DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Applicant's response, filed on 07/30/2025, 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.
Status of claims
Canceled:
2-3, 11
Amended:
1, 22-23
New:
24-25
Pending:
1, 4-10, 12-25
Withdrawn:
none
Examined:
1, 4-10, 12-25
Independent:
1, 24
Allowable:
none
Priority
As detailed on the 10/27/2020 filing receipt, this application claims priority to as early as 03/28/2018 the filing date of provisional application 62/648984.
Withdrawn Rejections/Objections
The objection to the disclosure because it contains an embedded hyperlink and/or other form of browser-executable code, in the Office action mailed 03/21/2025 is withdrawn in view of the amendments filed 07/30/2025.
Newly Applied USC 35 103 Claims Rejection
No prior art was applied to claims 1, 4-10 and 12-23 in the office action mailed 03/21/2024. However, new USC 35 103 claim rejections are applied in view of claim amendments filed 07/30/2025 as indicated below.
Claim Rejections - 35 USC § 112
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, 4-10 and 12-25 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.
Claim 1 (page 5, line 25, predicting step) and claim 24 (page 11, line 7, predicting step) recites “predicting a clearance capacity of the subject based upon an analysis of the abundance of the xenobiotic clearance protein within the liver of the subject and a pharmacokinetic simulation model that is designed to predict exposure and effects of the given drug or pharmaceutical in humans or animals, the abundance of the xenobiotic clearance protein being used to define a starting point for the pharmacokinetic simulation model...” The specification does not disclose abundance of the xenobiotic clearance protein being used to define a starting point for the pharmacokinetic simulation model. The specification discloses “The augmented first input data is used to define the starting points for the simulation model of the invention, in terms of baseline levels of drug metabolizing, transporting and clearance protein or enzyme within the individual's tissues, optionally in combination with gene identity and expression data including allelic variation and whether certain genes are either up- or down- regulated compared to average (i.e. mean or median) levels within a given population.” (page 23, para. 2, line 22).
Claim 1 (page 6, line 3) recites “…administering the given drug or pharmaceutical compound in accordance with the dosage regimen that is optimized for the subject, so as to treat liver cancer, in the subject, in a personalized manner.” The specification does not disclose administering the given drug or pharmaceutical compound and the dosage regimen that is optimized for the subject for treating liver cancer.
These are new matter rejections.
Dependent claims are rejected for depending on rejected claim.
Claim Rejections - 35 USC § 112
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, 4-10 and 12-25 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.
Claim 1 (page 6, line 2) and claim 24 (Page 11, line 11) recite “…to achieve efficacy while lessening a risk of safety issues…” The recited “efficacy” and “lessening a risk” are subjective terms of relative or vague degree or form of association, neither defined in the specification, nor having a well-known and sufficiently particular definition in the art (See MPEP 2173.05(b)). A claim term that requires the exercise of subjective judgment without restriction may render the claim indefinite. In re Musgrave, 431 F.2d 882, 893, 167 USPQ 280, 289 (CCPA 1970) (See 2173.05(b)).
Claim 1 (page 4, line 21, normalizing step) and claim 24 (Page 10, line 9, normalizing step) recite “…genes that are expressed principally and consistently in the liver to ensure…” The recited “principally” and “consistently” are subjective terms of relative or vague degree or form of association, neither defined in the specification, nor having a well-known and sufficiently particular definition in the art (See MPEP 2173.05(b)). A claim term that requires the exercise of subjective judgment without restriction may render the claim indefinite. In re Musgrave, 431 F.2d 882, 893, 167 USPQ 280, 289 (CCPA 1970) (See 2173.05(b)).
Dependent claims are rejected for depending on rejected claim.
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, 4-10 and 12-25 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Mental processes recited include:
Claims 1, 14, 22 and 24 recites: determining a dosage regimen that is optimized for a subject and that is tailored for personalized treatment of liver cancer; identifying a xenobiotic clearance protein that contributes to pharmacokinetics of a given drug or pharmaceutical that is suitable for treating liver cancerin a human or animal; analysing the isolated cfRNATOTAL in order to determine an amount of the first cfRNA present within the cfRNATOTAL; performing an analysis of the cfRNATOTAL...; determining SCF as the mean concentration of mRNA...; identifying an abundance of the xenobiotic clearance protein...; ...comparing the amount of first cfRNA encoding the xenobiotic clearance protein with an abundance curve for the abundance of the xenobiotic clearance protein in the liver and predicting a clearance capacity of the subject based upon an analysis of the abundance of the xenobiotic clearance protein within the liver of the subject; and a pharmacokinetic simulation model that is designed to predict exposure and effects of the given drug or pharmaceutical in humans or animals, the abundance of the xenobiotic clearance protein being used to define a starting point for the pharmacokinetic simulation model; generating a dosage regimen for the given drug or pharmaceutical compound..." The process of identifying, analyzing, determining and comparing are acts of evaluating information that could be practically performed in the human mind or with pen and paper. Generating a dosage regimen involves developing a plan that requires using judgements, which could be practically performed in the human mind or with pen and paper.
Claim 10 recite: abundance curve is generated by comparison of matched samples. The process of comparing is an act of evaluating information that could be practically performed in the human mind or with pen and paper.
Claim 12 recites: wherein the SCF is determined... The process of determining is an act of evaluating information that could be practically performed in the human mind or with pen and paper.
Claim 13 recites: three marker genes are selected in order to determine the SCF. The process of selecting and determining are involved with evaluating and analyzing data that could be practically performed in the human mind or with pen and paper.
Mathematical concepts recited include:
Claims 1, 14 and 22 recites: performing a normalizing function on the amount of the first cfRNA present against a RNA organ Shedding Correction Factor (SCF) that is determined for the subject; ...quantify an amount of mRNA present within the cfRNArnTAL... and determining SCF as the mean concentration of mRNA of the each of two or more marker genes present within the cfRNATOTAL. These limitations are mathematical concepts that requires performing a series of mathematical calculations.
Claim 12 recites: ...formula A... Where N is equal to a number of marker genes quantified. These limitations are mathematical concepts and formulas that requires performing a series of mathematical calculations.
Claims 2-9, 15-21 and 23 do not recite JEs.
The processes of claims 1, 14 and 22 include identifying, analyzing, determining and comparing are acts of evaluating information that could be practically performed in the human mind or with pen and paper. Claim 1 also includes the process of generating a dosage regimen involves developing a plan that requires using judgements, which could also be practically performed in the human mind or with pen and paper. Claim 10 is involved with the process of comparing, which is an act of evaluating information. Claims 12 and 13 involves the process of determining and is an act of evaluating information. Acts of evaluating and analyzing data could be practically performed in the human mind and/or with pen and paper because they merely require making observations, evaluations, judgments, and opinions (See MPEP 2106.04(a)(2) subsection III). Therefore, under the broadest reasonable interpretation, claims 1, 10, 12-14 and 22 could be practically carried out in the human mind or with pen and paper as claimed, which falls under the "Mental processes" grouping of abstract ideas.
Claim 1 recites a computer implemented method, claim 14 recites an input device, for inputting data relating to the subject and a non-transitory computer readable medium containing program instructions and claim 22 recites a computer server comprising: a computer readable medium containing program instructions configured to embody steps of claim 1, wherein execution of the program instructions results in one or more processors of the server. The recited computer components of claims 1, 14 and 22 equate to generic computer components. Although claims 1, 14 and 22 recite performing the steps as part of a method executed on a computer there are no additional imitations to indicate that anything other than a generic computer is required. Merely requiring that the steps are carried out with a generic computer does not negate the mental nature of these steps and equates rather to merely using a computer as a tool to perform the mental process.
Claims 1, 12, 14, and 22 recites mathematical concepts and formulas as discussed above. The process of normalizing and quantifying requires carrying out a series of mathematical calculations and the recited formula is a mathematical concept and formula that requires carrying out a series of mathematical calculations to utilize the formula to obtain a value. Therefore, claims 1, 12, 14, and 22 recite claim elements that falls under the “mathematical concepts” grouping of abstract ideas.
As such, claims 1, 4-10 and 12-25 recite an abstract idea (Step 2A, Prong 1: YES).
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). The above indicated judicial exceptions are not integrated into a practical application because the claims do not recite an additional elements that apply, rely on or use the judicial exception in such a manner to amount to integration into a practical application. For example, there are no limitations that reflect an improvement to technology or applies or uses the recited judicial exception in some other meaningful way. Rather, the instant claims recite additional elements that equate to mere instructions to implement an abstract idea or insignificant extra solution activity. Specifically, the instant claims recite the following additional elements:
claims 1, 14 and 22: the recited "isolating total cell free RNA (cfRNATOTAL) from the liquid biopsy... administering the given drug or pharmaceutical compound in accordance with the dosage regimen that is optimized for the subject, so as to treat liver cancer, in the subject, in a personalized manner." step/element. Isolating total cell free RNA is a data gathering step and administering the given drug or pharmaceutical compound is not particular and is merely instructions to "apply" the exception in a generic way (See MPEP 2106.04(d)(2))."
Claim 1: the recited "a computer"
claim 14: the recited "input device, for inputting data relating to the subject," "output device for presenting a model," "a non-transitory computer readable medium" and "processors" step/element.
Claim 15: the recited "input device" and "output device" step/element.
Claim 16: the recited "input device," "output device" and "user interface device" step/element.
Claim 20: the recited "first server" and "second server" step/element.
Claim 21: the recited "second server" step/element.
claim 22: the recited "computer server," "a computer readable medium," "processors," "server," "medium is non-transitory" and "telecommunication module" step/element.
Claims 4-10, 13, 17-19 and 23 do not recite additional elements in addition to the JEs.
Claims 17-19 and 23 are providing information on the location of the computer readable medium and server.
Claims 4-9 are providing information on what the data represents and do not change the character of the data obtaining step beyond mere data gathering activity.
These elements of claims 1, 14-16 and 20-22 equate to insignificant extra solutional activities of data gathering, data inputting and data outputting. The limitations of obtaining data serves as input to the recited judicial exception in the claims. The recited computer components of claims 1, 14-16 and 20-22 equate to generic computer components. The step of administering the given drug or pharmaceutical compound of laims 1, 14 and 22 are not particular and is merely instructions to "apply" the exception in a generic way (See MPEP 2106.04(d)(2)). As such, as currently recited, the claims do not appear to recite an improvement to technology or apply or use the recited judicial exception in some other meaningful way. Therefore, claims 1, 4-10 and 12-25 are directed to an abstract idea (Step 2A, Prong 2: NO).
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 claims recite additional elements that equate to well-understood, routine and conventional activities, insignificant extra-solution activity or mere instructions to implement the abstract idea on a generic computer. The instant claims recite the following additional elements:
claims 1, 14 and 22: the recited "isolating total cell free RNA (cfRNATOTAL) from the liquid biopsy... administering the given drug or pharmaceutical compound in accordance with the dosage regimen that is optimized for the subject, so as to treat liver cancer, in the subject, in a personalized manner." step/element. Isolating total cell free RNA is a data gathering step and administering the given drug or pharmaceutical compound is not particular and is merely instructions to "apply" the exception in a generic way (See MPEP 2106.04(d)(2)).
Claim 1: the recited "a computer"
claim 14: the recited "input device, for inputting data relating to the subject," "output device for presenting a model," "a non-transitory computer readable medium" and "processors" step/element.
Claim 15: the recited "input device" and "output device" step/element.
Claim 16: the recited "input device," "output device" and "user interface device" step/element.
Claim 20: the recited "first server" and "second server" step/element.
Claim 21: the recited "second server" step/element.
claim 22: the recited "computer server," "a computer readable medium," "processors," "server," "medium is non-transitory" and "telecommunication module" step/element.
The additional elements indicated above do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Limitations that equate to mere data gathering and outputting via generic computer components, such as receiving data at a computer or outputting data, amount to insignificant extra-solution activity as set forth by the courts in Mayo, 566 U.S. at 79, 101 USPQ2d at 1968 and OIP Techs., Inc, v, Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015). Also, the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application or provide significantly more as identified by the courts in Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit). Additionally, the courts have recognized that the laboratory technique of determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017) is a well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity (see MPEP 2106.05(d)(II)). Also, Schwarzenbach (as cited on the 03/21/2025 PTO-892 form) teaches that the isolating and using cell-free RNA to identify biomarkers related to cancer are known methods. Schwarzenbach discussed the latest developments in the use of circulating microRNAs as prognostic and predictive biomarkers and discusses their utility in personalized medicine (Abstract) and that the advantages of using cfmiRNAs in cancer diagnosis include the low cost and ease of the assays used for cfmiRNAs analysis, as well as the quick results using PCR-based methods from the first day of diagnosis and before any therapeutic intervention (Page 145, col. 1, para. 1). The step of administering the given drug or pharmaceutical compound in claim 1 is not particular and is merely instructions to "apply" the exception in a generic way (See MPEP 2106.04(d)(2)). Overall, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 1, 4-10 and 12-25 are not patent eligible.
