DETAILED ACTION
Applicant’s response filed 4/29/2026 has been fully considered. The following rejections and/or objections are either reiterated or newly applied.
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 .
Claim Status
Claims 21-26 are cancelled by Applicant.
Claims 1-20 are currently pending and are herein under examination.
Claims 1-20 are rejected.
Priority
The instant application does not claim benefit of priority to any earlier filed applications. As such, the effective filing date for claims 1-20 is 05/27/2021.
Information Disclosure Statement
The IDS filed 4/29/2026 follows the provisions of 37 CFR 1.97 and has been considered in full. A signed copy of the list of references cited from this IDS is included with this Office Action.
Withdrawn Rejections
35 USC 112(b)
The rejection of claim 17 under 35 USC 112(b) is withdrawn in view of claim amendment.
35 USC 102
The rejection of claims 1-2, 5-6, 10, and 13-15 under 35 U.S.C. 102(a)(1) as being anticipated by Fritsch et al. as evidenced by Goodwine is withdrawn in view of claim amendments.
35 USC 103
The rejection of claims 3-4, 11-12 and 19-20 under 35 U.S.C. 103 as being unpatentable over Fritsch et al., as evidenced by Goodwine, in view of Mo et al. is withdrawn in view of claim amendments.
The rejection of claim 9 under 35 U.S.C. 103 as being unpatentable over Fritsch et al., as evidenced by Goodwine, in view of Stanford et al. is withdrawn in view of claim amendments.
Claim Objections
The objection to claims 13 and 20 are withdrawn in view of claim amendments.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Any newly recited portions herein are necessitated by claim amendment.
Step 1:
Step 1 asks whether the claims recite statutory subject matter. In the instant application, claims 1-4 recite a system, claims 5-12 recite a method, and claims 13-20 recite a CRM. As such, these claims recite statutory subject matter (Step 1: YES).
Step 2A, Prong 1:
Claims that recite statutory subject matter are analyzed under Step 2A, Prong 1 to determine if they recite any concepts that equate to an abstract idea, law of nature or natural phenomena. The instant claims recite the following limitations that equate to one or more categories of judicial exception:
Claim 1 recites “determine, for a subject, different peptides to be assigned to different groups of cancer vaccines for the subject, wherein each group comprises two or more different peptides; determine a peptide property of a peptide from the different peptides, the peptide property comprising at least one of: a class I immunogenicity score, a class II immunogenicity score, or an amino acid sequence length; define a first group of the different groups by assigning first peptides from the different peptides to the first group based at least in part on an assignment process, wherein: the first group has a first group property that comprises a measure of at least one of: class I immunogenicity scores, class II immunogenicity scores, or amino acid sequence lengths of the first peptides; the first group property is within a similarity range relative to a second group property of a second group from the different groups; and the assignment process comprises (i) ranking the different peptides based at least in part on the peptide property, (ii) assigning, to the first group, a highest-ranked peptide and a lowest-ranked peptide based at least in part on the ranking, and (iii) determining that assigning the first peptides to the first group results in the first group property being within the similarity range; and generate a plurality of vaccine plans by shuffling peptide assignments, each vaccine plan identifying a different assignment of the different peptides to the different groups; select a vaccine plan from the plurality of vaccine plans based at least in part on whether peptide groups of the vaccine plan satisfy a co-solubility constraint and a constraint that no peptide group includes more than one peptide having more than one cysteine in its amino acid sequence, the vaccine plan comprising the first group and the second group; and generate information indicating the vaccine plan, the information enabling manufacturing of a vaccine that includes the first group and the second group.”
Claim 2 recites “determine a sorted order of the different peptides based at least in part on individual peptide properties; associate, based at least in part on the sorted order, a first subset of the different peptides with a first tier and a second subset of the different peptides with a second tier, the peptide being a first peptide associated to the first tier; and assign, to the first group, the first peptide associated with the first tier and a second peptide associated with the second tier.”
Claim 3 recites “wherein the sorted order indicates that the first peptide has a top-ranked peptide property and the second peptide has a worst-ranked peptide property.”
Claim 4 recites “execute a combinatorial optimization algorithm configured to (i) determine potential assignments of the different peptides to the different groups, (ii) compute, for each group of the different groups, a group property based at least in part on peptide properties of peptides potentially assigned to the group, and (iii) reduce a difference between group properties of the different groups.”
