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 .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-12, in the reply filed on 12 June 2026 is acknowledged.
Claim 13 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12 June 2026
Claims 1-12 are under consideration in the instant Office action.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
The information disclosure statement (IDS) submitted on 22September 2023 has been considered by the examiner.
Drawings
The drawings are objected to because they do not comply with 37 CFR 1.84(a)(1) and (l) which requires that black ink be used for drawings and that every line, number and letter must be clean, black, sufficiently dense and dark and uniformly thick and well-defined. All 3 Figures appear to have extraneous lines running through them and letters and text appear fuzzy and not well-defined. Corrected drawing sheets in compliance with 37 CFR 1.121(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 37 CFR 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.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. See at least pages 2-3 of the specification.
Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The use of the term Distiller® at page 12 of the specification, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
The use of the term Evidence Investigator® at pages 13-14 of the specification, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
The use of the term RStudio® at page 14 of the specification, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claim 9 is objected to because of the following informalities: the claim refers to CKD-EPI eGFR but does not explain what the abbreviation stands for. All abbreviations should be spelled out at first usage for clarity purposes. Appropriate correction is required.
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 2-6 are rejected under 35 U.S.C. 101 because the claimed invention is directed to the judicial exception of law of nature/natural phenomenon and abstract idea without significantly more. The judicial exception is not integrated into a practical application and the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception for the reasons that follow.
Applicant’s attention is directed to the USPTO January 7, 2019 Revised Patent Subject Matter Eligibility Guidance (i.e. Guidance) available at URL: https://www.govinfo.gov/content/pkg/FR-2019-01-07/pdf/2018-28282.pdf.
Also, the U.S. Patent and Trademark Office recently revised the MPEP with regard to § 101 (see the MPEP at 2106). Regarding the MPEP at 2106, in determining what concept the claim is “directed to,” we first look to whether the claim recites:
(1) any judicial exceptions, including certain groupings of abstract ideas (i.e., mathematical concepts, certain methods of organizing human activity such as a fundamental economic practice, or mental processes); and
(2) additional elements that integrate the judicial exception into a practical application (see MPEP § 2106.05(a)-(c), (e)-(h)).
Only if a claim (1) recites a judicial exception and (2) does not integrate that exception into a practical application, do we then look to whether the claim contains an “inventive concept’ sufficient to ‘transform’ the claimed judicial exception into a patent-
eligible application of the judicial exception. Alice, 573 U.S. at 221 (quoting Mayo, 566 U.S. at 82). In so doing, we thus consider whether the claim:
(3) adds a specific limitation beyond the judicial exception that is not
“well-understood, routine, conventional” in the field (see MPEP § 2106.05(d)): or
(4) simply appends well-understood, routine, conventional activities
previously known to the industry, specified at a high level of generality, to the
judicial exception.
See MPEP 2106.
Regarding Step 1 of the Guidance, the claims are directed to the statutory category of a process as the claims are directed to methods.
Regarding Step 2A, prong one, the claims are directed to and recite the judicial exception of a law of nature/natural phenomenon in claims 2-6.
