DETAILED ACTION
Notice of 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 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.
Status of the Claims
Claims 1-13, 28-35, 38-41, 43-50, and 53-64 are cancelled.
Claims 14-27, 36-37, 42, and 51-52 are pending.
Claims 14, 24, 36, and 51 are independent.
Claims 14, 16, 19, 23, 36-37, 42 and 51-52 are objected to.
Claims 14-27, 36-37, 42, and 51-52 are rejected.
Priority
This US Application 17/795,465 (07/26/2022) is a 371 of PCT/US21/16508 (02/04/2021) and claims benefit from US Application 62/970,480 (02/05/2020), as reflected in the filing receipt mailed on 04/14/2023. The claims to the benefit of priority are acknowledged; and the effective filing date of claims 14-27, 36-37, 42, and 51-52 is 02/05/2020.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 03/06/2025 was considered.
Drawings
The drawings are objected to as failing to comply with 37 CPR 1.84(p)(5) because Fig. 6F and Fig. 14 include illegible labels. Corrected drawing sheets in compliance with 37 CPR 1.12l(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as "amended." If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either "Replacement Sheet" or "New Sheet" pursuant to 3 7 CPR 1.121 ( d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim objections
Claims 14, 16, 19, 23, 36-37, 42 and 51-52 are objected to because of the following informalities related to grammar/punctuation. Appropriate correction is required.
Claim 14 is missing a conjunction between the penultimate (i.e. step (iii)) and the final list item (i.e. step (iv)).
In claim 14, the use of commas/semi-colons is inconsistent. For example, the recited "i) … diabetes, ii) … antagonist, iii) …" should read "i) … diabetes; ii) … antagonist; iii) …". In contrast, claim 14 step (iii) does not present the same issue.
Claim 23 repeats the issue for "… disease, and wherein …"
Claims 37, 42, and 52 repeat the issue above for "… subject, and graphically …"
Claim 19 is missing a space between "Lofexidine," and the conjunction "and" for proper punctuation.
In claim 51, a semi-colon should be a comma, i.e. the recited " … b) … concentration; and iii) … system; and c) …" should read " … b) … concentration, and iii) … system; and c) …" for proper punctuation. In contrast, claim 36 does not present the same issue.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION —The specification shall conclude with one or more claims
particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
Claims 16, 21-27, 36-37, 42, and 51-52 are rejected under 35 U.S.C. 112(b)as being indefinite for failing to particularly point out and distinctly claim the subject matter the invention. Dependent claims are rejected similarly, unless otherwise noted below. The following issues cause the respective claims to be rejected under 112(b) as indefinite:
Claim 16 recites just "PSA," and each abbreviation should be defined in the claims the first time it occurs.
claim 27 is rejected similarly.
The following recitations require but lack antecedent basis, rendering their claims indefinite:
claims 21-22, 36, and 51, "the group consisting of" should read "a group..."
claims 24, 36, and 51, "the concentration" should read "a concentration..."
claim 37, "the level of trimethylamine N-oxide (TMAO)" should read "a level..."
claim 42, "the level of N6-trimethyl- lysine (TML)"
claim 52, "the level of choline"
Claim 23 is missing punctuation at the end of the claim. It is unclear if the claim recites a closed list of items or not, making the relationship between the items unclear.
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 14-23, 36-37, 42, and 51-52 are rejected under 35 USC § 101 because the claimed inventions are directed to one or more Judicial Exceptions (JEs) without significantly more. Regarding JEs, "Claims directed to nothing more than abstract ideas..., natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 §I). Abstract ideas include mathematical concepts and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)).
101 background
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Analysis of instant claims
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Claim 14 is directed to a 101 process, here a "method," with process steps such as "identifying," etc. Claims 24, 36 and 51 and their dependents are analyzed similarly.
[Step 1: claims 14-27, 36-37, 42, and 51-52: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Background
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
Analysis of instant claims
Mathematical concepts recited in instant claims 36-37, 42 and 51-52, include the terms:
• "level" or "risk" "… higher than …" (claims 36-37, 42 and 51-52) and
• "minimum value" (claims 36-37, 42 and 51-52).