Response to 35 USC §101 (Remarks received 07/30/2025, pages 13-17)
Applicant argues that the claims recite eligible subject matter under MPEP 2106 and are not directed to Judicial Exception (Step 2A, Prong One). Applicant argues that claims 1 and 24 do not recite a law of nature, nor do they recite a mathematical formula, mental process, or method of organizing human activity, but are directed to biological measurement, normalization, and simulation, all for the clinical purpose of tailoring treatment to a patient with liver cancer.
Applicant discusses that each claim recites multiple technological steps that are not mental or conventional business practices. Applicant states that the claims represent a technical diagnostic and therapeutic process, grounded in molecular biology and pharmacokinetics and are not abstract in nature. Applicant also states that the claims require physical processing of a liquid biopsy sample, RNA isolation, normalization against a defined liver-specific gene set, and use of that normalized RNA data to simulate liver function in the context of a pharmacokinetic model.
In response, Applicant’s argument is not persuasive. As indicated above in the 101 rejection section, the claims include mental and mathematical concepts. Examples of mental processes recited in claim 1 include “identifying a xenobiotic clearance protein…,” “analysing the isolated cfRNATOTAL…” and “comparing the amount of first cfRNA…” The process of identifying, analyzing, determining and comparing are acts of evaluating and analyzing information that could be practically performed in the human mind or with pen and paper. Examples of mathematical concepts recited in claim 1 include “determining SCF as the mean concentration of mRNA of the each of two or more marker genes present within the cfRNATOTAL…” which requires performing a series of mathematical calculations to determine the mean concentration of mRNA. Additionally, the courts have recognized that the laboratory technique of determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017) is a well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity (see MPEP 2106.05(d)(II)). Also, Schwarzenbach (as cited on the attached PTO-892 form) teaches that the isolating and using cell-free RNA to identify biomarkers related to cancer are known methods. Schwarzenbach discussed the latest developments in the use of circulating microRNAs as prognostic and predictive biomarkers and discusses their utility in personalized medicine (Abstract) and that the advantages of using cfmiRNAs in cancer diagnosis include the low cost and ease of the assays used for cfmiRNAs analysis, as well as the quick results using PCR-based methods from the first day of diagnosis and before any therapeutic intervention (Page 145, col. 1, para. 1).
Applicant argues that the claims integrate any alleged abstract idea into practical application of Particular treatment or prophylaxis for a disease or medical condition (Step 2A, Prong Two) because claim 1 includes an "administering" step, which aligns directly with USPTO Example 29. Applicant states that both claims 1 and 24 include normalization using a fixed panel of liver-specific genes - a concrete biochemical operation that reflects an improvement to the field of personalized pharmacology, and not merely a "conventional data analysis step."
Applicant further argues that the claims recite significantly more than any alleged abstract idea (Step 2B). Applicant states the following:
* The use of liquid biopsies, quantification of cfRNA, normalization against specific gene markers, and estimation of liver enzyme abundance are not conventional clinical practices.
* The use of subject-specific cfRNA data to parameterize a pharmacokinetic simulation model constitutes a non-routine and non-generic implementation of machine learning and modeling in clinical care.
* The generation of a personalized dosage regimen, and especially its administration in claim 1, ensures the method does not merely recite a concept, but puts it into action to achieve therapeutic benefit.
In response, Applicants’ arguments that the claims integrate the judicial exception into a practical application by applying or using a judicial exception to affect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2) under Step 2A, Second Prong, 2nd consideration of the 101 analysis have been fully considered and are not persuasive. According to MPEP 2106.04(d)(2), Examples of "treatment" and prophylaxis" limitations encompass limitations that treat or prevent a disease or medical condition, including, e.g., acupuncture, administration of medication, dialysis, organ transplants, phototherapy, physiotherapy, radiation therapy, surgery, and the like. For example, an immunization step that integrates an abstract idea into a specific process of immunizing that lowers the risk that immunized patients will later develop chronic immune-mediated diseases is considered to be a particular prophylaxis limitation that practically applies the abstract idea. See, e.g., Classen Immunotherapies, Inc. v. Biogen IDEC, 659 F.3d 1057, 1066–68, 100 USPQ2d 1492, 1500-01 (Fed. Cir. 2011). In order to qualify as a "treatment" or "prophylaxis" limitation for purposes of this consideration, the claim limitation in question must affirmatively recite an action that effects a particular treatment or prophylaxis for a disease or medical condition. An example of such a limitation is a step of "administering amazonic acid to a patient" or a step of "administering a course of plasmapheresis to a patient." If the limitation does not actually provide a treatment or prophylaxis, e.g., it is merely an intended use of the claimed invention or a field of use limitation, then it cannot integrate a judicial exception under the "treatment or prophylaxis" consideration. For example, a step of "prescribing a topical steroid to a patient with eczema" is not a positive limitation because it does not require that the steroid actually be used by or on the patient, and a recitation that a claimed product is a "pharmaceutical composition" or that a "feed dispenser is operable to dispense a mineral supplement" are not affirmative limitations because they are merely indicating how the claimed invention might be used. Additionally, the treatment or prophylaxis limitation must be "particular," i.e., specifically identified so that it does not encompass all applications of the judicial exception(s). For example, consider a claim that recites mentally analyzing information to identify if a patient has a genotype associated with poor metabolism of beta blocker medications. This falls within the mental process grouping of abstract ideas enumerated in MPEP § 2106.04(a). The claim also recites "administering a lower than normal dosage of a beta blocker medication to a patient identified as having the poor metabolizer genotype." This administration step is particular, and it integrates the mental analysis step into a practical application. Conversely, consider a claim that recites the same abstract idea and "administering a suitable medication to a patient." This administration step is not particular, and is instead merely instructions to "apply" the exception in a generic way. Thus, the administration step does not integrate the mental analysis step into a practical application. (See MPEP 2106.04(d)(2)).
Although amended claim 1 recites an action that effects a particular treatment or prophylaxis for a disease or medical condition with an administration step, the administration step of amended claim 1 is not particular because the treatment is not specifically identified so that it does not encompass all applications of the judicial exception(s). Amended claim 1 recites a step of “administering the given drug or pharmaceutical compound in accordance with the dosage regimen that is optimized for the subject, so as to treat liver cancer, in the subject, in a personalized manner.” This administration step of amended claim 1 is similar to the example of “administering a suitable medication to a patient” provided by MPEP 2106.04(d)(2) mentioned above that was found to not be particular, and is instead merely instructions to "apply" the exception in a generic way. Thus, the administration step does not integrate the JEs into a practical application. (See MPEP 2106.04(d)(2)).
Additionally, the courts have recognized that the laboratory technique of determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017) is a well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity (see MPEP 2106.05(d)(II)). Also, Schwarzenbach (as cited on the attached PTO-892 form) teaches that the isolating and using cell-free RNA to identify biomarkers related to cancer are known methods. Schwarzenbach discussed the latest developments in the use of circulating microRNAs as prognostic and predictive biomarkers and discusses their utility in personalized medicine (Abstract) and that the advantages of using cfmiRNAs in cancer diagnosis include the low cost and ease of the assays used for cfmiRNAs analysis, as well as the quick results using PCR-based methods from the first day of diagnosis and before any therapeutic intervention (Page 145, col. 1, para. 1). Therefore, isolating and quantifying mRNA estimating of liver enzyme abundance are conventional methods. The generation of a personalized dosage regimen appears to be instructions to generally apply the exception, and the pharmacokinetic simulation model is itself a JE (mathematical concepts, i.e., this does not amount to a practical application as inputting into a statistical model further does not apply, rely on or use the JE(s) in a meaningful way, rather is just further performing additional mathematical calculations). Therefore, the JEs of claim 1 are not integrated into a practical application.
It is understood that Applicant argues that the claims of USPTO Subject Matter Eligibility Example 29 is similar to the claims of the instant application because both sets of claims recite an administration step. Applicant’s arguments are not persuasive. In Example 29, titled Diagnosing and Treating Julitis, claims 5 and 6 that include an administration step that are eligible because the claims include the claim limitation of administering a specific type of unconventional treatment to the patient. In claim 5 of Example 29, administering topical vitamin D was found to be an unconventional step that is more than a mere instruction to “apply” the judicial exception using well-understood, routine or conventional techniques in the field. For claim 6 of Example 29, the additional elements of the claim as a whole adds meaningful limits on the use of the judicial exception. The steps include the recitation of a particular treatment (administration of an effective amount of anti-TNF antibodies) integrate the exception into the diagnostic and treatment process, and amount to more than merely diagnosing a patient with julitis and instructing a doctor to generically “treat it.” Further, the combination of steps, which is not routine and conventional, ensures that patients who have julitis will be accurately diagnosed (due to the detection of JUL-1 in their plasma) and properly treated with anti-TNF antibodies, as opposed to being misdiagnosed as having rosacea as was previously commonplace. As discussed above, claim 1 recites a general form of treatment of a given drug or pharmaceutical compound, which is merely merely instructions to "apply" the exception in a generic way and does not integrate a judicial exception under the "treatment or prophylaxis" consideration.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1, 4-10, 12-21 and 24-25 are rejected under 35 U.S.C. 103 as being unpatentable over Nerenberg (WO 2017/156310 A1, published 14 September 2017; cited on the 10/20/2020 IDS Document), in view of Gao (Gao, Jie, et al. "Changes in cytochrome P450s-mediated drug clearance in patients with hepatocellular carcinoma in vitro and in vivo: a bottom-up approach." Oncotarget 7.19 (2016): 28612., published 2016; cited on the attached “Notice of References Cited” form 892); Gharbi (Identification of Reliable Reference Genes for Quantification of MicroRNAs in Serum Samples of Sulfur Mustard-Exposed Veterans. Cell J. 2015 Fall;17(3):494-501., published 2015; cited on the 10/20/2020 IDS Document); Anderson ("A comparison of selected mRNA and protein abundances in human liver." Electrophoresis 18.3‐4 (1997): 533-537; cited on the attached “Notice of References Cited” form 892.); Zhang (Content and activity of human liver microsomal protein and prediction of individual hepatic clearance in vivo. Sci Rep 5, 17671 (2015); cited on the attached “Notice of References Cited” form 892). Any newly recited portions herein are necessitated by claim amendment.
Regarding independent claim 1, Nerenberg teaches the claim limitation of quantifying an amount of a first cell free RNA (cfRNA) present in a liquid biopsy obtained from the subject with Nerenberg’s Claim 34 (b). Claim 34(b) “measuring a quantity of liver ribonucleic acids (RNA) in the biological fluid.”
Nerenberg teaches the claim limitation of wherein the first cfRNA originates from a liver of the subject, and wherein the first cfRNA codes for the xenobiotic clearance protein with Nerenberg’s claim 54. Claim 54 “The method of claim 34, wherein the liver RNA corresponds to a gene selected from the group consisting of: 1810014F10RIK, A1BG, ABCC2, ABCC6, ABCG5, ANG, ANGPTL3, ACOX2, ACSM2A, ADH1A, ADH1C, ADH6, AFM, AFP, AGXT, AHSG, AKR1C4 …”
Nerenberg teaches the claim limitation of isolating total cell free RNA (cfRNATOTAL) from the liquid biopsy using (a) a density gradient medium to isolate lymphocytes from peripheral blood, (b) an RNA extraction kit to collect total nucleic acid from the lymphocytes, and/or (c) a DNA extraction kit to remove DNA from the total nucleic acid with “Some methods disclosed herein comprise isolating at least one marker and/or at least one tissue-specific polynucleotide. In some cases, the at least one marker and/or at least one tissue- specific polynucleotide comprise a cell-free polynucleotide. In some cases, isolating the cell- free polynucleotide comprises fractionating the sample from the subject. Some methods comprise removing intact cells from the sample. For example, some methods comprise centrifuging a blood sample and collecting the supernatant that is serum or plasma, or filtering the sample to remove cells. In some embodiments, cell-free polynucleotides are analyzed without fractionating the sample from the subject. For example, urine, cerebrospinal fluid or other fluids that contain little to no cells may not require fractionating. Some methods comprise sufficiently purifying the cell-free polynucleotides in order to detect/quantify/analyze the cell- free polynucleotides. Various reagents, methods and kits can be used to purify the cell-free polynucleotides. Reagents are known in the art and include, but are not limited to, Trizol, phenol-chloroform, glycogen, sodium iodide, and guanidine resin. Kits include, but are not limited to, Thermo Fisher ChargeSwitch® Serum Kit, Qiagen RNeasy Kit, ZR serum DNA kit, Puregene DNA purification system, QIAamp DNA Blood Midi kit, QIAamp Circulating Nucleic Acid Kit, and QIAamp DNA Mini kit.” (para. [0061])
Nerenberg teaches the claim limitation of analysing the isolated cfRNATOTAL in order to determine an amount of the first cfRNA present within the cfRNATOTAL with Nerenberg’s claim 44. Claim 44. “The method of claim 34, wherein measuring the quantity of liver RNA comprises measuring the relative contribution of liver RNA to a nucleic acid population selected from total RNA of the biological fluid and total nucleic acids of the biological fluid.”
