DETAILED ACTION
Applicant’s response, filed Feb 18 2026, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. 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 .
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Claim Status
Claims 39-43 are pending.
Claims 1-38 are canceled.
Claims 39-43 are rejected.
Priority
The instant Application claims domestic benefit to US provisional application 62/562,978, filed Sep 25 2017. Accordingly, each of claims 39-43 are afforded the effective filing date of the Sep 25 2017.
Information Disclosure Statement
The information disclosure statement (IDS) filed on Feb 18 2026 is in compliance with the provisions of 37 CFR 1.97 and has therefore been considered. A signed copy of the IDS document is included with this Office Action.
Claim Rejections- 35 USC § 112
The outstanding rejections to the claims are withdrawn in view of the amendments submitted herein.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 39-43 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more. Any newly recited portions are necessitated by claim amendment.
The instant rejection reflects the Guidance published in the Federal Register notice titled
2019 Revised Patent Subject Matter Eligibility Guidelines (Vol. 84, No. 4, Monday January
7, 2019 at 50) and the October 2019 Updated Subject Matter Eligibility Guidance (hereinafter both referred to as the “Guidance”), as outlined in the MPEP at 2106.04.
Framework with which to Evaluate Subject Matter Eligibility:
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter;
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
Step 1
With respect to Step 1: yes, the claims are directed to methods [Step 1: YES; See MPEP § 2106.03].
Step 2A, Prong One
With respect to Step 2A, Prong One, the claims recite abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found herein to recite abstract ideas that fall into the grouping of mental processes (in particular procedures for observing, analyzing, and organizing information) and mathematical concepts (in particular mathematical relationships and formulas).
The claim steps to abstract ideas of mental processes and mathematical concepts are as follows:
Independent claim 39: (b) generating… corrected sequencing data for the sequencing data received in (a) by applying an attribution rule set to the sequencing data, wherein the attribution rule set comprises attributing an occurrence in the sequencing data of:
(i) a putative sequence encoding the at least one CDR to a parent sequence based on sequence similarity and relative abundance of the parent sequence over the putative sequence, wherein the putative sequence and the parent sequence are associated with the same molecular label sequence;
(ii) a molecular label sequence associated with a putative sequence encoding the at least one CDR to a parent molecular label sequence associated with the putative sequence encoding the at least one CDR based on sequence similarity and relative abundance of the parent molecular label sequence over the molecular label sequence; and
(iii) a putative sequence encoding the at least one CDR to a chimeric sequence, wherein the chimeric sequence is associated with a molecular label sequence associated with (A) the putative sequence encoding the at least one CDR, and (B) at least one other putative sequence encoding a different CDR,
wherein attributing the occurrence of (i) and (ii) is applied to the sequencing data recursively, and wherein the putative sequence whose occurrence has been attributed to the chimeric sequence is excluded from the corrected sequencing data, such that a variation in sequences encoding the at least one CDR in the corrected sequencing data is reduced.
Dependent claim 41: wherein the attribution rule set further comprises attributing an occurrence in the sequencing data of (iv) a combination sequence to a parent combination sequence when the combination sequence is within a third directional adjacency threshold of the parent molecular label sequence, wherein each combination sequence comprises a putative sequence encoding the at least one CDR and an associated molecular label sequence, and when an occurrence of the parent combination sequence is greater than or equal to a third directional adjacency occurrence threshold relative to the occurrence of the combination sequence, and wherein attributing the occurrence of (iv) is applied to the sequencing data recursively.
Dependent claim 43: discriminating between signal and noise molecular label sequences among the molecular label sequences associated with sequences in the corrected sequencing data; and
removing sequences associated with the noise molecular label sequences from the corrected sequencing data.
Dependent claims 40 and 42 recite additional steps that further limit the judicial exceptions in independent claim 39 and, as such, are further directed to abstract ideas. For example, claim 40 further limits the actions taken in steps (b) (i-iii) of claim 39 to attributing occurrences of the difference sequences, and claim 42 further limits the first and second directional adjacency occurrence thresholds.