Said terms are being identified as mathematical concepts. The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one having ordinary skill in the art. Thus, the recited terms corresponds to verbal equivalents of mathematical concepts because they constitute actions executed by a group of mathematical steps in a form of a mathematical algorithm; thus mathematical concepts (MPEP 2106.04(a)(2)). A mathematical concept need not be expressed in mathematical symbols, because "words used in a claim operating on data to solve a problem can serve the same purpose as a formula." In re Grams, 888 F.2d 835, 837 and n.1, 12 USPQ2d 1824, 1826 and n.1 (Fed. Cir. 1989).
Mental processes, defined as concepts or steps practically performed in the human mind such as steps of observations, evaluations, judgments, analysis, opinions or organizing information include "identifying a subject as having increased levels of at least one compound compared to control levels" (claim 14).
Under the BRI, the recited limitations are mental processes because a human mind is sufficiently capable of evaluate data to identify increasing levels of a compound and introduce a sample into a device.
Dependent claims 15-16 recite further details about "identifying increased levels of a compound"; not reciting any additional non-abstract elements; all reciting further aspects of the information being analyzed, the manner in which that analysis is performed. Hence, the claims explicitly recite numerous elements that, individually and in combination, constitute abstract ideas. The instant claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d)).
[Step 2A Prong One: claims 14-23, 36-37, 42, and 51-52: Yes – claims 24-27: No due to no judicial exceptions identified]
Step 2A, 1st prong, 1st Mayo/Alice question: natural law-- MPEP 2106.04(b).
The instant claims recite a natural correlation by correlating the measurement of an amount of a metabolite naturally found in the body with a diabetes status. (see MPEP 2106.04(b).I).
[Step 2A, 1st prong, law of nature: 36-37, 42, and 51-52: Yes]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Background
MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
Analysis of instant claims
Instant claims 14, 36, and 51 recite additional elements that are not abstract ideas:
• "treating said subject" (claim 14);
• "obtaining a sample" (claims 36 and 51);
• "introducing .. sample into an analytical device" (claims 36 and 51); and
• "graphically displaying said subject's risk" (claims 36 and 51).
Dependent claims 17-23 recite further details about "treating the subject"; dependent claims 37, 42, and 52 recite further details about "sample analysis"; and dependent claims 42 and 52 recite further details about "graphically displaying."
The recited limitations in these claims are interpreted to require multiple computer parts (processor/ memory), not requiring specialized hardware other than a generic computer, which does not integrate the abstract idea into a practical application. Hence, the claims explicitly recite steps executed by computers and therefore can be described as computer functions.
The recited "obtaining a sample" for further analysis read on data gathering activities or the type of data being gathered; not amounting to a practical application. The type of data doesn’t change that it is mere data gathering. The recited "introducing .. sample into an analytical device" (claims 36 and 51) reads on a physical step.
Claims directed to "graphically displaying" read on outputting data via a computer (Symantec, 838 F.3d at 1321 - MPEP 2106.05(a) pertains), which constitutes just necessary data gathering and outputting and therefore correspond to insignificant extra-solution activity.
Hence, these are mere instructions to apply the abstract idea using a computer and insignificant extra-solution activity and therefore the claims do not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; 2106.05(f); and 2106.05(g)). The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc .... are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (MPEP 2106.05(f)).
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In this Step 2A, Prong Two immediately above claim steps and/or elements were identified as part of one or more additional elements. Additional elements are further discussed in Step 2B below.
Here in Step 2A, Prong Two, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
At this point in examination it is not yet the case that any of the Step 2A, Prong Two considerations enumerated above clearly demonstrates integration of the identified JE(s) into a practical application. Referring to the considerations above, none of 1. an improvement, 2. treatment, 3. a particular machine or 4. a transformation is clear in the record.
For example, regarding the first consideration at MPEP 2106.04(d)(1) and an improvement over the previous state of the technology field, the record, including for example the specification, does not yet clearly disclose an explanation of improvement over the previous state of the technology field. The claims do not yet clearly result in such an improvement.