Claim 5 recites “determining a peptide property of a peptide from different peptides that are to be assigned to different groups of vaccines; ranking the different peptides based at least in part on the peptide property; determining that the peptide is to be assigned to a first group from the different groups based at least in part on an assignment process, the first group having a first group property that is based at least in part on peptide properties of first peptides to be assigned to the first group, the first group property being within a similarity range relative to a second group property of a second group from the different groups, the assignment process assigning a highest-ranked peptide and a lowest-ranked peptide to the first group based at least in part on the ranking and on a determination that assigning the first peptides instead of a different set of peptides to the first group results in the first group property is within the similarity range; and generating information for a vaccine plan in which the peptide is assigned to the first group, the information enabling manufacturing of a vaccine that includes the first group and the second group.”
Claim 6 recites “determining that the different peptides are associated with a subject, wherein the different groups are assigned a same number of peptides and are defined for a cancer vaccine of the subject.”
Claim 7 recites “determining that the peptide is also assigned to the second group; and removing the second group from a candidate set of groups of vaccines.”
Claim 8 recites “determining that the second group is assigned more than one peptide having a particular amino acid; and removing the second group from a candidate set of groups of vaccines.”
Claim 9 recites “defining the different groups by assigning the different peptides to the different groups, wherein only a subset of the different groups is assigned PADRE peptides, and wherein no more than one PADRE peptide is assigned per group of the subset.”
Claim 10 recites “defining the different groups by assigning the different peptides to the different groups, wherein the different peptides comprise a neo-antigen peptide, and wherein the neo-antigen peptide is assigned to only one of the different groups.”
Claim 11 recites “determining that the peptide is a neo-antigen peptide that has a peptide property score larger than a threshold score, wherein the peptide property score comprises at least one of: a class I immunogenic response score or a class II immunogenic response score; and defining the different groups by assigning the different peptides to the different groups, wherein the neo-antigen peptide is assigned to more than one group based at least in part on the peptide property score being larger than the threshold score.”
Claim 12 recites “determining that the different peptides are associated with a subject that has a tumor in an area; determining that the peptide is a neo-antigen peptide that has a peptide property score larger than a threshold score; and associating the first group with the area based at least in part on the neo-antigen peptide being assigned to the first group.”
Claim 13 recites “determining a peptide property of a peptide from different peptides that are to be assigned to different groups of vaccines; ranking the different peptides based at least in part on the peptide property; determining that the peptide is to be assigned to a first group from the different groups based at least in part on an assignment process, the first group having a first group property that is based at least in part on peptide properties of first peptides to be assigned to the first group, the first group property being within a similarity range relative to a second group property of a second group from the different groups, the assignment process assigning a highest-ranked peptide and a lowest-ranked peptide to the first group based at least in part on the ranking and on a determination that assigning the first peptides instead of a different set of peptides to the first group results in the first group property is within the similarity range; and generating information for a vaccine plan in which the peptide is assigned to the first group, the information enabling manufacturing of a vaccine that includes the first group and the second group.”
Claim 14 recites “defining the different groups by assigning the different peptides to the different groups, wherein the different groups are assigned a same number of peptides.”
Claim 15 recites “determining a sorted order of the different peptides based at least in part on individual peptide properties; associating, based at least in part on the sorted order, a first subset of the different peptides with a first tier and a second subset of the different peptides with a second tier, the peptide being a first peptide associated to the first tier; and assigning, to the first group, the first peptide associated with the first tier and a second peptide associated with the second tier.”
Claim 16 recites “wherein the second tier is associated with second peptides having a second sorted order . . . determining an updated order of the second subset by shuffling the second sorted order; defining an updated first group based at least in part on the updated order; and associating the first group with a first vaccine plan and the updated first group with a second vaccine plan.”
Claim 17 recites “determining that each group associated with the first vaccine plan is not assigned more than one peptide having a particular amino acid; and generating information indicating that the first vaccine plan is preferred relative to the second vaccine plan.”
Claim 18 recites “wherein the first tier and the second tier are sorted in a second sorted order . . . determining an updated order of the first tier and the second tier by shuffling the second sorted order; and defining an updated first group based at least in part on the updated order.”
