DETAILED ACTION
This is a FINAL Office Action (“Action”) in reply to the response filed Aug. 17, 2026 (“Aug. Resp.”). In the Aug. Resp. claims 1-9, 16, and 41-44 are pending. The following is a status listing of the pending claims:
Claim 1-9, 16, and 41-44 are rejected under 35 U.S.C. § 112(a) for lack of written description.
Claims 1-9, 16, and 41-44 are rejected under 35 U.S.C. § 112(b) as indefinite.
Claims 1-9, 16, and 41-44 are rejected under 35 U.S.C. § 101 as being directed to patent ineligible subject matter.
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 .
Response to Arguments and Amendments
Applicant responds to the previously presented 35 U.S.C. §§ 112(b) and 101 claim rejections. Notwithstanding any specific argument against a particular limitation, the claims have been amended in the Aug. Resp. to overcome the section 112(b) and 101 claim rejections. See Aug. Resp. at 7 and 9. Since these amendments have not yet been considered, any specific argument is addressed in the updated rejections below in light of the Aug. Resp. claim amendments. Additionally, the claim amendments raise additional issues as also presented below.
Claim Objections
Claims 1-9, 16, and 41-44 are objected to for the following reasons, where claims 3-9, 16, and 41-44 are objected only for their dependencies from respective claims 1 and 2.
Claim 1
Claim 1 should be amended for clarity as follows, for example:
a) sequencing [[the]] first circulating tumor DNA from a first biological sample of a subject before administration of the immunogenic composition to generate first circulating tumor DNA sequence data;
b) sequencing second circulating tumor DNA from a second biological sample of a subject after administration of the immunogenic composition to generate second circulating tumor DNA sequence data.
Additionally, the words “and” should be inserted after step “d)” but before step “e)”.
Any changes made to the limitations of at least claim 1 are notwithstanding the 35 U.S.C. §§ 112(a) and (b) rejections below, and should also be propagated throughout the entirety of the claims as necessary, as should any changes made to overcome the section 112(a) and (b) rejections. Appropriate correction is required.
Claim 2
Claim 2, step “g)” was amended in the Aug. Resp. to include additional limitations but these newly added limitations were not underlined. As a result, claim 2 is objected to for improper claim amendment formatting. See MPEP § 714; see also 37 CFR § 1.121(c). Despite this objection, the claims are nonetheless entered and any subsequent claim amendments should be based on the claims filed in the Aug. Resp. as they were filed.
Claim Rejections – 35 USC § 112(a) – Lack of Written Description
The following is a quotation of the first paragraph 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.
Claims 1-9, 16, and 41-44 are rejected under 35 U.S.C. § 112(a) as failing to comply with the written description requirement.
Claims 1-9, 16, and 41-44 contain 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 at the time the application was filed had possession of the claimed invention.
Claim 1 has been amended to recite, in part:
a) sequencing the circulating tumor DNA from a biological sample of a subject before administration of the immunogenic composition to generate circulating tumor DNA sequence data;
b) sequencing circulating tumor DNA from a biological sample of a subject after administration of the immunogenic composition to generate circulating tumor DNA sequence data; and
c) analyzing the circulating tumor DNA sequence data to quantify one or more ctDNA mutations in the circulating tumor DNA encoding one or more tumor-specific neoantigens in the immunogenic composition and generating a numerical probability score of the prevalence of each tumor-specific neoantigen before and after administration of the immunogenic composition using a machine learning platform;
…
d) generating an individual score of each tumor-specific neoantigen based on the predicted response of specific CD8+ T cells or CD4+ T cells using a machine learning model.
Claim 2 has been amended to recite, in part:
c) analyzing the circulating tumor DNA sequence data to quantify one or more ctDNA mutations in the circulating tumor DNA encoding one or more tumor-specific neoantigens;
…
e) generating an individual score of each tumor-specific neoantigen based on the predicted response of specific CD8+ T cells or CD4+ T cells using a machine learning model.