For example, regarding the second consideration at MPEP § 2106.04(d)(2), the record, including for example the specification, does not yet clearly disclose an explanation of a particular treatment or prophylaxis for a disease or medical condition. Steps directed to "treating a sample/subject" do not integrate the abstract idea into a practical application because there are no additional limitations to indicate details of exactly how the judicial exception ("identifying levels of a compound") is determining the details of how the treating step is applied. The claims do not yet clearly result in such treatment (e.g. specification: pgs. 8-11).
[Step 2A Prong Two: claims 14-23, 36-37, 42, and 51-52: No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception.
A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during examination that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
Further, the courts have found that the additional elements regarding receiving and displaying/outputting data are well-understood, routine, and conventional functions of a computer when claimed in a generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versa ta Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93, as discussed in MPEP 2106.05(d)(Il)(i)).
As explained above, the instant claims constitute insignificant extra solution activity, and when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(g)). Hence, these elements, when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(d)).
As discussed above regarding the treatment limitations, these limitations do not integrate the abstract idea into a practical application. The conventionality is only evaluated for those additional elements that are part of the broadest reasonable interpretation of the claim.
When the claims are considered as a whole, they do not improve a technology by allowing the technology to perform a function that it previously was not capable of performing. See MPEP 2106.05(a) and 2106.05(h).
[Step 2B: claims 14-23, 36-37, 42, and 51-52: No]
Conclusion: Instant claims are directed to non-statutory subject matter
For the reasons above, the claims in the instant application, when the limitations are considered individually and as a whole, are directed to an abstract idea and lack an inventive concept. Hence, the claimed invention does not constitute significantly more than the abstract idea, so instant claims 14-23, 36-37, 42, and 51-52 are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless -
(a)(l) the claimed invention was patented, described in a printed publication, or in public use, on sale,
or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 14 and 16-27 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Clendinen ("Preoperative metabolic signatures of prostate cancer recurrence following radical prostatectomy" Journal of proteome research 18(3):1316-1327 (2019)), as cited on the attached Form PTO-892.
Clendinen discloses a correlation analysis on metabolite abundances (i.e. increased levels) - including PGA - detected on serum samples collected prior to surgery from prostate cancer patients (i.e. a prostate cancer therapeutic) (pg. 1316 para. 1).
Bullet points indicate the teachings of the instant features over the prior art. Instantly claimed elements which are considered to be equivalent to the prior art teachings are described in bold for all claims.
Claim 14 recites:
a) identifying a subject as having increased levels of at least one compound compared to control levels, wherein said at least one compound comprises phenylacetyl glutamine (PAG); and
b) treating said subject with at least one of the following:
i) a first agent or procedure that treats cardiovascular disease (CVD), heart failure, asthma, and/or thrombosis, wherein said subject is chronic kidney disease (CKD) free and/or has diabetes,
ii) a second agent selected from: a beta-adrenergic blocking agent, an alpha 2 adrenergic receptor agonist, and an alpha 2 adrenergic receptor antagonist,
iii) an antibiotic or antibiotic cocktail, wherein said subject does not have an active infection;
iv) a third agent or second procedure selected from: a prostate cancer therapeutic, brachytherapy, radiation therapy, and prostatectomy.
• Clendinen teaches correlation analysis on metabolite abundances (i.e. increased levels) detected on serum samples collected prior to surgery from prostate cancer patients (i.e. a prostate cancer therapeutic) showed significant alterations in a number of pathways, including amino acid metabolism (pg. 1316 para. 1); wherein phenylacetylglutamine is identified as a predictor of prostate cancer compared to healthy patients (i.e. identifying a subject as having increased levels of at least one compound compared to control levels, wherein said at least one compound comprises phenylacetyl glutamine (PAG)) and correlated with the presence of prostate cancer (pg. 1324 col. 1 para. 2).
Claim 16 recites:
wherein said at least one compound further comprises PSA, choline, and/or betaine, and said subject has prostate cancer.