The abstract ideas recited in the claims are evaluated under the Broadest Reasonable Interpretation (BRI) and determined herein to each cover performance either in the mind and/or performance by mathematical operation because the steps involve nothing more than instructions for a user to manually generated corrected sequencing data based on sequence similarities. There are no specifics as to the methodology involved in “generating”, “attributing”, “discriminating”, and “removing”, and thus, under the BRI, one could simply, for example, generate corrected sequencing data by attributing an occurrence in the sequencing data of a putative sequence to a parent sequence based on sequence similarity and abundance, attributing a molecular label sequence associated with a putative sequence to a parent molecular label sequence based on sequence similarity and relative abundance, and attributing a putative sequence to a chimeric sequence, in the mind or with pen and paper as an aid. Even though the received sequencing data comprises a molecular label sequence of 5-10 nucleotides in length, sequences of at least 200 nucleotides, stochastic barcodes collectively represent at least 103 unique molecular label sequences, and an average sequencing depth of at least 100, as recited in (a), it is considered that such data could be manipulated with the aid of pen and paper or a computer, and does not alter the mental processes which occur when analyzing such data. It is further noted that the claims require only “attributing an occurrence in the sequencing data” such that all of the sequencing data may not be required to be processed through steps (i-iii). Even though the claim recites that the attributing is applied to the sequencing data recursively, there is no condition set forth in the claim for how many times the attributing must be repeated.
Some steps, including those directed to “attributing… based on… relative abundance” in claim 39, attributing when an occurrence of the sequence is greater than or equal to a first or second directional adjacency occurrence threshold relative to the occurrence of the putative sequence or molecular label sequence and when the putative sequence has an occurrence smaller than a chimeric occurrence threshold in claim 40, attributing an occurrence of a combination sequence when the when an occurrence of the parent combination sequence is greater than or equal to a third directional adjacency occurrence threshold relative to the occurrence of the combination sequence in claim 41, and the first directional adjacency occurrence threshold is twice the occurrence of the putative sequence less one, and/or the second directional adjacency occurrence threshold is twice the occurrence of the molecular label sequence less one in claim 42 are performed using mathematical techniques as their only embodiment, as is supported by examples in the Specification, such as Hamming distance [0190]; thresholding analyses [0193]; and, generally, from [0188-0234].
Therefore, claims 39 and those claims dependent therefrom recite an abstract idea [Step 2A, Prong 1: YES; See MPEP § 2106.04].
Step 2A, Prong Two
Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two, provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the 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 is said to fail to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
With respect to the instant recitations, the claims recite the following additional elements:
Independent claim 39: (a) receiving, with the computer system, sequencing data of stochastically barcoded mRNA targets from a sample of T-cells, wherein the MRNA targets encode immune receptors comprising at least one complementarity-determining region (CDR), and each of the stochastically barcoded mRNA targets comprising a stochastic barcode that comprises a molecular label sequence of 5-10 nucleotides in length, wherein the sequencing data comprises sequences of at least 200 nucleotides, wherein the stochastic barcodes collectively represent at least 103 unique molecular label sequences, and wherein an average sequencing depth of each of the stochastically barcoded mRNA targets is at least 100.
The claims also include the following non-abstract computer elements. Claim 39 is a computer-implemented method with a computer system comprising: a hardware processor; and a non-transitory memory having instructions stored thereon, which when executed by the hardware processor cause the processor to perform the method.
With respect to Step 2A, Prong Two, the additional elements of the claims do not integrate the judicial exceptions into a practical application for the following reasons. Those steps directed to data gathering, such as “receiving” data, perform functions of collecting the data needed to carry out the abstract idea. Data gathering does not impose any meaningful limitation on the abstract idea, or on how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)).
Further steps directed to additional non-abstract computer elements do not describe any specific computational steps by which the “computer parts” perform or carry out the judicial exceptions, nor do they provide any details of how specific structures of the computer, such as the computer-readable recording media, are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the judicial exceptions. Hence, these are mere instructions to apply the judicial exceptions using a computer, and therefore the claim does not integrate that judicial exceptions into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc.… are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (MPEP 2106.05(f)).
