DETAILED ACTION
Applicant' s response, filed 19 March 2026, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 19 March 2026 has been entered.
Claim Status
Claims 3-10 and 14-16 are pending and examined herein.
Claims 3-10 and 14-16 are rejected.
Claims 3 and 4 are objected to.
Priority
Claims 3-10 and 14-16 are not granted the claim to the benefit of priority to U.S. application 13/279990 filed 24 October 2011 or previous applications in which priority is claimed because there is no disclosure of “combining the classification scores of each N biomarker to generate a plurality of N classification scores” and “comparing the plurality of N classification scores to a predetermined threshold”. Thus, the effective filling date of claims 3-10 and 14-16 is given the date of the effective filling date of the instant disclosure 21 September 2021.
Claim Objections
The objection of claims 3 and 4 in Office action mailed 22 December 2025 is withdrawn in view of the amendments of “wherein each of the capture reagents of the set of capture reagents” and “wherein the biomarker levels comprise a plurality of biomarker values” received 19 March 2026.
The objection below is newly recited necessitated by amendment.
Claims 3 and 4 are objected to because of the following informalities:
Claims 3 and 4 recite “combining the classification scores of each N biomarker…” in step e) of the claims should read “combining the classification scores of each of the N biomarkers”.
Appropriate correction is required.
Claim Interpretation
Claims 3 and 4 recite “measuring the level of biomarkers in a biological sample of an individual, comprising contacting the biological sample with a set of capture reagents, wherein each of the set of capture reagents bind to a different biomarker chosen from…”. This limitation is interpreted as the step of contacting the biological sample with a set of capture reagents is open-ended (i.e., does not exclude additional, unrecited elements or method steps see MPEP 2111.03(I)) while the different biomarkers chosen from the group in the claim is a closed group (i.e., excludes any element not specified in the claim see MPEP 2111.03(II)). Therefore, the BRI of the claim encompasses contacting the biological sample additional capture reagents that target other biomarkers not listed in the claim but must include capture reagents that bind to biomarkers chosen from the group specified in the claim.
Claims 3 and 4 recite “retrieving on a computer the measured level of each of the biomarkers captured by the set of capture reagents in the biological sample from the individual, wherein the biomarker level comprises a plurality of biomarker values that each correspond to one of at least N biomarkers chosen from…”. This limitation is interpreted as the biomarker levels retrieved by the computer is open-ended (i.e., does not exclude additional, unrecited elements or method steps see MPEP 2111.03(I)) while the N biomarkers chosen from the group in the claim is a closed group (i.e., excludes any element not specified in the claim see MPEP 2111.03(II)). Therefore, the BRI of the claim encompasses retrieving biomarker levels of additional biomarkers not listed in the claim but must include a plurality of biomarker values that each correspond to one of at least N biomarkers chosen from the group specified in the claim.
Claim Rejections - 35 USC § 112
112/a New Matter
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.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
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.
The rejection below is newly recited necessitated by amendment.
Claims 3-10 and 14-16 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 applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 3 and 4 recite “combining the classification scores of each N biomarker to generate a plurality of N classification scores, comparing the plurality of N classification scores to a predetermined threshold” which constitutes as new matter. The is not an adequate written description of combining classification scores of each N biomarker to generate a plurality of N classification scores or comparing the plurality of N classification scores to a predetermined threshold. The instant disclosure provides “once a biomarker has been detected and a biomarker value assigned each marker is scored or classified as described in detail herein and the marker scores are then combined to provide a total diagnostic score” (instant disclosure [0109]), “combining the assigned scores for each biomarker quantified to obtain a total score” (instant disclosure [0260] and [0261]), and comparing a total score with a predetermined score (instant disclosure [0260] and [0261]). The instant disclosure provides that combining classification scores generates a singular total score and that the total score is then compared to a predetermined threshold. However, there is no disclosure of combining the classification scores of each biomarker to generate a plurality of N classification scores or comparing the plurality of N classification scores to a predetermined threshold. Thus, these limitations constitute as new matter. Dependent claims 5-10 and 14-16 are rejected by virtue of their dependency on a rejected claim without alleviating the rejection.
112/b
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.
The rejections below are newly recited necessitated by amendment.