Nerenberg teaches the claim limitation of normalizing the amount of the first cfRNA present against a plurality of marker genes that are expressed principally and consistently in the liver to ensure correct measurement of enzyme expression and determining a Shedding Correction Factor (SCF) for the subject by: (i) performing an analysis of the cfRNATOTAL in order to quantify an amount of mRNA present within the cfRNATOTAL that corresponds to each of the plurality of marker genes with “In some cases, the methods comprise normalizing cell-free transcript values. This involves reseating cell-free transcript values to housekeeping gene transcript values. Next, the sample's total RNA is assessed against the panel of tissue-specific genes using quadratic programming in order to determine the tissue-specific relative contributions to the sample's cell - free transcriptome. The following constraints are employed to obtain the estimated relative contributions during the quadratic programming analysis: a) the RNA contributions of different tissues are greater than or equal to zero, and b) the sum of all contributions to the cell -free transcriptome equals one.” (para. [0079]).
Nerenberg teaches the claim limitation of wherein each of the plurality of marker genes is with “In most cases, liver RNA disclosed herein is RNA that is predominantly expressed in a human liver. In most cases, liver RNA disclosed herein is RNA expressed substantially higher in liver than in any other tissue of the human subject. In some cases, liver RNA corresponds to a gene selected from the group consisting of: 1810014F10RIK, A1BG, ABCC2, ABCC6, ABCG5, ANG, ANGPTL3, ACOX2, ACSM2A, ADHl A, ADHIC, ADH6, AFM, AFP, AGXT, AHSG, AKR1C4, AKR1D1, ALB, ALDH1B1, ALDH4A1, ALDOB, AMBP, AOC3, APCS, APOAl, APOA2, APOA5, APOB, APOC1, APOC2, APOC3, APOC4, APOE, APOF, APOH, APOM, ARID 1 A, ARSE, ASL, AQP9, ASGR1, ASGR2, ATF5, C4A, C4BPA, C6, C8A, C8B, C8G, C9, CAPN5, CES1, CES2, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CHD2, CIDEB, CPN1, CRLF1, CRYAA, CYP1A2, CYP27A1, CYP2A13, CYP2A6, CYP2A7, CYP2B6, CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2E1, CYP3A4, CYP4A11, CYP4A22, CYP4F12, DIOl, DAK, DCXR, F10, F12, F2, F9, FAH, FCN2, FETUB, FGA, FGB, FGG, FM03, FTCD, G6PC, GPC3, GALKl, GAMT, GBA, GBP7, GCKR, GLYAT, GNMT, GPT, GSTM1, HAAO, HAMP, HAOl, HGD, HGFAC, HMGCS2, haptoglobin, HPN, HPR, HPX, HRG, HSDl lBl, HSD17B6, HLF, IGF2, ILIRN, IGFALS, IQCE, ITIHl, ITIH2, ITIH4, JCLN, KHK, KLK13, LBP, LECT2, LOC55908, LP A, MASP2, MBL2, MGMT, MUPCDH, NHLH2, NNMT, NSFL1C, OATP1B1, ORM2, PCK1, PEMT, PGC, PLG, PKLR, PLGLB2, POLR2C, PON1, PON3, PROC, PXMP2, RBP4, RDH16, RET, SAA4, SARDH, SDS, SDSL, SEC14L2, SERPINA4, SERPINA7, SERPINA10, SERPF A11, SERPINC1, SERPF D1, SLC01B1, SLC10A1, SLC22A1, SLC22A7, SLC22A10, SLC25A47, SLC27A5, SLC38A3, SLC6A12, SPP2, TAT, TBX3, TF, TEVI2, TMEM176B, TST, UPB1, UROC1, VTN, WNT7A, C2, C20RF72, CPB2, CYP4F11, CYP4F2, DUSP9, GABBRl, HP, HPD, IGSF1, IL17RB, ITIH2, ITIH3, LCAT, LGALS4, MAT1A, MST1, MSTP9, NR0B2, NR1I2, ORM1, RELN, RGN, RHBG, SAA4, SERPF A5, SERPINA7, SERPINC1, SERPFNF2, SLC2A2, SULT1A2, SULT2A1, TCP10L, TNNI2, UGT2B15, and UGT2B17…” (para. [0004]).
Nerenberg teaches the claim limitation of generating, based on the clearance capacity of the subject, a dosage regimen for the given drug or pharmaceutical compound that is optimized for the subject to achieve efficacy while lessening a risk of safety issues and administering the given drug or pharmaceutical compound in accordance with the dosage regimen that is optimized for the subject, so as to treat liver cancer, in the subject, in a personalized manner with with “Further provided herein are systems. Such systems comprise: (a) a memory unit configured to store results of (i) an assay for detecting at least one marker of each of at least one condition in a first sample of a subject, and (ii) an assay for detecting at least one tissue-specific RNA in a second sample of a subject, wherein each of the at least one tissue-specific RNA is a cell-free RNA specific to a tissue; (b) at least one processor programmed to: (i) quantify a level of the at least one marker; (ii) quantify a level of the at least one tissue-specific polynucleotide; (iii) compare the level of each of the at least one marker to a corresponding reference level of the marker; (iv) compare the level of each of the at least one tissue-specific polynucleotide to a corresponding reference level of the tissue-specific polynucleotide; and (v) determine presence of or relative change in damage of the tissue by the at least one condition based on the comparing; and (c) an output unit that delivers a report to a recipient, wherein the report provides results generated by the processor in (b). Optionally, reports comprise a recommendation for medical action based on the generated by the processor in (b). In some instances, medical action comprises recommended treatment. In many instances, the at least one tissue-specific polynucleotide comprises at least one tissue specific RNA.” (para. [0006]) and “Multiple diseases and tissues may be assessed simultaneously using the kits, systems and methods disclosed herein. In this way, the kits, systems and methods disclosed herein may be used to assess the presence or absence of at least one condition and identify both affected and unaffected tissues. In some embodiments, methods comprise selecting or recommending a medical action based on results produced by the methods, systems or kits disclosed herein. In some embodiments, a customized medical action is recommended, and optionally taken, based on the determination. In some instances, customized medical action comprises directly treating a tissue under duress, e.g., with radiation or injection of the tissue. Non-limiting examples of medical actions include performing additional tests (e.g., biopsy, imaging, surgery), treating the subject for the disease or condition, and modifying a treatment of the subject (e.g. altering the dose of a pharmaceutical composition, ceasing administration of a pharmaceutical composition, administering a different or additional pharmaceutical composition).” (para. [0020]) and “In some embodiments, the methods disclosed herein comprise detecting and/or analyzing at least one polynucleotide (e.g., RNA, DNA) associated with a liver-associated disease or condition. The at least one polynucleotide may comprise a gene or genetic transcript or portions thereof associated with a liver-associated disease or condition. The portion of the gene or genetic transcript thereof may comprise a sufficient number of nucleotides to determine the portion of the gene or genetic transcript thereof is associated with a gene of interest, mutants thereof, chemical modifications thereof, and splice variants thereof. The polynucleotide may encode a protein or identifiable portion thereof. The gene of interest, by way of non-limiting example, may be selected from a gene associated with a cellular function selected from lipid metabolism, lipid storage, lipid transport (uptake/efflux), cholesterol metabolism, cholesterol storage, cholesterol transport (cellular uptake/efflux), inflammation, extracellular matrix formation, drug metabolism, drug transport (cellular uptake/efflux), vitamin storage, vitamin uptake, vitamin metabolism, and apoptosis.” (para. [00183]).
Nerenberg does not explicitly teach the claim limitation of identifying a xenobiotic clearance protein that contributes to pharmacokinetics of a given drug or pharmaceutical that is suitable for treating liver cancer in a human or animal; determining the SCF as a mean concentration of mRNA of the plurality of marker genes present within the cfRNATOTAL; identifying an abundance of the xenobiotic clearance protein within the liver of the subject by comparing the amount of first cfRNA encoding the xenobiotic clearance protein with an abundance curve for the abundance of the xenobiotic clearance protein in the liver; predicting identifying a clearance capacity of the subject based upon an analysis of the abundance of the xenobiotic clearance protein within the liver of the subject; and a pharmacokinetic simulation model that is designed to predict exposure and effects of the given drug or pharmaceutical in humans or animals, the abundance of the xenobiotic clearance protein being used to define a starting point for the pharmacokinetic simulation model of claim 1. However, these limitations are taught by Gao, Gharbi, Anderson and Zhang as discussed below.
Gao teaches the claim limitation of identifying a xenobiotic clearance protein that contributes to pharmacokinetics of a given drug or pharmaceutical that is suitable for treating liver cancer in a human or animal with “…assessments of changes in clearance values for CYPs may be useful not only for designing personalized HCC treatments, but also for identifying dosage regimens for drugs that are used to treat HCC patients who suffer from other diseases.” (page 28612, col. 1, para. 1) and with Table 2, page 28620. Table 2 depicts CYPs, drugs and clearance.
Gharbi teaches the claim limitation of determining the SCF as a mean concentration of mRNA of the plurality of marker genes present within the cfRNATOTAL with “Finally, geometric mean of two reference genes were applied as a separate normalizer, and its stability was compared with other single candidate genes using Genorm and Normfinder programs. The data revealed that the stability of the geometric mean normalizer is significantly higher than each candidate, even when the least stable reference gene, 5S rRNA, was included (Figs.3, 4). As shown in figure 3, standard deviation (SD) of 5S rRNA was decreased from 2.3 to 0.51 after adding its geometric mean with miR-423-3p. Similar observation was made after adding obtaining the geometric mean of 5S rRNA with that of miR-423 using geNorm software (Fig.4).” (page 498, col 1, para 2 to page 498, col 2, para 1)
Anderson teaches the claim limitation of identifying an abundance of the xenobiotic clearance protein within the liver of the subject by comparing the amount of first cfRNA encoding the xenobiotic clearance protein with an abundance curve for the abundance of the xenobiotic clearance protein in the liver with Figure 3. Relative abundance distributions of the top-ranked 100 mRNAs and proteins detected in human liver. The first (leftmost)molecule is the most abundant, followed by molecules of decreasing abundance through the 100th rank (at the right). Abundances of both mRNAs and proteins are plotted as a percentage of total detected molecules on a log scale. Message and protein points at the same rank are not, in general, products of the same gene (page 535).
Zhang teaches the claim limitation of predicting a clearance capacity of the subject based upon an analysis of the abundance of the xenobiotic clearance protein within the liver of the subject with “In order to assess the utility of individual parameters in predicting in vivo clearance rates, we assessed the metabolism of the sulfonylurea drug tolbutamide in liver samples. Tolbutamide is the probe of CYP2C9, which is one of the most abundant CYPs in human liver and is responsible for the metabolism of many drugs3 . While the effects of genetic polymorphisms on CYP2C9 activities have been widely reported, experimental information demonstrating individual variations in tolbutamide metabolism in vitro are rather limited. An analysis of tolbutamide metabolism in HLM can be used not only to assess individual variations, but also to predict in vivo clearance rates. Such data will be informative for the design of personalized medicines.” (page 2, para. 5).
Zhang teaches the claim limitation of a pharmacokinetic simulation model that is designed to predict exposure and effects of the given drug or pharmaceutical in humans or animals, the abundance of the xenobiotic clearance protein being used to define a starting point for the pharmacokinetic simulation model with “Recently, the PBPK program in the Division of Pharmacometrics at the FDA decided to bring PBPK models into the drug review process (http://www.fda.gov/aboutfda/centersoffices/officeofmedicalproductsandtobacco/cder/ucm365118.htm). However, valid predictions for in vivo clearance that are based on PBPK models require large numbers of different individual parameters. Although many individual characteristics can influence the outcomes of these predictions, the greatest attention has been given to variations that occur in drug metabolism, particularly that mediated by the liver26. The five most important parameters in predicting hepatic clearances (CLH) are: i) MPPGL, ii) in vitro metabolic clearance (CLint , in vitro), iii) liver weight (LW), iv) hepatic blood flow (QH) and v) body weight (BW).” (page 2, para. 4).
It would have been prima facia obvious to combine the teachings of Nerenberg and Gao to arrive at the claimed invention. Gao’s bottom-up approach allowed for the prediction of pharmacokinetics in patients with HCC accompanied by fibrosis or cirrhosis and exploration of the reasons for changes in CYPs clearance at different levels (Page 28618, Col. 2, Para. 2). A person of ordinary skill in the art would have been motivated to combine the method of Nerenberg by including the step of identifying a clearance protein that contributes to pharmacokinetics of a drug for treating liver cancer as taught by Gao to improve the data used to predict pharmacokinetics. Furthermore, there would have been a reasonable expectation of success, since Nerenberg and Gao teach methods that pertain to the analysis of liver proteins.
It would have also been prima facia obvious to combine the teachings of Nerenberg and Gharbi to arrive at the claimed invention. A person of ordinary skill in the art would have been motivated to combine the method of Nerenberg to use two or more marker genes and determining the mean concentration of mRNA of the each of two or more marker genes present within the cfRNAtotal as taught by Gharbi to increase the stability of reference genes because the reference genes’ stability increases when two or more are used (page 496, col. 2, para 3). Furthermore, there would have been a reasonable expectation of success, since Nerenberg and Gharbi teach methods that pertain to the analysis of circulating RNA.
