DETAILED ACTION
Claims 1-7, 9, 113-120, and 122-123 are pending.
Status of Claims
Claims 1-7, 9, 113-120, and 122-123 are pending. Claims 1 and 117 have been amended.
Claims 1-7, 9, 113-120, and 122-123 are under examination.
Withdrawn Claim Objections and/or Rejections
The rejection of claims 1-9 and 113-123 under 35 USC 112(a) for failing to comply with the enablement requirement on p. 2-7 of the previous office action (mailed on 04/06/2026) has been withdrawn in view of the amended claims (filed on 07/02/2026). The amendments overcome the 112(a) because the newly amended claims recite explicitly what an analyte sample consists of and what a negative sample consists of.
Claim Rejections - 35 USC § 101-Maintained.
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 and 113-123 are rejected under 35 U.S.C. 101 because the claimed method is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract
idea) without significantly more. The judicial exception is not integrated into a practical
application and the claim(s) does/do not include additional elements that are sufficient to
amount to significantly more than the judicial exception.
Step 1
This part of the eligibility analysis evaluates whether the claim falls within any statutory
category per MPEP 2106.03
Regarding instant claims 1-9 and 113-123, Example 43 of “2019 PEG” is particularly
enlightening because the fact pattern of claim 1 of example 43 is most similar to the instant
application claims1-9 and 113-123.
Regarding claim 1 of example 43 of the “2019 PEG” and per Step 1, the claim is
directed to a process, which is one of the statutory categories of invention as the claim recites
“A treatment method comprising: (a) calculating a ratio of C11 to C13 levels measured in a
blood sample from a patient diagnosed with Nephritic Autoimmune Syndrome Type 3 (NAS-3)
to identify the patient as having a non-responder phenotype; (b) administering a treatment to the
patient having a non-responder phenotype.” (Step 1: YES).
Similarly instant claims 1-9 and 113-123 are directed to a statutory method that
measures naturally occurring proteins and correlates the levels of the naturally occurring
proteins with the quality of a sample (Step 1: YES).
Step 2A, Prong 1: Does the claim recite a judicial exception?
This part of the eligibility analysis evaluates whether the claim recites a judicial
exception. As explained in MPEP 2106.04(II) and the October 2019 Update, a claim “recites” a
judicial exception when the judicial exception is “set forth” or “described” in the claim.
Regarding instant claims 1-9 and 113-123, Example 43 of the “2019 PEG” shows a similar fact pattern.
Regarding claim 1 in Example 43 of the “2019 PEG” and per Step 2A, prong 1, the
claim recites the judicial exception of “calculating a ratio of C11 to C13 levels measured in a
blood sample from a patient diagnosed with Nephritic Autoimmune Syndrome Type 3 (NAS-3)
to identify the patient as having a non-responder phenotype,” and according to broadest
reasonable interpretation (BRI), an arithmetic calculation of a division is required to obtain the
ratio of C11 to C13 that can be used to identify whether the patient has the non-respondent
phenotype.
Specifically, limitation (a) in claim 1 of Example 43 of the “2019 PEG” recites “calculating
a ratio of C11 to C13 levels measured in a blood sample from a patient diagnosed with Nephritic
Autoimmune Syndrome Type 3 (NAS-3) to identify the patient as having a non-responder
phenotype,” which has a BRI that requires performing an arithmetic calculation (division) in order to obtain the ratio of C11 to C13 levels, and then using this ratio to identify whether the
patient has the non-responder phenotype (i.e., the patient has a calculated ratio of 3:1 or
greater and thus is not responding, or will not respond, to glucocorticoids). This limitation
therefore recites a mathematical calculation. The grouping of “mathematical concepts” in the
2019 PEG includes “mathematical calculations” as an exemplar of an abstract idea. 2019 PEG
Section I, 84 Fed. Reg. at 52. Thus, limitation (a) falls into the “mathematical concept” grouping
of abstract ideas. In addition, this type of simple arithmetic calculation (division) can be
practically performed in the human mind, and is in fact performed in the human mind on a daily
basis, for instance by school-aged children studying mathematics. Note that even if most
humans would use a physical aid (e.g., pen and paper, a slide rule, or a calculator) to help them
complete the recited calculation, the use of such physical aid does not negate the mental nature
of this limitation. Thus, limitation (a) also falls into the “mental process” groupings of abstract
ideas.
In addition, limitation (a) describes a naturally occurring relationship between the ratio
of C11 to C13 and the non-responder phenotype, and thus may also be considered to recite a
law of nature. Accordingly, limitation (a) recites a judicial exception (an abstract idea that falls
within the mathematical concept and mental process groupings in the “2019 PEG”, and a law of
nature), and the analysis must therefore proceed to Step 2A Prong Two.