Applicant points to paragraphs [0025], [0026], [0029], [0044]-[0055], [0058], and [0148] of the specification, which is assumed to be the specification as filed and not the U.S. Patent Application Publication having number 2024/0360515. See Aug. Resp. at 6, §I. Looking at these sections in light of the rest of the specification, at least the limitations noted above do not have adequate written description support in the specification as originally filed.
With respect to claim 1, limitations “a)” through “c)” require “sequencing circulating tumor DNA” of two different “biological samples,” one “before administration of [an] immunogenic composition” and one after to “generate [respective] circulating tumor DNA sequence data,” and then “analyzing the circulating tumor DNA sequence data to quantify one or more ctDNA mutations in the circulating tumor DNA encoding one or more tumor-specific neoantigens.” In other words, to satisfy the written description requirement, the specification as filed must show possession of a single embodiment describing the corresponding steps “before” and “after” administration of the immunogenic composition and “quantify[ing] ctDNA mutations” and “encoding one or more tumor-specific neoantigens.” However, none of the cited paragraphs or any other part of the specification as filed describes an embodiment in which a biological sample is taken before administration of the immunogenic composition and one that is taken after for comparison to the one taken before.
For example, paragraph [0025] states, with emphasis:
The approach begins with sequencing circulating tumor DNA from a biological sample of a subject. The subject may have been previously administered an immunogenic composition. Alternatively, the subject will be administered an immunogenic composition.
The subsequent and additional descriptions in the specification also only focus on one biological sample. There is no discussion of taking more than one biological sample and comparing analysis or assignment of numerical probability scores based on these samples. Since there is no single embodiment that embodies all the limitations of at least claim 1, the proposed claim amendments result in claim 1 having a lack of written description under section 112(a). See MPEP § 2163; see also UMC Elecs. Co. v. United States, 816 F.2d 647, 652, 2 USPQ2d 1465, 1468 (Fed. Cir. 1987) (“[T]here cannot be a reduction to practice of the invention ... without a physical embodiment which includes all limitations of the claim.”).
Additionally, while the specification links the cellular prevalence with the tumor-specific neoantigens in the circulating tumor DNA (see e.g., Spec. as filed ¶¶[0009], [0045]), there does not appear to be any description linking the quantity of “ctDNA mutations” with “one or more tumor-specific neoantigens in the immunogenic composition,” as recited in claim 1. (Emphasis added.) Moreover, it is not entirely clear what it means to, nor does there appear to be any description in the specification of “quantify[ing] one or more ctDNA mutations in the circulating tumor DNA encoding one or more tumor-specific neoantigens,” as recited in claims 1 and 2, such that the quantifying the ctDNA mutations somehow results in “encoding one or more tumor-specific neoantigens.” As a result, this limitation also does not appear to have adequate written description support under section 112(a) in the original specification as filed.
Claims 1 and 2 recite, “generating an individual score of each tumor-specific neoantigen based on the predicted response of specific CD8+ T cells or CD4+ T cells using a machine learning model.” Paragraphs [0057], [0068], and [0077] are the only parts of the specification that mention CD8+ and CD4+ T cells. None of these paragraphs, however, described “generating an individual score of each tumor-specific neoantigen based on the predicted response of specific CD8+ T cells or CD4+ T cells.” Moreover, none of these paragraphs discuss any “predicted response of specific CD8+ T cells or CD4+ T cells” or using such predicted responses in a machine learning model. As a result, this limitation also does not appear to have adequate written description support under section 112(a) in the original specification as filed.
The remaining claims 3-9, 16, and 41-44 depend directly or indirectly from either claims 1 or 2. Thus, these claims have the same features of claims 1 and 2, including those that do not have adequate written description support in the specification as originally filed.
For at least these reasons, claims 1-9, 16, and 41-44 are rejected under section 112(a) for lacking proper written description.
If Applicant believes there is adequate written description support, it is respectfully requested that these portions of the specification be particularly pointed out and discussed in any subsequent response.
