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 .
Detailed Action
Summary
This is a Non-Final Office Action based on application 18/247865 response filed 03/30/2026.
Claims 17-19, 26-29 & 38-40 have been examined and fully considered.
Claims 20-25 & 30-37 have been cancelled.
Claims 38-40 have been newly added.
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 17-19, 26-29 & 38-40 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1: Independent Claims 17, 26 & 38 are directed towards methods.
Step 2A, Prong One: Independent Claims 17, 26 & 38 recite abstract ideas which are “comparing,” the measured level of biomarker to the level in a control sample. Comparing is a mental process which is an abstract idea. Though not a diagnostic or natural correlation claim and instead including an abstract idea, the independent claims follow a similar analysis to that of Example 29 of the USPTO subject matter eligibility examples, which was found ineligible.
Comparison to a control is a mental process or at best, a mathematical comparison using an equation. Formulas or equations are mathematical concepts, which are an enumerated abstract idea (MPEP § 2106.04(a)).
Step 2A, Prong Two: The abstract idea in independent Claims 17, 26 & 38 are not integrated into a practical application because upon or after the comparison, nothing further is done to practically apply. Claims 17, 26 & 38 do not involve a and therefore does not practically apply it. Further, as claimed it is not clear if the claim and particular and specific treatment or anything else which practically applies the comparison (abstract idea judicial exception).
Also- the claimed measuring/measurement steps as instantly claimed as just data gathering to perform the judicial exceptions. Data gathering is considered to be extra-solution activity, and does not practically apply the judicial exception. See MPEP 2106.05 (g).
Step 2B: There is nothing in independent Claims 17, 26 & 38 which add something which is non routine and conventional or significantly more to the claimed abstract idea judicial exception.
“Measuring,” especially as generally claimed instantly claimed is well understood routine and conventional (WURC) in the art. This is evidenced by SAVIDGE in US 20140296134---which teaches in paragraph 0095—"Extracted samples may be analyzed using any suitable method known in the art. Biological samples or extracts of biological samples can be analyzed on essentially any mass spectrometry platform, either by direct injection or following chromatographic separation. Typical mass spectrometers are comprised of a source that ionizes molecules within the sample, and a detector for detecting the ionized molecules or fragments of molecules. Non-limiting examples of common sources include electron impact, electrospray ionization (ESI), atmospheric pressure chemical ionization (APCI), atmospheric pressure photo ionization (APPI), matrix assisted laser desorption ionization (MALDI), surface enhanced laser desorption ionization (SELDI), and derivations thereof. Common mass separation and detection systems can include quadrupole, quadrupole ion trap, linear ion trap, time-of-flight (TOF), magnetic sector, ion cyclotron (FTMS), orbitrap, and derivations and combinations thereof. Ionization used in-line with liquid chromatography is referred to as Liquid Chromatography Mass Spectrometry (LC-MS). In certain aspects a mass spectrometer consisting of an electrospray ionization (ESI) source and linear ion-trap (LIT) mass analyzer is used.”
See MPEP 2106.05(d)- “laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner.”
The dependent claims are analyzed the same way as above.
Claim 18 recites specifics about the comparison. This is part of the judicial exception so does nothing to practically apply at step 2A/2, nor to add significantly more at step 2B.
Claim 19 recites what the sample is which is measured from and in which the data gathering is done from however does to practically apply at step 2A/2, nor to add significantly more at step 2B.
Claim 27 recites that more generic measuring and comparison is added to the measuring and comparison in the independent claim. These elements carry the same analysis as in the independent claim so does nothing to practically apply at step 2A/2, nor to add significantly more at step 2B.
Claim 28 recites specifics about the comparison. This is part of the judicial exception so does nothing to practically apply at step 2A/2, nor to add significantly more at step 2B.
Claim 29 recites what the sample is which is measured from and in which the data gathering is done from however does to practically apply at step 2A/2, nor to add significantly more at step 2B.
Claim 39 recites that more generic measuring and comparison is added to the measuring and comparison in the independent claim. These elements carry the same analysis as in the independent claim so does nothing to practically apply at step 2A/2, nor to add significantly more at step 2B.
Claim 40 recites that more generic measuring and comparison is added to the measuring and comparison in the independent claim. These elements carry the same analysis as in the independent claim so does nothing to practically apply at step 2A/2, nor to add significantly more at step 2B.
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 17-19, 27-28 & 38-39 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.