Claims 3-10 and 14-16 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 3 and 4 recite “applying, with the computer, a random forest classifier to the retrieved biomarker values to identify a subset of N biomarkers relevant to cancer classification wherein N is greater than or equal to 3 and less than or equal to 12…” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because it is unclear if “a subset of N biomarkers” is meant to be a subset of the N biomarkers chosen from the group of biomarkers provided in the retrieving step or if “a subset of N biomarkers” can be any subset of N biomarkers in the retrieved data which encompasses biomarker values of biomarkers not listed in the retrieving step (i.e., it is unclear if the subset of N biomarkers can include only biomarkers which are not listed in the claim as long as they are identified by the random forest classifier as being relevant to cancer classification). Dependent claims 5-10 and 14-16 are rejected by virtue of their dependency on a rejected claim without alleviating the indefiniteness. For the sake of furthering examination, the subset of N biomarkers is interpreted as being a subset of the N biomarkers chosen from the group of biomarkers in the retrieving step which are identified by the random forest classifier.
Claim 3 recites “at least two of the N biomarkers are CRP and AKR7A2” and claim 4 recites “at least two of the N biomarkers are CA6 and AKR7A2” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because it is unclear if “the N biomarkers are CRP and AKR7A2” (in claim 3) and “the N biomarkers are CA6 and AKR7A2” (in claim 4) are referring to the “at least N biomarkers chosen from KLK3-SRPINA3…” in the retrieving step or if “the N biomarkers are CRP and AKR7A2” (in claim 3) and “the N biomarkers are CA6 and AKR7A2” (in claim 4) are referring to the “subset of N biomarkers” identified by the random forest. Further, it is unclear if the biomarkers CRP and AKR7A2 (in claim 3) and CA6 and AKR7A2 (in claim 4) are required to be identified by the random forest classifier or if they are only required to be retrieved. Dependent claims 5-10 and 14-16 are rejected by virtue of their dependency on a rejected claim without alleviating the indefiniteness. For the sake of furthering examination, the N biomarkers are CRP and AKR7A2 (in claim 3) is interpreted as referring to the subset of N biomarkers identified by the random forest, and the N biomarkers are CA6 and AKR7A2 (in claim 3) is interpreted as referring to the subset of N biomarkers identified by the random forest.
Claims 3 and 4 recite “for each of the N biomarkers, computing a classification score…” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because it is unclear if “the N biomarkers” is referring to the “subset of N biomarkers relevant to cancer classification” or if “the N biomarkers” is referring to the “at least N biomarkers chosen from KLK3-SERPINA3…” in the retrieving step. Dependent claims 5-10 and 14-16 are rejected by virtue of their dependency on a rejected claim without alleviating the indefiniteness. For the sake of furthering examination, this limitation will be interpreted as for each of the N biomarkers in the subset identified as being relevant to cancer classification, computing a classification score.
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.
The rejection below has been modified necessitated by amendment.
Claims 3-10 and 14-16 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.
(Step 1)
Claims 3-10 and 14-16 fall under the statutory category of a process.
(Step 2A Prong 1)
Under the BRI, the instant claims recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mental process”, such as procedures for evaluating, analyzing or organizing information, and forming judgement or an opinion. The instant claims further recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mathematical concept”, such as mathematical relationships and mathematical equations. The instant claims further recite judicial exceptions that are a natural correlation.
Independent claim 3 recites a mental process of identifying a subset of N biomarkers relevant to cancer classification, wherein N is greater than or equal to 3 and less than or equal to 12, and at least two of the N biomarkers are CRP and AKR7A2, combining the classification scores of each N biomarker to generate a plurality of N classification scores, comparing the plurality of N classifications scores to a predetermined threshold, and indicating a likelihood that said individual has cancer based upon the plurality of N classification scores.
Independent claim 4 recites a mental process of identifying a subset of N biomarkers relevant to cancer classification, wherein N is greater than or equal to 3 and less than or equal to 12, and at least two of the N biomarkers are CA6 and AKR7A2, combining the classification scores of each N biomarker to generate a plurality of N classification scores, comparing the plurality of N classifications scores to a predetermined threshold, and indicating a likelihood that said individual has cancer based upon the plurality of N classification scores.
Independent claims 3 and 4 recite mathematical concepts of for each N biomarkers, computing a classification score based on a class-dependent probability distribution derived from training data and combining the classification scores of each N biomarker to generate a plurality of N classification scores.