Claim Rejections - 35 USC § 112(b) – Indefiniteness
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.
Claims 1-9, 16, and 41-44 are rejected under 35 U.S.C. § 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claims 1 and 2: New Limitations
Claim 1 recites, among other limitations, “analyzing the circulating tumor DNA sequence data to quantify one or more ctDNA mutations in the circulating tumor DNA encoding one or more tumor-specific neoantigens in the immunogenic composition.” Claim 2 recites, “analyzing the circulating tumor DNA sequence data to quantify one or more ctDNA mutations in the circulating tumor DNA encoding one or more tumor-specific neoantigens.” As explained above, there is no description in the specification that appears to link “quantify[ing] circulating tumor DNA sequence data” with “encoding one or more tumor-specific neoantigens.” There is also no description of what it means to “encode” tumor-specific neoantigens. Thus, it is unclear how this limitation should be interpreted. Additionally, the specification seems to describe the “tumor-specific neoantigens” as coming from the biological sample, not “the immunogenic composition,” as recited in claim 1. As such, claim 1 is additionally indefinite for this reason.
For the reasons above, claims 1 and 2 are indefinite.
Claim 1: Numerical Probabilities
Claim 1 recites, among other limitations:
wherein a higher numerical probability score relative to a low numerical probability score indicates that the one or more tumor-specific neoantigens is present in the circulating tumor DNA and that the one or more tumor-specific neoantigens has a lower prevalence in a tumor of the subject relative to before administration of the immunogenic composition; and
wherein a lower numerical probability score relative to a higher numerical probability score indicates that the one or more tumor specific neoantigens is present in a low amount or not present in the circulating tumor DNA and that the one or more tumor-specific neoantigens has a higher prevalence in the tumor of the subject relative to before administration of the immunogenic composition.
As explained in the prior non-final Office action, the terms “higher” and “lower” are relative terms, but the claims do not provide any context on what would constitute a “higher” or “lower” probability score other than comparison against another score. However, the claim does not actively recite or link any two scores for comparison. It is not clear from the claim language which two scores would be compared to determine whether they are “higher” or “lower” than the other. For example, it is not clear if there are two sets of probability scores generated for each tumor-specific neoantigen, one set for before administration of the immunogenic composition and one set for after. Even if the claims did require numerical probabilities for each set (i.e., “before administration” and “after administration” sets), it is not clear which probability scores are compared to each other. The claims are silent whether the comparison is of scores from the same set, different sets, or whether the scores are compared for the same tumor-specific neoantigens or not. Thus, it is not clear from the claim language what exactly would constitute a “higher” or “lower” score. For at least this reason, claim 1 is indefinite.
Claim 1: Antecedent Basis
Claim 1 recites the limitation “analyzing the circulating tumor DNA sequence data,” but there are two previously recited instances of “circulating tumor DNA sequence data” that this limitation may be referencing. Thus, this limitation lacks a clear antecedent basis and should be amended for clarity.
Dependent Claims 3-9, 16, and 41-44
Claims 3-9, 16, and 41-44 depend directly or indirectly from either claims 1 or 2, thus, they have the same limitations as either claims 1 or 2. And since none of claims 3-9, 16, and 41-44 resolve the section 112(b) indefiniteness issues noted above, they too are rejected as indefinite under section 112(b) for the same reasons as claims 1 and 2.
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 1-9, 16, and 41-44 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
To determine whether claimed subject matter is patent eligible section 2106 of the MPEP requires specific evaluation of the limitations recited. In step 1, a determination is made as to whether a claim is directed to a statutory category (i.e., a process, machine, manufacture, and composition of matter). If so, then a determination is made as to whether the claim is directed to patent ineligible subject matter, such as an abstract idea, using a three part test: First, in step 2A, prong 1 the abstract idea is identified; Second, in step 2A, prong 2 the abstract idea is determined to be integrated into a practical application or not; and Third, in step 2B the additional claim limitations are evaluated individually and as a whole to determine if they amount to an inventive concept (i.e., determining whether the limitations are significantly more than the abstract idea itself).
