DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restriction
Applicants’ election without traverse of Group I drawn to claims 1, 2, 5, 7, 8, 10, 11, 12, 16, 19, 21-24, 27, 30, and 34, filed 11/06/2025 is acknowledged. Applicants’ election without traverse of Species I drawn to claim 2, filed 11/06/2025 is acknowledged.
Claims 19, 21, 23, 24, 27, 36, 39, and 42 are hereby withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Status of Claims
Claims 1, 2, 5, 7, 8, 10, 11, 12, 16, 30, and 34 are under examination.
Claims 3, 4, 6, 9, 13-15, 17, 18, 20, 25, 26, 28, 29, 31-33, 35-42 are cancelled via applicant’s amendment. Claims 19, 21, 23, 24, 27 are withdrawn.
Priority
Applicant’s claim for the benefit of priority under 35 U.S.C. 119(a)-(d) is acknowledged. This application is the National Stage filing under 35 USC 371 of PCT/US2022/015275, filed 02/04/2022 and claims priority to earlier filed Provisional Application No. 63/146,392, filed 02/05/2021. Receipt is acknowledged of papers submitted under 35 U.S.C. 119(a)-(d), which papers have been placed of record in the file.
Drawings
The drawings filed 03/25/2022 are acceptable.
Information Disclosure Statement(s)
The information disclosure statement (IDS) document(s) submitted on 06/29/2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS document(s) has/have been fully considered by the examiner.
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, 2, 5, 7, 8, 10, 11, 12, 16, 30, and 34 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
The United States Patent and Trademark Office published revised guidance on the application of 35 U.S.C. § 101. USPTO’s 2019 Revised Patent Subject Matter Eligibility Guidance (“Guidance”). Under the Guidance, in determining what concept the claim is “directed to,” we first look to whether the claim recites:
(1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human activity such as a fundamental economic practice, or mental processes) (Guidance Step 2A, Prong 1); and
(2) additional elements that integrate the judicial exception into a practical application (see MPEP § 2106.05(a)-(c), (e)-(h)) (Guidance Step 2A, Prong 2).
Only if a claim (1) recites a judicial exception and (2) does not integrate that exception into a practical application, do we then look to whether the claim contains an “‘inventive concept’ sufficient to ‘transform’” the claimed judicial exception into a patent-eligible application of the judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82). In so doing, we thus consider whether the claim:
(3) adds a specific limitation beyond the judicial exception that are not “well-understood, routine and conventional in the field” (see MPEP § 2106.05(d)); or 2019 Revised Patent Subject Matter Eligibility Guidance, 84 Fed. Reg. 50-57 (January 7, 2019).
(4) simply appends well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception.(Guidance Step 2B). See Guidance, 84 Fed. Reg. at 54-56.
Guidance Step 1:
The instant invention (claim 1 being representative) is directed to a method for ranking tumor-specific neoantigens that performs a series of processes. Thus, the claims are directed to one of the statutory categories of invention. MPEP 2106.03.
A. Guidance Step 2A, Prong 1
The Revised Guidance instructs us first to determine whether any judicial exception to patent eligibility is recited in the claim. The Revised Guidance identifies three judicially-excepted groupings identified by the courts as abstract ideas: (1) mathematical concepts, (2) certain methods of organizing human behavior such as fundamental economic practices, and (3) mental processes. Regarding claim(s) 1, the claimed steps that are part of the abstract idea are as follows:
b) for an individual somatic mutation in the plurality of somatic mutations: i) determining a best short neoantigen from an initial plurality of short neoantigens based at least in part on an immunogenicity score of the best short neoantigen; ii) determining a best long neoantigen from an initial plurality of long neoantigens based at least in part on an immunogenicity score of the best long neoantigen; iii) adding the best short neoantigen to a list of short neoantigen candidates; and iv) adding the best long neoantigen to a list of long neoantigen candidates;
c) performing step b for the plurality of somatic mutations, wherein the list of short neoantigen candidates when completed includes the respective best short neoantigens for the plurality of somatic mutations, and wherein the list of long neoantigen candidates when completed includes the respective best long neoantigens for the plurality of somatic mutations;
d) ranking the list of short neoantigen candidates by descending immunogenicity score; e) ranking the list of long neoantigen candidates by descending immunogenicity score.
