DETAILED CORRESPONDENCE
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 .
This action is in response to the papers filed March 16, 2026. Currently, claims 22, 24-27, 30-36, 38-39 are pending.
All arguments have been thoroughly reviewed but are deemed non-persuasive for the reasons which follow. This action is made FINAL.
Any objections and rejections not reiterated below are hereby withdrawn.
The 102 rejection over Rupp has been withdrawn in view of the amendment to Claim 22 requiring particular primers and polymorphisms.
Election/Restrictions
Applicant's election of Group I, claims 22-36 and SNP 653 in the paper filed July 31, 2025 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.03(a)).
The requirement is still deemed proper and is therefore made FINAL.
Priority
This application is a 371 of PCT/AU2021/050038, filed January 22, 2021 and claims priority to Australia 2020900167, filed January 22, 2020.
Drawings
The drawings are acceptable.
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 A(1) 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.
Page 71 contains a list of references.
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 22, 24-27, 30-36, 38-39 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
35 U.S.C. § 101 requires that to be patent-eligible, an invention (1) must be directed to one of the four statutory categories, and (2) must not be wholly directed to subject matter encompassing a judicially recognized exception. M.P.E.P. § 2106. Regarding judicial exceptions, “[p]henomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Gottschalk v. Benson, 409 U.S. 63, 67 (1972); see also M.P.E.P. § 2106, part II.
Based upon consideration of the claims as a whole, as well as consideration of elements/steps recited in addition to the judicial exception, the present claims fail to meet the elements required for patent eligibility.
Question 1
The claimed invention is directed to a process that involves a natural principle and a judicial exception.
Question 2A Prong I
The claims are taken to be directed to an abstract idea, a law of nature and a natural phenomenon.
Claim 22 is directed to “a method of determining the quantity or concentration of a bacterium in a sample” by amplifying a target nucleic acid comprising16S rRNA and a SNP, calculating a quantity or concentration by comparing to a reference level and determining copy number from the quantity or concentration.
Claim 22 is directed to a process that involves the judicial exceptions of an abstract idea (i.e. the abstract steps of “calculating a quantity or concentration or a target nucleic acid”, “comparing the quantity or concentration with a reference level” and “determining copy number”).
Claims 24-25 are directed to “generating the reference level” which is deemed an abstract idea and may be performed mentally.
Claim 33 is directed to determining a prognosis for an infection by quantifying the bacterium in a sample. This determining is a mental process and the associated of the quantity of bacterium in a sample and prognosis of infection is a natural correlation.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception for the reasons that follow.
Herein, the claims recite numerous patent-ineligible concepts of an abstract process. Claim 22 requires performing the step of “determining the quantity, “identifying the bacterium”. Neither the specification nor the claims set forth a limiting definition for "determining" or “identifying” and the claims do not set forth how “determining” or “identifying” is accomplished. As broadly recited the determining and identifying steps may be accomplished mentally by thinking about an amplification assay result and making the determination and identification. Thus, the determining step constitutes an abstract process idea.
Claim 22 further recites a comparison between the target nucleic acid in the sample and a reference level that is deemed an abstract idea (see MPEP 2106.04(a)(2)(III)(A); • claims to “comparing BRCA sequences and determining the existence of alterations,” where the claims cover any way of comparing BRCA sequences such that the comparison steps can practically be performed in the human mind, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 763, 113 USPQ2d 1241, 1246 (Fed. Cir. 2014)).
Even more, the claim requires a calculating and determining copy number being a function of or correlated to the quantity of the bacterium in the sample. This is a mathematical calculation. Claim 30 clearly recites a mathematical formula for calculation of copy number.
A correlation that preexists in the human is an unpatentable phenomenon. The association between quantity of bacterium and prognosis for an infection is a law of nature/natural phenomenon. The "evaluating” step which tells users of the process to predict prognosis for an infection in the sample, amounts to no more than an "instruction to apply the natural law". This assessing step is no more than a mental step. Even if the step requires something more such as to verbalize the discovery of the natural law, this mere verbalization is not an application of the law of nature to a new and useful end. The "assessing" step does not require the process user to do anything in light of the correlation. The "assessing" step fails to provide the “practical assurance” sought by the Prometheus Court that the “process is more than a drafting effort designed to monopolize the law of nature itself.”