The Specification does not disclose a clear explanation for how the additional elements provide any improvements. Therefore, the additional elements do not clearly improve the functioning of a computer, or comprise an improvement to any other technical field. Further, the additional elements do not clearly effect a particular treatment; they do not clearly require or set forth a particular machine; they do not clearly effect a transformation of matter; nor do they clearly provide a nonconventional or unconventional step (MPEP2106.04(d)).
Thus, none of the claims recite additional elements which would integrate a judicial exception into a practical application, and the claims are directed to an abstract idea [Step 2A, Prong 2: NO; See MPEP § 2106.04(d)].
Step 2B
As such, the claims are lastly evaluated using the Step 2B analysis, wherein it is determined that because the claims recite abstract ideas which are not integrated into a practical application, the claims also lack a specific inventive concept. Applicant is reminded that the judicial exceptions alone cannot provide the inventive concept or the practical application and that the identification of whether the additional elements amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception. (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements of data gathering described above do not rise to the level of significantly more than the judicial exception. As directed in the Berkheimer memorandum of 19 April 2018 and set forth in the MPEP, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant claims, the courts have found that receiving data is a well-understood, routine, and conventional function of a computer when claimed in a merely generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information) and buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network) as discussed in MPEP 2106.05(d)(II)(i)).
Further, the non-abstract general purpose computer elements or do not rise to the level of significantly more than the judicial exception. The specification as published also notes that computer system is commercially available or widely ([0028; 0270]; Fig. 10). The additional elements are set forth at such a high level of generality that they can be met by a general purpose computer. Therefore, the computer components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than the judicial exceptions (see MPEP 2106.05(b)I-III).
Taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself [Step 2B: NO; See MPEP § 2106.05].
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
Response to Applicant Arguments
At p. 5-,8, par. 1, Applicant submits that claim 39 is patent eligible because it does not recite a judicial exception. Applicant submits that the alleged finding that the claim recites a mental process is an impermissible expansion of the mental grouping to include limitations that cannot practically be performed in the mind, pointing to the USPTO Memorandum dated Aug 4 2025. Applicant submits that claim 39 cannot be performed mentally because it recites specific ways of attributing an occurrence in the sequencing data of a putative sequence, a molecular label sequence, and a putative sequence encoding a chimeric sequence in a recursive manner. Applicant submits that the rejection overly simplifies the claim in an impermissible expansion of the abstract idea grouping. Applicant submits that the claims recite that the received sequencing data comprises a molecular label sequence of 5-10 nucleotides in length, sequences of at least 200 nucleotides, stochastic barcodes collectively represent at least 103 unique molecular label sequences, and an average sequencing depth of at least 100, and that a human mind could not sort through the entirety of such a sequencing dataset to apply the attribution rule set to generate the corrected sequencing data. Applicant further submits that such an analysis requires a base-by-base comparison which a human mind is not equipped to perform. Applicant submits that the previous response that the use of a computer to perform a large number of actions as an “apply it" step is an oversimplification of the claim limitations and the Examiner should consider whether the claim recites only the idea or solution of an outcome, or whether the claim invokes computers merely as a tool to perform an existing process. Applicant submits that the claims recite a particular solution to the problem of overestimating immune receptor diversity in sequencing data, and represents an improvement in existing technology.
It is respectfully submitted that this is not persuasive. First, the claims recite only “attributing an occurrence in the sequencing data” according to the attribute rule set described in (i-iii), where the attributing is applied to the sequencing data recursively. The claims do not set forth requirements for how many times the attribute rule set must be applied to the sequencing data, and as one of ordinary skill in the art would understand “recursive” to mean only the repeated performance of a method, the claims do not require the attribute rule set to be applied to all of the sequencing data, but only, at minimum, two occurrences in the sequencing data. It is maintained that a human mind would be capable of performing the recited attribute rule set in the claims to two sequences, even if such an action would require a base-by-base comparison of the sequences to a parent sequence. Therefore, the claims recite a mental process at Step 2A, Prong 1.
However, even supposing that the claims did require the attribute rule set to be applied to all of the sequencing data, such limitations would still be considered to recite a mental action. That the claims attempt to require the performance of the attribute rule set on a large number of sequences does not alter the fact that the performance of the actions on one sequence can be done mentally, with or without the aid of pen and paper or a computer. Therefore, expansion of the mental process to a larger number of sequences could be performed mentally by one person over a longer period of time, or by a number of people. Repetition of a mental process does not change the process to something that a human mind is not equipped to perform.