It would have also been prima facia obvious to combine the teachings of Nerenberg and Anderson to arrive at the claimed invention. A person of ordinary skill in the art would have been motivated to combine the method of Nerenberg to compare the amount of first cfRNA encoding the xenobiotic clearance protein with an abundance curve as taught by Anderson to easily visualize and determine the distribution of the top ranked mRNAs and proteins detected in the liver. Furthermore, there would have been a reasonable expectation of success, since Nerenberg and Anderson teach methods that pertain to the analysis of circulating RNA and proteins of the liver.
It would have also been prima facia obvious to combine the teachings of Nerenberg and Zhang to arrive at the claimed invention. A person of ordinary skill in the art would have been motivated to combine the method of Nerenberg to compare the amount of first cfRNA encoding the xenobiotic clearance protein with an abundance curve as taught by Zhang to easily determine the distribution of the top ranked mRNAs and proteins detected in the liver. Furthermore, there would have been a reasonable expectation of success, since Nerenberg and Zhang teach methods that pertain to the analysis of circulating RNA and proteins of the liver.
Regarding claim 4, Nerenberg teaches the claim limitation of wherein the xenobiotic clearance protein is selected from a group consisting of: a xenobiotic metabolising enzyme and a xenobiotic transporting protein with Nerenberg’s claim 54. “Claim 54. The method of claim 34, wherein the liver RNA corresponds to a gene selected from the group consisting of: 1810014F10RIK, A1BG, ABCC2, ABCC6, ABCG5, ANG, ANGPTL3, ACOX2, ACSM2A, ADH1A, ADH1C, ADH6, AFM, AFP, AGXT, AHSG, AKR1C4, AKR1D1, ALB, ALDH1B1, ALDH4A1, ALDOB, AMBP, AOC3, APCS, APOAl, APOA2, APOA5, APOB, APOCl, APOC2, APOC3, APOC4, APOE, APOF, APOH, APOM, ARID 1 A, ARSE, ASL, AQP9, ASGRl, ASGR2, ATF5, C4A, C4BPA, C6, C8A, C8B, C8G, C9, CAPN5, CES1, CES2, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CHD2, CIDEB, CPN1, CRLF1 , CRYAA, CYP1A2, CYP27A1, CYP2A13, CYP2A6, CYP2A7, CYP2B6, CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2E1, CYP3A4, CYP4A11, CYP4A22, CYP4F12, DIOl, DAK, DCXR, F10, F12, F2, F9, FAH, FCN2, FETUB, FGA, FGB, FGG, FM03, FTCD, G6PC, GPC3, GALK1, GAMT, GBA, GBP7, GCKR, GLYAT, GNMT, GPT, GSTM1, HAAO, HAMP, HAOl, HGD, HGFAC, HMGCS2, haptoglobin, HPN, HPR, HPX, HRG, HSDl IB 1, HSD17B6, HLF, IGF2, IL1RN, IGFALS, IQCE, ITIH1, ITffl2, ITffl4, JCLN, KHK, KLK13, LBP, LECT2, LOC55908, LP A, MASP2, MBL2, MGMT, MUPCDH, NHLH2, NNMT, NSFL1C, OATP1B 1, ORM2, PCK1, PEMT, PGC, PLG, PKLR, PLGLB2, POLR2C, PON1, PON3, PROC, PXMP2, RBP4, RDH16, RET, SAA4, SARDH, SDS, SDSL, SEC14L2, SERPF A4, SERPINA7, SERPINA10, SERPINA11, SERPINC1, SERPINDl, SLC01B1, SLC10A1, SLC22A1, SLC22A7, SLC22A10, SLC25A47, SLC27A5, SLC38A3, SLC6A12, SPP2, TAT, TBX3, TF, TIM2, TMEM176B, TST, UPB1, UROC1, VTN, WNT7A, C2, C20RF72, CPB2, CYP4F11, CYP4F2, DUSP9, GABBRl, HP, HPD, IGSF1, IL17RB, ITffl2, ITffl3, LCAT, LGALS4, MAT1A, MST1, MSTP9, NR0B2, NR1I2, ORM1, RELN, RGN, RHBG, SAA4, SERPINA5, SERPINA7, SERPINC1, SERPF F2, SLC2A2, SULT1A2, SULT2A1, TCP10L, TNNI2, UGT2B15, and UGT2B17.”
Regarding claim 5, Nerenberg teaches the claim limitation of wherein the xenobiotic metabolising enzyme comprises a cytochrome P450 monooxygenase (CYP) protein with Nerenberg’s claim 54. “Claim 54. The method of claim 34, wherein the liver RNA corresponds to a gene selected from the group consisting of: 1810014F10RIK, A1BG, ABCC2, ABCC6, ABCG5, ANG, ANGPTL3, ACOX2, ACSM2A, ADH1A, ADH1C, ADH6, AFM, AFP, AGXT, AHSG, AKR1C4, AKR1D1, ALB, ALDH1B1, ALDH4A1, ALDOB, AMBP, AOC3, APCS, APOAl, APOA2, APOA5, APOB, APOCl, APOC2, APOC3, APOC4, APOE, APOF, APOH, APOM, ARID 1 A, ARSE, ASL, AQP9, ASGRl, ASGR2, ATF5, C4A, C4BPA, C6, C8A, C8B, C8G, C9, CAPN5, CES1, CES2, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CHD2, CIDEB, CPN1, CRLF1 , CRYAA, CYP1A2, CYP27A1, CYP2A13, CYP2A6, CYP2A7, CYP2B6, CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2E1, CYP3A4, CYP4A11, CYP4A22, CYP4F12, DIOl, DAK, DCXR, F10, F12, F2, F9, FAH, FCN2, FETUB, FGA, FGB, FGG, FM03, FTCD, G6PC, GPC3, GALK1, GAMT, GBA, GBP7, GCKR, GLYAT, GNMT, GPT, GSTM1, HAAO, HAMP, HAOl, HGD, HGFAC, HMGCS2, haptoglobin, HPN, HPR, HPX, HRG, HSDl IB 1, HSD17B6, HLF, IGF2, IL1RN, IGFALS, IQCE, ITIH1, ITffl2, ITffl4, JCLN, KHK, KLK13, LBP, LECT2, LOC55908, LP A, MASP2, MBL2, MGMT, MUPCDH, NHLH2, NNMT, NSFL1C, OATP1B 1, ORM2, PCK1, PEMT, PGC, PLG, PKLR, PLGLB2, POLR2C, PON1, PON3, PROC, PXMP2, RBP4, RDH16, RET, SAA4, SARDH, SDS, SDSL, SEC14L2, SERPF A4, SERPINA7, SERPINA10, SERPINA11, SERPINC1, SERPINDl, SLC01B1, SLC10A1, SLC22A1, SLC22A7, SLC22A10, SLC25A47, SLC27A5, SLC38A3, SLC6A12, SPP2, TAT, TBX3, TF, TIM2, TMEM176B, TST, UPB1, UROC1, VTN, WNT7A, C2, C20RF72, CPB2, CYP4F11, CYP4F2, DUSP9, GABBRl, HP, HPD, IGSF1, IL17RB, ITffl2, ITffl3, LCAT, LGALS4, MAT1A, MST1, MSTP9, NR0B2, NR1I2, ORM1, RELN, RGN, RHBG, SAA4, SERPINA5, SERPINA7, SERPINC1, SERPF F2, SLC2A2, SULT1A2, SULT2A1, TCP10L, TNNI2, UGT2B15, and UGT2B17.”
Regarding claim 6, Nerenberg teaches the claim limitation of wherein CYP is selected from a group consisting of: CYP1A1, CYP1A2, CYP1B1, CYP2A6, CYP2A7, CYP2A13, CYP2B6, CYP2C8, CYP2C9, CYP2C18, CYP2C19, CYP2D6, CYP2E1, CYP3A4, CYP3A5, and CYP3A7 with Nerenberg’s claim 54. “Claim 54. The method of claim 34, wherein the liver RNA corresponds to a gene selected from the group consisting of: 1810014F10RIK, A1BG, ABCC2, ABCC6, ABCG5, ANG, ANGPTL3, ACOX2, ACSM2A, ADH1A, ADH1C, ADH6, AFM, AFP, AGXT, AHSG, AKR1C4, AKR1D1, ALB, ALDH1B1, ALDH4A1, ALDOB, AMBP, AOC3, APCS, APOAl, APOA2, APOA5, APOB, APOCl, APOC2, APOC3, APOC4, APOE, APOF, APOH, APOM, ARID 1 A, ARSE, ASL, AQP9, ASGRl, ASGR2, ATF5, C4A, C4BPA, C6, C8A, C8B, C8G, C9, CAPN5, CES1, CES2, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CHD2, CIDEB, CPN1, CRLF1 , CRYAA, CYP1A2, CYP27A1, CYP2A13, CYP2A6, CYP2A7, CYP2B6, CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2E1, CYP3A4, CYP4A11, CYP4A22, CYP4F12, DIOl, DAK, DCXR, F10, F12, F2, F9, FAH, FCN2, FETUB, FGA, FGB, FGG, FM03, FTCD, G6PC, GPC3, GALK1, GAMT, GBA, GBP7, GCKR, GLYAT, GNMT, GPT, GSTM1, HAAO, HAMP, HAOl, HGD, HGFAC, HMGCS2, haptoglobin, HPN, HPR, HPX, HRG, HSDl IB 1, HSD17B6, HLF, IGF2, IL1RN, IGFALS, IQCE, ITIH1, ITffl2, ITffl4, JCLN, KHK, KLK13, LBP, LECT2, LOC55908, LP A, MASP2, MBL2, MGMT, MUPCDH, NHLH2, NNMT, NSFL1C, OATP1B 1, ORM2, PCK1, PEMT, PGC, PLG, PKLR, PLGLB2, POLR2C, PON1, PON3, PROC, PXMP2, RBP4, RDH16, RET, SAA4, SARDH, SDS, SDSL, SEC14L2, SERPF A4, SERPINA7, SERPINA10, SERPINA11, SERPINC1, SERPINDl, SLC01B1, SLC10A1, SLC22A1, SLC22A7, SLC22A10, SLC25A47, SLC27A5, SLC38A3, SLC6A12, SPP2, TAT, TBX3, TF, TIM2, TMEM176B, TST, UPB1, UROC1, VTN, WNT7A, C2, C20RF72, CPB2, CYP4F11, CYP4F2, DUSP9, GABBRl, HP, HPD, IGSF1, IL17RB, ITffl2, ITffl3, LCAT, LGALS4, MAT1A, MST1, MSTP9, NR0B2, NR1I2, ORM1, RELN, RGN, RHBG, SAA4, SERPINA5, SERPINA7, SERPINC1, SERPF F2, SLC2A2, SULT1A2, SULT2A1, TCP10L, TNNI2, UGT2B15, and UGT2B17.”
Regarding claim 7, Nerenberg teaches the claim limitation of wherein the xenobiotic metabolising enzyme comprises a transferase selected from one of a group consisting of: a methyltransferase; a sulfotransferase; an N-acetyltransferase; a glucuronosyltransferase selected from a group consisting of UGT1 A1, UGT1 A3, UGT1A4, UGT1A6, UGT1A9, UGT2B4, UGT2B7, and UGT2B15; a glutathione-S- transferase; and a choline acetyl transferase with Nerenberg’s claim 54. “Claim 54. The method of claim 34, wherein the liver RNA corresponds to a gene selected from the group consisting of: 1810014F10RIK, A1BG, ABCC2, ABCC6, ABCG5, ANG, ANGPTL3, ACOX2, ACSM2A, ADH1A, ADH1C, ADH6, AFM, AFP, AGXT, AHSG, AKR1C4, AKR1D1, ALB, ALDH1B1, ALDH4A1, ALDOB, AMBP, AOC3, APCS, APOAl, APOA2, APOA5, APOB, APOCl, APOC2, APOC3, APOC4, APOE, APOF, APOH, APOM, ARID 1 A, ARSE, ASL, AQP9, ASGRl, ASGR2, ATF5, C4A, C4BPA, C6, C8A, C8B, C8G, C9, CAPN5, CES1, CES2, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CHD2, CIDEB, CPN1, CRLF1 , CRYAA, CYP1A2, CYP27A1, CYP2A13, CYP2A6, CYP2A7, CYP2B6, CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2E1, CYP3A4, CYP4A11, CYP4A22, CYP4F12, DIOl, DAK, DCXR, F10, F12, F2, F9, FAH, FCN2, FETUB, FGA, FGB, FGG, FM03, FTCD, G6PC, GPC3, GALK1, GAMT, GBA, GBP7, GCKR, GLYAT, GNMT, GPT, GSTM1, HAAO, HAMP, HAOl, HGD, HGFAC, HMGCS2, haptoglobin, HPN, HPR, HPX, HRG, HSDl IB 1, HSD17B6, HLF, IGF2, IL1RN, IGFALS, IQCE, ITIH1, ITffl2, ITffl4, JCLN, KHK, KLK13, LBP, LECT2, LOC55908, LP A, MASP2, MBL2, MGMT, MUPCDH, NHLH2, NNMT, NSFL1C, OATP1B 1, ORM2, PCK1, PEMT, PGC, PLG, PKLR, PLGLB2, POLR2C, PON1, PON3, PROC, PXMP2, RBP4, RDH16, RET, SAA4, SARDH, SDS, SDSL, SEC14L2, SERPF A4, SERPINA7, SERPINA10, SERPINA11, SERPINC1, SERPINDl, SLC01B1, SLC10A1, SLC22A1, SLC22A7, SLC22A10, SLC25A47, SLC27A5, SLC38A3, SLC6A12, SPP2, TAT, TBX3, TF, TIM2, TMEM176B, TST, UPB1, UROC1, VTN, WNT7A, C2, C20RF72, CPB2, CYP4F11, CYP4F2, DUSP9, GABBRl, HP, HPD, IGSF1, IL17RB, ITffl2, ITffl3, LCAT, LGALS4, MAT1A, MST1, MSTP9, NR0B2, NR1I2, ORM1, RELN, RGN, RHBG, SAA4, SERPINA5, SERPINA7, SERPINC1, SERPF F2, SLC2A2, SULT1A2, SULT2A1, TCP10L, TNNI2, UGT2B15, and UGT2B17.”