With respect to Claim 17, 27, & 38-39, they claim things in “()”’s. In some instances, the things in “()’s are abbreviations of a longer written out name of biomarker. In other instances though, they seem to be specifying that only 1 type of structure for the biomarker, “isoform 2,” of for instance (18:1/18:1) can be detected, however in these instances what is in “()”’s is not an abbreviation. Therefore--- the “()”’s are confusing and make the claims not clear as it is unclear in many instances what exactly the applicant intends the exact biomarker to be.
With respect to Claims 18 & 28, they claim that the biomarkers are “statistically significant,” but it does not say what they are statistically significant for. Is something really statistically significant if it is not said what the significance is in relation to or for? Or what the relationship of statistical significance is for? Statistical significance and “significance,” in general is a relative terminology and would mean something different to different people, especially without stating what the significance is specific for. This is unclear in the claim and makes the claim confusing.
Claims 18-19, 28 & 39 are also rejected due to their dependency on an unclear base claim.
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 non-obviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 17-19, 26-29 & 38-40 are rejected under 35 U.S.C. 103 as being obvious over SAVIDGE in US 20140296134 in view of CIRULLI in US 20190310269
With respect to Claim 17, SAVIDGE teaches of a method of determining a metabolite profile and then of assessing the status of a subject based on the sample. SAVIDGE focuses on stool, samples, but the sample can also be blood (abstract, paragraph 0031).
SAVIDGE further teaches of measuring at least one metabolic marker as claimed, which includes 3-phenylpropionate (paragraph 0087), anthranilate (paragraph 0088), and p-cresol sulfate (paragraph 0089) among other biomarkers.
SAVIDGE further teaches of comparing the measured level of the biomarker to a control including a healthy control sample (paragraph 0100, 0127, 0057, 0030), however since SAVIDGE focuses on using models, if comparison to a healthy control sample is unclear to one of ordinary skill, CIRULLI is used to remedy this.
CIRULLI teaches methods for diagnosis or prognosis of subjects for obesity or a disease related thereto (abstract) in which the disease related thereto can be inflammation (paragraph 0042). CIRULLI further teaches of comparison to a healthy control sample for the measured samples (paragraph 0092, 0090), and that the biomarkers can include cinnamoyl glycine and adenosine monophosphate (AMP) (Table 11).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention to measure AMP and cinnamoyl glycine as is done in CIRULLI and compare the levels of all biomarkers to a healthy control sample as is done in CIRULLI, due to the advantage the biomarkers have has for showing relationship with BMI and associated conditions such as inflammation (table 11) and due to the advantage this offers for comparison with a subject who is not suffering from the condition (CIRULLI, paragraph 0092).
With respect to Claim 18, SAVIDGE teaches of determining if the biomarkers are elevated or decreased by determining statistically significant differences (paragraph 0119, & 0116-0119, 0030). SAVIDGE teaches of calculating p-values for the measured biomarkers 3-phenylpropionate (paragraph 0087), anthranilate (paragraph 0088), and p-cresol sulfate (paragraph 0089) among other biomarkers.
With respect to Claim 19, SAVIDGE teaches that the sample can be blood (abstract, paragraph 0031).
With respect to Claim 26, SAVIDGE teaches of a method of determining a metabolite profile and then of assessing the status of a subject based on the sample. SAVIDGE focuses on stool, samples, but the sample can also be blood (abstract, paragraph 0031).
SAVIDGE further teaches of measuring at least one metabolic marker as claimed, which includes 3-phenylpropionate (paragraph 0087), anthranilate (paragraph 0088), and p-cresol sulfate (paragraph 0089) among other biomarkers. SAVIDGE also teaches of detection of indole-3-acetic acid which is also known as 1H-indole-3-ylacetate, which makes the instant 1H-indole-7-acetic acid obvious (paragraph 0086-0088).
SAVIDGE further teaches of comparing the measured level of the biomarker to a control (paragraph 0100, 0127, 0057, 0030), however since SAVIDGE focuses on using models, if comparison to a healthy control sample is unclear to one of ordinary skill, CIRULLI is used to remedy this.
CIRULLI teaches methods for diagnosis or prognosis of subjects for obesity or a disease related thereto (abstract) in which the disease related thereto can be inflammation (paragraph 0042). CIRULLI further teaches of comparison to a healthy control sample for the measured samples (paragraph 0092, 0090), and that the biomarkers can include cinnamoyl glycine and adenosine monophosphate (AMP) (Table 11).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention to measure AMP and cinnamoyl glycine as is done in CIRULLI and compare the levels of all biomarkers to a healthy control sample as is done in CIRULLI, due to the advantage the biomarkers have has for showing relationship with BMI and associated conditions such as inflammation (table 11) and due to the advantage this offers for comparison with a subject who is not suffering from the condition (CIRULLI, paragraph 0092).