Claim 2 is directed to a method of determining the prognosis of chronic kidney disease in a patient which comprises the steps of: (a) measuring the amount of complement 3a des-arginine (C3a-desArg) in a sample, and (b) comparing the level in the sample to a reference value, wherein a decreased level of C3a-desArg in the sample compared to the reference value is indicative of an adverse outcome. Claim 3 is directed to a method of determining the prognosis of chronic kidney disease in a patient which comprises the steps of: (a) measuring the amount of complement 3a des-arginine (C3a-desArg) in a sample, (b) measuring the amount of one or both of soluble tumor necrosis factor receptor 1 (sTNFR1) and neutrophil gelatinase-associated lipocalin (NGAL) and establishing the significance of the level of the measured proteins via a mathematical model to indicate CKD prognosis. Claim 4 is directed to a method of determining the prognosis of chronic kidney disease in a patient which comprises the steps of: (a) measuring the amount of complement 3a des-arginine (C3a-desArg) in a sample, (b) measuring the amount of one or both of soluble tumor necrosis factor receptor 1 (sTNFR1) and neutrophil gelatinase-associated lipocalin (NGAL) and (c) comparing the level of sTNFR1 in the sample to a reference value, wherein an increase in sTNFR1 is indicative of an adverse outcome. Claim 5 is directed to a method of determining the prognosis of chronic kidney disease in a patient which comprises the steps of: (a) measuring the amount of complement 3a des-arginine (C3a-desArg) in a sample, (b) measuring the amount of one or both of soluble tumor necrosis factor receptor 1 (sTNFR1) and neutrophil gelatinase-associated lipocalin (NGAL) and (c) comparing the level of NGAL in the sample to a reference value, wherein an increase in NGAL is indicative of an adverse outcome. Claim 6 is directed to a method of determining the prognosis of chronic kidney disease in a patient which comprises the steps of: (a) measuring the amount of complement 3a des-arginine (C3a-desArg) in a sample, (b) measuring the amount of one or both of soluble tumor necrosis factor receptor 1 (sTNFR1) and neutrophil gelatinase-associated lipocalin (NGAL) and (c) comparing the level of C3a-desArg, sTNFR1 and NGAL in the sample to a reference value, wherein an increase in sTNFR1, an increase in NGAL and a decrease in C3a-desArg is indicative of an adverse outcome. Therefore, the claims recite the relationship between amounts of C3a-desArg, sTNFR1 and NGAL in a sample from a subject and an increased risk of an adverse outcome (prognosis) in a subject with chronic kidney disease.
As in Mayo Collaborative Services v. Prometheus, the recited relationships are natural phenomenon that exist apart from any human action.
The claims are also directed to and recite the judicial exception of an abstract idea and particularly mental processes.
Note that the Courts have held that steps that can be performed by a human using mental processes or basic critical thinking, or intangible verbal communication are types of activities that represent abstract ideas. Claims 2 and 4-6 all require a comparison to be made although it is not recited as an active step in the claims. The broadest reasonable interpretation of the "compared to a reference value" limitation is that this comparison may be accomplished mentally by critical thinking processes. Such mental processes are abstract, having no particular concrete or tangible form. For instance, one may read information in a report or database regarding protein levels for a subject and making the comparison to some reference value. Thus, the "compared to a reference value” limitation encompasses an abstract idea/process.
Claim 3 recites “establishing the significance of the level of the biomarkers by inputting each of the biomarker concentration values into a statistical methodology to produce an output value”. The broadest reasonable interpretation of this limitation is that this process may be accomplished mentally as this reads on a mathematical calculation. Such mental processes are abstract, having no particular concrete or tangible form. Thus, the limitation encompasses an abstract idea/process.
Applicant’s attention is directed to the Association for Molecular Pathology (AMP) and ACLU v. USPTO and Myriad Genetics (Fed. Cir. 2012)) wherein it is stated at 56-57:
We renew our conclusion that Myriad’s claims to “comparing” or “analyzing” two gene sequences fall out-side the scope of § 101 because they claim only abstract mental processes. See Benson, 409 U.S. at 67 (“Phenomena of nature, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.”). The claims recite, for example, a “method for screening a tumor sample,” by “comparing” a first BRCA1 sequence from a tumor sample and a second BRCA1 sequence from a non-tumor sample, wherein a difference in sequence indicates an alteration in the tumor sample. ’001 patent claim 1. This claim thus recites nothing more than the abstract mental steps necessary to compare two different nucleotide sequences: one looks at the first position in a first sequence; determines the nucleotide sequence at that first position; looks at the first position in a second sequence; determines the nucleotide sequence at that first position; determines if the nucleotide at the first position in the first sequence and the first position in the second sequence are the same or different, wherein the latter indicates an alteration; and repeats the process for the next position. (Emphasis added).