While the claims fall within at least one of the four statutory categories of patent eligible subject matter (i.e., step 1 is satisfied because independent claims 1 and 2 are directed to processes and the remaining claims all depend from these claims), they are nonetheless patent ineligible for being directed to an abstract idea without reciting significantly more.
Initially, the following explanation is based not only on the guidance in the MPEP, but also the “2024 Guidance Update on Patent Subject Matter Eligibility, Including on Artificial Intelligence,” published on July 17, 2024 (89 FR 58128) (AI-SME Update). Moreover, the Office has provided examples of patent ineligible subject matter that are relevant to the claimed subject matter of this application. In particular, example 491, is relevant to the discussion below of claims 1-9, 16, and 41-44 and should be reviewed for further guidance and support of the determination that these claims are directed to patent ineligible subject matter.
Step 2A, Prong 1: Independent Claims 1 and 2
Claims 1 and 2 recite limitations directed to an abstract idea, specifically the recitation of mathematical concepts and mental processes. See MPEP 2106.04(a)(2), subsections I and III.
Claim 1 recites in its entirety:
A method for evaluating the efficacy of an immunogenic composition, comprising:
a) sequencing the circulating tumor DNA from a biological sample of a subject before administration of the immunogenic composition to generate circulating tumor DNA sequence data;
b) sequencing circulating tumor DNA from a biological sample of a subject after administration of the immunogenic composition to generate circulating tumor DNA sequence data;
c) analyzing the circulating tumor DNA sequence data to quantify one or more ctDNA mutations in the circulating tumor DNA encoding one or more tumor-specific neoantigens in the immunogenic composition and generating a numerical probability score of the prevalence of each tumor-specific neoantigen and after administration of the immunogenic composition using a machine learning platform;
wherein a higher numerical probability score relative to a low numerical probability score indicates that the one or more tumor-specific neoantigens is present in the circulating tumor DNA and that the one or more tumor-specific neoantigens has a lower prevalence in a tumor of the subject relative to before administration of the immunogenic composition; and
wherein a lower numerical probability score relative to a higher numerical probability score indicates that the one or more tumor specific neoantigens is present in a low amount or not present in the circulating tumor DNA and that the one or more tumor-specific neoantigens has a higher prevalence in the tumor of the subject relative to before administration of the immunogenic composition;
d) generating an individual score of each tumor-specific neoantigen based on the predicted response of specific CD8+ T cells or CD4+ T cells using a machine learning model; [and]
e) inputting the numerical probability score and the individual score into an objective function to receive an output of a summation, wherein the summation is a value of a weighted sum corresponding to the efficacy of the immunogenic composition.
Claim 2 recites in its entirety:
A method for treating cancer, comprising:
a) administering to a subject in need thereof a first immunogenic composition;
b) sequencing circulating tumor DNA from a biological sample from a subject to generate circulating tumor DNA sequence data;
c) analyzing the circulating tumor DNA sequence data to quantify one or more ctDNA mutations in the circulating tumor DNA encoding one or more tumor-specific neoantigens;
d) generating a numerical probability score of cellular prevalence of each tumor-specific neoantigen using a machine learning platform;
e) generating an individual score of each tumor-specific neoantigen based on the predicted response of specific CD8+ T cells or CD4+ T cells using a machine learning model;
f) sorting the one or more tumor-specific neoantigens by ξαςα, wherein ξα is the cellular prevalence and ςα is the individual score of each tumor-specific neoantigen; and
g) generating a second immunogenic composition based on the sorting of the one or more tumor-specific neoantigens.
There are no limitations or elements in claims 1 and 2 directed to a structural element that may execute or carry out the method steps. The following are the broadest reasonable interpretations consistent with the specification of various claim terms and limitations of the claim. The limitations are given their “plain meaning” or “ordinary and customary meaning given to the term[s] by those of ordinary skill in the art at the relevant time.” See MPEP § 2111.01. Notwithstanding the 35 U.S.C. §§ 112(a) and 112(b) rejections of claims 1 and 2 in this Action, and giving the limitations a reading that provides a plain meaning that is as clear as possible, the limitations of the claims are interpreted as discussed below, and if not mentioned, they are given their plain meaning. The instant application has published as U.S. Patent Application Publication No. 2024/0360515, and will be referenced as “PgPub” and cited below as needed.