Similarly, instant claims 1-9 and 113-123 recites “measuring analyte level” of proteins
and using the measurements to assess the samples quality, which describes a naturally
occurring relationship between the protein biomarker and the sample quality, and thus is
considered a law of nature. Further, claims 1-9 and 113-123 recite “wherein the classification
decides if a sample is an analysis sample or a negative sample and wherein the classification
decision is based on a predetermined decision criteria based on analyte level patterns”, which is
directed toward an abstract idea that falls under the mental process grouping (i.e., concepts
performed in the human mind (including an observation, evaluation, judgement, opinion). Comparing collected information to a predetermined threshold, which is an act of evaluating
information that can be practically performed in the human mind. Consequently, claims 1-9 and
113-123 recite the judicial exception of applying and using a law of nature and an abstract idea.
Dependent instant claims 8 and 121 contain limitations that fall under a judicial
exception. The instant claims 8 and 121 recite using the protein levels to “predict” the length of
time between the sample collection from the human subject and sample centrifugation and/or
the length of time between sample centrifugation and sample decanting. The language “predict”
is directed to a judicial exception as it is an abstract idea that falls under the mental process
grouping (i.e., concepts performed in the human mind (including an observation, evaluation,
judgement, opinion). Comparing collected information from a random forest model to a
predetermined threshold which is an act of evaluating information that can be practically
performed in the human mind. Further, claims 8 and 121 describes a naturally occurring
relationship between nature-based products and correlating it to the prediction of length of time
between sample collection from the human subject and sample centrifugation and/or the length
of time between sample centrifugation and sample decanting, and thus is considered to recite a
law of nature.
Accordingly, instant claims 1-9 and 113-123 recite a judicial exception (a law of nature
and an abstract idea that falls within the mental process grouping) and the analysis must
therefore proceed to Step 2A Prong Two.
Step 2A Prong 2: Does the claim recite additional elements that integrate the exception into a practical application?
Regarding instant claims 1-9 and 113-123, Example 43 of “2019 PEG” shows a similar
fact pattern.
In claim 1 of example 43 of the “2019 PEG” and per Step 2A, prong 2, the claim as a
whole does not integrate the recited judicial exception into a practical application of the exception. This evaluation is performed by (a) identifying whether there are any additional
elements recited in the claim beyond the judicial exception, and (b) evaluating those additional
elements individually and in combination to determine whether the claim as a whole integrates
the exception into a practical application. Besides the abstract idea, the claim 1 of example 43
of the “2019 PEG” recites the additional element of “(b) administering a treatment to the patient
having a non-responder phenotype”. Although this limitation indicates that a treatment is to be
administered, it does not provide any information as to how the patient is to be treated, or what
the treatment is, but instead covers any possible treatment that a doctor decides to administer
to the patient. In fact, this limitation is recited at such a high level of generality that it does not
even require a doctor to take the calculation step’s outcome (the patient’s phenotype) into
account when deciding which treatment to administer, making the limitation’s inclusion in this
claim at best nominal. Thus, limitation (b) of example 43 of the “2019 PEG” fails to
meaningfully limit the claim because it does not require any particular application of the recited
calculation, and is at best the equivalent of merely adding the words “apply it” to the judicial
exception. Accordingly, limitation (b) of example 43 of the “2019 PEG” does not integrate the
recited judicial exception into a practical application and the claim is therefore directed to the
judicial exception.
Similarly, instant claims 1-9 and 113-123 do not have additional elements that would
integrate the judicial exception cited above into a practical application. In comparison to claim
43, Example 43 did not pass step 2A prong 2 with step of general treatment, instant claims 1-9
and 113-123 do not even recite a correlation to any disease. Instant claims 1-9 and 113-123 do note recite any additional elements other than the law of nature and the abstract idea. Example 43 failed with the step of a general treatment, instant claims 1-9 and 113-123 do not even recite a further active step, let alone a step for treatment.
Therefore, instant claims 1-9 and 113-123 do not integrate the judicial exception into a
practical application.
Step 2B: Does the claim recite significantly more?
Regarding instant claims 1-9 and 113-123, this part of the eligibility analysis evaluates
whether the claim as a whole amounts 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. MPEP 2106.05. As explained with respect to Step 2A Prong Two, the
claim does not recite any active steps. Instant claims 8 and 121 do recite “predicting”, however,
that language is still directed to a judicial exception as it is an abstract idea that falls under the
mental process grouping (i.e., concepts performed in the human mind (including an observation,
evaluation, judgement, opinion). Comparing collected information to a predetermined threshold,
which is an act of evaluating information that can be practically performed in the human mind.
