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 .
Status of the Claims
Claims 1-2, 10, 14-15, 17, and 19-25 are pending in the application.
Claims 19-20 are withdrawn.
Claims 1-2, 10, 14-15, 17, and 21-25 are the subject of this office action.
Claim Rejections - 35 USC § 112(a)
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.
Claims 1-2, 10, 14-15, 17, and 21-25 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.
Independent claims 1, 2, and 10 all contain the limitation “wherein the mRNA biomarkers are measured under sample hold-time and temperature conditions for which TBP expression stability matched to GBP5 and DUSP3 to maintain a stable score, as supported by the cartridge protocol”, this limitation does not appear in the specification, and the specification contains no recitation of a “cartridge protocol”. This is a new matter rejection.
Dependent claims 14-15, 17, and 21-25 are rejected because they depend from a rejected claim and fail to remedy its deficiencies.
Claims 1-2, 10, 14-15, 17, and 21-25 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for determination of whether a patient is positive or negative for TB infection, does not reasonably provide enablement for the full scope of the claims which encompasses determination of TB risk. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make or use the invention commensurate in scope with these claims.
In In re Wands, the Court set forth a non-exhaustive list of factors to be considered in determining whether undue experimentation would be involved in making and/or using the claimed invention. These factors include, but are not limited to:
(a) the breadth of the claims; (b) the nature of the invention; (c) the state of the prior art; (d) the level of one of ordinary skill; (e) the level of predictability in the art; (f) the amount of direction provided by the inventor; (g) the existence of working examples; and (h) the quantity of experimentation needed to make or use the invention based on the content of the disclosure.
Breadth of the claims and nature of the invention: The claims are directed to methods of identifying, evaluating, and treating TB infection, wherein all of the methods recite determining a patient’s risk of TB infection. The methods comprise measuring mRNA expression levels of the biomarkers GBP5, DUSP3, and TBP to identify the presence or risk of TB infection. The claims recite calculating a score which is compared to predetermined cutoff values. The claims (with the exception of claims 21 and 24) do not specifically define the cutoff values used in determining presence or risk of TB infection. The claims (with the exception of claim 23) do not establish how comparison of a calculated score to a threshold value is used to determine disease presence or risk. There are no claims within the application which both define the predetermined cutoff values and define how comparison of the calculated score and the cutoff value is used to draw diagnostic or prognostic conclusions regarding disease presence and risk. Claim 25 recites outputting certain triage instructions depending on the relationship between the calculated score and the cutoff values, but does not relate these scores, cutoff values, or triage instructions to risk in a way that definitively clarifies what it means for a patient to be high or low risk.
It is also noted that claim 10 recites classifying a patient into one of four different groups (active TB, high risk, low risk, negative) based only on comparison of a single calculated score to two predetermined cutoff values. It is not clear how comparison of one score to only two different cutoff values can yield accurate classification into four different groups (i.e. a calculated score can only really compare to two cutoff values in one of three ways: the score can be higher than both cutoffs; in between the two cutoffs; or lower than both cutoffs. How would this comparison be used to reliably yield classification into four different groups?).
State of the prior art/level of one or ordinary skill/level of predictability in the art: The prior art provides some examples of GBP5, DUSP3, and TBP expression levels used in the diagnosis of tuberculosis: see Nygren et al (US 2022/0106627 A1), Par. 4. The prior art contains other examples of GBP5 and DUSP3 expression levels used to diagnose or treat tuberculosis in the absence of TBP: see Khatri et al (US 2018/0291452 A1), Par. 7. However, the methods taught by Nygren include the measurement of additional biomarkers which are not specifically included in the instant claims. Nygren does not provide particular support or reduction to practice for the diagnosis of TB infection or risk based specifically on measurement of GBP5, DUSP3, and TBP in the absence of any other biomarkers.
Further, while the prior art teaches that these markers may be used in diagnosis of tuberculosis infection, it does not teach their use in classifying patients into particular high and low risk groups. While Nygren contains some discussion of evaluating risk, (see Par. 104) it does not explicitly discuss or reduce to practice the use of the particular biomarkers to determine a specific risk group. Criteria for high and low risk groups are not explicitly defined, and no particular thresholds or relationships in biomarker expression are identified for classifying patients into high and low risk groups based on particular biomarker expression data.