Claim 19 recites “determining a total number of peptides to assign to the different groups; generating a peptide set by associating the peptide with the peptide set and dissociating a second peptide from the different peptides with the peptide set, wherein a size of the peptide set is equal to the total number; defining the different groups by assigning subsets of the peptide set to the different groups; generating an updated peptide set by disassociating the peptide with the peptide set and associating the second peptide with the peptide set, wherein a size of the updated peptide set is equal to the total number; and defining additional groups by assigning subsets of the updated peptide set to the additional groups.”
Claim 20 recites “executing a combinatorial optimization algorithm configured to (i) determine potential assignments of the different peptides to the different groups, (ii) compute, for each group of the different groups, a group property based at least in part peptide properties of peptides potentially assigned to the group, and (iii) and reduce a difference between group properties of the different groups.”
Limitations reciting a mental process
The limitations in claims 1-20 of determining, defining, generating information, associating, assigning, executing a combinatorial optimization algorithm, and removing are recited at such a high level of generality that they equate to a mental process because they are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), which the courts have identified as concepts that can be practically performed in the human mind.
The broadest reasonable interpretation (BRI) of these limitations includes using a dataset of peptides with associated peptide properties to group the peptides into different groups based upon their peptide properties. The BRI also includes determining whether some groupings are within a similarity range by, for example, calculating averages of the group properties. The BRI of the assignment processor includes mental processes as it requires ranking peptides, assigning them to groups, and determining that groups are within similar ranges by comparing values. Generating vaccine plans by shuffling includes assigning different peptides to different groups, which is a mental process. Selecting a vaccine plan based on whether co-solubility and cysteine constraints are satisfied includes analyzing data derived from a manufacture to determine if the peptide groups have satisfied the requirements, particularly because there is no active step of determining co-solubility. Information can be generated by using pen and paper to list the groupings. These limitations can be practically performed by a human using pen and paper because they merely require observation, evaluation, judgement, and opinion (MPEP 2106.04(a)(2)).
A human could also practically perform a combinatorial optimization algorithm, as recited in claims 4 and 20, such as a loss function, as recited in para. [50] of the instant specification, using pen and paper. Therefore, these limitations equate to reciting a mental process.
It is also noted that the following limitation in claims 1, 5 and 13 equates to an intended use and is thus not required by the claims: “the information enabling manufacturing of a vaccine that includes the first group and the second group.”
Limitations reciting a mathematical concept
The limitations cited directly above in claims 4 and 20 equate to a mathematical concept because these limitations are similar to the concepts of organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)), which the courts have identified as mathematical concepts.
The BRI of “(ii) compute, for each group of the different groups, a group property based at least in part on peptide properties of peptides potentially assigned to the group, and (iii) reduce a difference between group properties of the different groups” includes performing calculations. Computing a group property includes calculating an immunogenicity score. Reducing a difference between group properties includes using a loss function as recited in specification para. [50].
As such, claims 1-20 recite an abstract idea (Step 2A, Prong 1: YES).
Additional Elements:
Once limitations have been identified that recite a judicial exception, the claims are evaluated for additional elements. The additional elements are then analyzed under Step 2A, Prong 2 then Step 2B. The instant claims recite the following additional elements:
Claim 1 recites “A system, comprising: one or more processors; and one or more memories storing computer-readable instructions that, upon execution by the one or more processors, configure the system to:”
Claims 2 and 4 recite “The system of claim 1, wherein the one or more memories store further computer-readable instructions that, upon execution by the one or more processors, configure the system to:”
Claim 3 recites “The system of claim 2”.
Claim 13 recites “One or more non-transitory computer-readable storage media storing instructions that, upon execution on a system, cause the system to perform operations comprising:”
Claims 14 and 15 recite “The one more non-transitory computer-readable storage media of claim 13, further storing additional instructions that, upon execution on the system, cause the system to perform operations comprising:”
Claim 16 recites “The one more non-transitory computer-readable storage media of claim 15 . . . wherein one more non-transitory computer-readable storage media store further instructions that, upon execution on the system, cause the system to perform operations comprising:”
Claim 17 recites “The one more non-transitory computer-readable storage media of claim 16 storing additional instructions that, upon execution on the system, cause the system to perform additional operations comprising”
Claim 18 recites “The one more non-transitory computer-readable storage media of claim 15 . . . and wherein one more non-transitory computer-readable storage media store further instructions that, upon execution on the system, cause the system to perform operations comprising:”
Claims 19 and 20 recite “The one or more non-transitory computer-readable storage media of claim 13, further storing additional instructions that, upon execution on the system, cause the system to perform operations comprising:”
These above recited additional elements are analyzed below under both Step 2A, Prong 2 and Step 2B:
Step 2A, Prong 2:
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exception is not integrated into a practical application because the claims do not recite additional elements that reflect an improvement to a computer, technology, or technical field (MPEP § 2106.04(d)(1) and 2106.5(a)), require a particular treatment or prophylaxis for a disease or medical condition (MPEP § 2106.04(d)(2)), implement the recited judicial exception with a particular machine that is integral to the claim (MPEP § 2106.05(b)), effect a transformation or reduction of a particular article to a different state or thing (MPEP § 2106.05(c)), nor provide some other meaningful limitation (MPEP § 2106.05(e)). Rather, the claims include limitations that equate to an equivalent of the words “apply it” and/or to instructions to implement an abstract idea on a computer (MPEP § 2106.05(f)). The paragraphs below discuss the additional elements recited above in the instant claims.