Regarding claim 8, Nerenberg teaches the claim limitation of wherein the xenobiotic transporting protein is an ATP-binding cassette (ABC) transporter with Nerenberg’s claim 54. “Claim 54. The method of claim 34, wherein the liver RNA corresponds to a gene selected from the group consisting of: 1810014F10RIK, A1BG, ABCC2, ABCC6, ABCG5, ANG, ANGPTL3, ACOX2, ACSM2A, ADH1A, ADH1C, ADH6, AFM, AFP, AGXT, AHSG, AKR1C4, AKR1D1, ALB, ALDH1B1, ALDH4A1, ALDOB, AMBP, AOC3, APCS, APOAl, APOA2, APOA5, APOB, APOCl, APOC2, APOC3, APOC4, APOE, APOF, APOH, APOM, ARID 1 A, ARSE, ASL, AQP9, ASGRl, ASGR2, ATF5, C4A, C4BPA, C6, C8A, C8B, C8G, C9, CAPN5, CES1, CES2, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CHD2, CIDEB, CPN1, CRLF1 , CRYAA, CYP1A2, CYP27A1, CYP2A13, CYP2A6, CYP2A7, CYP2B6, CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2E1, CYP3A4, CYP4A11, CYP4A22, CYP4F12, DIOl, DAK, DCXR, F10, F12, F2, F9, FAH, FCN2, FETUB, FGA, FGB, FGG, FM03, FTCD, G6PC, GPC3, GALK1, GAMT, GBA, GBP7, GCKR, GLYAT, GNMT, GPT, GSTM1, HAAO, HAMP, HAOl, HGD, HGFAC, HMGCS2, haptoglobin, HPN, HPR, HPX, HRG, HSDl IB 1, HSD17B6, HLF, IGF2, IL1RN, IGFALS, IQCE, ITIH1, ITffl2, ITffl4, JCLN, KHK, KLK13, LBP, LECT2, LOC55908, LP A, MASP2, MBL2, MGMT, MUPCDH, NHLH2, NNMT, NSFL1C, OATP1B 1, ORM2, PCK1, PEMT, PGC, PLG, PKLR, PLGLB2, POLR2C, PON1, PON3, PROC, PXMP2, RBP4, RDH16, RET, SAA4, SARDH, SDS, SDSL, SEC14L2, SERPF A4, SERPINA7, SERPINA10, SERPINA11, SERPINC1, SERPINDl, SLC01B1, SLC10A1, SLC22A1, SLC22A7, SLC22A10, SLC25A47, SLC27A5, SLC38A3, SLC6A12, SPP2, TAT, TBX3, TF, TIM2, TMEM176B, TST, UPB1, UROC1, VTN, WNT7A, C2, C20RF72, CPB2, CYP4F11, CYP4F2, DUSP9, GABBRl, HP, HPD, IGSF1, IL17RB, ITffl2, ITffl3, LCAT, LGALS4, MAT1A, MST1, MSTP9, NR0B2, NR1I2, ORM1, RELN, RGN, RHBG, SAA4, SERPINA5, SERPINA7, SERPINC1, SERPF F2, SLC2A2, SULT1A2, SULT2A1, TCP10L, TNNI2, UGT2B15, and UGT2B17.”
Regarding claim 9, Nerenberg teaches the claim limitation of wherein the xenobiotic transporting protein is a solute carrier (SLC) transporter with Nerenberg’s claim 54. “Claim 54. The method of claim 34, wherein the liver RNA corresponds to a gene selected from the group consisting of: 1810014F10RIK, A1BG, ABCC2, ABCC6, ABCG5, ANG, ANGPTL3, ACOX2, ACSM2A, ADH1A, ADH1C, ADH6, AFM, AFP, AGXT, AHSG, AKR1C4, AKR1D1, ALB, ALDH1B1, ALDH4A1, ALDOB, AMBP, AOC3, APCS, APOAl, APOA2, APOA5, APOB, APOCl, APOC2, APOC3, APOC4, APOE, APOF, APOH, APOM, ARID 1 A, ARSE, ASL, AQP9, ASGRl, ASGR2, ATF5, C4A, C4BPA, C6, C8A, C8B, C8G, C9, CAPN5, CES1, CES2, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CHD2, CIDEB, CPN1, CRLF1 , CRYAA, CYP1A2, CYP27A1, CYP2A13, CYP2A6, CYP2A7, CYP2B6, CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2E1, CYP3A4, CYP4A11, CYP4A22, CYP4F12, DIOl, DAK, DCXR, F10, F12, F2, F9, FAH, FCN2, FETUB, FGA, FGB, FGG, FM03, FTCD, G6PC, GPC3, GALK1, GAMT, GBA, GBP7, GCKR, GLYAT, GNMT, GPT, GSTM1, HAAO, HAMP, HAOl, HGD, HGFAC, HMGCS2, haptoglobin, HPN, HPR, HPX, HRG, HSDl IB 1, HSD17B6, HLF, IGF2, IL1RN, IGFALS, IQCE, ITIH1, ITffl2, ITffl4, JCLN, KHK, KLK13, LBP, LECT2, LOC55908, LP A, MASP2, MBL2, MGMT, MUPCDH, NHLH2, NNMT, NSFL1C, OATP1B 1, ORM2, PCK1, PEMT, PGC, PLG, PKLR, PLGLB2, POLR2C, PON1, PON3, PROC, PXMP2, RBP4, RDH16, RET, SAA4, SARDH, SDS, SDSL, SEC14L2, SERPF A4, SERPINA7, SERPINA10, SERPINA11, SERPINC1, SERPINDl, SLC01B1, SLC10A1, SLC22A1, SLC22A7, SLC22A10, SLC25A47, SLC27A5, SLC38A3, SLC6A12, SPP2, TAT, TBX3, TF, TIM2, TMEM176B, TST, UPB1, UROC1, VTN, WNT7A, C2, C20RF72, CPB2, CYP4F11, CYP4F2, DUSP9, GABBRl, HP, HPD, IGSF1, IL17RB, ITffl2, ITffl3, LCAT, LGALS4, MAT1A, MST1, MSTP9, NR0B2, NR1I2, ORM1, RELN, RGN, RHBG, SAA4, SERPINA5, SERPINA7, SERPINC1, SERPF F2, SLC2A2, SULT1A2, SULT2A1, TCP10L, TNNI2, UGT2B15, and UGT2B17.”
Regarding claim 14, Nerenberg teaches the claim limitation of an input device, for inputting data relating to the subject; a non-transitory computer readable medium containing program instructions for implementing the method of claim 1, wherein execution of the program instructions results in one or more processors of the system carrying out steps of the method; and an output device for presenting a model of clearance capacity for the given drug or pharmaceutical for the subject with “The systems disclosed herein may be used with any one of the kits or devices disclosed herein. The systems may be integrated with any one of the kits or devices disclosed herein. The devices disclosed herein may comprise any one of the systems disclosed herein. In some embodiments, the system comprises a computer system. A computer for use in the system may comprise at least one processor. Processors may be associated with at least one controller, calculation unit, and/or other unit of a computer system, or implanted in firmware as desired. If implemented in software, the routines may be stored in any computer readable memory such as in RAM, ROM, flashes memory, a magnetic disk, a laser disk, or other suitable storage medium. Likewise, this software may be delivered to a computing device via any known delivery method including, for example, over a communication channel such as a telephone line, the internet, a wireless connection, etc., or via a transportable medium, such as a computer readable disk, flash drive, etc. The various steps may be implemented as various blocks, operations, tools, modules and techniques which, in turn, may be implemented in hardware, firmware, software, or any combination of hardware, firmware, and/or software. When implemented in hardware, some or all of the blocks, operations, techniques, etc. may be implemented in, for example, a custom integrated circuit (IC), an application specific integrated circuit (ASIC), a field programmable logic array (FPGA), a programmable logic array (PLA), etc. A client-server, relational database architecture can be used in embodiments of the system. A client-server architecture is a network architecture in which each computer or process on the network is either a client or a server. Server computers are typically powerful computers dedicated to managing disk drives (file servers), printers (print servers), or network traffic (network servers). Client computers include PCs (personal computers) or workstations on which users run applications, as well as example output devices as disclosed herein. Client computers rely on server computers for resources, such as files, devices, and even processing power. In some embodiments, the server computer handles all of the database functionality. The client computer can have software that handles all the front-end data management and can also receive data input from users.” (para. [00127]) and “The disclosure provides a computer-readable medium comprising code that, upon execution by at least one processor, implements a method of the present disclosure. A machine readable medium comprising computer-executable code may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium or physical transmission medium. Non- volatile storage media include, for example, optical or magnetic disks, such as any of the storage devices in any computers) or the like, such as may be used to implement the databases, etc. Volatile storage media include dynamic memory, such as main memory of such a computer platform. Tangible transmission media include coaxial cables; copper wire and fiber optics, including the wires that comprise a bus within a computer system. Carrier-wave transmission media may take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (IR) data communications. Common forms of computer-readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD- ROM, any other optical medium, punch cards paper tape, any other physical storage medium with patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer may read programming code and/or data. Many of these forms of computer readable media may be involved in carrying at least one sequence of at least one instruction to a processor for execution.” (para. [00130]).
Regarding claim 15, Nerenberg teaches the claim limitation of wherein the input device and the output device are the same device with “A computer for use in the system may comprise at least one processor. ...Client computers include PCs (personal computers) or workstations on which users run applications, as well as example output devices as disclosed herein.” (para. [00127]).
Regarding claim 16, Nerenberg teaches the claim limitation of wherein the input device and the output device comprise a user interface device with “A computer for use in the system may comprise at least one processor. ...Client computers include PCs (personal computers) or workstations on which users run applications, as well as example output devices as disclosed herein.” (para. [00127]).
Regarding claim 17, Nerenberg teaches the claim limitation of wherein the non-transitory computer readable medium is located with a first server with “A client-server, relational database architecture can be used in embodiments of the system. A client-server architecture is a network architecture in which each computer or process on the network is either a client or a server. Server computers are typically powerful computers dedicated to managing disk drives (file servers), printers (print servers), or network traffic (network servers). Client computers include PCs (personal computers) or workstations on which users run applications, as well as example output devices as disclosed herein. Client computers rely on server computers for resources, such as files, devices, and even processing power. In some embodiments, the server computer handles all of the database functionality. The client computer can have software that handles all the front-end data management and can also receive data input from users.” (para. [00127]).
Regarding claim 18, Nerenberg teaches the claim limitation of wherein the first server is located remotely from the input device with “Systems disclosed herein may be configured to receive a user request to perform a detection reaction on a sample. The user request may be direct or indirect. Examples of direct request include those transmitted by way of an input device, such as a keyboard, mouse, or touch screen). Examples of indirect requests include transmission via a communication medium, such as over the internet (either wired or wireless).” (para. [00128]).
Regarding claim 19, Nerenberg teaches the claim limitation of wherein the first server is located remotely from the output device with “Further provided herein are systems. Such systems comprise: (a) a memory unit configured to store results of (i) an assay for detecting at least one marker of each of at least one condition in a first sample of a subject, and (ii) an assay for detecting at least one tissue-specific RNA in a second sample of a subject, wherein each of the at least one tissue-specific RNA is a cell-free RNA specific to a tissue; (b) at least one processor programmed to: (i) quantify a level of the at least one marker; (ii) quantify a level of the at least one tissue-specific polynucleotide; (iii) compare the level of each of the at least one marker to a corresponding reference level of the marker; (iv) compare the level of each of the at least one tissue-specific polynucleotide to a corresponding reference level of the tissue-specific polynucleotide; and (v) determine presence of or relative change in damage of the tissue by the at least one condition based on the comparing; and (c) an output unit that delivers a report to a recipient, wherein the report provides results generated by the processor in (b).” (para. [0006]).
Regarding claim 20, Nerenberg teaches the claim limitation of wherein the first server is configured to communicate with at least a second server with “Systems disclosed herein may be configured to receive a user request to perform a detection reaction on a sample. The user request may be direct or indirect. Examples of direct request include those transmitted by way of an input device, such as a keyboard, mouse, or touch screen). Examples of indirect requests include transmission via a communication medium, such as over the internet (either wired or wireless).” (para. [00128]).