The claim includes limitations which encompass purely mental actions as set forth in the above rejections. In MPEP 2106.04(a)(2), section III(A), examples that cannot practically be performed in the mind are provided, and include a method for calculating an absolute position of a GPS receiver and an absolute time of reception of satellite signals, detecting suspicious activity by using network monitors and analyzing network packets, specific data encryption method for computer communication involving a several-step manipulation of data, a method for rendering a halftone image of a digital image where the method required the manipulation of computer data structures and the output of a modified computer data structure. In contrast, the MPEP notes that the limitations that can practically be performed in the human mind, including for example, observations, evaluations, judgments, and opinions. The MPEP therefore makes clear that limitations which cannot practically be performed in the mind are those in which the human mind is not equipped to perform the claim limitations. The term practical is not meant to indicate that as a matter of practicality, one would perform a method preferentially on a computer rather than mentally. The MPEP makes clear that “practical” indicates that a human mind is not capable of performing the recited action. That the performance of such a task would be cumbersome or take a large amount of time because of the scale of the data to be analyzed is not changed by the fact that the human mind is capable of performing the task. Further, the use of a physical aid, such as a computer, does not negate the mental and mathematical nature of said limitations at Step 2A, Prong 1 (see MPEP 2106.05(f)).
Regarding the Aug 2025 Memo, it is noted that the considerations discussed therein are already present in MPEP 2106.05(f) in regards to Step 2A, Prong 2, and Step 2B, and were considered in the analysis of the claims during the formulation of the above rejection. Applicant erroneously applies the assessment of whether the claim recites the mere idea of a solution or outcome to the entirety of the claim. The assessment is not to whether the claim itself, especially in the judicial exceptions, recites details of how a solution to a problem is accomplished, but whether the additional elements of the claim do so. In the instant claims, the additional element of the computer system is merely applied to the performance of the steps which recite judicial exceptions. The claims do not provide details for how the computer system performs these steps, just that it does. Therefore, the claims merely recite the outcome of using a computer system to perform the judicial exceptions. Second, as discussed above, the limitations of the claims are considered to recite mental processes, and the computer is included in the claim merely as a tool to perform the existing process. The functioning of the computer is not changed by the performance of the steps in the claim; therefore the functioning of the computer is not improved. Applicant’s argument that the problem of overestimating immune receptor diversity in sequencing data is not convincing because analyzing sequencing data encompasses judicial exceptions, as set forth in the above rejection, and is not a technological field which can be improved. The supposed improvement also doesn’t arise from the additional elements of the claim, which include only receiving data and the computing system, but from the judicial exceptions themselves.
The courts have made clear that a judicial exception is not eligible subject matter (Bilski, 561 U.S. at 601, 95 USPQ2d at 1005-06 (quoting Chakrabarty, 447 U.S. at 309, 206 USPQ at 197 (1980)) if there are no additional claim elements besides the judicial exception, or if the additional claim elements merely recite another judicial exception that is insufficient to integrate the judicial exception into a practical application. See, e.g., RecogniCorp, LLC v. Nintendo Co., 855 F.3d 1322, 1327, 122 USPQ2d 1377 (Fed. Cir. 2017) ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016) (eligibility "cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself."). For a claim reciting a judicial exception to be eligible, it is the additional elements (if any) in the claim that must "transform the nature of the claim" into a patent-eligible application of the judicial exception, Alice Corp., 573 U.S. at 217, 110 USPQ2d at 1981, either at Prong Two or in Step 2B. If there are no additional elements in the claim, then it cannot be eligible.
Ultimately, it is not agreed that the analysis of the claims constitutes an oversimplification of the claims to impermissibly expand the mental process grouping of judicial exceptions, but that the analysis has correctly identified that the claims merely recite mental processes at Step 2A, Prong 1, which are applied to a generic computer at Step 2A, Prong 2, and Step 2B, and are not patent eligible.