Regarding the above cited limitations in claims 1-4 and 13-20 of a system comprising one or more processors and one or more memories storing computer-readable instructions, one or more non-transitory computer-readable storage media storin instructions. There are no limitations that these systems or computer readable media require anything other than a generic computing system. As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer, which the courts have established does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984.
As such, claims 1-20 are directed to an abstract idea (Step 2A, Prong 2: NO).
Step 2B:
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). These claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because these claims recite additional elements that equate to instructions to apply the recited exception in a generic way and/or in a generic computing environment (MPEP § 2106.05(f)) and to well-understood, routine and conventional (WURC) limitations (MPEP § 2106.05(d)). The paragraphs below discuss the additional elements recited above in the instant claims.
Regarding the above cited limitations in claims 1-4 and 13-20 of a system comprising one or more processors and one or more memories storing computer-readable instructions, one or more non-transitory computer-readable storage media storin instructions. These limitations equate to instructions to implement an abstract idea on a generic computing system, which the courts have established does not provide an inventive concept in Intellectual Ventures I LLC v. Capital One Bank (USA), 792 F.3d 1363, 1367, 115 USPQ2d 1636, 1639 (Fed. Cir. 2015). Additionally, storing code on a non-transitory computer readable medium as stated in claims 13-20 equates to storing information in memory, which the courts have established as a WURC function of a generic computer in Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015).
When these additional elements are considered individually and in combination, they do not provide an inventive concept because they all equate to WURC functions/components of a generic computer and/or generic computing system and because they equate to instructions to apply the judicial exception on a generic computer. Therefore, these additional elements do not transform the claimed judicial exception into a patent-eligible application of the judicial exception and do not amount to significantly more than the judicial exception itself (Step 2B: No).
As such, claims 1-20 are not patent eligible.
Response to Arguments under 35 USC 101
Applicant's arguments filed 4/29/2026 have been fully considered but they are not persuasive.
Applicant argues improvement in vaccine manufacturing technology that cannot be achieved by using manual or heuristic methods (pg. 10, last para.) Applicant’s argument is not persuasive because:
The assignment process, generating a plurality of vaccine plans, selecting a vaccine plan, and generating information all recite mental processes. A human can practically perform these limitations as described above in section Step 2A, Prong 1. MPEP 2106.05(a) recites “the judicial exception alone cannot provide the improvement.” Thus, these abstract ideas do not integrate into a practical application.
Claims 1, 5 and 13 recite “the information enabling manufacturing of a vaccine” which is an intended use. Thus these claims do not require an active step of manufacturing the vaccines.
Applicant argues a solution to a technical problem of assigning peptides into vaccine groups for manufacture and that the solution transforms raw peptide data and predicted properties into a concrete arrangement of peptide groups used for manufacturing patient-specific vaccines, which is a transformation into a real-world utility (pg. 11, para. 1). Applicant’s argument is not persuasive because:
The limitations Applicant lists on pg. 11, para. 1 all recite a mental process. The judicial exception alone cannot provide an improvement to a technical field or other technology (MPEP 2106.05(a). MPEP 2106.05(a).II also recites “an improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology.”
Regarding argument for concrete real-world utility, MPEP 2106.I recites “eligibility should not be evaluated based on whether the claim recites a ‘useful, concrete, and tangible result’”. The instant claims analyze and organize data in the abstract. There is no requirement for generation of peptides or vaccines. The limitation of “the information enabling manufacturing of a vaccine” is an intended use, and there is no active step of manufacturing the vaccines.