Question 2A Prong II
The exception is not integrated into a practical application of the exception. The claims do not recite any additional elements that integrate the exception into a practical application of the exception. While the claim recites amplifying a target nucleic acid comprising bacterial 16S rRNA and a SNP, this is not an integration of the exception into a practical application. Instead, these elements are data gathering required to perform the method. Thus, the claim is “directed to” the exception.
Claims 34-36 are directed to methods of treating an infection and evaluating treatment efficacy however these treatments are general in nature and not particular treatments. Claim 34 also includes discontinuing treatment which is essentially “not administering treatment”. This is thus not a treatment method. Claim 35 requires quantifying a bacterium and determining whether or not the treatment is efficacious. This is not an integration of the exceptions (see MPEP 2106.04(d)(2)(c)). The administration of a treatment in order to gather data for the mental analysis step is extra-solution activity and does not integrate the judicial exception into a practical application.
Question 2B
The second step of Alice involves determining 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).
The claims are not sufficiently defined to provide a method which is significantly more from a statement of a natural principle for at least these reasons:
The claims do not include applying the judicial exception, or by use of, a particular machine. The claims do not tie the steps to a “particular machine" and therefore do not meet the machine or transformation test on these grounds. The use of machines generally does not impose a meaningful limit on claim scope.
The claims also do not add a specific limitation other than what is well-understood, routine and conventional in the field. The amplification of a bacterium from a sample is mere data gathering step that amounts to extra solution activity to the judicial exception. It merely tells the users of the method to determine the sequence of a sample without further specification as to how the sample should be analyzed. The claim does not recite a new, innovative method for such determination. The determining step essentially tells users to determine the markers through whatever known processes they wish to use.
The step of determining the quantity or concentration was well known in the art at the time the invention was made. The steps are recited at a high level of generality. The claim merely instructs a scientist to use any amplification analysis to determine the status of the bacteria. The claim does not require the use of any particular non-conventional reagents. When recited at this high level of generality, there is no meaningful limitation that distinguishes this step from well understood, routine and conventional activities engaged in by scientists prior to applicant’s invention and at the time the application was filed.
Further it is noted that the courts have recognized the following laboratory techniques as 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.
Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546;
Amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014)
For these reasons the claims are rejected under section 101 as being directed to non-statutory subject matter.
Response to Arguments
The response traverses the rejection. The response asserts the claims are directed to a specific lab method for detecting and quantifying bacteria in a sample rather than a mere natural correlation or abstract idea. This argument has been considered but is not convincing because the claims recite several judicial exceptions, namely calculating, comparing and determining copy number and correlating with quantity or concentration of bacterium in the sample. The response does not address these judicial exceptions.
The response also argues the claims require the use of defined primer sequences and specific SNP positions. This argument has been reviewed but is not persuasive. As discussed in the rejection, amplification has been found to be well understood routine and conventional by the courts. With regard to the instant primers and SNP positions, the prior art teaches each of these primers and positions (see particularly WO2018/209398, for example.). Thus the primers and the method of amplifying were well understood routine and conventional prior to the instant application.
The steps in addition to the judicial exception are not a practical application of molecular biology techniques, instead they were mere data collection by well understood routine methods. Thus, this is not patent eligible subject matter.
Thus for the reasons above and those already of record, the rejection is maintained.
Claim Rejections - 35 USC § 112-Scope of Enablement
The following is a quotation 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.
Claims 22, 24-27, 30-36, 38-39 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for methods of determining the presence of an amplification product, does not reasonably provide enablement for determining the quantity or concentration or a bacterium using a SNP in the 16S rRNA. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Factors to be considered in determining whether a disclosure meets the enablement requirement of 35 USC 112, first paragraph, have been described by the court in In re Wands, 8 USPQ2d 1400 (CA FC 1988). Wands states at page 1404,
“Factors to be considered in determining whether a disclosure would require undue experimentation have been summarized by the board in Ex parte Forman. They include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.”
The nature of the invention and breadth of claims
The claims are drawn to methods of determining the quantity or concentration of a bacterium in a sample. This requires differentiating a bacteria from other bacteria to make the quantification or concentration determination.
The invention is in a class of invention which the CAFC has characterized as “the unpredictable arts such as chemistry and biology.” Mycogen Plant Sci., Inc. v. Monsanto Co., 243 F.3d 1316, 1330 (Fed. Cir. 2001).