Mental Processes
Under the broadest reasonable interpretation, the above italicized steps amount to observing data, manipulating data (via scoring), and ordering/ranking the data. Notably, claims do not impose any boundaries on how the italicized functions are actually being achieved. In addition, the instant specification describes mathematical equations associated with at least some of the claimed functions [0040-0057]. As such, the specification provides sufficient evidence that the claims are directed to an abstract idea since the specific descriptions provided for accomplishing these tasks include only data reception and analysis. Accordingly, the above steps clearly fall within the mental process groupings of abstract ideas because they cover concepts performed in the human mind, including observation, evaluation, judgment, and opinion. See MPEP 2106.04(a)(2), subsection III [Step 2A, Prong 1: YES].
B. Guidance Step 2A, Prong 2
This part of the eligibility analysis evaluates whether the claim as a whole integrates the recited judicial exception into a practical application of the exception or whether the claim is “directed to” the judicial exception. This evaluation is performed by (1) identifying whether there are any additional steps/elements recited in the claim beyond the judicial exception, and (2) evaluating those additional steps/elements individually and in combination to determine whether the claim as a whole integrates the exception into a practical application. See MPEP 2106.04(d).
The additional steps/elements recited in the claim beyond the judicial exception are as follows: a) identifying a plurality of somatic mutations present in the tumor;
In this case, this step is recited at a high of generality (without any details regarding how it is being performed) and results in nothing more than collecting data for use by the abstract idea. Accordingly, this step amounts to insignificant extra-solution activity and is not indicative of an integration into a practical application. See MPEP 2106.05(g). See MPEP 2106.04(d)(1) for a list of considerations when evaluating whether additional elements integrate a judicial exception into a practical application. [Step 2A, Prong 2: NO].
C. Guidance Step 2B:
This part of the eligibility analysis evaluates whether the claim as a whole amount to significantly more than the recited exception i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim. See MPEP 2106.05. In addition, a review of the specification teaches routine and conventional sequencing method for determining mutations [0023-0026, 0063-0065]. Therefore, even upon reconsideration, there is nothing unconventional with regards to the above non-abstract step. See MPEP 2106.05(d)(Part II). Thus, the independent claim(s) as a whole do not amount to significantly more than the exception itself. Therefore, the claim(s) is/are not patent eligible. [Step 2B: NO].
D. Dependent Claims
Dependent claims 2, 5, 7, 8, 10, 11, 12, 16, 30, and 34 have also been considered under the two-part analysis but do not include additional steps/elements appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception(s) for the following reasons. In particular, claims 2, 5, 7, 8, 10, 11, 12, 16, 30, and 34 are entirely directed to limitations that further limit the specificity of the abstract idea or the type of data being used by the abstract idea. Accordingly, these claims are also directed to an abstract idea for the reasons set forth above (Step 2A, prong 1, analysis). Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea without significantly more.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), first paragraph:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same and shall set forth the best mode contemplated by the inventor of carrying out his invention.
This is a written description rejection.
Claims 1, 2, 5, 7, 8, 10, 11, 12, 16, 30, and 34 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement.
The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The written description requirement is separate and distinct from the enablement requirement. The specification must: (1) describe the claimed invention in a manner understandable to a person of ordinary skill in the art, and (2) show that the inventor actually invented the claimed subject matter.