Applicant argues that claims do not recite WURC limitations and that some limitations are not abstract (pg. 11, para. 2). Applicant’s argument is not persuasive because:
The assignment process and generating the vaccine plans by shuffling recite mental processes not additional elements. Only additional elements are evaluated for whether they are WURC under Step 2B. See MPEP 2106.05(d). As of record, the only additional elements in claim 1 are the system comprised of processors and memories, which equates to WURC components of a generic computer.
The BRI of selecting a vaccine plan based on whether peptide groups satisfy co-solubility and cysteine constraints includes mental processes. First, there is no requirement for an active step of testing for co-solubility. Rather, the BRI of this limitation includes determining whether a peptide group satisfied a co-solubility by analyzing data from a manufacturer that previously tested for co-solubility, as described in specification para. [33]. Second, the BRI of satisfying a cysteine constraint includes counting cysteines in an amino acid, which is a mental process. Third, claim 1 does not require that the vaccine be manufactured based on these requirements. Rather, claim 1 recites an intended use of enabling manufacture.
Applicant argues that the claims are not mere instructions to implement an abstract idea on a computer (pg. 11, para. 2). Applicant’s argument is not persuasive because:
The additional elements in claim 1 are a system comprised of processors and memories configured to perform abstract ideas. This equates to mere instructions to implement an abstract idea on a generic computer which does not integrate the judicial exception into a practical application or provide significantly more. See MPEP 2106.05(f).
Applicant argues that the claims do not preempt all forms of peptide grouping or vaccine design but are limited to a specific computational process for generating groupings according to defined criteria (pg. 11, para. 2). Applicant’s argument is not persuasive because:
Although claim 1 may not preempt all forms of peptide grouping or vaccine design, it is still ineligible after evaluation under the Alice/Mayo test. MPEP 2106.04.I recites “While preemption is the concern underlying the judicial exceptions, it is not a standalone test for determining eligibility … Instead, questions of preemption are inherent in and resolved by the two-part framework from Alice Corp. and Mayo … It is necessary to evaluate eligibility using the Alice/Mayo test, because while a preemptive claim may be ineligible, the absence of complete preemption does not demonstrate that a claim is eligible.” Diamond v. Diehr, 450 U.S. 175, 191-92 n.14, 209 USPQ 1, 10-11 n.14 (1981) ("We rejected in Flook the argument that because all possible uses of the mathematical formula were not pre-empted, the claim should be eligible for patent protection").
Conclusion
No claims are allowed.
Claims 1-20 are free from the prior art because the prior art does not fairly teach or suggest the following limitations: in claim 1 “(ii) assigning, to the first group, a highest-ranked peptide and a lowest-ranked peptide based at least in part on the ranking, and (iii) determining that assigning the first peptides to the first group results in the first group property being within the similarity range.” In claim 5 “assigning a highest-ranked peptide and a lowest-ranked peptide to the first group based at least in part on the ranking and on a determination that assigning the first peptides instead of a different set of peptides to the first group results in the first group property being within the similarity range.” In claim 13 “assigning a highest-ranked peptide and a lowest-ranked peptide to the first group based at least in part on the ranking and on a determination that assigning the first peptides instead of a different set of peptides to the first group results in the first group property being within the similarity range.” The closest prior art is Fritsch et al. (“Fritsch”; US 2016/0310584 A1; US App. No. 2 cited on IDS filed 10/03/2022; previously cited) and Mo et al. (“Mo”; US 2023/0338491 A1; effective filing date 03/08/2021; previously cited on PTO892 mailed 4/4/2025).
Fritsch formulates peptide vaccines, wherein each vaccine contains a pool of peptides [514]. Peptides are predicted to bind specific HLA alleles wherein the peptides are grouped based upon their predicted binding [442-452]. However, Fritsch does not generate top-ranked and worst-ranked peptides. Mo screens individualized tumor neoantigen peptides and vaccines then arranges peptides in descending order according to their immunogenic score, wherein peptides are selected for a vaccine from top to bottom (abstract). However, Fritsch in view of Mo does not render obvious assigning into the same vaccine a top-ranked and worst-ranked property predicted peptide, wherein the assignment of the ranked peptides, instead of assignment of other peptides, results in a first group property being within a similarity range of another group property.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/N.A.A./Examiner, Art Unit 1687
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685
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