At p. 8, par. 2 through p. 9, par. 1, Applicant disagrees with the previous response that the claims are not analogous to those at issue in Synopsys 839 F.3d at 1148 because Synopsis was cited for recognizing that a method that involved "a several-step manipulation of data that, except in its most simplistic form, could not conceivably be performed in the human mind or with pencil and paper." Applicant submits that it has not been explained why the claims are not analogous to those in Synopsys.
It is respectfully submitted that this is not persuasive. In the previous reply, it was stated that Synopsys recites steps for a specific data encryption method for computer communication, which is not present in the instant claims. It is further noted that MPEP 2106.04(a)(2) points to this case as an example for a claim being directed to an abstract idea because the claims read on an individual performing the steps mentally or with pencil and paper as no computer elements were present in the claims. It is submitted that the instant claims are more analogous to this use case of Synopsys.” Applicant has not provided arguments for why Synopsys would not be relevant to provide support for interpreting the instant claims as mere mental processes applied to a computer. At MPEP 2106.04(a)(2)(III)(A), Synopsis is included as an example of a claim that does not recite mental processes because they cannot be practically performed in the human mind because it recites a claim to a specific data encryption method for computer communication involving a several-step manipulation of data. The instant claims may recite a several-step manipulation of data, but they do not recite a specific data encryption method for computer communication. There is nothing in the claims in addition to the judicial exceptions that recite a several-step manipulation of data to provide a practical application. Beyond these facts, Applicant has provided no more evidence for why Synopsis should be considered to be relevant. It is noted that ultimately the decision in Synopsys was that the “claims are directed to an abstract mental process and contain no inventive concept” and are not patent eligible under 35 USC 101.
At p. 9, par. 2 through p. 10, par. 1, Applicant submits that the claims are analogous to Example 48 because they do not recite mathematical processes. Applicant submits that Example 48 highlights the distinction between a claim which recites mathematical processes and which merely relies on mathematical processes. Applicant submits that the specific technology of Example 48 is irrelevant to their argument that the instant claims do not recite mathematical processes. Applicant submits that the previous reply did not provide a substantive reasoning why the claims recite mathematical processes. Applicant submits that the previous Office Action conceded that claim 39 does not recite a mathematical process, and that there is no evidence that directional adjacency recites a mathematical process as asserted in the rejection. Applicant submits that even directional adjacency did involve a mathematical process, the claims do not recite a mathematical concept.
It is respectfully submitted that this is not persuasive. In the previous rejection, it is stated that “Instant claim 35 at least recite “thresholding the molecular label sequences based on a distribution of the molecular label sequences such that each molecular label sequence in the corrected sequencing data is identified as a signal or noise molecular label sequence”, where examining distributions is an inherently mathematical process. It is further submitted that although the actions of claim 39 may not recite mathematical processes directly, it is noted that at least dependent claim 40 does limit the action of attributing an occurrence to using directional adjacency thresholds, which is considered to recite a mathematical process. The actions of discriminating and thresholding as recited in claim 35 are also still considered to recite a mathematical process because they, similarly to claim 40, directly recite using directional adjacency to perform these steps. Directional adjacency is an inherently mathematical process and cannot be interpreted in any different manner.” Although claim 35 has been canceled, claims 39-42 recite similar processes, including steps of comparing numbers to thresholds.
The claims recite the following limitations which recite mathematical concepts: “attributing… based on… relative abundance” in claim 39, attributing when an occurrence of the sequence is greater than or equal to a first or second directional adjacency occurrence threshold relative to the occurrence of the putative sequence or molecular label sequence and when the putative sequence has an occurrence smaller than a chimeric occurrence threshold in claim 40, attributing an occurrence of a combination sequence when the when an occurrence of the parent combination sequence is greater than or equal to a third directional adjacency occurrence threshold relative to the occurrence of the combination sequence in claim 41, and the first directional adjacency occurrence threshold is twice the occurrence of the putative sequence less one, and/or the second directional adjacency occurrence threshold is twice the occurrence of the molecular label sequence less one in claim 42 are performed using mathematical techniques as their only embodiment, as is supported by examples in the Specification, such as Hamming distance [0190]; thresholding analyses [0193]; and, generally, from [0188-0234]. While these limitations do not recite mathematical symbols, it is important to note that a mathematical concept need not be expressed in mathematical symbols. The instant claims recite words operating on data to solve a problem, which serves the same purpose as a formula (see MPEP 2106.04(a)(2)). Finally, the limitations require the use of mathematical concepts as their only embodiment for performance. There is no way to compare numbers to a threshold (i.e., another number) without performing a mathematical process. Therefore, at least these limitations explicitly recite a mathematical process.
