FINAL ACTION
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 responsive to the Amendment and Response filed 03 November 2025, as well as the Terminal Disclaimer filed 03 November 2025. Claims 14 and 18 have been amended, claims 1-13 and 16-17 have been canceled, and claims 21-29 have been added. Claims 14-15 and 18-29 are now pending and under consideration. The nonstatutory double patenting rejection has been withdrawn in view of the acceptance of the Terminal Disclaimer (see also paragraph 5 below). Applicant’s amendments and arguments have been thoroughly reviewed, and have overcome the following objections/rejections set forth in the prior Office action:
The objection to claims 18-20 in view of Applicant’s corrective amendment;
The rejection of claims 35 USC 112(d), in view of Applicant’s amendment to claim 18 (although it is noted that the manner in which claim 18 was amended has raised a new issue under 35 USC 112(a), as indicated below);
The rejection of claims under 35 USC 102(a)(1) and 35 USC 102(a)(2) in view of the amendment of the claims to require a combination of primer pairs and probes as set forth in independent claim 14 (which now requires all of a)-e) of the claim); and
The rejection of claim 18 and claims dependent therefrom under 35 USC 101, in view of the amendment of claim 18 to require the step of “contacting said biological sample with the kit of claim 14” (as the claim now requires an active step that cannot reasonably be considered as well-understood, routine, and conventional activity as of Applicant’s effective filing date).
Claims 14-15 and 18-29 remain rejected for the reasons given below, which include new grounds of rejection necessitated by Applicant’s amendments. Any rejections and/or objections not reiterated in this action have been withdrawn. This action is FINAL.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Terminal Disclaimer
The terminal disclaimer filed on 03 November 2025 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of US Patent No. 11,098,376 has been reviewed and is accepted. The terminal disclaimer has been recorded.
Election/Restrictions
Applicant’s election without traverse of the primer pair/probe combination of SEQ ID Nos 1-3 in the reply filed on July 8, 2025 is again acknowledged. However, it is noted that all pending claims now require the combination of primer pairs/probes set forth in independent claim 14 (which includes the originally elected primer pair/probe and four other combinations of primer pairs/probes).
Claim Rejections - 35 USC § 112(b)/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.
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.
THE FOLLOWING INCLUDES NEW GROUNDS OF REJECTION NECESSITATED BY APPLICANT’S AMENDMENTS:
Claims 14-15 and 18-29 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.
Claims 14-15 and 18-29 are indefinite over the recitation in independent claim 14 of the limitation “wherein the one or more oligonucleotide probes comprise a detectable moiety selected from the group consisting of a fluorescence emitter moiety, a fluorescence quencher moiety, a fluorophore, biotin, radionucleotide, radioactive label, and a chemiluminescent agent”. First, as the limitation “one or more oligonucleotide probes” is not previously employed in the claim, clear antecedent basis is lacking for the reference to “the one or more oligonucleotide probes”. Second, the claim as amended recites 5 different oligonucleotide probes – see a)-e) of the claim, noting that the claim as amended now recites “kit comprising” and “and” rather than “and/or” at the end of d), such that all recited primers/probes are now required – and it is not clear whether the recitation of “the one or more oligonucleotide probes” is referring to, e.g., one of these particular probes, all of these probes, some other kit component, etc. Accordingly, the manner in which this “wherein” clause further limits the claim is also generally unclear. Further clarification is therefore required.
Claim 25 is indefinite over the recitation of the limitation “the at least one pair of primers capable of hybridizing to the 16S rRNA gene of BVAB2a”, as there is insufficient antecedent basis for this limitation in the claims (due to what appears to be a typographical error). Clarification is required.
Claim 29 is indefinite over the recitation of the limitation “wherein each primer is flanked by complementary sequences comprising a fluorophore at the 5’ end, or a fluorescence quencher at the 3’ end, or both”, as it is not clear what is required by this language. While it is noted that the reference to “each primer” is interpreted as referring to each of the primers set forth in claim 14, the reference to “complementary sequences” is not sufficiently clear, as there is no indication of any target sequence(s) to which such sequences must be “complementary” (i.e., a required point of reference is lacking, such that it is not clear whether the additional sequences are complementary to, e.g., each other, to the same target sequence to which the corresponding primer is complementary, etc.). Further, the requirement that each primer is “flanked” by sequences “comprising a fluorophore at the 5’ end, or a fluorescence quencher at the 3’ end, or both” is also confusing, as it is not clear whether this refers to the 5’ and 3’ end of each “complementary sequence” or of each primer, and because it is not clear whether the claim does/does not actually require additional sequences “flanking” each primer, given the recitation of a fluorophore or a quencher “or both”. Accordingly, clarification is required regarding several aspects of claim 29.
Claim Rejections – 35 USC § 112(a)/first paragraph
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.
THE FOLLOWING ARE NEW GROUNDS OF REJECTION NECESSITATED BY APPLICANT’S AMENDMENTS:
Claims 18-22 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed Invention. This is a new matter rejection.