Independent claims 3 and 4 recite a natural correlation between the levels of the recited biomarkers and a likelihood of cancer.
The claims recite steps analyzing/evaluating data as identify a subset of N biomarkers which are relevant to cancer classification, combining the classification scores of each N biomarker to generate a plurality of N classification scores, comparing the plurality of N classifications scores to a predetermined threshold, and indicating a likelihood that said individual has cancer based upon the plurality of classifications. The human mind is capable of build decision trees with numerical thresholds to identify biomarkers which are able to discriminate between classes based on the data used (i.e., relevant to cancer classification), combining classification scores to generate a plurality of scores, comparing the plurality of classification scores to a predetermined threshold and indicating a likelihood that an individual has cancer based upon the plurality of classifications.
The claims recite mathematical calculations as for each of the N biomarkers, computing a classification score based on a class-dependent probability distribution derived from training data (instant disclosure [0237]-[0239] shows mathematical equations for computing classification scores utilizing a class-dependent probability distribution derived from training data) and combining classification scores of each N biomarker encompasses a mathematical operation such as summing (instant disclosure [0109], [0260], and [0261]). The MPEP states there is no particular word or set of words that indicates a claim recites a mathematical calculation. That is, a claim does not have to recite the word "calculating" in order to be considered a mathematical calculation. For example, a step of "determining" a variable or number using mathematical methods or "performing" a mathematical operation may also be considered mathematical calculations when the broadest reasonable interpretation of the claim in light of the specification encompasses a mathematical calculation (see MPEP 2106.04(a)(2)(I)(C)).
Dependent claims 9, 10, 15, and 16 further limit the mental process/mathematical concept and natural correlation recited in the independent claim but do not change their nature as a mental process/mathematical concept and natural correlation. Therefore, claims 3-10 and 14-16 recite an abstract idea.
(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). Integration into a practical application is evaluated by identifying whether there are any additional elements recited in the claim and evaluating those additional elements to determine whether they integrate the exception into a practical application.
The additional element in claims 3 and 4 of using a generic computer to perform judicial exceptions does not integrate the judicial exception into a practical application because this is simply applying the judicial exception to a generic computer without an improvement to computer technology (see MPEP 2106.04(d)(1)). The additional element of the generic computer only interacts with the judicial exceptions in manner of utilizing the generic computer as a tool to perform judicial exceptions.
The additional element in claims 3 and 4 of using a random forest classifier does not integrate the judicial exceptions into a practical application because this constitutes are mere instructions to apply an exception on a computer (see MPEP 2106.05(f) and Example 47). This additional element amounts to mere instructions to apply the exception because the claim recites only the idea of a solution or outcome without details of how the solution is accomplished. Further, this additional element is generally linking the judicial exception of identifying a subset of N biomarkers to the technological environment of random forests (see MPEP 2106.05(h)).
The additional element in claims 3 and 4 of measuring the level of biomarkers in a biological sample of an individual, comprising contacting the biological sample with a set of capture reagents, wherein each of the set of capture reagents bind to a different biomarker chosen from KLK3-SERPINA3, EGFR, BMPER, FGA-FGB-FGG, C9, STX1A, AKR7A2, CKB-CKM, DDC, CA6, IGFBP2, IGFBP4, FN1, BMP1, CRP, KIT, CNTN1, SERPINA1, BDNF, GHR, ITIH4, NME2, MMP12, MMP7, and CNDP1, the additional element in claim of retrieving on a computer the measured level of each of the biomarkers, captured by the set of capture reagents in the biological sample from the individual, wherein the biomarker level comprises a plurality of biomarker values that each correspond to the one of at least N biomarkers chosen from KLK3-SERPINA3, EGFR, BMPER, FGA-FGB-FGG, C9, STX1A, AKR7A2, CKB-CKM, DDC, CA6, IGFBP2, IGFBP4, FN1, BMP1, CRP, KIT, CNTN1, SERPINA1, BDNF, GHR, ITIH4, NME2, MMP12, MMP7, and CNDP1 wherein N is greater than or equal to 3 and less than or equal to 12, and at least one of the N biomarkers is CRP, the additional element in claim 7 of wherein measuring the level of biomarkers is obtained by measuring protein levels from the biological sample from the individual in an in vitro assay, the additional element in claim 8 of wherein the biological sample is serum, the additional element in claim 14 of wherein the set of capture reagents are aptamers comprising a 5-position pyrimidine modification do not integrate the judicial exceptions into a practical application because these steps are insignificant extra solution activity of data gathering. These additional elements are insignificant extra solution activity of data gathering because they only interact with the judicial exceptions by providing data to be processed by the judicial exceptions. It is noted that the content of the data in the retrieving step (i.e., what the data abstractly represents (biomarker values)) does not change the active step of retrieving data in a generic computer environment.