With respect to Claim 27, SAVIDGE further teaches of measuring at least one metabolic marker as claimed, which includes 3-phenylpropionate (paragraph 0087), anthranilate (paragraph 0088), and p-cresol sulfate (paragraph 0089) among other biomarkers.
With respect to Claim 28, SAVIDGE teaches of using the biomarkers 3-phenylpropionate (paragraph 0087), anthranilate (paragraph 0088), and p-cresol sulfate (paragraph 0089) among other biomarkers, to identify and/ or classify (diagnose) CDI (clostridium difficile infection, which is a disease or a disorder as claimed) (paragraph 0092, 0004). SAVIDGE teaches of determining if the biomarkers are elevated or decreased by determining statistically significant differences (paragraph 0119, & 0116-0119, 0030). SAVIDGE teaches of calculating p-values for the measured biomarkers 3-phenylpropionate (paragraph 0087), anthranilate (paragraph 0088), and p-cresol sulfate (paragraph 0089) among other biomarkers.
With respect to Claim 29, SAVIDGE teaches that the sample can be blood (abstract, paragraph 0031).
With respect to Claim 38, SAVIDGE teaches of a method of determining a metabolite profile and then of assessing the status of a subject based on the sample. SAVIDGE focuses on stool, samples, but the sample can also be blood (abstract, paragraph 0031).
SAVIDGE further teaches of measuring at least one metabolic marker as claimed, which includes 3-phenylpropionate (paragraph 0087), anthranilate (paragraph 0088), and p-cresol sulfate (paragraph 0089) among other biomarkers. SAVIDGE also teaches of detection of indole-3-acetic acid which is also known as 1H-indole-3-ylacetate, which makes the instant 1H-indole-7-acetic acid obvious (paragraph 0086-0088).
SAVIDGE further teaches of comparing the measured level of the biomarker to a control (paragraph 0100, 0127, 0057, 0030), however since SAVIDGE focuses on using models, if comparison to a healthy control sample is unclear to one of ordinary skill, CIRULLI is used to remedy this.
CIRULLI teaches methods for diagnosis or prognosis of subjects for obesity or a disease related thereto (abstract) in which the disease related thereto can be inflammation (paragraph 0042). CIRULLI further teaches of comparison to a healthy control sample for the measured samples (paragraph 0092, 0090), and that the biomarkers can include cinnamoyl glycine and adenosine monophosphate (AMP) (Table 11).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention to measure AMP and cinnamoyl glycine as is done in CIRULLI and compare the levels of all biomarkers to a healthy control sample as is done in CIRULLI, due to the advantage the biomarkers have has for showing relationship with BMI and associated conditions such as inflammation (table 11) and due to the advantage this offers for comparison with a subject who is not suffering from the condition (CIRULLI, paragraph 0092).
With respect to Claim 39, SAVIDGE teaches of a method of determining a metabolite profile and then of assessing the status of a subject based on the sample. SAVIDGE focuses on stool, samples, but the sample can also be blood (abstract, paragraph 0031).
SAVIDGE further teaches of measuring at least one metabolic marker as claimed, which includes 3-phenylpropionate (paragraph 0087), anthranilate (paragraph 0088), and p-cresol sulfate (paragraph 0089) among other biomarkers. SAVIDGE also teaches of detection of indole-3-acetic acid which is also known as 1H-indole-3-ylacetate, which makes the instant 1H-indole-7-acetic acid obvious (paragraph 0086-0088).
SAVIDGE further teaches of comparing the measured level of the biomarker to a control (paragraph 0100, 0127, 0057, 0030), however since SAVIDGE focuses on using models, if comparison to a healthy control sample is unclear to one of ordinary skill, CIRULLI is used to remedy this.
CIRULLI teaches methods for diagnosis or prognosis of subjects for obesity or a disease related thereto (abstract) in which the disease related thereto can be inflammation (paragraph 0042). CIRULLI further teaches of comparison to a healthy control sample for the measured samples (paragraph 0092, 0090), and that the biomarkers can include cinnamoyl glycine and adenosine monophosphate (AMP) (Table 11).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention to measure AMP and cinnamoyl glycine as is done in CIRULLI and compare the levels of all biomarkers to a healthy control sample as is done in CIRULLI, due to the advantage the biomarkers have has for showing relationship with BMI and associated conditions such as inflammation (table 11) and due to the advantage this offers for comparison with a subject who is not suffering from the condition (CIRULLI, paragraph 0092).