Nerenberg does not teach the claim limitation of wherein the abundance curve is generated by comparison of matched samples comprising the liquid biopsy and a tissue biopsy from a reference individual of claim 10; wherein the SCF is determined according to a formula A… where N is equal to a number of marker genes quantified of claim 12; wherein at least three marker genes are selected in order to determine the SCF of claim 13 wherein the at least a second server provides additional modelling capability, including at least one physiologically-based pharmacokinetic (PBPK) model of claim 21. However, these limitations are taught by Anderson, Hakooz and Zhang.
Regarding claim 10, Anderson teaches the claim limitation of wherein the abundance curve is generated by comparison of matched samples comprising the liquid biopsy and a tissue biopsy from a reference individual with “Figure 3. Relative abundance distributions of the top-ranked 100mRNAs and proteins detected in human liver. The first (leftmost)molecule is the most abundant, followed by molecules of decreasing abundance through the 100th rank (at the right). Abundances of both mRNAs and proteins are plotted as a percentage of total detected molecules on a log scale. Message and protein points at the same rank are not, in general, products of the same gene” (page 535).
Regarding claim 12, Hakooz teaches the claim limitation of wherein the SCF is determined according to a formula A… where N is equal to a number of marker genes quantified with “For hepatocytes the scale up process is a very straightforward procedure, as data are expressed per million cells; hence multiplication by the hepatocellularity of the entire liver [120 million cells per gram (8,9)] will achieve this step (3,4). For hepatic microsomes the procedure is more complicated due to the destructive nature of the procedure involved in isolating microsomes. However, the steps are analogous. Data from hepatic microsomes, conventionally expressed per milligram of microsomal protein, are normalized per mole of P450, and this number in turn may be multiplied by the P450 content per gram liver (obtained from a whole-homogenate analysis). In practice, these two steps are usually carried out as one, and hence a scaling factor is employed that is the ratio of the nanomoles of P450 per gram liver divided by the nanomoles of P450 per milligram of microsomal protein with units of milligrams of microsomal protein per gram of liver. It should be remembered that this scaling factor is not a measure of microsomal recovery in the traditional sense as there are no corrections for dilution, yet it does allow correction for the inefficiency of the subcellular fractionation procedure and hence loss of microsomal P450.” (page 533, col. 2, para. 3 to page 534, col. 1, para. 1).
Regarding claim 13, Hakooz teaches the claim limitation of wherein at least three marker genes are selected in order to determine the SCF with “For hepatocytes the scale up process is a very straightforward procedure, as data are expressed per million cells; hence multiplication by the hepatocellularity of the entire liver [120 million cells per gram (8,9)] will achieve this step (3,4). For hepatic microsomes the procedure is more complicated due to the destructive nature of the procedure involved in isolating microsomes. However, the steps are analogous. Data from hepatic microsomes, conventionally expressed per milligram of microsomal protein, are normalized per mole of P450, and this number in turn may be multiplied by the P450 content per gram liver (obtained from a whole-homogenate analysis). In practice, these two steps are usually carried out as one, and hence a scaling factor is employed that is the ratio of the nanomoles of P450 per gram liver divided by the nanomoles of P450 per milligram of microsomal protein with units of milligrams of microsomal protein per gram of liver. It should be remembered that this scaling factor is not a measure of microsomal recovery in the traditional sense as there are no corrections for dilution, yet it does allow correction for the inefficiency of the subcellular fractionation procedure and hence loss of microsomal P450.” (page 533, col. 2, para. 3 to page 534, col. 1, para. 1).
Regarding claim 21, Zhang teaches the claim limitation of wherein the at least a second server provides additional modelling capability, including at least one physiologically-based pharmacokinetic (PBPK) model with “Recently, the PBPK program in the Division of Pharmacometrics at the FDA decided to bring PBPK models into the drug review process (http://www.fda.gov/aboutfda/centersoffices/officeofmedicalproductsandtobacco/cder/ucm365118.htm). However, valid predictions for in vivo clearance that are based on PBPK models require large numbers of different individual parameters. Although many individual characteristics can influence the outcomes of these predictions, the greatest attention has been given to variations that occur in drug metabolism, particularly that mediated by the liver26. The five most important parameters in predicting hepatic clearances (CLH) are: i) MPPGL, ii) in vitro metabolic clearance (CLint , in vitro), iii) liver weight (LW), iv) hepatic blood flow (QH) and v) body weight (BW).” (page 2, para. 4).
It would have also been prima facia obvious to combine the teachings of Nerenberg and Anderson to arrive at the claimed invention. A person of ordinary skill in the art would have been motivated to combine the method of Nerenberg to compare samples comprising the liquid biopsy and a tissue biopsy from a reference individual as taught by Anderson to easily visualize and determine the distribution of mRNAs and proteins detected in the liver. Furthermore, there would have been a reasonable expectation of success, since Nerenberg and Anderson teach methods that pertain to the analysis of circulating RNA and proteins of the liver.
It would have also been prima facia obvious to combine the teachings of Nerenberg and Hakooz to arrive at the claimed invention. A person of ordinary skill in the art would have been motivated to combine the method of Nerenberg to determine a SCF or a scaling factor for human liver as taught by Hakooz to accurately predict drug clearance. Furthermore, there would have been a reasonable expectation of success, since Nerenberg and Hakooz teach methods that pertain to the analysis of liver proteins.
Regarding independent claim 24, Nerenberg teaches the claim limitation of wherein the xenobiotic clearance protein is selected from the list consisting of: CYP1A1, CYP1A2, CYP1B1, CYP2A6, CYP2A7, CYP2A13, CYP2B6, CYP2C8, CYP2C9, CYP2C18, CYP2C19, CYP2D6, CYP2E1, CYP3A4,CYP3A5, and CYP3A7 with Nerenberg’s claim 54. “Claim 54. The method of claim 34, wherein the liver RNA corresponds to a gene selected from the group consisting of: 1810014F10RIK, A1BG, ABCC2, ABCC6, ABCG5, ANG, ANGPTL3, ACOX2, ACSM2A, ADH1A, ADH1C, ADH6, AFM, AFP, AGXT, AHSG, AKR1C4, AKR1D1, ALB, ALDH1B1, ALDH4A1, ALDOB, AMBP, AOC3, APCS, APOAl, APOA2, APOA5, APOB, APOCl, APOC2, APOC3, APOC4, APOE, APOF, APOH, APOM, ARID 1 A, ARSE, ASL, AQP9, ASGRl, ASGR2, ATF5, C4A, C4BPA, C6, C8A, C8B, C8G, C9, CAPN5, CES1, CES2, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CHD2, CIDEB, CPN1, CRLF1 , CRYAA, CYP1A2, CYP27A1, CYP2A13, CYP2A6, CYP2A7, CYP2B6, CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2E1, CYP3A4, CYP4A11, CYP4A22, CYP4F12, DIOl, DAK, DCXR, F10, F12, F2, F9, FAH, FCN2, FETUB, FGA, FGB, FGG, FM03, FTCD, G6PC, GPC3, GALK1, GAMT, GBA, GBP7, GCKR, GLYAT, GNMT, GPT, GSTM1, HAAO, HAMP, HAOl, HGD, HGFAC, HMGCS2, haptoglobin, HPN, HPR, HPX, HRG, HSDl IB 1, HSD17B6, HLF, IGF2, IL1RN, IGFALS, IQCE, ITIH1, ITffl2, ITffl4, JCLN, KHK, KLK13, LBP, LECT2, LOC55908, LP A, MASP2, MBL2, MGMT, MUPCDH, NHLH2, NNMT, NSFL1C, OATP1B 1, ORM2, PCK1, PEMT, PGC, PLG, PKLR, PLGLB2, POLR2C, PON1, PON3, PROC, PXMP2, RBP4, RDH16, RET, SAA4, SARDH, SDS, SDSL, SEC14L2, SERPF A4, SERPINA7, SERPINA10, SERPINA11, SERPINC1, SERPINDl, SLC01B1, SLC10A1, SLC22A1, SLC22A7, SLC22A10, SLC25A47, SLC27A5, SLC38A3, SLC6A12, SPP2, TAT, TBX3, TF, TIM2, TMEM176B, TST, UPB1, UROC1, VTN, WNT7A, C2, C20RF72, CPB2, CYP4F11, CYP4F2, DUSP9, GABBRl, HP, HPD, IGSF1, IL17RB, ITffl2, ITffl3, LCAT, LGALS4, MAT1A, MST1, MSTP9, NR0B2, NR1I2, ORM1, RELN, RGN, RHBG, SAA4, SERPINA5, SERPINA7, SERPINC1, SERPF F2, SLC2A2, SULT1A2, SULT2A1, TCP10L, TNNI2, UGT2B15, and UGT2B17.”
Nerenberg teaches the claim limitation of wherein the given drug includes a compound that is selected from the list consisting of caffeine, tacrine, theophylline, melatonin, clozapine, lidocaine, bilirubin, cotinine, coumarin, benzphetamine, bupropion, methamphetamine, temazepam, amodiaquine, paclitaxel, ibuprofen, diclofenac, irbesartan, valsartan, tamoxifen, tolbutamide, hexobarbital, imipramine, omeprazole, diazepam, codeine, dihydrocodeine, amphetamine, loratadine, oxycodone, paroxetine, risperidone, aniline, chlorzoxazone, halothane, isoflurane, para-nitrophenol, vinyl chloride, alfentanil, alprazolam, atorvastatin, cortisol, cholesterol, dasatinib, dexamethasone, midazolam, prednisolone, quinine, sildenafil, testosterone, triazolam, and vincristine with “Treating the subject for NAFLD may comprise administering a pharmaceutical targeting steatosis or insulin resistance. By way of non-limiting example, a pharmaceutical targeting steatosis or insulin resistance is metformin or an analog thereof. A pharmaceutical targeting steatosis or insulin resistance may be a statin. The statin, by way of non-limiting example, may be selected from atorvastatin, pravastatin, rosuvastatin, and tetrahydrolipstatin, or an analog thereof. A pharmaceutical targeting steatosis or insulin resistance may be a fibrate, e.g., gemfibrozil or an analog thereof. A pharmaceutical targeting steatosis or insulin resistance may be a thiazolidinedione or peroxisome proliferator activated receptor (PPAR) agonist (e.g., pioglitazone, rosiglitazone, GFT505 or an analog thereof). A pharmaceutical targeting steatosis or insulin resistance may be a bile acid or analog thereof, e.g., ursodiol, 6a-ethyl- chenodeoxycholic acid. A pharmaceutical targeting steatosis or insulin resistance may be a vitamin or analog thereof, e.g., vitamin E, vitamin D or vitamin C, or analogues thereof.” (para. [0088]).
Nerenberg teaches the claim limitation of quantifying an amount of a first cell free RNA (cfRNA) present in a liquid biopsy obtained from the subject with Nerenberg’s Claim 34 (b). Claim 34(b) “measuring a quantity of liver ribonucleic acids (RNA) in the biological fluid.”
Nerenberg teaches the claim limitation of wherein the first cfRNA originates from a liver of the subject, and wherein the first cfRNA codes for the xenobiotic clearance protein with Nerenberg’s claim 54. Claim 54 “The method of claim 34, wherein the liver RNA corresponds to a gene selected from the group consisting of: 1810014F10RIK, A1BG, ABCC2, ABCC6, ABCG5, ANG, ANGPTL3, ACOX2, ACSM2A, ADH1A, ADH1C, ADH6, AFM, AFP, AGXT, AHSG, AKR1C4 …”
Nerenberg teaches the claim limitation of isolating total cell free RNA (cfRNATOTAL) from the liquid biopsy using (a) a density gradient medium to isolate lymphocytes from peripheral blood, (b) an RNA extraction kit to collect total nucleic acid from the lymphocytes, and/or (c) a DNA extraction kit to remove DNA from the total nucleic acid with “Some methods disclosed herein comprise isolating at least one marker and/or at least one tissue-specific polynucleotide. In some cases, the at least one marker and/or at least one tissue- specific polynucleotide comprise a cell-free polynucleotide. In some cases, isolating the cell- free polynucleotide comprises fractionating the sample from the subject. Some methods comprise removing intact cells from the sample. For example, some methods comprise centrifuging a blood sample and collecting the supernatant that is serum or plasma, or filtering the sample to remove cells. In some embodiments, cell-free polynucleotides are analyzed without fractionating the sample from the subject. For example, urine, cerebrospinal fluid or other fluids that contain little to no cells may not require fractionating. Some methods comprise sufficiently purifying the cell-free polynucleotides in order to detect/quantify/analyze the cell- free polynucleotides. Various reagents, methods and kits can be used to purify the cell-free polynucleotides. Reagents are known in the art and include, but are not limited to, Trizol, phenol-chloroform, glycogen, sodium iodide, and guanidine resin. Kits include, but are not limited to, Thermo Fisher ChargeSwitch® Serum Kit, Qiagen RNeasy Kit, ZR serum DNA kit, Puregene DNA purification system, QIAamp DNA Blood Midi kit, QIAamp Circulating Nucleic Acid Kit, and QIAamp DNA Mini kit.” (para. [0061])
Nerenberg teaches the claim limitation of analysing the isolated cfRNATOTAL in order to determine an amount of the first cfRNA present within the cfRNATOTAL with Nerenberg’s claim 44. Claim 44. “The method of claim 34, wherein measuring the quantity of liver RNA comprises measuring the relative contribution of liver RNA to a nucleic acid population selected from total RNA of the biological fluid and total nucleic acids of the biological fluid.”