Additionally, in In re BRCA1- & BRCA2-Based Hereditary Cancer Test Patent Litigation, 774 F.3D 755 (2014), the Court held that:
Having determined that the comparison steps of claims 7 and 8 are abstract ideas, we move to the second step of Alice and ask whether the particular mechanism for the comparisons added by claims 7 or 8 renders the claims patent-eligible. For this step, Alice dictates that we ask whether the remaining elements, either in isolation or combination with the other non-patent-ineligible elements, are sufficient to “‘transform the nature of the claim’ into a patent-eligible application.” Alice, 134 S. Ct. at 2355 (quoting Mayo, 132 S. Ct. at 1297). There must be a further inventive concept to take the claim into the realm of patent-eligibility. Id. at 2355. The second paragraph of claim 7 describes the way in which the sequences are compared: they are compared by 1) hybridizing a BRCA gene probe and 2) detecting the presence of a hybridization product. Similarly, claim 8 requires 1) amplification of the BRCA1 gene and 2) sequencing of the amplified nucleic acids. The non-patent-ineligible elements of claims 7 and 8 do not add “enough” to make the claims as a whole patent- eligible. (Emphasis added).
Thus, the claims recite and are directed to the patent-ineligible concepts of abstract processes and a law of nature / natural phenomenon.
Regarding Step 2A, prong two, having determined that the claims recite a judicial exception, it is then determined whether the claims recite additional elements that integrate the judicial exception into a practical application. Here, the claims do not integrate the recited judicial exceptions into a practical application of the exception(s). For example, the claims do not practically apply the recited law of nature/natural phenomenon by including a step of treatment. The claims do not integrate the judicial exception into a practical application because it does not rely on, use or implement the judicial exception in any manner.
The method includes mental steps as they could be performed by merely reviewing data mentally or using a computer. In addition, such steps are judicial exceptions as given their broadest reasonable interpretation, they do not clearly go beyond mental activity and add nothing specific to the law of nature/natural phenomenon other than what is well-understood, routine, conventional data gathering and analysis, previously engaged in by those in the field.
Regarding Step 2B, the next question is whether the remaining elements/steps – i.e., the non-patent-ineligible elements/steps – either in isolation or combination, amount to significantly more than the judicial exception. Here, the claims as a whole are not considered to recite any additional steps or elements that amount to significantly more than routine and conventional activity and do not add something “significantly more” so as to render the claims patent-eligible. The claims do not require performing any specific, non-conventional transformative active process steps.
The claims encompass performing any type of method of measuring the recited protein levels. However, methods for measuring protein levels were well-known, routine and conventional in the prior art as evidenced by the instant specification beginning at page 8. Specifically, the specification states:
The determination of the level of biomarkers in the sample may be determined by immunological methods such as an ELISA-based assay. The methods of the current invention preferably comprise the following steps; the biomarkers binding to a probe(s), adding a detector probe(s) and detecting and measuring the biomarker/probe complex
signal(s), placing these values into a machine algorithm and analysing the output value, said value indicating the patient's prognosis. Preferably, the methods of the present invention use a solid-state device for determining the level of biomarkers in the sample isolated from the patient.
The solid-state device comprises a substrate having a probe or multiple different probes immobilised upon it that bind specifically to a biomarker. The interactions between a biomarker and its respective probe can be monitored and quantified using various techniques that are well-known in the art. The term "probe" refers to a molecule that is capable of specifically binding to a target molecule such that the target molecule can be detected as a consequence of said specific binding. Probes that can be used in the present invention include, for example, antibodies, aptamers, phages and oligonucleotides. In a preferred embodiment of the current invention the probe is an antibody.
The claims do not recite actual physical steps related to the determination of the recited protein levels. The judicial exception is the correlation of protein levels being indicative of and adverse outcome in patients with CKD. “Elements or steps that are well-understood, purely conventional, and routinely taken by others in order to apply the natural principle, or that only limit the use to a particular technological environment (filed-of-use), would not be sufficiently specific. See Mayo, 566 U.S. at , 132 S.Ct. at 1294, 101 USPQ2d at 1968.”