Thus, the level of predictability in the art for supporting the full scope of the claims is low, especially as it relates to identifying whether a patient has high or low risk of TB using only the three recited biomarkers. The prior art does not provide a predictable relationship between a score calculated from the expression levels of DUSP3, GBP5, and TBP and diagnosis of tuberculosis infection and risk. The prior art does not identify specific cutoff values for all three biomarkers which could be used to make these determinations and classifications, and does not provide guidance which would allow one of ordinary skill in the art to determine the specific cutoff values for the recited risk groups and differential diagnoses. The prior art does not teach calculation of a score using the formula recited in the instant claims.
Amount of direction provided by the inventor/existence of working examples: The most relevant direction and reduction to practice in the specification is provided in Examples 1-5 of the instant specification. The data and reduction to practice demonstrates differentiation of patients into 4 risk categories: positive, high risk, low risk, and negative, as shown in Example 5 and Fig. 5. Fig. 5 shows an X axis which represents whether a patient is determined to be positive or negative for TB infection based on MTB/RIF Ultra (i.e. a previously known and used method of diagnosing TB) and a Y axis which indicates a score calculated from GBP5, DUSP3, and TBP mRNA expression levels, wherein the score is compared to predetermined cutoff values to determine the risk group of the patient.
Example 5 in the specification provides one example of calculating a score and comparing it to cutoff values which are calculated based on their specificity and sensitivity. Results of this example are further displayed in Fig. 5. The results show a wide distribution of biomarker expression scores for both the positive group and the negative group (as determined by MTB/RIF Ultra). The data shows that some patients determined to be negative by MTB/RIF Ultra have biomarker expression scores which would indicate positive infection with TB. The data shows that many of the patients determined to be TB positive by MTB/RIF Ultra have biomarker expression scores which align with high risk, low risk, or even negative classifications. Both the positive and the negative groups show significant overlap in biomarker expression scores throughout all four risk classifications.
Additionally, while Example 5 provides exemplary cutoff values which are used to determine risk groups, these are exemplary and not explicitly limiting. That is, example 5 is not sufficiently representative of the full scope of the instantly claimed methods, which do not particularly define or place parameters on the cutoff values used, how they are calculated, or what relationship between a particular cutoff value and particular calculated score is required to draw a particular conclusion about a patient’s disease state or risk. While some of the dependent claims limit some of these features, there is no claim which defines and supports all of these features.
As such, the reduction to practice provided in the instant application is insufficient to fully support and fully enable the methods as claimed. That is, the quantity of experimentation needed to make or use the invention based on the content of the disclosure is considered undue because one cannot reliably or consistently draw a conclusion of TB risk classification based only on the limitations and steps of the methods as claimed. This is especially true of the independent claims which provide no specific limitation or definition of what the cutoff values or are how their comparison to a calculated score impacts drawing a conclusion of TB infection or risk.
Claim Rejections - 35 USC § 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.
Claims 1-2, 10, 14-15, 17, and 21-25 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 1-2, 10, 14-15, 17, and 21-25 are rejected as indefinite. The claims recite the terms “high risk” and “low risk” which are relative terms with unclear metes and bounds such that one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. The independent claims recite that a patient’s risk is determined by comparing a calculated score to predetermined cutoff values, however, what these values are, how they are determined, what they represent, and what relationship between each cutoff value and the calculated score is used to determine risk group is not defined in the claims and thus is unclear.
Dependent claim 21 defines specific first and second predetermined cutoff values, but does not provide or establish a specific relationship between these cutoff values and the recited risk classifications, such that the determination of risk made in the comparison step of the method is still unclear.
Dependent claim 23 establishes particular comparison steps and relationships between cutoff values and risk groups, but does not contain any definition of what the cutoff values are or how they are determined, such that what is actually being compared to draw a conclusion about patient risk of TB is still unclear.
Dependent claim 24 establishes that the first, second, and third predetermined cutoff values are based on particular thresholds of specificity and sensitivity, but these are not clearly defined (i.e. specificity and sensitivity for what?). Additionally, this claim still does not establish a particular or defined relationship between a patient’s risk group and each cutoff value.