Nerenberg teaches the claim limitation of normalizing the amount of the first cfRNA present against a plurality of marker genes that are expressed principally and consistently in the liver to ensure correct measurement of enzyme expression and determining a Shedding Correction Factor (SCF) for the subject by: (i) performing an analysis of the cfRNATOTAL in order to quantify an amount of mRNA present within the cfRNATOTAL that corresponds to each of the plurality of marker genes with “In some cases, the methods comprise normalizing cell-free transcript values. This involves reseating cell-free transcript values to housekeeping gene transcript values. Next, the sample's total RNA is assessed against the panel of tissue-specific genes using quadratic programming in order to determine the tissue-specific relative contributions to the sample's cell - free transcriptome. The following constraints are employed to obtain the estimated relative contributions during the quadratic programming analysis: a) the RNA contributions of different tissues are greater than or equal to zero, and b) the sum of all contributions to the cell -free transcriptome equals one.” (para. [0079]).
Nerenberg teaches the claim limitation of wherein each of the plurality of marker genes is with “In most cases, liver RNA disclosed herein is RNA that is predominantly expressed in a human liver. In most cases, liver RNA disclosed herein is RNA expressed substantially higher in liver than in any other tissue of the human subject. In some cases, liver RNA corresponds to a gene selected from the group consisting of: 1810014F10RIK, A1BG, ABCC2, ABCC6, ABCG5, ANG, ANGPTL3, ACOX2, ACSM2A, ADHl A, ADHIC, ADH6, AFM, AFP, AGXT, AHSG, AKR1C4, AKR1D1, ALB, ALDH1B1, ALDH4A1, ALDOB, AMBP, AOC3, APCS, APOAl, APOA2, APOA5, APOB, APOC1, APOC2, APOC3, APOC4, APOE, APOF, APOH, APOM, ARID 1 A, ARSE, ASL, AQP9, ASGR1, ASGR2, ATF5, C4A, C4BPA, C6, C8A, C8B, C8G, C9, CAPN5, CES1, CES2, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CHD2, CIDEB, CPN1, CRLF1, CRYAA, CYP1A2, CYP27A1, CYP2A13, CYP2A6, CYP2A7, CYP2B6, CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2E1, CYP3A4, CYP4A11, CYP4A22, CYP4F12, DIOl, DAK, DCXR, F10, F12, F2, F9, FAH, FCN2, FETUB, FGA, FGB, FGG, FM03, FTCD, G6PC, GPC3, GALKl, GAMT, GBA, GBP7, GCKR, GLYAT, GNMT, GPT, GSTM1, HAAO, HAMP, HAOl, HGD, HGFAC, HMGCS2, haptoglobin, HPN, HPR, HPX, HRG, HSDl lBl, HSD17B6, HLF, IGF2, ILIRN, IGFALS, IQCE, ITIHl, ITIH2, ITIH4, JCLN, KHK, KLK13, LBP, LECT2, LOC55908, LP A, MASP2, MBL2, MGMT, MUPCDH, NHLH2, NNMT, NSFL1C, OATP1B1, ORM2, PCK1, PEMT, PGC, PLG, PKLR, PLGLB2, POLR2C, PON1, PON3, PROC, PXMP2, RBP4, RDH16, RET, SAA4, SARDH, SDS, SDSL, SEC14L2, SERPINA4, SERPINA7, SERPINA10, SERPF A11, SERPINC1, SERPF D1, SLC01B1, SLC10A1, SLC22A1, SLC22A7, SLC22A10, SLC25A47, SLC27A5, SLC38A3, SLC6A12, SPP2, TAT, TBX3, TF, TEVI2, TMEM176B, TST, UPB1, UROC1, VTN, WNT7A, C2, C20RF72, CPB2, CYP4F11, CYP4F2, DUSP9, GABBRl, HP, HPD, IGSF1, IL17RB, ITIH2, ITIH3, LCAT, LGALS4, MAT1A, MST1, MSTP9, NR0B2, NR1I2, ORM1, RELN, RGN, RHBG, SAA4, SERPF A5, SERPINA7, SERPINC1, SERPFNF2, SLC2A2, SULT1A2, SULT2A1, TCP10L, TNNI2, UGT2B15, and UGT2B17…” (para. [0004]).
Nerenberg teaches the claim limitation of generating, based on the clearance capacity of the subject, a dosage regimen for the given drug or pharmaceutical compound that is optimized for the subject to achieve efficacy while lessening a risk of safety issues with “Further provided herein are systems. Such systems comprise: (a) a memory unit configured to store results of (i) an assay for detecting at least one marker of each of at least one condition in a first sample of a subject, and (ii) an assay for detecting at least one tissue-specific RNA in a second sample of a subject, wherein each of the at least one tissue-specific RNA is a cell-free RNA specific to a tissue; (b) at least one processor programmed to: (i) quantify a level of the at least one marker; (ii) quantify a level of the at least one tissue-specific polynucleotide; (iii) compare the level of each of the at least one marker to a corresponding reference level of the marker; (iv) compare the level of each of the at least one tissue-specific polynucleotide to a corresponding reference level of the tissue-specific polynucleotide; and (v) determine presence of or relative change in damage of the tissue by the at least one condition based on the comparing; and (c) an output unit that delivers a report to a recipient, wherein the report provides results generated by the processor in (b). Optionally, reports comprise a recommendation for medical action based on the generated by the processor in (b). In some instances, medical action comprises recommended treatment. In many instances, the at least one tissue-specific polynucleotide comprises at least one tissue specific RNA.” (para. [0006]) and “Multiple diseases and tissues may be assessed simultaneously using the kits, systems and methods disclosed herein. In this way, the kits, systems and methods disclosed herein may be used to assess the presence or absence of at least one condition and identify both affected and unaffected tissues. In some embodiments, methods comprise selecting or recommending a medical action based on results produced by the methods, systems or kits disclosed herein. In some embodiments, a customized medical action is recommended, and optionally taken, based on the determination. In some instances, customized medical action comprises directly treating a tissue under duress, e.g., with radiation or injection of the tissue. Non-limiting examples of medical actions include performing additional tests (e.g., biopsy, imaging, surgery), treating the subject for the disease or condition, and modifying a treatment of the subject (e.g. altering the dose of a pharmaceutical composition, ceasing administration of a pharmaceutical composition, administering a different or additional pharmaceutical composition).” (para. [0020]) and “In some embodiments, the methods disclosed herein comprise detecting and/or analyzing at least one polynucleotide (e.g., RNA, DNA) associated with a liver-associated disease or condition. The at least one polynucleotide may comprise a gene or genetic transcript or portions thereof associated with a liver-associated disease or condition. The portion of the gene or genetic transcript thereof may comprise a sufficient number of nucleotides to determine the portion of the gene or genetic transcript thereof is associated with a gene of interest, mutants thereof, chemical modifications thereof, and splice variants thereof. The polynucleotide may encode a protein or identifiable portion thereof. The gene of interest, by way of non-limiting example, may be selected from a gene associated with a cellular function selected from lipid metabolism, lipid storage, lipid transport (uptake/efflux), cholesterol metabolism, cholesterol storage, cholesterol transport (cellular uptake/efflux), inflammation, extracellular matrix formation, drug metabolism, drug transport (cellular uptake/efflux), vitamin storage, vitamin uptake, vitamin metabolism, and apoptosis.” (para. [00183]).
Nerenberg does not explicitly teach the claim limitation of identifying a xenobiotic clearance protein that contributes to pharmacokinetics of a given drug or pharmaceutical that is suitable for treating liver cancer in a human or animal; determining the SCF as a mean concentration of mRNA of the plurality of marker genes present within the cfRNATOTAL; identifying an abundance of the xenobiotic clearance protein within the liver of the subject by comparing the amount of first cfRNA encoding the xenobiotic clearance protein with an abundance curve for the abundance of the xenobiotic clearance protein in the liver; predicting identifying a clearance capacity of the subject based upon an analysis of the abundance of the xenobiotic clearance protein within the liver of the subject; and a pharmacokinetic simulation model that is designed to predict exposure and effects of the given drug or pharmaceutical in humans or animals, the abundance of the xenobiotic clearance protein being used to define a starting point for the pharmacokinetic simulation model of claim 1. However, these limitations are taught by Gao, Gharbi, Anderson and Zhang as discussed below.
Gao teaches the claim limitation of identifying a xenobiotic clearance protein that contributes to pharmacokinetics of a given drug or pharmaceutical that is suitable for treating liver cancer in a human or animal with “…assessments of changes in clearance values for CYPs may be useful not only for designing personalized HCC treatments, but also for identifying dosage regimens for drugs that are used to treat HCC patients who suffer from other diseases.” (page 28612, col. 1, para. 1) and with Table 2, page 28620. Table 2 depicts CYPs, drugs and clearance.
Gao also teaches the claim limitation of wherein the given drug includes a compound that is selected from the list consisting of caffeine, tacrine, theophylline, melatonin, clozapine, lidocaine, bilirubin, cotinine, coumarin, benzphetamine, bupropion, methamphetamine, temazepam, amodiaquine, paclitaxel, ibuprofen, diclofenac, irbesartan, valsartan, tamoxifen, tolbutamide, hexobarbital, imipramine, omeprazole, diazepam, codeine, dihydrocodeine, amphetamine, loratadine, oxycodone, paroxetine, risperidone, aniline, chlorzoxazone, halothane, isoflurane, para-nitrophenol, vinyl chloride, alfentanil, alprazolam, atorvastatin, cortisol, cholesterol, dasatinib, dexamethasone, midazolam, prednisolone, quinine, sildenafil, testosterone, triazolam, and vincristine with Table 2, page 28620. Table 2 depicts CYPs, drugs and clearance.
Gharbi teaches the claim limitation of determining the SCF as a mean concentration of mRNA of the plurality of marker genes present within the cfRNATOTAL with “Finally, geometric mean of two reference genes were applied as a separate normalizer, and its stability was compared with other single candidate genes using Genorm and Normfinder programs. The data revealed that the stability of the geometric mean normalizer is significantly higher than each candidate, even when the least stable reference gene, 5S rRNA, was included (Figs.3, 4). As shown in figure 3, standard deviation (SD) of 5S rRNA was decreased from 2.3 to 0.51 after adding its geometric mean with miR-423-3p. Similar observation was made after adding obtaining the geometric mean of 5S rRNA with that of miR-423 using geNorm software (Fig.4).” (page 498, col 1, para 2 to page 498, col 2, para 1)
Anderson teaches the claim limitation of identifying an abundance of the xenobiotic clearance protein within the liver of the subject by comparing the amount of first cfRNA encoding the xenobiotic clearance protein with an abundance curve for the abundance of the xenobiotic clearance protein in the liver with Figure 3. Relative abundance distributions of the top-ranked 100 mRNAs and proteins detected in human liver. The first (leftmost)molecule is the most abundant, followed by molecules of decreasing abundance through the 100th rank (at the right). Abundances of both mRNAs and proteins are plotted as a percentage of total detected molecules on a log scale. Message and protein points at the same rank are not, in general, products of the same gene (page 535).
Zhang teaches the claim limitation of predicting a clearance capacity of the subject based upon an analysis of the abundance of the xenobiotic clearance protein within the liver of the subject with “In order to assess the utility of individual parameters in predicting in vivo clearance rates, we assessed the metabolism of the sulfonylurea drug tolbutamide in liver samples. Tolbutamide is the probe of CYP2C9, which is one of the most abundant CYPs in human liver and is responsible for the metabolism of many drugs3 . While the effects of genetic polymorphisms on CYP2C9 activities have been widely reported, experimental information demonstrating individual variations in tolbutamide metabolism in vitro are rather limited. An analysis of tolbutamide metabolism in HLM can be used not only to assess individual variations, but also to predict in vivo clearance rates. Such data will be informative for the design of personalized medicines.” (page 2, para. 5).
Zhang teaches the claim limitation of a pharmacokinetic simulation model that is designed to predict exposure and effects of the given drug or pharmaceutical in humans or animals, the abundance of the xenobiotic clearance protein being used to define a starting point for the pharmacokinetic simulation model with “Recently, the PBPK program in the Division of Pharmacometrics at the FDA decided to bring PBPK models into the drug review process (http://www.fda.gov/aboutfda/centersoffices/officeofmedicalproductsandtobacco/cder/ucm365118.htm). However, valid predictions for in vivo clearance that are based on PBPK models require large numbers of different individual parameters. Although many individual characteristics can influence the outcomes of these predictions, the greatest attention has been given to variations that occur in drug metabolism, particularly that mediated by the liver26. The five most important parameters in predicting hepatic clearances (CLH) are: i) MPPGL, ii) in vitro metabolic clearance (CLint , in vitro), iii) liver weight (LW), iv) hepatic blood flow (QH) and v) body weight (BW).” (page 2, para. 4).