The additional element in claim 5 of displaying data on a computer display does not integrate the judicial exception into a practical application because this is adding a step of insignificant extra solution activity of outputting data. This additional element is insignificant extra solution activity of outputting data because it only interacts with the judicial exceptions by outputting the processed data of the judicial exceptions (i.e., solution of the abstract idea). It is noted that the content of the data being outputted does not change the active step of outputting the data on a display.
The additional element in claim 6 of wherein for an individual identified as having a likelihood of cancer, the method further comprises the step of administering to the individual a cancer treatment selected from the group consisting of a drug therapy, a siRNA, a cancer vaccine, and any combination thereof does not integrate the judicial exception into a practical application because this step does not provide a particular treatment and is mere instructions to apply the exception because of the generality of the application of the judicial exception (see MPEP 2106.04(d)(2) and 2106.05(f)). This step does not constitute as a particular treatment and constitutes as mere instructions to apply the exception because the administering step is broad and only based on a likelihood of cancer. The likelihood encompasses any value of the likelihood (such as low values or zero) and does not limit the treatment to a subset of individuals with cancer. Further, this step constitutes as mere instructions to apply the exception because of the generality of the recited treatments of a drug therapy, a siRNA, a cancer vaccine, and any combination thereof.
Thus, the additional elements do not integrate the judicial exceptions into a practical application and claims 3-10 and 14-16 are directed to the abstract idea.
(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). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because:
The additional element in claims 3 and 4 of measuring the level of biomarkers in a biological sample of an individual, comprising contacting the biological sample with a set of capture reagents, wherein each of the set of capture reagents bind to a different biomarker chosen from KLK3-SERPINA3, EGFR, BMPER, FGA-FGB-FGG, C9, STX1A, AKR7A2, CKB-CKM, DDC, CA6, IGFBP2, IGFBP4, FN1, BMP1, CRP, KIT, CNTN1, SERPINA1, BDNF, GHR, ITIH4, NME2, MMP12, MMP7, and CNDP1, , the additional element in claim 7 of wherein measuring the level of biomarkers is obtained by measuring protein levels from the biological sample from the individual in an in vitro assay, the additional element in claim 8 of wherein the biological sample is serum, the additional element in claim 14 of wherein the set of capture reagents are aptamers comprising a 5-position pyrimidine modification is conventional as shown by Ostroff et al. (PLoS one, Decmeber 2010, 5:e1500; previously cited) and Gold and Ayers et al. (Nature Precedings (2010); previously cited) which shows the use of modified aptamers to capture biomarkers and to measure levels of biomarkers. Further, the instant application shows measuring biomarker levels in a biological sample by disclosing any means known in the art can be used to detect a biomarker value by detecting the aptamer component of an aptamer affinity complex (instant disclosure [0169]).
The additional element in claims 3 and 4 of using a generic computer to perform judicial exceptions and using a random forest classifier (which amounts to mere instructions to apply the judicial exception to a computer) is conventional as shown by MPEP 2106.05(b) and MPEP 2106.05(d)(II).
The additional element in claims 3 and 4 of the additional element in claim of retrieving on a computer the measured level of each of the biomarkers, captured by the set of capture reagents in the biological sample from the individual, wherein the biomarker level comprises a plurality of biomarker values that each correspond to the one of at least N biomarkers chosen from KLK3-SERPINA3, EGFR, BMPER, FGA-FGB-FGG, C9, STX1A, AKR7A2, CKB-CKM, DDC, CA6, IGFBP2, IGFBP4, FN1, BMP1, CRP, KIT, CNTN1, SERPINA1, BDNF, GHR, ITIH4, NME2, MMP12, MMP7, and CNDP1 wherein N is greater than or equal to 3 and less than or equal to 12, and at least one of the N biomarkers is CRP is conventional as shown by MPEP 2106.05(b) and MPEP 2106.05(d)(II). It is noted that the content of the data in the retrieving step (i.e., what the data abstractly represents (biomarker values)) does not change the active step of retrieving data in a generic computer environment.