The specification provides some clarification on the relationship between risk groups and predetermined cutoff values in Example 5 and Fig. 5 (see, especially Par. 431), however, this definition is presented as exemplary, and is not established as limiting or representative of the full scope of the claims as written (see, e.g. Par. 84 of the specification which indicates that cutoff values may be modified), such that provision of this singular example of specific cutoff values and their specific relationship to determining patient risk groups does not clarify the full scope of the claims which do not include these particular provisions and definitions and which (in most of the claims) do not establish any particular relationship between a particular cutoff value and a particular risk group.
Claim 24 is rejected as indefinite because it recites that predetermined cutoff values are defined by thresholds of specificity and sensitivity but does not establish what the specificity and sensitivity is relevant to, such that the scope of the claim is unclear.
Claims 1-2 and 10 are rejected as indefinite over the recitation “identifying the patient by the cartridge or the instrument” because it is not clear exactly what the limitation means or requires. Clarification is required.
Claims 1-2 and 10 are vague regarding “the cartridge protocol”. There is no previous introduction of a “cartridge protocol” in the claim, and as such there is insufficient antecedent basis for this limitation. Additionally, this makes the recitation “wherein the mRNA biomarkers are measured under sample hold-time and temperature conditions for which TBP exhibits expression stability matched to GBP5 and dESP3 to maintain a stable score, as supported by the cartridge protocol” unclear as what the cartridge protocol is and how it supports biomarker measurement is unclear, such that it is not clear what exactly this limitation requires or what conditions it implies.
Claim 14 is rejected as indefinite because it recites determining whether the patient is responding to treatment by comparing the levels of expression of biomarkers, but it does not indicate how the determination is made or what relationship between levels of expression would indicate whether or not a patient is responding to treatment.
Dependent claims 14-15, 17, and 21-25 are rejected as indefinite because they depend from a rejected claim and fail to remedy its deficiencies
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-2, 10, 14-15, 17, and 21-25 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more.
The claims are directed to methods of identifying and/or treating tuberculosis which comprise measuring biomarkers (DUSP3, GBP5, TBP) in a sample from a patient and comparing them to predetermined cutoff values in order to determine, the presence and/or risk of tuberculosis infection. As such, independent claims 1, 2, and 10 comprise multiple judicial exceptions: wherein the relationship between particular biomarkers and a particular disease state comprises a natural phenomena/law of nature; the calculation of a score based on biomarker expression and a mathematical formula comprises an abstract idea; and drawing a conclusion regarding the disease state of a patient based on biomarker expression comprises a mental process which may be performed in the human mind, and thus comprises an abstract idea.
Similar concepts have been held by the courts to constitute law of nature/natural phenomena, as in the identification of a correlation between the presence of myeloperoxidase in a bodily sample (such as blood or plasma) and cardiovascular disease risk in Cleveland Clinic Foundation v. True Health Diagnostics LLC, 859, F.3d 1352, 1361, 123 USPQ2d 1081, 1087 (Fed. Cir. 2017), and the natural relationship between a patient’s CYP2D6 metabolizer genotype and the risk that the patient will suffer QTc prolongation after administration of iloperidone in Vanda Pharmaceuticals Inc v. West-Ward Pharmaceuticals, 887 F.3d 1117, 1135-36, 126 USPQ2d 1266, 1281 (Fed. Cir. 2018). (See MPEP 2106.04(b)).
The correlation is naturally occurring and is a judicial exception because it exists in principle apart from any human action. The correlation itself (between biomarker expression levels and TB infection or risk) therefore cannot form the basis of eligibility.
Similarly, the identification and evaluation of tuberculosis infection which is a conclusion drawn based on the calculation of a score from a disclosed formula (which is itself a mathematical concept/abstract idea) constitutes and abstract idea and a mental process, wherein the claims encompass a practitioner drawing a certain conclusion based on certain data, a process which may be performed in the human mind. It is noted that the courts do not distinguish between mental processes performed by humans and claims that recite mental processes performed on a computer. See MPEP 2106.04(a)(2)(III).
As such, the identification of disease state and risk to which independent claims 1 and 10 and their dependent claims are directed to a judicial exception which cannot form the basis of eligibility.
Regarding claim 2 and its dependent claims, these are directed to a recited method of treating tuberculosis in a patient. While integration of a judicial exception into a particular method of treatment may serve to integrate recited judicial exceptions into a practical application, this is not the case with instant claims 2, 14, and 17.