The steps are labeled “a),” “b),” “c),” etc. and are understood to be an ordered set of steps starting with “a).”
Claim 1, steps “a)” and “b),” and claim 2, step “b)” are understood as simply sequencing circulating tumor DNA from a biological sample to generate a data sequence. The Specification admits this concept is well known in the art. See Spec. ¶¶17, 40; see also PgPub ¶¶18, 41.
Claim 1, step “c),” and claim 2, step “c)” and “d)” are understood to be analyzing the generated data sequence to count (i.e., “quantify”) “one or more ctDNA mutations” as they relate to “one or more tumor-specific neoantigens,” and generate a “numerical probability score.” The term “numerical probability score” is understood to be a probability ranging from 0 to 1 (or 0% to 100%) that a corresponding neoantigen is present in the circulating tumor DNA. See Spec. as filed, ¶30; see also PgPub, ¶31. As a result, while not expressly described in the specification, a person of ordinary skill in the art would be well equipped with the general knowledge to measure a concentration or amount of neoantigens (i.e., the circulating tumor DNA, see Spec. ¶39; see also PgPub ¶40) in a known amount of a biological sample (see Spec. ¶38; see also PgPub ¶39) and easily count the number of something and calculate a probability or ratio of neoantigens to total sample, and thus, generate a “numerical probability score.” The biological samples may be taken at different time points, including prior to treatment and during treatment, thus, a single neoantigen may have several “numerical probability scores” associated with it over time. See Spec. as filed ¶¶18, 53; see also PgPub ¶¶19, 54. This data gathering, counting, score generation, and comparison may be carried out for any neoantigen under examination. After gathering the samples over time and calculating various neoantigen numerical probability scores, the scores can be compared. See Spec. ¶34; see also PgPub ¶35.
Claim 1, step “b),” and claim 2, step “a),” are understood to include administration or giving a patient an “immunogenic composition.” Claim 2, step “d),” is understood to be generating or deriving a “second immunogenic composition” albeit “based on the sorting of the one or more tumor-specific neoantigens.”
Lastly, claim 1 recites, “generating an individual score of each tumor-specific neoantigen based on the predicted response of specific CD8+ T cells or CD4+ T cells using a machine learning model” and “inputting the numerical probability score and the individual score into an objective function to receive an output of a summation, wherein the summation is a value of a weighted sum corresponding to the efficacy of the immunogenic composition.” Claim 2 recites, “generating an individual score of each tumor-specific neoantigen based on the predicted response of specific CD8+ T cells or CD4+ T cells using a machine learning model,” and “sorting the one or more tumor-specific neoantigens by ξαςα, wherein ξα is the cellular prevalence and ςα is the individual score of each tumor-specific neoantigen.” These limitations are understood to relate the tumor-specific antigens to the generation of scores based on “responses” of CD8+ T cells and CD4+ T cells, but do not require any specifics.
With the above in mind, claims 1 and 2 are directed to the abstract idea of assigning a probability score of the prevalence of tumor-specific antigens in a biological sample, generating another score (which is not defined in the claims) using a machine learning model (which is also not defined in the claims), sorting data, and inputting these scores into a function. These are all mathematical steps in nature and can be performed in the human mind or on paper. As noted above, determining a ratio or probability of “circulating tumor DNA sequence data” present in a biological sample to the overall size of the biological sample is a simple probabilistic calculation, which can be carried out in the human mind or on paper, assigning scores without detail on how these scores are assigned, sorting without more detail, and inputting these scores into a mathematical function are abstract. See MPEP §§ 2106.05(b), subsection III, 2106.05(b).