With respect to Claim 40, SAVIDGE teaches of a method of determining a metabolite profile and then of assessing the status of a subject based on the sample. SAVIDGE focuses on stool, samples, but the sample can also be blood (abstract, paragraph 0031).
SAVIDGE further teaches of measuring at least one metabolic marker as claimed, which includes 3-phenylpropionate (paragraph 0087), anthranilate (paragraph 0088), and p-cresol sulfate (paragraph 0089) among other biomarkers. SAVIDGE also teaches of detection of indole-3-acetic acid which is also known as 1H-indole-3-ylacetate, which makes the instant 1H-indole-7-acetic acid obvious (paragraph 0086-0088).
SAVIDGE further teaches of comparing the measured level of the biomarker to a control (paragraph 0100, 0127, 0057, 0030), however since SAVIDGE focuses on using models, if comparison to a healthy control sample is unclear to one of ordinary skill, CIRULLI is used to remedy this.
CIRULLI teaches methods for diagnosis or prognosis of subjects for obesity or a disease related thereto (abstract) in which the disease related thereto can be inflammation (paragraph 0042). CIRULLI further teaches of comparison to a healthy control sample for the measured samples (paragraph 0092, 0090), and that the biomarkers can include cinnamoyl glycine and adenosine monophosphate (AMP) (Table 11).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention to measure AMP and cinnamoyl glycine as is done in CIRULLI and compare the levels of all biomarkers to a healthy control sample as is done in CIRULLI, due to the advantage the biomarkers have has for showing relationship with BMI and associated conditions such as inflammation (table 11) and due to the advantage this offers for comparison with a subject who is not suffering from the condition (CIRULLI, paragraph 0092).
Response to Arguments
Applicant's arguments filed 03/30/2026 have been fully considered but they are not fully persuasive.
With respect to the 101 rejection, it is noted that applicant cancelled the claims which were priorly rejected under 101. However, upon consultation with the examiner’s SPE, the examiner has added a 101 rejection for all pending claims which was not done before. Therefore, the instant rejection is made Non-Final. The reasons for this are above in the rejection.
With respect to the prior 112 (a) rejection, the claims which were rejected under this statute were cancelled. Therefore, this rejection is withdrawn.
With respect to the 112 (b) rejection, some of the prior issues were overcome, however one is maintained and further explained for clarity as shown above. Specifically—statistically significant and significant/significance in general is a relative term and would mean something different to different people. Therefore, use of this term or phrase in the claim causes clarity issues. The examiner further notes with respect to this though that applicant should be careful of considering to amend what the significance is specific to ( gut dysbiosis or inflammation) into the claims--- as natural correlations are considered laws of nature, which are commonly rejected under 101 if not practically applied in the claim and if significantly more is not added in the claims.
With respect 103 rejection, though the examiner does not agree with applicant--- the prior art rejection has been adjusted and a new reference added as shown above. Therefore applicant’s arguments do not apply to the current grounds of rejection made, in this Non-Final office action.
All claims remain rejected.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
VENEGAS in Short Chain Fatty Acids (SCFAs)-Mediated Gut Epithelial and Immune Regulation and It’s Relevance for Inflammatory Bowel Diseases (as cited on IDS dated 04/24/2023)
VENEGAS is used to remedy this and more specifically teaches of a method of detection of Irritable Bowel Disease (IBD) by investigating microbial short chain fatty acids in the intestinal mucosa (Page 1, abstract). Further, VENEGAS teaches of detecting acetate, propionate and butyrate (Page 1, abstract), and even further of diagnosing gut dysbiosis, especially in relation to clostridium difficile cases (Page 10, column 1, paragraph 1 & abstract).
VOROS in US 20190391131
VOROS is used to remedy this and teaches of methods for evaluating a human subject for having atherosclerotic coronary artery disease (ASCAD) or as having a coronary atherosclerotic plaque (abstract). VOROS further teaches of biomarkers for the disease being guanidinosuccinate, imidazole propionate, and 4-hydroxyphenylacetate (paragraph 0175) among other biomarkers. VOROS further teaches of treating with an effective amount of statin (paragraph 0196). It would have been obvious to one of ordinary skill in the art before the effective filing date of the instant invention to treat with an effective amount of statin as is done in VOROS in the methods of SAVIDGE and VENEGAS due to the advantage statins are known to have for improving cardiovascular health (paragraph 0196).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to REBECCA M FRITCHMAN whose telephone number is (303)297-4344. The examiner can normally be reached 9:30-4:30 MT Monday-Friday.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Maris Kessel can be reached on 571-270-7698. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/REBECCA M FRITCHMAN/Primary Examiner, Art Unit 1758