Regarding claim(s) 1, the specification fails to provide written description support for the following steps:
b) for an individual somatic mutation in the plurality of somatic mutations: i) determining a best short neoantigen from an initial plurality of short neoantigens based at least in part on an immunogenicity score of the best short neoantigen; ii) determining a best long neoantigen from an initial plurality of long neoantigens based at least in part on an immunogenicity score of the best long neoantigen; iii) adding the best short neoantigen to a list of short neoantigen candidates; and iv) adding the best long neoantigen to a list of long neoantigen candidates;
c) performing step b for the plurality of somatic mutations, wherein the list of short neoantigen candidates when completed includes the respective best short neoantigens for the plurality of somatic mutations, and wherein the list of long neoantigen candidates when completed includes the respective best long neoantigens for the plurality of somatic mutations;
With regards to the claimed “determining” steps (b and c), it is unclear how the “best short neoantigen” and “best long neoantigen” are being determined. The claim does not recite any particular operations or functions for achieving the claimed results, e.g. equations for calculating scores or criteria for determining optimal neoantigens. A review of the specification teaches probability-based equations for calculating a short score [0045-0052]. However, these limitations are not commensurate in scope with what is being claimed and it is improper to import narrowing limitations into the claims. MPEP 2111.01. In other words, the claimed method is essentially a black box for determining optimal “best short” and “best long” neoantigens. In addition, one of ordinary skill in the art would recognize that methods for determining optimal “neoantigens” are not trivial. For example, Gopanenko et al. (Cancers 2020, 12, 2879, pp.1-28) teaches methods for identifying neoantigens. Unlike the claimed method, which is not limited to any particular computational acts or algorithms, Gopanenko teaches that elaborate bioinformatics pipelines are required to overcome all the obstacles involved in selecting the best neoantigen candidates [page 3, ¶1, page 4, ¶3, page 5, ¶3, and Figure 1] and further teaches that scoring and ranking candidate peptides (i.e. neoantigens) based on identified variants requires using specific tools (e.g. MHC binding estimators or affinity binding methods) [Figure 1 and page 8, ¶1]. Therefore, given the breadth of what is claimed, the specification does not provide sufficient written description such that one of skill in the art would have been aware that applicants were actually in possession of computational methods/techniques configured to perform the full scope of what is being claimed.
Regarding claim(s) 5, 8, 10, 11, 12, 16, these claims are directed to determining a probability based on an individual allele being present in at least one neoantigen in the set of short neoantigens or based on data from an MHC Class II machine learning model. However, in each case, it is unclear how these scores are actually being determined as the claims do not recite any particular equations, parameters, or prose equivalent for achieving the claimed results. Moreover, one of ordinary skill in the art would recognize that the development of machine learning models for calculating probabilities as claimed is not trivial. For example, Wu et al. (Front. Immunol., 31 October 2019, pp.1-11) teaches deep learning methods for predicting neoantigens. Unlike the claimed method, Wu teaches using particular HLA binding data and immunogenicity data for training and validating well-defined machine learning models [See entire]. At best, the specification teaches a limited embodiment of probability-based equations for calculating immunogenicity scores [0045-0052]. However, these limitations are not commensurate in scope with what is being claimed and it is improper to import narrowing limitations into the claims. MPEP 2111.01. Therefore, given the breadth of what is claimed, the specification does not provide sufficient written description such that one of skill in the art would have been aware that applicants were actually in possession of computational methods/techniques configured to perform the full scope of what is being claimed.
For the reasons discussed above, the specification does not satisfy the written description requirement with respect to the full scope of what is being claimed. For more information regarding the written description requirement, see MPEP §2161.01- §2163.07(b).
Claim rejections - 35 USC § 112, 2nd Paragraph
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 2, 5, 7, 8, 10, 11, 12, 16, 30, and 34 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 pre-AIA the applicant regards as the invention. Claims that depend directly or indirectly from claim(s) 1 are also rejected due to said dependency.