• Clendinen teaches correlation analysis on metabolite abundances (i.e. increased levels) detected on serum samples collected prior to surgery from prostate cancer patients (pg. 1316 para. 1); wherein panel included median PSA levels (pg. 1318 Table 1).
Claim 17 recites:
wherein said subject is a human having heart failure, asthma, cardiovascular disease, or prostate cancer.
• Clendinen teaches the recitation as applied for claim 14 above.
Claim 24 recites:
a) obtaining a sample, wherein said sample is from a human subject who is optionally chronic kidney disease (CKD) free and/or has diabetes; and
b) treating said sample under conditions such that the concentration of at least one compound is determined, wherein said at least one compound comprises phenylacetyl glutamine (PAG).
• Clendinen teaches serum sample collection from a cohort of 80 male subjects (pg. 1317 col. 2 para. 2); wherein samples are analyzed via ultraperformance liquid chromatography coupled to high-resolution tandem mass spectrometry (i.e. treating said sample under conditions such that the concentration of at least one compound is determined) (pg. 1317 col. 2 para. 4) and phenylacetylglutamine is identified as a predictor of prostate cancer compared to healthy patients and correlated with the presence of prostate cancer (i.e. at least one compound comprises phenylacetyl glutamine (PAG)) (pg. 1324 col. 1 para. 2).
Claim 25 recites:
wherein said concentration of said PAG in said sample is determined by mass spectrometry.
• Clendinen teaches serum sample analyzed via ultraperformance liquid chromatography coupled to high-resolution tandem mass spectrometry (pg. 1317 col. 2 para. 4).
Claim 26 recites:
wherein said wherein said subject has heart failure, asthma, cardiovascular disease, or prostate cancer.
• The described recitation as applied for claim 14 above.
Claim 27 recites:
wherein said at least one compound further comprises trimethylamine-n-oxide (TMAO) and/or N6-trimethyl-lysine (TML) and/or PSA and/or choline, and/or betaine.
• Clendinen teaches the recitation as applied for claim 16 above.
Claim Rejections - 35 USC § 103
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 pre-AIA 35 U.S.C. 103(a) 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.
Claim 15 is rejected under 35 U.S.C. 103(a) as being unpatentable over Clendinen as applied to claim 14 in the 102 rejection above further in view of Kuligowski ("Metabolomic analysis of gastric cancer progression within the Correa’s Cascade using Ultraperformance liquid chromatography–mass Spectrometry" Journal of Proteome Research 15(8):2729-2738 (2016)), as cited on the attached Form PTO-892.
Claim 15 recites:
wherein said identifying comprises receiving a report that said subject has increased PAG levels compared to a control.
• Kuligowski teaches significant increased relative levels in the gastric cancer subjects compared to control (pg. 2734 col. 2 para. 1) with values reported via ultraperformance liquid chromatography-mass spectrometry chromatogram reports (pg. 2735 Fig. 2).
Rationale for combining (MPEP §2142-2143)
Regarding claim 15, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Clendinen in view of Kuligowski because all references disclose methods for the investigation of plasma metabolites and its correlation to disease. The motivation would have been to allow the identification of discriminant plasma metabolites (pg. 2736 col. 2 para. 3 Kuligowski). Therefore it would have been obvious to one of ordinary skill in the art to substitute the allelic imbalance analysis method of Clendinen to the methods by Kuligowski because such a substitution is no more than the simple substitution of one known element for another. One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for investigation of plasma metabolites and its correlation to disease.
No prior art has been applied to the following claims
Claims 36-37, 42, and 51-52 are free of the analogous art at least because close art, e.g. Clendinen as well as art cited on the IDSs and in the search histories either individually or in obvious combination, does not teach the recited combination of "iii) an anti-PAG antibody-based detection system" disclosed before the effective filling date.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to FRANCINI A FONSECA LOPEZ whose telephone number is (571)270-0899. The examiner can normally be reached Monday - Friday 8AM - 5PM ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia Wise can be reached at (571) 272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/F.F.L./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685