Claim 18 (from which claims 19-22 depend) has been amended to recite the limitation “contacting said biological sample with the kit of claim 14”. While it is noted that this amendment was intended to overcome another rejection, the application as filed – while clearly disclosing methods employing primers/probes of the invention, including methods in which such primers/probes are contacted with a biological sample – does not disclose methods including a step of contacting a biological sample with a kit per se (i.e., a product in which primers/probes are contained or packaged, as compared to the components/reagents present within a kit). The acts of contacting a sample with primers/probes is not equivalent to contacting a sample with a “kit” comprising those materials, and the application as filed does not disclose other activities that could reasonably be considered as equivalent to contacting a sample with a “kit”. While it is noted that the application does not provide a limiting definition for the term “kit” – such that the term is not necessarily limited to typical, packaged types of “kits” – such embodiments are clearly not excluded by the claim language, and thus there are at least some embodiments of the invention as now claimed that do not find basis in the application as filed. Accordingly, the amendment of 03 November 2025 adds new matter to the claims.
Claim Rejections – 35 USC § 101
THE FOLLOWING INCLUDES NEW GROUNDS OF REJECTION NECESSITATED BY APPLICANT’S AMENDMENTS
Claims 14-15 and 23-29 remain/are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon/law of nature without significantly more.
Initially, it is reiterated that claims 14 and 29 are indefinite for the reasons given above, and it is not clear the recitations of the “wherein” clause of claim 14, and of the flanking complementary sequences of claim 29, actually further limit the products being claimed (such that the claims as presently written at least potentially encompass kits including any “one or more oligonucleotide probes” comprising a detectable moiety, and [regarding claim 29] any labeled complementary sequences, as opposed to, e.g., probes/primers defined by SEQ ID NOS as set forth in the claims that also require such modifications).
Amended independent claim 14 (from which claims 15 and 23-29 depend) is drawn to a kit comprising multiple primers pairs and probes (specifically set forth as a)-e) in the claim), all of which correspond to fragments of naturally occurring bacterial nucleic acids (see, e.g., Table 1). Such oligonucleotides/nucleic acid fragments are products of nature falling under the law of nature/natural phenomenon judicial exception (JE). While the primers/probe of the claims must be present in a “kit”, the nucleic acids as claimed do not require any type of modifications rendering them markedly different from their naturally occurring counterparts, nor does packaging them together result in any kind of marked difference. While claim 14 has been amended to recite “wherein the one or more oligonucleotide probes comprise a detectable moiety…”, as noted above it is unclear how this language further limits what is claimed, such that the claims must be interpreted as encompassing, e.g., the inclusion in the claimed kit of any type of “one or more” probes including such moieties (as opposed to requiring that the specific probes set forth in a)-e) are so labeled).
This judicial exception is not integrated into a practical application because placing the product of nature (specifically, the primer pairs and probes of a)-e)) into a generic container such as a test tube or kit does not add a meaningful limitation as it is merely a nominal or token extra-solution component of the claim, and is nothing more than an attempt to generally link the product of nature to a particular technological environment. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because: a) the packaging together into kits of reagents for use together in nucleic acid detection was clearly well-known, routine, and conventional as of the effective filing date of applicant’s invention; and b) the packaging of an additional generic oligonucleotide probe (or probes) in kits was also well-known, routine and conventional as of Applicant’s effective filing date (such that this additional claim limitation does not add something “significantly more” to the JEs to which the claims are directed).
With further regard to dependent claims 15 and 24-28, these claims simply require more specific fragments of naturally occurring nucleic acids; the analysis above therefore also applies to these claims. With further regard to claim 23, directed to a kit that further includes “a DNA polymerase and/or a plurality of dNTPs”, the requirement for inclusion of additional natural products also fails to render the claimed product markedly different from a product of nature, and such kits do not integrate the judicial exception into a practical application for the same reasons noted above (as the claim encompasses, e.g., separate materials packaged together in a kit). Additionally, such kits of reagents for use together in detection/amplification do not amount to something significantly more than a JE, as they were well-known, routine and conventional as of applicant’s effective filing date. Finally, with regard to dependent claim 29, it is reiterated that it is not clear what is encompassed by this claim; thus, the claim has been interpreted as potentially encompassing, e.g., the inclusion of generic (and undefined) “complementary sequences” comprising labels, which does not clearly render what is claimed “markedly different” than a natural product, impart a requirement for any kind of practical application, or add anything that clearly amounts to “significantly more” than a JE.
Thus, none of claims 14-15 and 23-29 as presently written is directed to patent eligible subject matter.
The reply of 03 November 2025 traverses the prior rejection of claims (including claims 14-15) under 35 USC 101 on the grounds that claim 14 ‘has been amended to introduce markedly different detectable moieties”, such that claim 14 and its dependent claims “now include additional elements that are sufficient to amount to significantly more than” a judicial exception (Reply page 7).
This argument has been thoroughly considered but is not persuasive. While Applicant’s amendment to claim 14 is noted, as discussed above it is not clear how the new claim language referenced in Applicant’s arguments actually further limits the products being claimed. Further, even if some embodiments embraced by the claims may correspond to patent eligible subject matter, a “claim whose BRI covers both statutory and non-statutory embodiments embraces subject matter that is not eligible for patent protection and therefore is directed to non-statutory subject matter” (MPEP 2106.03(II)). Thus, these arguments are non-persuasive given what is actually encompassed by the present claims.
Conclusion
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 DIANA B JOHANNSEN whose telephone number is (571)272-0744. The examiner can normally be reached Monday-Friday, 7:30 am-3:30 pm EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached at (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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/DIANA B JOHANNSEN/Primary Examiner, Art Unit 1682