It would have been prima facia obvious to combine the teachings of Nerenberg and Gao to arrive at the claimed invention. Gao’s bottom-up approach allowed for the prediction of pharmacokinetics in patients with HCC accompanied by fibrosis or cirrhosis and exploration of the reasons for changes in CYPs clearance at different levels (Page 28618, Col. 2, Para. 2). A person of ordinary skill in the art would have been motivated to combine the method of Nerenberg by including the step of identifying a clearance protein that contributes to pharmacokinetics of a drug for treating liver cancer as taught by Gao to improve the data used to predict pharmacokinetics. Furthermore, there would have been a reasonable expectation of success, since Nerenberg and Gao teach methods that pertain to the analysis of liver proteins.
It would have also been prima facia obvious to combine the teachings of Nerenberg and Gharbi to arrive at the claimed invention. A person of ordinary skill in the art would have been motivated to combine the method of Nerenberg to use two or more marker genes and determining the mean concentration of mRNA of the each of two or more marker genes present within the cfRNAtotal as taught by Gharbi to increase the stability of reference genes because the reference genes’ stability increases when two or more are used (page 496, col. 2, para 3). Furthermore, there would have been a reasonable expectation of success, since Nerenberg and Gharbi teach methods that pertain to the analysis of circulating RNA.
It would have also been prima facia obvious to combine the teachings of Nerenberg and Anderson to arrive at the claimed invention. A person of ordinary skill in the art would have been motivated to combine the method of Nerenberg to compare the amount of first cfRNA encoding the xenobiotic clearance protein with an abundance curve as taught by Anderson to easily visualize and determine the distribution of the top ranked mRNAs and proteins detected in the liver. Furthermore, there would have been a reasonable expectation of success, since Nerenberg and Anderson teach methods that pertain to the analysis of circulating RNA and proteins of the liver.
It would have also been prima facia obvious to combine the teachings of Nerenberg and Zhang to arrive at the claimed invention. A person of ordinary skill in the art would have been motivated to combine the method of Nerenberg to compare the amount of first cfRNA encoding the xenobiotic clearance protein with an abundance curve as taught by Zhang to easily determine the distribution of the top ranked mRNAs and proteins detected in the liver. Furthermore, there would have been a reasonable expectation of success, since Nerenberg and Zhang teach methods that pertain to the analysis of circulating RNA and proteins of the liver.
Regarding claim 25, Nerenberg teaches the claim limitation of wherein the plurality of marker genes includes at least eight marker genes with “In most cases, liver RNA disclosed herein is RNA that is predominantly expressed in a human liver. In most cases, liver RNA disclosed herein is RNA expressed substantially higher in liver than in any other tissue of the human subject. In some cases, liver RNA corresponds to a gene selected from the group consisting of: 1810014F10RIK, A1BG, ABCC2, ABCC6, ABCG5, ANG, ANGPTL3, ACOX2, ACSM2A, ADHl A, ADHIC, ADH6, AFM, AFP, AGXT, AHSG, AKR1C4, AKR1D1, ALB, ALDH1B1, ALDH4A1, ALDOB, AMBP, AOC3, APCS, APOAl, APOA2, APOA5, APOB, APOC1, APOC2, APOC3, APOC4, APOE, APOF, APOH, APOM, ARID 1 A, ARSE, ASL, AQP9, ASGR1, ASGR2, ATF5, C4A, C4BPA, C6, C8A, C8B, C8G, C9, CAPN5, CES1, CES2, CFHR1, CFHR2, CFHR3, CFHR4, CFHR5, CHD2, CIDEB, CPN1, CRLF1, CRYAA, CYP1A2, CYP27A1, CYP2A13, CYP2A6, CYP2A7, CYP2B6, CYP2C19, CYP2C8, CYP2C9, CYP2D6, CYP2E1, CYP3A4, CYP4A11, CYP4A22, CYP4F12, DIOl, DAK, DCXR, F10, F12, F2, F9, FAH, FCN2, FETUB, FGA, FGB, FGG, FM03, FTCD, G6PC, GPC3, GALKl, GAMT, GBA, GBP7, GCKR, GLYAT, GNMT, GPT, GSTM1, HAAO, HAMP, HAOl, HGD, HGFAC, HMGCS2, haptoglobin, HPN, HPR, HPX, HRG, HSDl lBl, HSD17B6, HLF, IGF2, ILIRN, IGFALS, IQCE, ITIHl, ITIH2, ITIH4, JCLN, KHK, KLK13, LBP, LECT2, LOC55908, LP A, MASP2, MBL2, MGMT, MUPCDH, NHLH2, NNMT, NSFL1C, OATP1B1, ORM2, PCK1, PEMT, PGC, PLG, PKLR, PLGLB2, POLR2C, PON1, PON3, PROC, PXMP2, RBP4, RDH16, RET, SAA4, SARDH, SDS, SDSL, SEC14L2, SERPINA4, SERPINA7, SERPINA10, SERPF A11, SERPINC1, SERPF D1, SLC01B1, SLC10A1, SLC22A1, SLC22A7, SLC22A10, SLC25A47, SLC27A5, SLC38A3, SLC6A12, SPP2, TAT, TBX3, TF, TEVI2, TMEM176B, TST, UPB1, UROC1, VTN, WNT7A, C2, C20RF72, CPB2, CYP4F11, CYP4F2, DUSP9, GABBRl, HP, HPD, IGSF1, IL17RB, ITIH2, ITIH3, LCAT, LGALS4, MAT1A, MST1, MSTP9, NR0B2, NR1I2, ORM1, RELN, RGN, RHBG, SAA4, SERPF A5, SERPINA7, SERPINC1, SERPFNF2, SLC2A2, SULT1A2, SULT2A1, TCP10L, TNNI2, UGT2B15, and UGT2B17…” (para. [0004]).
Claims 22-23 are rejected under 35 U.S.C. 103 as being unpatentable over Nerenberg (WO 2017/156310 A1, published 14 September 2017; cited on the 10/20/2020 IDS Document), in view of Gao (Gao, Jie, et al. "Changes in cytochrome P450s-mediated drug clearance in patients with hepatocellular carcinoma in vitro and in vivo: a bottom-up approach." Oncotarget 7.19 (2016): 28612., published 2016; cited on the attached “Notice of References Cited” form 892); Gharbi (Identification of Reliable Reference Genes for Quantification of MicroRNAs in Serum Samples of Sulfur Mustard-Exposed Veterans. Cell J. 2015 Fall;17(3):494-501., published 2015; cited on the 10/20/2020 IDS Document); Anderson ("A comparison of selected mRNA and protein abundances in human liver." Electrophoresis 18.3‐4 (1997): 533-537; cited on the attached “Notice of References Cited” form 892.); Zhang (Content and activity of human liver microsomal protein and prediction of individual hepatic clearance in vivo. Sci Rep 5, 17671 (2015); cited on the attached “Notice of References Cited” form 892) as applied to claims 1, 4-10, 12-21 and 24-25 above and in further view of Sheikh-Bahaei (“Enabling clearance predictions to emerge from in silico actions of quasi-autonomous hepatocyte components.” Drug Metabolism and Disposition, Vol. 39, Issue 10. P. 1910-1920 (October, 2011). Epub July 18, 2011; cited on the attached “Notice of References Cited” form 892).
Nerenberg, Gao, Gharbi, Anderson and Zhang are applied to claims 1, 4-10, 12-21 and 24-25 as discussed above.
Regarding claim 22, Nerenberg teaches the claim limitation of A computer server comprising: a computer readable medium containing program instructions configured to embody steps of a computer readable medium containing program instructions configured to embody steps of claim 1, wherein execution of the program instructions results in one or more processors of the server carrying out steps of the method and producing an in silico model of clearance capacity of an individual subject for a given drug or pharmaceutical that is suitable for treating liver cancer, and wherein the in silico model is hosted on the computer server, wherein the computer readable medium is non-transitory and comprises instructions configured to embody the computer server; and a telecommunication module for communicating with a remotely located user interface device, thereby permitting a remotely located user to access the in silico model with “The systems disclosed herein may be used with any one of the kits or devices disclosed herein. The systems may be integrated with any one of the kits or devices disclosed herein. The devices disclosed herein may comprise any one of the systems disclosed herein. In some embodiments, the system comprises a computer system. A computer for use in the system may comprise at least one processor. Processors may be associated with at least one controller, calculation unit, and/or other unit of a computer system, or implanted in firmware as desired. If implemented in software, the routines may be stored in any computer readable memory such as in RAM, ROM, flashes memory, a magnetic disk, a laser disk, or other suitable storage medium. Likewise, this software may be delivered to a computing device via any known delivery method including, for example, over a communication channel such as a telephone line, the internet, a wireless connection, etc., or via a transportable medium, such as a computer readable disk, flash drive, etc. The various steps may be implemented as various blocks, operations, tools, modules and techniques which, in turn, may be implemented in hardware, firmware, software, or any combination of hardware, firmware, and/or software. When implemented in hardware, some or all of the blocks, operations, techniques, etc. may be implemented in, for example, a custom integrated circuit (IC), an application specific integrated circuit (ASIC), a field programmable logic array (FPGA), a programmable logic array (PLA), etc. A client-server, relational database architecture can be used in embodiments of the system. A client-server architecture is a network architecture in which each computer or process on the network is either a client or a server. Server computers are typically powerful computers dedicated to managing disk drives (file servers), printers (print servers), or network traffic (network servers). Client computers include PCs (personal computers) or workstations on which users run applications, as well as example output devices as disclosed herein. Client computers rely on server computers for resources, such as files, devices, and even processing power. In some embodiments, the server computer handles all of the database functionality. The client computer can have software that handles all the front-end data management and can also receive data input from users.” (para. [00127]) and “The disclosure provides a computer-readable medium comprising code that, upon execution by at least one processor, implements a method of the present disclosure. A machine readable medium comprising computer-executable code may take many forms, including but not limited to, a tangible storage medium, a carrier wave medium or physical transmission medium. Non- volatile storage media include, for example, optical or magnetic disks, such as any of the storage devices in any computers) or the like, such as may be used to implement the databases, etc. Volatile storage media include dynamic memory, such as main memory of such a computer platform. Tangible transmission media include coaxial cables; copper wire and fiber optics, including the wires that comprise a bus within a computer system. Carrier-wave transmission media may take the form of electric or electromagnetic signals, or acoustic or light waves such as those generated during radio frequency (RF) and infrared (IR) data communications. Common forms of computer-readable media therefore include for example: a floppy disk, a flexible disk, hard disk, magnetic tape, any other magnetic medium, a CD-ROM, DVD or DVD- ROM, any other optical medium, punch cards paper tape, any other physical storage medium with patterns of holes, a RAM, a ROM, a PROM and EPROM, a FLASH-EPROM, any other memory chip or cartridge, a carrier wave transporting data or instructions, cables or links transporting such a carrier wave, or any other medium from which a computer may read programming code and/or data. Many of these forms of computer readable media may be involved in carrying at least one sequence of at least one instruction to a processor for execution.” (para. [00130]) and “Systems disclosed herein may be configured to receive a user request to perform a detection reaction on a sample. The user request may be direct or indirect. Examples of direct request include those transmitted by way of an input device, such as a keyboard, mouse, or touch screen). Examples of indirect requests include transmission via a communication medium, such as over the internet (either wired or wireless).” (para. [00128]).
Nerenberg does not explicitly teach the claim limitation of in silico model of clearance capacity of an individual subject for a given drug or pharmaceutical in claim 22. However, this limitation is taught by Sheikh-Bahaei.
Sheikh-Bahaei teaches the claim limitation of in silico model of clearance capacity of an individual subject for a given drug or pharmaceutical with “We demonstrate the feasibility of using in silico hepatocyte cultures (ISHCs) to provide predictions of the intrinsic clearance (CL) of compounds in hepatocyte cultures.” (abstract).
Regarding claim 23, Nerenberg teaches the claim limitation of wherein the computer server is located remotely from the user interface device with “Systems disclosed herein may be configured to receive a user request to perform a detection reaction on a sample. The user request may be direct or indirect. Examples of direct request include those transmitted by way of an input device, such as a keyboard, mouse, or touch screen). Examples of indirect requests include transmission via a communication medium, such as over the internet (either wired or wireless).” (para. [00128]).
It would have been prima facia obvious to combine the teachings of Nerenberg and Sheikh-Bahaei to arrive at the claimed invention. Sheikh-Bahaei’s bottom-up approach allowed for the prediction of pharmacokinetics in patients with HCC accompanied by fibrosis or cirrhosis and exploration of the reasons for changes in CYPs clearance at different levels (Page 28618, Col. 2, Para. 2). A person of ordinary skill in the art would have been motivated to combine the method of Nerenberg by including in silico model of clearance capacity of an individual subject for a given drug or pharmaceutical as taught by Sheikh-Bahaei to improve the ability to anticipate the clearance properties of new compounds (page 1919, col. 2, para. 2). Furthermore, there would have been a reasonable expectation of success, since Nerenberg and Sheikh-Bahaei teach methods that pertain to the analysis of liver proteins.
Conclusion
No claims are allowed.
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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/K.K./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686