The unpredictability of the art and the state of the prior art
The art teaches many 16S rRNA share the same SNP and thus, quantifying a particular bacterium would be unpredictable. For example, the 779 SNP illustrated in Figure 4 demonstrates the A allele is present in Brucella abortus, Ochrobacterium guangzhouense, Peudochrobactrum accharolyticum, Pseudochrobactrum asaccharolytium, Ochrobactrum anthropic etc (see Gopaul et al. (BMC Microbiology, Vol. 8 No. 86, 2008)). Gopaul does not provide any guidance for determining the quantity or any particular bacterium in the samples.
Guidance in the Specification.
The specification provides no evidence that the skilled artisan could quantify or determine the concentration of a particular bacterium in a sample by amplifying a target nucleic acid with a SNP by the mere presence or absence of a SNP. Table 2 and 3 illustrates SNP positions in the 16S rRNA and it clear that a single SNP (and even combinations of SNPs) are unable to distinguish a particular bacterium. In particular E. coli, S. pneumonia, S. agalactiae, S. pyogenes each have a “T” at position 653. The skilled artisan would be unable to quantify any one of these bacteria without similarly detecting and quantifying the other bacterium. There is no guidance how the skilled artisan could quantify E. coli, a bacterium, from the sample and not also quantify the other bacterium in the sample. The guidance provided by the specification amounts to an invitation for the skilled artisan to try and follow the disclosed instructions to make and use the claimed invention.
Quantity of Experimentation
The quantity of experimentation in this area is extremely large since there is significant number of parameters which would have to be studied to enable the skilled artisan to practice the claimed invention as broadly as claimed. As discussed above, the SNPs disclosed in the specification, including elected 653, are not particular to a bacterium. Thus, the skilled artisan would be unable to quantify “a bacterium” using a SNP. This would require significant inventive effort, with each of the many intervening steps, upon effective reduction to practice, not providing any guarantee of success in the succeeding steps.
Level of Skill in the Art
The level of skill in the art is deemed to be high.
Conclusion
Thus given the broad claims in an art whose nature is identified as unpredictable, the unpredictability of that art, the large quantity of research required to define these unpredictable variables, the lack of guidance provided in the specification, the absence of a working example and the negative teachings in the prior art balanced only against the high skill level in the art, it is the position of the examiner that it would require undue experimentation for one of skill in the art to perform the method of the claim as broadly written.
Response to Arguments
The response traverses the rejection. The response asserts step (a) of Claim 22 is directed to amplifying using particular primers at particular positions, namely elected 653. The examiner agrees this step is enabled. However, step (b) that requires identifying the bacterium based on the presence of absence of the elected SNP 653 is not enabled. As discussed in the rejection above, the SNPs disclosed in the specification, including elected 653, are not particular to a bacterium. Thus, the skilled artisan would be unable to quantify “a bacterium” using a SNP. It is unpredictable which bacterium should be identified if the SNP at position 653 is a “T”. Table 3 on page 15 illustrates at least 10 different bacterial species that have a T at position 653. Thus, the mere detection of a T at position 653 would not allow identification of the bacterium in the sample. The skilled artisan would be unable to identify the bacterium in the sample by analyzing the amplification product for the presence or absence of one or a plurality of SNPs as required by the claims.
Thus for the reasons above and those already of record, the rejection is maintained.
Claim Rejections - 35 USC § 112- Second Paragraph
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 22, 24-27, 30-36, 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 pre-AIA the applicant regards as the invention.
The preamble of Claim 22 is directed to determining the quantity or concentration of a bacterium in a sample. Step (c) requires calculating the quantity or concentration. The claim then continues to add another step for determining a copy number of the bacterial 16S rRNA. It is unclear what the method requires. It is unclear whether the claim requires determining a copy number or the method only requires determining the quantity or concentration of the bacterium. The claims depending thereon are similarly indefinite. The metes and bounds of the claimed invention are unclear.
Response to Arguments
The response traverses the rejection. The response asserts the claims have been amended to overcome the rejection. This argument has been considered but is not convincing because the claim is still not clear what is required. It is unclear whether copy number of the bacterial 16S rRNA is the function of the method or whether determining concentration and quantity of a bacteria is the objective. Thus for the reasons above and those already of record, the rejection is maintained.
Conclusion
No claims allowable.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEANINE ANNE GOLDBERG whose telephone number is (571)272-0743. The examiner can normally be reached Monday-Friday 6am-3:30pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng (Winston) Shen can be reached on (571) 272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JEANINE A GOLDBERG/Primary Examiner, Art Unit 1682
May 15, 2026
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