Regarding whether integration of the judicial exception into a method of treatment comprises integration of the judicial exception into a practical application, MPEP 2106.04(d)(2) provides the following: “One way to demonstrate such integration is when the additional elements apply or use the recited judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition. The application or use of the judicial exception in this manner meaningfully limits the claim by going beyond generally linking the use of the judicial exception to a particular technological environment, and thus transforms a claim into patent-eligible subject matter. Such claims are eligible at Step 2A, because they are not “directed to” the recited judicial exception”. Regarding the particularity of the treatment step, the MPEP indicates that recitation of an abstract idea in conjunction with a step of, for example, “administering a suitable medication to a patient” does not integrate the judicial exception into a practical application because the treatment step is general (not particular) and is merely instruction to “apply” the judicial exception in a generic way.
As it applies to the instant case, the claimed treatment step recites “administering at least one tuberculosis treatment to the patient when the patient is identified as having tuberculosis”. Claim 2 and its dependents (excluding claim 15) do not identify any particular type of treatment or intervention, beyond administering a tuberculosis treatment to a patient determined to have tuberculosis. As such, the recitation of a generic treatment step is insufficient to integrate the recited judicial exceptions of these claims into a practical application.
Additional dependent claims in the application provide further limitations on how tuberculosis is diagnosed and how risk is classified, monitoring responsiveness to treatment (i.e. measuring expression levels of biomarkers over time and comparing them), sample type and preparation, and conditions of biomarker quantification. Some of these additional limitations are judicial exceptions themselves, and none of these limitations is sufficient to integrate the recited judicial exceptions into a practical application.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception. The amended claims recite limitations on cartridge device used to measure mRNA biomarker expression, and these are considered according to the “particular machine” guidance provided in MPEP 2106.05. While consideration of whether a judicial exception is applied with or by use of a particular machine is an important clue, it is not a standalone test for eligibility. The MPEP notes that integral use of a machine to achieve performance of a method may integrate the recited judicial exception into a practical application or provide significantly more, in contrast to where the machine is merely an object on which the method operates, which does not integrate the exception into a practical application or provide significantly more.
As it applies to the instant case, the particular machine (i.e. the cartridge and instrument) is only used to gather data which is used to support a diagnostic conclusion (i.e. judicial exception). The MPEP further notes that additional elements that invoke computers or other machinery as a tool to perform an existing process (in the instant case, a well-known and routine PCR method for measuring mRNA biomarkers in a sample) will generally not amount to significantly more than the judicial exception. In order for a machine to add significantly more than a judicial exception, it must play a significant part in permitting the claimed method to be performed, rather than function solely as an obvious mechanism for permitting a solution to be achieved more quickly. Use of a machine that contributes only nominally to execution of the claimed method (e.g. in a data gathering step) would not be sufficient to integrate a judicial exception into a practical application or provide significantly more. As such, the particular machine (i.e. cartridge and instrument) which is recited in the instant claims and is used in the method to perform data gathering in support of the judicial exception and to automate a process of drawing a conclusion (i.e. a mental process which could be performed in the human mind) is not sufficient to integrate the recited judicial exceptions into a practical application or provide significantly more than the judicial exceptions.
In addition to the judicial exceptions, claims further recite limitations which include detection of biomarkers in a sample and which limit the particular sample type and preparation and the particular method of biomarker detection. Neither the independent claims nor the additional limitations provided in the dependent claims are sufficient to constitute significantly more than the judicial exception because they amount to mere data gathering in support of the judicial exceptions (i.e. in order to detect or evaluate the disease state (abstract idea), one must gather data about biomarker expression and apply the naturally occurring relationship between biomarker levels and disease state/severity (law of nature)). Similarly, in order to calculate a score using the recited formula, one must gather data about biomarker expression. Such mere data gathering in support of a judicial exception has been identified by the courts as insignificant extra solution activity which cannot constitute significantly more than the judicial exception. See MPEP 2106.05(g).
Furthermore, detection of any biomarker in the blood has been identified by the courts to be routine and conventional activity in the life sciences arts (see MPEP 2106.05(d)(II)), such that it cannot constitute significantly more than the recited judicial exceptions.