Claim 1 also recites two “wherein” clauses that compare the generated probability scores and identify meaning based on the values and/or comparison of these scores. While these limitations are more limiting than just generating a probability score, they still do not provide meaningful limits on the abstract idea because they too themselves are evaluations that are mathematical in nature and can be performed in the human mind. For example, determining if one value is higher or lower than another, and then looking up the meaning behind such a comparison can be done in the mind. Thus, these “wherein” clauses are also abstract ideas.
With respect to the other steps in claims 1 and 2 they are addressed below.
For the reasons above, claims 1 and 2 fall within the meaning of mental processes and mathematical concepts, and are taken together as a single abstract idea to which the claims are directed, even if part of an ordered set of steps. Thus, prong one of step 2A is satisfied and the analysis continues below.
Step 2A, Prong 2: Independent Claims 1 and 2
The last two paragraphs of the “Background” section of the application as filed (Spec. ¶¶6, 7; PgPub ¶¶7, 8) describes the invention as having the advantage (“practical application”) of:
The reliable detection of neoantigens (i.e., mutations) in cancer genomes is important for developing effective therapies as well as guiding treatment choices for cancer, such as immunogenic compositions. Identification of somatic mutations is challenged by the heterogeneous composition of tumors. Evaluating heterogeneity to guide choice and sequence of therapy could be achieved by tumor biopsies, but this is impractical due to the associated risk of complications and costs. Alternatively, circulating tumor-derived DNA (ctDNA) can be used to monitor cancer dynamics noninvasively. Circulating tumor derived DNA is DNA originating from tumor cells (e.g., from primary tumors, micrometastases, and overt metastases) that is released into the circulation. Fiala et al., (2018), The Journal of Applied Laboratory Medicine, 3(2):300-313. However, the sensitivity of circulating DNA analysis is limited by extremely low amounts of tumor DNA concentrations in the blood and by the methods of detection. Id. Currently, circulating tumor DNA is unlikely to perform at the high level of sensitivity and specificity required to apply clinically. Id.
Accordingly, there is a significant unmet need for an integrated method that characterizes tumor genomic material to identify neoantigens and selects which neoantigens are likely to be suitable for effective immunogenic compositions
However, none of the steps in claims 1 and 2 describes or links analyzing the circulating tumor DNA for neoantigens and selecting or identifying neoantigens for generation of any immunogenic composition.
Claim 1, in steps “a)” and “b),” recite “sequencing circulating tumor DNA from a biological sample” both before and after administration of an immunogenic composition and then “generat[ing] circulating tumor DNA sequence data.” Sequencing tumor DNA to obtain circulating tumor DNA sequence data, without any detail on how this is done, is well-understood, routine, and conventions. See MPEP § 2106.05(d), subsection II.
Claim 2 in step “a)” requires “administering to a subject in need thereof a first immunogenic composition.” (Claim 1 impliedly includes administering an immunogenic composition, but such a step is not actively required.) However, this limitation is the first step in the set of ordered steps (and is routine in that administering a composition or treatment to a patient who needs it is the exact way medicine treats many diseases and conditions, see Spec. ¶68; PgPub ¶69), moreover, this step is not later referenced by any other later-recited steps. As a result, this step in claim 2 does not meaningfully limit the abstract idea or other limitations, and at best would be nothing more than a mere application of an abstract idea, which does not make the claimed invention patent eligible. See MPEP § 2106.04(d)(2).
Claim 2 in step “d)” also recites “generating a second immunogenic composition based on [] sorting [] one or more tumor-specific neoantigens.” However, this is recited at a high level of generality. While the “second immunogenic composition” is generated based on “sorting [] one or more tumor-specific neoantigens,” there is no detail recited in the claim how this sorting results in generation of the “second immunogenic composition.” Additionally, generating an immunogenic composition is nothing more than generating a treatment for administration to a patient to treat a medical condition, which is well-known since this is exactly how medicine treats many conditions. See Spec. ¶68; PgPub ¶69. There are no additionally recited specifics on how the immunogenic composition is generated. Thus, this step does not meaningfully limit the abstract idea and does not make the abstract idea patent eligible.