The additional element in claim 5 of displaying data on a computer display is conventional as shown by MPEP 2106.05(b) and MPEP 2106.05(d)(II). It is noted that the content of the data being outputted does not change the active step of outputting the data on a display.
The additional element in claim 6 of administering to the individual a cancer treatment selected from the group consisting of a drug therapy, a siRNA, a cancer vaccine, and any combination thereof is conventional as shown by Hammerschmidt et al. (Dtsch Arztebl Int. 2009 Dec;106(49):809-18; previously cited) which reviews cancer treatment for lung cancer which includes drug therapy.
Thus, the additional elements are not sufficient to amount to significantly more than the judicial exception because they are conventional.
Response to Arguments
Applicant's arguments filed 19 March 2026 have been fully considered but they are not persuasive.
Argument 1:
Applicant argues that amended claim 3 and 4 are applicable under Pathway A because the claims are directed towards improvements in the relevant art and because the claims do not seek to prevent others from practicing the judicial exception (Reply p. 7-8).
This argument has been fully considered but found to be not persuasive. The MPEP states “The results of the streamlined analysis will always be the same as the full analysis, thus the streamlined analysis is not a means of avoiding a finding of ineligibility that would occur if a claim were to undergo the full eligibility analysis” (MPEP 2106.06). Amended claims 3 and 4 are not applicable under pathway A for the reasons provided below. Further, even if the streamlined analysis was applicable the full analysis would provide the same result as the streamlined result.
The MPEP states at 2106.05(a) “It is important to note, the judicial exception alone cannot provide the improvement. The improvement can be provided by one or more additional elements… In addition, the improvement can be provided by the additional element(s) in combination with the recited judicial exception”. The determination of an improvement to technology has two steps, the identification of additional elements (which define the technology) and the evaluation of the additional elements to determine if the improvement is provided by or realized in the additional elements either by the additional elements themselves or the additional element in combination with the judicial exception (i.e. the interaction between the judicial exceptions and the additional elements). As show under Step 2A Prong 2 above the identified additional elements include retrieving abstract data in a computer environment, wet lab steps, displaying/outputting the solution of the abstract idea which only interact with the judicial exceptions in a manner to provide data to be analyzed by the judicial exceptions (and outputting the solution of the abstract idea) which amounts to insignificant extra solution activity of data gathering/ data outputting. The additional elements alone or in combination with the judicial exceptions do not provide an improvement in how the computer environment retrieves (or outputs the solution) the abstract data or how the wet lab steps are performed in which the wet lab steps are improved. The improvement falls under the judicial exception itself of processing data to provide an abstract solution of the likelihood of a subject having cancer which is not an improvement to technology because the judicial exception alone cannot provide the improvement (see MPEP 2106.05(a)). Further, the identified additional element of using a generic computer to perform judicial exceptions only interacts with the judicial exceptions as being utilized as tool to perform judicial exceptions. The additional element of the generic computer does not interact with the judicial exceptions in a manner where the computer itself functions in a different or improved manner.
The MPEP provides an example of a claim that recites an abstract idea which eligibility is self-evident, the claim being directed to a robotic arm assembly having a control system that operates using certain mathematical relationships which is clearly not an attempt to tie up use of the mathematical relationships and would not require a full analysis to determine eligibility (MPEP 2106.06(a)). In contrast to the example of a claim in which eligibility is self-evident in the MPEP, the instant claim recites performing mental processes and mathematical calculations to analyze numerical data to generate an abstract solution based on the numerical data (rather than a control system for a physical assembly which utilizes mathematical relationships). The eligibility of the instant claims are not self-evident because the instant claims are directed to gathering numerical data from a wet lab assay and performing abstract ideas to analyze the collected numerical data to generate an abstract solution of a likelihood of a subject having cancer.
Argument 2:
Applicant argues amended claims 3 and 4 recite steps that go well beyond merely analyzing data or determining disease status and instead recite a diagnostic process utilizing both physical laboratory operations and specific computer- implemented methods (Reply p. 8). Applicant argues the claims do not seek to "tie up" any alleged judicial exception (Reply p. 8). Applicant further argues amended claims 3 and 4 now recite specific limitations that meaningfully restrict the scope of the claims and prevent preemption of any abstract idea by limiting how biomarker data are selected, scored, combined, and evaluated, including the use of a random forest classifier for biomarker selection and scoring based on class-dependent probability distributions derived from training data (Reply p. 8).