Additionally, as set forth in the above rejection, directional adjacency is considered to recite an inherently mathematical process, as supported by the instant specification. The specification as published describes directionally adjacency as a process where occurrences of sequences are counted, clustered based on sequence similarity, and evaluated based on numerical distances [0234]. Therefore, directional adjacency, as understood by one of ordinary skill in the art, when read in light of the specification, involves the comparison of numerical descriptions of sequence similarity and abundance. It is considered that “directional adjacency” therefore also recites a mathematical process.
While these claims were not explicitly called out as reciting mathematical processes in the previous Office Action, it is not agreed that such formulation “conceded” that claims 39-42 did not recite mathematical processes. The claims that were noted in the previous Office Action were merely exemplary to show the types of limitations which recite mathematical processes. Claims 39-42 recites similar steps to those described in the previous Office Action for claims 27-30, which are now deleted, and have always been considered to recite mathematical processes. It is noted that MPEP 2106.04(I) notes that when identifying judicial exceptions, “it is sufficient for this analysis for the examiner to identify that the claimed concept (the specific claim limitation(s) that the examiner believes may recite an exception) aligns with at least one judicial exception.”.
At p. 10, par. 2 through p. 11, par. 3, Applicant disagrees with the finding in the previous rejection that, at Step 2A, Prong 2, the additional elements in the claim (receiving data, a computer system) do not provide a practical application because the improvement in the claim is provided by the additional elements in combination with the judicial exception. Applicant submits that the invention discloses an unconventional technical solution to generate corrected sequencing data which would mitigate over-estimation of immune receptor diversity when compared to sequencing data analyzed with a prior art method.
It is respectfully submitted that this is not persuasive. The claims are considered as a whole at Step 2A, Prong 2, which requires an analysis of how the additional elements contribute to the claim in relation to the judicial exception. As set forth in the above rejection, the step of receiving data merely recites a data gathering step which does not provide a practical application because the data is required by the judicial exception for its performance. The additional element of the computer system merely applies the judicial exception to a computer system and does not provide a practical application. Ultimately, neither of the additional elements in the claim are altered or affected by the performance of the judicial exceptions. It is considered that the improvement in in the claim flows from the judicial exceptions and results in improved data or results, which is not a technical field which can be improved, rather than an improvement in the additional elements of the claims. While the combination of additional elements and judicial exceptions may provide an improvement, the improvement must not flow only from the judicial exception or it must result in an improvement in the additional elements. Therefore, the instant claims are directed to a judicial exception at Step 2A, Prong 2.
MPEP 2106.05(d) sets forth that, at Step 2B, it is the additional elements which are examined to determine whether they are well-understood, routine, conventional activities previously known to the industry. The analysis at Step 2A, Prong 2, considers the claims as a whole, i.e., the additional elements in combination with the judicial exceptions (see MPEP 2106.05(a)), although the integration or improvement provided in the claim must flow from the additional elements and not the judicial exceptions to be considered persuasive. However, Step 2B requires examining only the additional elements, either alone or in combination with one another, for conventionality. An “inventive concept” is furnished by an element or combination of elements that is recited in the claim in addition to (beyond) the judicial exception, and is sufficient to ensure that the claim as a whole amounts to significantly more than the judicial exception itself (Alice Corp., 573 U.S. at 27-18, 110 USPQ2d at 1981 (citing Mayo, 566 U.S. at 72-73, 101 USPQ2d at 1966)). The limitations pointed to be Applicant are considered to recite a judicial exception as described above and are therefore not considered at Step 2B. The only additional elements in the claims, that of receiving data and of a computer system, recite conventional activities in the field and do not provide an inventive concept at Step 2B.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. 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.
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JANNA NICOLE SCHULTZHAUS whose telephone number is (571)272-0812. The examiner can normally be reached on Monday - Friday 8-4.
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/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685
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