Lastly, the claims also recite that some variables may be derived from “a machine learning model,” and the specification gives examples of some learning models. See Spec. ¶¶45, 48, 49, 132, 133; see also PgPub ¶¶46, 49, 50, 134, 135. However, there is no description in the specification of how these models are used in the described invention nor is there any description of any noted improvement to any computing device or processing because of these models. Moreover, simply using a machine learning model to generate an output is nothing more than reciting the purpose and results of using machine learning models. The claims do not explain in any detail how the model is used, except at a high level of generality of inputting values to obtain an output.
For these reasons, taking the limitations together or in combination, there is nothing that would show an integrated practical application of the abstract idea.
Step 2B: Independent Claims 1 and 2
As explained above, there are no other limitations, such as executing the method on a computer, etc., recited in claims 1 and 2, or any kind of improvement recited to a computer or computing device. Moreover, there are no other limitations recited in claims 1 and 2 of any type of integration into a practical application or that impart additional features that would amount to significantly more. Gathering a biological sample and sequencing genetic material are recited at a high level of generality and are well-known, such as being recognized by the courts as being routine laboratory techniques. See Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1377 (Fed. Cir. 2016)(analyzing DNA to provide sequence information or to detect allelic variants is conventional in the art); see also MPEP § 2106.05(d), subsection II. See Spec. as filed ¶¶18, 34, 53; see also PgPub ¶¶19, 35, 54.
Even as an ordered set of steps, the claim limitations provide no indication of any application of the invention or feature that would provide significantly more than the mathematical concepts and mental processes of the steps themselves. Comparing whether probability scores are higher or lower than one another is a basic mathematical concept and does not show any significant application of the abstract ideas.
Based on the analysis in steps 2A and 2B as explained above, claims 1 and 2 recite an abstract idea without significantly more and is directed to patent ineligible subject matter.
Dependent Claims 3-9, 16, and 41-44
Claims 3-9, 16, and 41-44 merely recite additional mathematical or mental process concepts without anything more, or do not add significantly more to the abstract ideas because they are well-known or are merely identifying a property or characteristic of a claimed element without integrating into any type of practical application or adding significantly more to the abstract idea.
Claims 3, 4, 16, 41, and 42 further recite generating a second immunogenic composition (claims 3 and 24), administering an immunogenic composition (claims 4 and 25), and identifying the source of the biological sample from a patient (claims 16, 41, and 42). As explained above, generating an immunogenic composition (without more) and administering an immunogenic composition are well-known and routine. They are not further limited nor do they relate back to any other claimed limitations. Identifying the source of the biological sample from a patient, as in claims 41 and 42, is nothing more than collecting a biological sample, which would be required for analyzing for genetic material and thus is well-known as explained above.
Claims 5-9 recite additional characteristics of the immunogenic compositions, but do not recite any further use or practical application of the immunogenic compositions. Nor do these limitations recite or define how these compositions are generated or how they link back to the generated probability scores. Thus, they provide no meaningful limit on the abstract idea.
Lastly, claims 43 and 44 further define the claimed “object function” of claim 3. But as seen, this is nothing more than further defining a mathematical concept with an explicit recitation of an equation. Thus, claims 43 and 44 are only directed to a more express recitation of the abstract idea and do not amount to significantly more.
For these reasons, claims 3-9, 16, and 41-44 do not add anything to the abstract idea that would show significantly more or an integrated practical application, and thus, claims 3-9, 16, and 41-44 are also directed to patent ineligible subject matter.
For the reasons explained above, none of claims 1-9, 16, and 41-44 are directed to patent eligible subject matter under section 101, and are thus, rejected.
Conclusion
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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/JOSHUA KADING/ Primary Patent Examiner, Art Unit 3993
1 https://www.uspto.gov/sites/default/files/documents/2024-AI-SMEUpdateExamples47-49.pdf.
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