Claim 1 recites “b) for an individual somatic mutation in the plurality of somatic mutations: i) determining a best short neoantigen from an initial plurality of short neoantigens based at least in part on an immunogenicity score of the best short neoantigen”. (1) It is unclear as to the metes and bounds of the term “immunogenicity score.” Neither the claim nor the specification provides any limiting definition that would serve to clarify the scope. Clarification is requested via amendment. (2) It is unclear in what way “determining” a best short neoantigen is “…based at least in part on an immunogenicity score of the best short neoantigen” such that the artisan would recognize what computational operations are encompassed. A review of the specification teaches an equation for calculating a short score [0045]. However, is improper to import narrowing limitations into the claims. MPEP 2111.01. Moreover, the claim does not recite any positive process limitation for calculating “immunogenicity scores” (or length scores) such that a determining of “best short” neoantigens can be made (i.e. the claim purport to be making a determination based on scores that have not been previously obtained). (3) As a result, the claim is also rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential steps/elements, such omission amounting to a gap between the steps. See MPEP § 2172.01. The omitted steps/elements appear to be directed to calculating scores associated with neoantigen length and/or immunogenicity. Clarification is requested via amendment. (4) The phrase “the best short neoantigen” is indefinite. The term "best short" is not defined by the claim and the specification does not provide a standard or criteria such that one of ordinary skill in the art would know the metes and bounds of “best short” neoantigens. Clarification is requested via amendment.
Claim 1 recites “ii) determining a best long neoantigen from an initial plurality of long neoantigens based at least in part on an immunogenicity score of the best long neoantigen.” This phrase is problematic for the following reasons. (1) It is unclear as to the metes and bounds of the term “immunogenicity score.” Neither the claim nor the specification provides any limiting definition that would serve to clarify the scope. Clarification is requested via amendment. (2) It is unclear in what way “determining a best long neoantigen is “…based at least in part on an immunogenicity score of the best long neoantigen” such that the artisan would recognize what computational operations are encompassed. A review of the specification teaches an equation for calculating a long score [0049]. However, is improper to import narrowing limitations into the claims. MPEP 2111.01. Moreover, the claim does not recite any positive process limitation for calculating “immunogenicity scores” such that a determining of “best long” neoantigens can be made (i.e. the claim purport to be making a determination based on scores that have not been previously obtained). (3) As a result, the claim is also rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential steps/elements, such omission amounting to a gap between the steps. See MPEP § 2172.01. The omitted steps/elements appear to be directed to calculating scores associated with neoantigen length and/or immunogenicity. Clarification is requested via amendment. (4) The phrase “the best long neoantigen” is indefinite. The term "best long" is not defined by the claim and the specification does not provide a standard or criteria such that one of ordinary skill in the art would know the metes and bounds of “best long” neoantigens. Clarification is requested via amendment.
Claim 1 recites “c) performing step b for the plurality of somatic mutations, wherein the list of short neoantigen candidates when completed includes the respective best short neoantigens for the plurality of somatic mutations, and wherein the list of long neoantigen candidates when completed includes the respective best long neoantigens for the plurality of somatic mutations.” The previously recited “step b)” requires determining a “best short neoantigen” and “best long neoantigen” for an individual somatic mutation in the plurality of somatic mutations. Therefore, it is unclear in what limiting effect is intended by “step c)” because it overlaps the same subject matter performed in “step b)” in at least one embodiment (e.g. for the “single” somatic mutation encompassed within the “plurality of somatic mutations”)”. In other words, “step c)” encompasses determining the “best short neoantigens” and “best long neoantigens” for the individual somatic mutation as well as the other remaining somatic mutations. Clarification is requested via amendment.
Claim 5 recites “wherein the probability is determined at least in part based on data from an MHC Class I machine learning model trained to determine a probability that a given allele in the plurality of HLA class I alleles presents a certain antigen”. In this case, there is lack of antecedent basis for “an MHC Class I machine learning model” since this feature has not been previously introduced (e.g. for generating data) and is not inherent to the process of determining a probability score. As a result, it is also unclear what limiting effect is intended by the above clause, i.e. in what way is the probability “based on data from an MHC Class I machine learning model” such that the artisan would recognize what computational operations are intended. A review of the specification [0041] merely reiterates the claim language and does not provide any additional guidance. Applicant is reminded that limitations directed to the nature of the data, per se, do not impose any actual boundaries on the scope of the claim. Clarification is requested via amendment.
Claim Rejections - 35 USC § 103
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 (i.e., changing from AIA to pre-AIA ) 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.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 2, 7, 30, and 34 are rejected under 35 U.S.C. 103 as being unpatentable over Nicosia et al. (WO 2020099614 A1; Pub. Date: 2020-05-22) in view of Biskbup et al. (WO 2020/043805; File Date: 08/28/2019; Pub. Date: 03/05/2020).