This argument has been fully considered but found to be not persuasive. The MPEP states at 2106.04(I) “While preemption is the concern underlying the judicial exceptions, it is not a standalone test for determining eligibility. Rapid Litig. Mgmt. v. CellzDirect, Inc., 827 F.3d 1042, 1052, 119 USPQ2d 1370, 1376 (Fed. Cir. 2016). Instead, questions of preemption are inherent in and resolved by the two-part framework from Alice Corp. and Mayo (the Alice/Mayo test referred to by the Office as Steps 2A and 2B)”. When analyzed under the two-part framework above the claims recite judicial exceptions which are not integrated into a practical application nor do the additional elements amount to significantly more.
The MPEP provides an example of a claim that recites an abstract idea which eligibility is self-evident, the claim being directed to a robotic arm assembly having a control system that operates using certain mathematical relationships which is clearly not an attempt to tie up use of the mathematical relationships and would not require a full analysis to determine eligibility (MPEP 2106.06(a)). In contrast to the example of a claim in which eligibility is self-evident in the MPEP, the instant claim recites performing mental processes and mathematical calculations to analyze numerical data to generate an abstract solution based on the numerical data (rather than a control system for a physical assembly which utilizes mathematical relationships). The eligibility of the instant claims are not self-evident because the instant claims are directed to gathering numerical data from a wet lab assay and performing abstract ideas to analyze the collected numerical data to generate an abstract solution of a likelihood of a subject having cancer. It is noted that further limiting the abstract ideas performed to analyze the abstract numerical data does not change the nature of the recited limitations being abstract ideas.
Argument 3:
Applicant argues claims 3 and 4 satisfy step 2A, Prong 2 because the claims integrate any alleged abstract idea into a practical application. Applicant further argues that claims 3 and 4 require physical manipulation and analysis of biological samples, followed by a specific computational workflow process that transforms biomarker measurements into classification scores and a diagnostic tool based on a determined scoring threshold. Applicant argues the interactions between the physical laboratory steps and defines computational operations constitute a practical application and are not insignificant extra solution activity (Reply p. 9).
This argument has been fully considered but found to be not persuasive. As state above, analysis of biomarker measurements (i.e., numerical data representing biomarker levels) using classification scores and comparing scores against a determined scoring threshold fall under the abstract idea itself (i.e., not an additional element). The MPEP states “Purely mental processes in which thoughts or human based actions are "changed" are not considered an eligible transformation. For data, mere "manipulation of basic mathematical constructs [i.e.,] the paradigmatic ‘abstract idea,’" has not been deemed a transformation. CyberSource v. Retail Decisions, 654 F.3d 1366, 1372 n.2, 99 USPQ2d 1690, 1695 n.2 (Fed. Cir. 2011) (quoting In re Warmerdam, 33 F.3d 1354, 1355, 1360, 31 USPQ2d 1754, 1755, 1759 (Fed. Cir. 1994))” (MPEP 2106.05(C)) which clarifies that the manipulation of data through mental processes and mathematical manipulation are not deemed a transformation in the sense of being a particular additional element which changes an article to a different state or thing. The determination of the physical laboratory steps being data gathering steps is because the interaction between the physical wet lab steps and the judicial exceptions of processing the numerical data is only being the collection of data so it can be provided to the abstract ideas to produce the abstract solution of determining the likelihood of a subject having cancer. Further, the MPEP provides an example of insignificant extra solution of data gathering as “Performing clinical tests on individuals to obtain input for an equation, In re Grams, 888 F.2d 835, 839-40; 12 USPQ2d 1824, 1827-28 (Fed. Cir. 1989)” (see MPEP 2106.05(g)) which is similar to the instant claims of collecting data through a test to obtain data for an abstract analysis of that data. Thus, the physical laboratory tests constitute as insignificant extra solution activity of data gathering.
Argument 4:
Applicant argues that the additional elements are not merely data gathering (Reply p. 9). Applicant states that amended claims 3 and 4 do not stop at collecting or retrieving data but require computing class-dependent classification scores, combining those scores and comparing them to a predetermined threshold to generate a diagnostic indication (Reply p. 9). Applicant further argues that the transformation of measured biomarker values into diagnostic scores are integral to the claimed diagnostic process and cannot be performed mentally or generically without the claimed computational framework (Reply p. 9).