Additionally, the specific measurement of GBP5, DUSP3, and TBP in a blood sample using a cartridge comprising a plurality of processing chambers in fluidic communication and a nucleic acid binding substrate for binding nucleic acid in fluidic communication with the processing chambers, wherein the processing chambers comprise regents for lysing cells from a sample, amplification and detection of nucleic acid from the sample, and a composition comprising sets of primers for detecting the biomarkers was known, routine, and conventional in the art before the effective filing date of the claimed invention, as demonstrated by Nygren et al (US 2022/0106627 A1; previously cited) and Khatri et al (US 2018/0291452 A1; previously cited) which establish GBP5, DUSP3, and TBP as known biomarkers which can be and have been detected by methods which are routine and conventional in the art (i.e. detection of mRNA expression levels of biomarkers in blood).
Both the instant specification and Nygren indicate that the cartridge used in the instantly claimed method may be a known and commercially available GeneXpert cartridge, wherein Nygren incorporates by reference US Pat Nos. 5,958,349; 6,403,037; 6,440,725; 6,783,736; 6,818,185; which describe this commercially available cartridge and have publication dates ranging from 1999-2004. See, especially, Pourahmadi et al (US 6,440,725 B1; IDS entered). Nygren further discusses methods of optimizing PCR conditions for the particular biomarkers detected, including optimization of incubation time, assay protocols, and cycling conditions (e.g. temperature, flow volume, rate, incubation time). See Nygren, Par. 13, 87, 93, 141-145, 203-215.
For all these reasons, the claimed elements, when taken alone or in combination, fail to include additional elements that are sufficient to either integrate the judicial exceptions into a practical application or amount to significantly more than the judicial exceptions.
Subject Matter Free of Prior Art
Claims 1-2, 10, 14-15, 17, and 21-25 are rejected as described above, but (as best interpreted in light of the 112(b) rejections identified above) appear to be free of the prior art.
The closest prior art is Nygren et al (US 2022/0106627 A1) and Khatri et al (US 2018/0291452 A1) which are discussed at length in the 102 and 103 rejections of the Non-Final Rejection of 30 October 2025.
Nygren and Khatri fail to meet the limitations of the instant independent claims 1, 2, and 10 because they do not teach or reasonably suggest the formula for calculating a score as recited in the claims.
Nygren and Khatri also fail to meet the limitation of the claims because they do not teach comparing the calculated score to cutoff values to determine a patient’s TB risk.
Response to Arguments
Applicant’s arguments filed 26 February 2026 have been fully considered.
The previous 112(a) written description rejection is withdrawn in view of the amendments to the claims which have narrowed the scope of the claims.
Regarding the 112(a) scope of enablement rejection, the previous grounds of rejection are withdrawn in favor of the new grounds of rejection presented above. Applicant’s arguments are largely based on the amendments to the claims, and these are specifically addressed in the new grounds of rejection presented above.
Regarding the 112(b) rejection of claim 14, applicant argues that claim 12 recites calculating scores at two timepoints using the same formula and comparing these scores. Applicant argues that one of ordinary skill in the art would understand that an increasing score indicates positive treatment response, as higher scores correlate with reduced TB infection severity. This argument is not persuasive because these relationships are not clearly established or defined within the claims themselves.
Regarding the 112(b) rejection of the terms high risk and low risk, Applicant argues that one of ordinary skill in the art would understand these terms correspond to specific numerical score ranges based on the specification’s teaching of the score formula and cutoff determination methodology, as shown in Specification Example 5. This argument is not persuasive for the reasons discussed at length in the 112(b) rejection above which addresses the amended claims.
The other previous 112(b) rejection are withdrawn in view of the cancellation and/or amendment of the rejected claims. New grounds of 112(b) rejection which address the amended claims are presented above.
Regarding the 101 rejection, Applicant argues that the amended claims of the application integrate the judicial exceptions into a practical application because performance of the recited methods with the amended cartridge limitations is an implementation of the judicial exception with or use of the judicial exception in conjunction with a particular machine or manufacture that is integral to the claim. This argument is not persuasive for the reasons discussed at length in the new grounds of 101 rejection presented above which addresses the amended claims and particular machine analysis.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ELLIS LUSI whose telephone number is (571)270-0694. The examiner can normally be reached M-Th 8am-6pm ET.
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/ELLIS FOLLETT LUSI/Examiner, Art Unit 1677
/BAO-THUY L NGUYEN/Supervisory Patent Examiner, Art Unit 1677 April 14, 2026
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