is added to the claims including the limitations of previous claim 18 and further requiring a processed biological sequence comprising a fingerprint marker associated with the fingerprint data string which represents the processed read, and constructing the processed biological sequence as a directional HYFT graph. The Applicant further presents similar arguments regarding claim 36 as have been previously presented in the foregoing arguments regarding previously presented claims (pages 21-25), and further states (page 21, para. 2) that claim 36 integrates any alleged abstract ideas into a practical application, and does not merely recite receive/compare/output on a generic computer, but recites a particular technical pipeline…that includes constructing the processed biological sequence as a directional HYFT graph…and that the 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 (page 21, bottom) that these features clearly provide an improvement to a technical field and control of a particular field, and so the claim integrates any abstract idea into a practical application at Prong Two, and further states (page 22, top) 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.
These arguments are not persuasive, for the reasons already provided in the foregoing responses to arguments and also in the above rejection, and further because, first, the new limitation (i.e., constructing a directed graph) in newly added claim 36 is identified as a judicial exception at Step 2A Prong One in the above rejection, and second, regarding the Applicant’s assertion that the Office action conflates the analysis at Step 2A Prong Two, it is noted that at Step 2A Prong Two, the claims are considered as a whole (i.e., the analysis takes into consideration all the claim limitations and how those limitations interact and impact each other when evaluating whether the exception is integrated into a practical application), and in the case of the instant claims, the eligibility analysis at Step 2A Prong Two determined that the claims do not recite any additional elements that would integrate the exceptions into a practical application when those additional elements were evaluated individually and in combination, using one or more of the considerations introduced in subsection I at 2106.04(d) of the MPEP, and discussed in more detail in MPEP §§ 2106.04(d)(1), 2106.04(d)(2), 2106.05(a) through (c) and 2106.05(e) through (h), and thus, do not provide an improvement to computer functionality itself, or an improvement to another technology or technical field, and therefore the improvement at best, is to be found in the abstract idea of searching a biological data sequence and designating subsequences as reference sequences for further search of within other biological sequence data.
The Applicant states on page 22/26 (paras. 3-4) of the Remarks that existing graph structures do not accurately represent sequence reads, however (page 23, para. 1) the current claims allow several technical improvements over known methods of biological sequencing, sequence similarity searching, biological sequence alignment, and biological sequence modelling (e.g., para. [156] in the specification). The Applicant further points to paragraph [161] in the specification, explaining that in contrast to sequence similarity searching in the prior art, where an alignment step is typically required and a measure of similarity is then established therefrom, alignment is not strictly necessary for similarity searching according to embodiments, and indeed, similar sequences can already be found by simply searching for sequences with the same fingerprints (optionally also taking into account their order and their interdistance), without alignment, which in turn allows to further speed up the search. The Applicant further states that the claimed steps reflect the improvements described in the disclosure, and thus, claim 36, as a whole, integrates the judicial exception into a practical application.
These arguments are not persuasive, for the reasons already provided in the foregoing responses to arguments and also in the above rejection, and further because, first, the new limitation (i.e., constructing a directed graph) in newly added claim 36 is identified as a judicial exception at Step 2A Prong One in the above rejection, and second, regarding the purported increased speed to searching due to not needing an alignment step, the claimed improvement comprises the limitations identified as judicial exceptions at Step 2A Prong One, and therefore cannot integrate the judicial exceptions into a practical application at Step 2A Prong Two.
The Applicant states on page 23/26 (bottom) of the Remarks that claim 36 recites significantly more than a generic computer, and further states that the recited nonconventional and non-generic arrangement of the claim limitations provide improvements to the underlying technology or technical field, and notably, the claimed limitations move from abstract scientific principle to specific application. The Applicant further states (page 24, para. 2) that claim 36, when considered as a whole, recites an additional element of a HYFT graph 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. 3) 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 further states (para. 4) 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 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.
These arguments are not persuasive, for the reasons already provided in the foregoing responses to arguments and also in the above rejection, and further because, first, the claim limitation reciting a so-called HYFT graph is not an additional element, but rather, is identified as a judicial exception at Step 2A Prong One, and therefore cannot integrate the judicial exceptions into a practical application at Step 2A Prong Two, and second, and as discussed above, the claims do not recite any additional elements that could be considered as providing an improvement to genomic sequencer technology, and third, the claims are directed to searching for subsequences of data within other sequences of data, with genomic sequencer used to gather the data necessary for searching for the claimed “characteristic biological subsequences” represented by so-called “fingerprint data strings.”
The Applicant states on page 24/26 (para. 5) of the Remarks that the claims are not directed to an abstract idea but recite an improvement in computer technology as in Enfish, and that the disclosure at least at paragraphs [05-14] 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 sequencing information in a meaningful way as described with respect to the improvements at least at paras. [19-29], [124], [130], [150], [156], and [164] of the disclosure (e.g., lossless compression, reduced computational requirements, increased flexibility/scalability, etc.). The Applicant further states on page 25 (para. 2) 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, 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, and (para. 3) taken together, 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, and further that the recited nonconventional and non-generic arrangement of the claim limitations provide improvements to the underlying technology or technical field, and therefore, notably, the claimed limitations move from abstract scientific principle to specific application.
These arguments are not persuasive, for the reasons already provided in the foregoing responses to arguments and also in the above rejection.
Conclusion
No claims are allowed.
This Office action is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this application.
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/S.W.B./Examiner, Art Unit 1687
/Joseph Woitach/Primary Examiner, Art Unit 1687