This argument has been fully considered but found to be not persuasive. It is noted that the collection and retrieving data does not constitute as data gathering because the method stops after collection and retrieving steps. These steps constitute as data gathering because the collection and retrieving steps only interact with the judicial exceptions of performing the steps of identifying a subset of N biomarkers, computing class-dependent classification scores, combining those scores, and comparing them to a predetermined threshold to generate a diagnostic indication is to provide data to this abstract data analysis. As stated above, the “transformation of measured biomarker values into a diagnostic score” is not an additional element of a transformation but rather falls under the judicial exception of analyzing abstract idea using mental processes and mathematical calculations (see above and MPEP 2106.05(C)). As described above under Step 2A prong 1, the claims recite mental processes (and mathematical concepts) and the further limitations to the abstract ideas do not change the nature of the limitations being abstract ideas. The human mind is capable of performing the operations recited in the claim denoted as mental processes. Thus, the physical wet lab steps are insignificant extra solution activity of data gathering because they only interact with the judicial exceptions by providing data to be processed by the abstract ideas.
Argument 5:
Applicant argues that amended claims 3 and 4 amount to significantly more than the judicial exception itself because the claims recite a combination of physical laboratory steps and specific computation operations that together form an inventive diagnostic process (Reply p. 9). Applicant argues that the use of a random forest classifier to identify a subset of biomarkers, followed by class-dependent scoring and evaluation of disease state based on a predetermined threshold, provides an unconventional approach to cancer detection (Reply p. 9).
This argument has been fully considered but found to be not persuasive. The MPEP states “Another consideration when determining whether a claim recites significantly more than a judicial exception is whether the additional element(s) are well-understood, routine, conventional activities previously known to the industry” (MPEP 2106.05(d)) which shows the analysis of conventionality is reserved for additional elements (i.e., not judicial exceptions). It is noted that the use of a random forest classifier to identify a subset of biomarkers, followed by class-dependent scoring and evaluation of disease state based on a predetermined threshold fall under the judicial exception itself (i.e., not additional elements). Thus, these limitations cannot provide significantly more than the judicial exceptions because these limitations are not additional elements and are not analyzed for conventionality under Step 2B of the 101 analysis.
Claim Rejections - 35 USC § 103
The rejection on the ground of 103 of claims 3, 5-10, and 14-16 as being unpatentable over Gold and Stanton et al. (US 20100070191 A1; previously cited) in view of Chaturvedi et al. (J Clin Oncol 28, 2719-2726 (2010); previously cited) in view of Díaz-Uriarte et al. (BMC Bioinformatics 7, 3 (2006); previously cited) in Office action mailed 22 December 2026 is withdrawn in view of the amendment of “combining the classification scores of each N biomarker to generate a plurality of N classification scores” and “comparing the plurality of N classification scores to a predetermined threshold” received 18 February 2026.
The rejection on the ground of 103 of claim 4 as being unpatentable over Gold and Stanton et al. (US 20100070191 A1; previously cited) in view of Zhang et al. (PLOS ONE 5(12): e15573. (Year: 2010); previously cited) in Office action mailed 22 December 2026 is withdrawn in view of the amendment of “combining the classification scores of each N biomarker to generate a plurality of N classification scores” and “comparing the plurality of N classification scores to a predetermined threshold” received 18 February 2026.
Conclusion
No claims are allowed.
Claims 3-10 and 14-16 is free of the prior art of record. Gold and Stanton et al. (US 20100070191 A1; previously cited) is the closest art of record which shows using capture reagents on protein biomarkers recited in the claim, retrieving biomarker level data in a computer, computing classification scores based on a class dependent probability distribution derived from training data and indicating a likelihood an individual has cancer. However, Gold and Stanton et al. (US 20100070191 A1; previously cited) does not show applying a random forest classifier to biomarker levels (or biomarkers such as CRP, CA6, or AKR7A2), combining the classification scores of each N biomarker to generate a plurality of N classification scores, and comparing the plurality of N classification scores to a predetermined threshold. Thus, claims 3-10 and 14-16 are free of the prior art of record.
This Office action is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this action.
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/J.E.H./Examiner, Art Unit 1685
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685
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