Applicant’s attention is again directed to the Federal Circuit decision for In re BRCA1- & BRCA2-Based Hereditary Cancer Test Patent Litigation which noted that
“the claims contain no otherwise new process for designing or using probes, primers or arrays beyond the use of BRCA1 and BRCA2 sequences in these processes.”
In other words, the naming of particular targets – e.g., the URI gene - does not add an inventive concept to the recited judicial exceptions since it was routine and conventional at the time the invention was made to use reagents that will detect particular targets.
See also Ariosa Diagnostics, Inc. v. Sequenom, Inc., F. Supp. 2d, 2013 WL 5863022, at *10 (N.D. Cal. Oct. 30, 2013) noting that "had the inventors of the [patent-in-suit] created an innovative method of performing DNA detection while searching for paternally inherited cffDNA, such as a new method of amplification or fractionation, those claims would be patentable.”
Note that this decision was affirmed by the Federal Circuit (No. 2014-1139, -1144. June 2015) wherein it is stated that “Where claims of a method patent are directed to an application that starts and ends with a naturally occurring phenomenon, the patent fails to disclose patent eligible subject matter if the methods themselves are conventional, routine and well understood applications in the art.”
Further, the steps of determining protein levels constitutes a data gathering step required to apply the law of nature / natural phenomenon.
In Mayo v. Prometheus, the Supreme Court stated: "[t]o put the matter more succinctly, the claims inform a relevant audience about certain laws of nature; any additional steps consist of well understood, routine, conventional activity already engaged in by the scientific community; and those steps, when viewed as a whole, add nothing significant beyond the sum of their parts taken separately."
This is similar to the present situation wherein the additional steps and elements are recited at a high degree of generality and are all routine, well understood and conventional in the prior art. The recited steps and elements do not provide the inventive concept necessary to render the claims patent eligible. See also Genetic Technologies Ltd. v. Merial L.L.C., 818 F.3d at 1377, 1379 (Fed. Cir. 2016).
For the reasons set forth above, when the claims are considered as a whole, the claims are not considered to recite something significantly more than a judicial exception and thereby are not directed to patent eligible subject matter.
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.
Claim 3 and dependent claims 4-6 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Claim 3 requires “establishing the significance of the level of the biomarkers by inputting each of the biomarker concentration values into a statistical methodology to produce an output value that indicates CKD prognosis for the patient” in step (b)(ii). However, the claimed method cannot be performed as the calculations which are to be made are not defined in the claim as the “statistical methodology” is not described. One of ordinary skill in the art would not be apprised of how to establish the significance level of the biomarkers without any guidance as to the statistical methodology to be used. The art of statistics can be quite complicated and knowing which methodology to be used is critical to the claimed method which requires the determination of a prognosis.
The claim recites that biomarker concentrations are inputted into “a statistical methodology to produce an output value that indicates CKD prognosis for the patient” but the claim does not indicate the statistical methodology to be used. Without any indication of which statistical methodology is to be used, a person of ordinary skill in the art would not be able to establish the significance of the level of biomarkers for arriving at a prognosis. Basically the claims appear to rely on an intended use of the biological markers to determine a prognosis without providing the actual necessary methods of how such information is to be used to determine the prognosis. The instant claims do not recite the necessary steps, parameters or statistical relationships to be determined in order to establish the significance of the level of biomarkers for arriving at a prognosis. Therefore, the instant claims as written are not enabled for the claimed method, absent evidence to the contrary.