Further, claims 1-9 and 113-123 describes a naturally occurring relationship between a nature-
based product and correlating it to the quality of the sample, and thus is considered to recite a
law of nature. Accordingly, instant claims 1-9 and 113-123 are not eligible (STEP 2B: NO).
Thus, instant claims 1-9 and 113-123 are rejected under 35 USC 101.
Response to Arguments
Applicant's arguments filed 07/02/2026 have been fully considered but they are not persuasive.
On p. 12-13 applicant argues that the claims are not directed merely to observing a natural correlation between biomarker levels and disease, nor are they directed merely to a mental comparison of data. Rather the claims are directed to a laboratory sample quality-control method in which analyte levels of a specific panel of proteins are measured in a physical sample from a human subject, a random forest classifier model comprising multiple decision trees is applied to the measured analyte levels to “predict a length of time between sample collection from the human subject and sample centrifugation and/or length between sample centrifugation and sample decanting.
However, while the claims do teach a laboratory sample quality-control method, the claims still recite judicial exceptions, and the recitation of a laboratory sample-quality control method does not add significantly more nor is it a practical application. Further, the method is directed at measuring naturally occurring markers and correlating those markers to the quality of the sample, which is direct to a judicial exception (law of nature), and then the using that judicial exception to “predict” the length of time between sample collection and centrifugation or decanting, which is directed to a judicial exception (abstract idea- mental process), by observing the results of a decision tree, which is also directed to a judicial exception (abstract idea-mental process). A judicial exception alone is not eligible subject matter, and if the additional claim elements merely recite another judicial exception, that is insufficient to integrate the judicial exception into a practical application.
On p. 13 applicant argues that the claims recite “using the sample” in a protein biomarker discovery analysis, protein expression level analysis, a diagnostic method or a prognostic method, and when the sample is identified as a negative sample, the method comprises “excluding the sample” from such downstream analysis.
However, merely reciting the words “applying it” with the judicial exception, or merely including instructions to implement an abstract idea does not integrate the judicial exception into a practical application.
On p. 14 applicants argue that the claims recite the classifier output being used to determine whether the physical sample is suitable or unsuitable for downstream analysis sample and excluded when identified as a negative sample. Applicant further argues that the amended claims are not properly characterized as a mental process because a random forest classifier modeling comprising multiple decision trees is used.
However, applying a random forest classifier is essentially making a series of data evaluations and making decisions based on those evaluations. Thus, the recitation of applying a random forest classifier does not amount to significantly more, as it makes a series of data evaluations, observing those evaluations, and making a decision based on those observations, which is directed to a judicial exception (abstract idea- mental process).
Conclusion
No claim is allowed.
Claims 1-9 and 112-123 are free of the prior art.
The prior art made of record and not relied upon is considered pertinent to applicant's
disclosure.
The closest prior art for claims 1-9 and 112-123 is Wilcox et al. (US 2013/0116150 A1)
(IDS filed on 10/07/2021).
Wilcox teaches a method that includes sample quality assessment, comprising a) measuring levels of proteins, and the levels of at least one, two, three, four, five, six, seven, eight, nine, ten, eleven, or twelve proteins in a sample from a human subject; and b) in order to assess sample quality, applying a forest decision tree, and based on the level of protein and the level of at least one, two, three, four, five, six, seven, eight, nine, ten, eleven, or twelve proteins.
Wilcox does not teach categorizing samples as “analysis sample” and “negative samples”. Wilcox does not teach measuring any combination of SHH, PTPN4, and the level of the one, two, three, four, five, six, seven, eight, nine, ten, eleven, or twelve proteins chosen from PGAM1, PGAM2, C4A.C4B, TNFSF14, FAM49B, RBP7, IHH, DDX39B, S100A12, IL21R, TMEM9 and ADAM9, which are proteins. Because proteins are a composition of matter, the markers SHH, PTPN4, and the level of the one, two, three, four, five, six, seven, eight, nine,
ten, eleven, or twelve proteins chosen from PGAM1, PGAM2, C4A.C4B, TNFSF14, FAM49B,
RBP7, IHH, DDX39B, S100A12, IL21R, TMEM9 and ADAM9. Further, Wilcox does not teach
wherein a measured analyte level leads a node to as classification or to one or more nodes each comprising another measured analyte level, and wherein the classification decides if a sample is an analysis sample or a negative sample, and wherein the classification decision is based on a predetermined decision criteria based on analyte level patterns.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MCKENZIE A DUNN whose telephone number is (571)270-0490. The examiner can normally be reached Monday-Tuesday 730 am -530pm, Wednesday-Friday 730 am-430 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gregory Emch can be reached at (571)272-8149. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/MCKENZIE A DUNN/ Examiner, Art Unit 1678
/GREGORY S EMCH/ Supervisory Patent Examiner, Art Unit 1678