Nicosia teaches a method for selecting cancer mutations for generation of a personalized vaccine [Abstract].
Regarding claim(s) 1, Nicosia teaches identifying a plurality of neoantigens in a sample of cancerous cells obtained from an individual and determining the mutation allele frequency of each mutations within the coding sequence for each neoantigen [ref. claim 1, step a and b], which broadly reads on identifying a plurality of somatic mutations since the artisan would recognize that neoantigens are directly generated from somatic mutations. Nicosia teaches determining allele frequency values and binding affinity values associated with said neoantigens [ref. claim 1, steps b and d], which are broadly interpreted as immunogenicity scores absent any limiting definition to the contrary. Nicosia teaches ranking neoantigens based on these values [ref. claim 1, step e], which broadly reads on determining best neoantigens based on immunogenicity scores for the plurality of mutations (which includes an individual mutation).
Nicosia does not specifically teaches determining best long and best short neoantigens, as in claim 1 (steps b and c). However, Nicosia teaches the above analysis includes ranking neoantigens consisting of amino acids with lengths covering 9 amino acids (i.e. short) to 40 amino acids (i.e. long) [ref. claim 1, step e], which at a minimum suggests determining the optimal short and long neoantigens absent any limiting definition to the contrary (and in view of the rejection under 35 USC 112b).
Furthermore, Biskup teaches methods for ranking and selecting tumor-specific neoantigens [Abstract] that include filtering out neoantigens based various parameter including binding affinity and length [ref. claim 8]. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to alter the method of Nicosia by additionally determining the best long or short neoantigens, as claimed, since methods for identifying long and short neoantigens were routine and conventional in the art, as taught by Biskup. The motivation would have been to improve the speed and accuracy of neoantigen selection by grouping short and long candidates.
Nicosia additionally teaches calculating rank sums from first, second, and third ranked lists of neoantigens from highest to lowest based on said binding affinity scores and selecting optimal neoantigens from said ranked list [ref. claim 1, steps f and g], which reads on ranking the list of long and short neoantigens by descending score as claimed.
Regarding claim(s) 2, Nicosia and Biskup makes obvious the feature of identifying shortest from longest neoantigens (for reasons set forth above); and Nicosia additionally teaches determining binding scores (i.e. neoantigen-allele scores) for the plurality of HLA class alleles [ref. claim 3]. Regarding claim(s) 7, Nicosia does not specifically teach removing short neoantigens with a lower score. However, Biskup explicitly teaches methods for filtering (i.e. removing) neoantigens based on length [ref. claim 8]. Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to alter the method of Nicosia by additionally removing short neoantigens that are low-scoring, as claimed, since Biskup teaches method for removing short (or long) neoantigens and since both Nicosia and Biskup teach methods for scoring neoantigens. The motivation would have been to improve the accuracy of neoantigen selection by removing sub-optimal candidates.
Regarding claim(s) 30, 34, Nicosia teaches determining MHC class binding affinity scores (i.e. neoantigen-allele scores) of the plurality of neoantigens [ref. claim 3], as claimed. Nicosia does not specifically teaches determining long and best short neoantigens, as claimed. However, as discussed above, Nicosia at a minimum suggests this feature because their analysis includes ranking neoantigens derived from tumors that consisting of amino acids with lengths covering 9 amino acids (i.e. short) to 40 amino acids (i.e. long) [ref. claim 1, step e].
Citation of Relevant Prior Art
The prior art made of record and not relied upon is considered pertinent to applicant' s disclosure.
Angiuoli et al. (US 20190189242 A1), which teaches a machine learning system and method for somatic mutation discovery are provided that provides improved identification of tumor-specific mutations.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to PABLO S WHALEY whose telephone number is (571)272-4425. The examiner can normally be reached between 1pm-9pm EST.
If attempts to reach the examiner by telephone are unsuccessful, the examiner's supervisor, Anita Coope can be reached at 571-270-3614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/PABLO S WHALEY/Primary Examiner, Art Unit 3619