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 1-10 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 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential steps, such omission amounting to a gap between the steps. See MPEP § 2172.01. The omitted steps are: a step that provides for the prognosis required by the claim. Claim 1 is directed to a method of determining the prognosis of chronic kidney disease in a patient but the only step is measuring the amount of protein from a sample. However, measuring the amount of protein in a sample does not indicate a prognosis without something more (such as a comparison to some value to indicate a particular prognosis). Claims 7-10 do not include limitations which would obviate this rejection, therefore, they are also indefinite for lacking an essential step.
The term “reference value” in claims 2 and 4-6 is a relative term which renders the claim indefinite. The term “reference value” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. The claims are indefinite as the comparison which is to be made cannot be performed without an understanding of the metes and bounds of “reference value”.
Claim 3 recites the limitation "the biomarkers" in line 4. There is insufficient antecedent basis for this limitation in the claim. Claim 3 depends from claim 1. Claim 1 measures C3a-desArg and claim 3 measures sTNFR1 and/or NGAL. Neither claim refers to these proteins as biomarkers and it is not clear which or if all of the proteins which are being measured are intended to be the biomarkers or not. Therefore, the metes and bounds of the claim are unclear.
Claim 10 recites the limitation "the statistical methodology" in line 2. There is insufficient antecedent basis for this limitation in the claim. Claim 10 depends from claim 1, but claim 1 does not recite “the statistical methodology”.
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)(1) 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.
Claim(s) 1, 3-5 and 7-12 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by WO 2015/049390 A2 (McConnell et al.).
McConnell et al. teach methods for detecting and staging chronic kidney disease (CKD) in a patient, where the levels of biomarkers in a sample obtained from a patient are elevated or reduced compared to the levels in a sample obtained from a healthy subject (see abstract). McConnell et al. teach that altered levels of individual biomarkers can be detected in serum from patients with stages 1-3 CKD compared with control individuals, including C3a desArg, NGAL and sTNFR1 (see page 4 , lines 10-30) and that altered levels compared to control indicates that the patient suffers from or is at risk of developing kidney disease (see page 8, lines 20-22). McConnell et al. teach that the method can be used for identifying patients at various stages of CKD or staging the progression of CKD by measuring 2 more markers which include C3a desArg, NGAL and sTNFR1 (see page 12, lines 14-22). McConnell et al. teach that NGAL and sTNFR1 are increased compared to controls in Stages 1, 2 and 3 of CKD (see Table 1).
McConnell et al. teach that the sample isolated from the patient is a serum sample, but may also be blood, plasma, urine or saliva (see page 11, lines 13-14).
Those of skill in the art would recognize that staging of CKD indicates prognosis as it provides a clear baseline for how the disease will behave overtime. McConnell et al. teach that there are 5 stages of CKD (see page 1 of the specification at lines 23-30). McConnell et al. teach that screening in early stages of CKD may reduce complications and associated heath conditions in subjects with CKD (see paragraph spanning pages 2-3). McConnell et al. teach that a GFR of 30-59 mL/min/1.73 m2 is associated with an increased risk of mortality (see page 3 of the specification, lines 31-32) and this GFR is associated with stage 3 of CKD and is > 40% decline in CKD-EPI eGFR (see claim 9).
Therefore, McConnell et al. teach a method of determining prognosis of chronic kidney disease in a patient suffering therefore by measuring the amount of C3a-desArg in a sample of said patient and comparing to a reference sample. While McConnell et al. do not specifically define a prognosis as an adverse outcome that consists of > 40% decline in CKD-EPI eGFR, doubling of serum creatinine, need for renal replacement therapy, or death, such outcomes are associated with particular stages of CKD, and therefore, would be inherent to the staging of CKD.
With regard to instant claims 3 and 10, McConnell et al. teach the use of an ROC graph in evaluating the diagnostic method, which is a statistic methodology using logistic regression.
Therefore, McConnell et al. anticipate the instant claims.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Christine J Saoud whose telephone number is (571)272-0891. The examiner can normally be reached M-F, 8am-4pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Julie Z Wu can be reached at 571-272-5205. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Christine J Saoud/Primary Examiner, Art Unit 1645
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