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 .
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 11/28/2025 has been entered.
Application Status
Claims 53,55-66, 125-138 are currently pending and claims 1-52,54,67-124 were cancelled.
The restriction of 12/4/2023, required species election for claims 53 and 125, where claims 53 and 125 are generic. Applicant responded on 1/30/2024, electing the transcript of N gonoorrhoeae gene with locus tag NG01812 and encoding major outer membrane protein (porB) and that claims 53-66 and 125-130 encompass the elected species.
An RCE was filed on 11/23/2025, and another restriction of 7/1/2025 was presented, which is now withdrawn.
Maintained Rejection, modified in view of amendments.
Improper Markush
Claims 53 and 125 are rejected on the basis that they contain an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush groupings of claims 53 and 125 are improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: the various recited transcripts, or probes or primers thereto, do not have a same physical structure or the same specific structural elements relevant to their function, nor do they perform the same functions. Claims 55-66, and 126-138 depend from claims 53 and 125 and are rejected for the same reason.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims1 and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Claim Objections
Claims 53, 58, 125, 132-136 are objected to because of the following informalities:
Claims 53 and 125 recite, “ a sequence having at least 80% identity…”. If the intent is for this to be a nucleotide sequence, add this descriptor.
Claim 58 recites, “selected from expression value of a reference RNA, DNA, number of cells, number of samples effective amount of sample used and/or a ratio of the a reference RNA DNA…”. A comma is necessary between “RNA” and “DNA”.
Claims 123-136 recite “RNA.has”, which includes a period between RNA and has, that should not be present.
Appropriate correction is required.
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.
Claim 58 is 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 58 recites, normalizing….” with a reference measurement selected from expression value of a reference RNA,DNA, number of cells, number of samples, effective amount of sample used and/or a ratio of the a reference RNA DNA, number of cells, number of samples, effective amount of sample used in a control and in a treated sample… As stated, (and presuming a missing comma between RNA and DNA), it is not clear how, for example, normalizing from expression value of a reference DNA occurs, and it is further unclear what the “a ratio of the a reference RNA DNA, number of cells, number of samples, effective amount of sample used in a control and in a treated sample is referencing as “a ratio”.
Claim Rejections - 35 USC § 101
5. 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 53, 55-58 are rejected under 35 U.S.C. 101 because the claimed invention is directed to the judicial exception of a law of nature or a natural phenomenon, and an 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 reasons that follow.
The unpatentability of laws of nature was confirmed by the U.S. Supreme Court in Mayo Collaborative Services v. Prometheus Laboratories, Inc., No. 10-1150 (March 20, 2012).
The unpatentability of abstract ideas was confirmed by the U.S. Supreme court in Bilski v. Kappos, No. 08-964, 2010 WL 2555192 (June 28, 2010) and in Alice Corp. v. CLS Bank Int’l, 134 S. Ct. 2347, 2354 (2014).
Applicant’s attention is directed to MPEP 2106 “Patent Subject Matter Eligibility.”
Re: Step 1, the claims are directed to the statutory category of a process (a method).
Re: Step 2A, prong I, the claims are directed to a judicial exception, here a law of nature, or a natural correlation between quantitative bacterial transcript expression (or a downshift in expression) of a marker and antibiotic susceptibility, in a method to detect a marker of N. gonorrhoeae.
Re: Step 2A, prong II, the claims do not recite additional elements that integrate the judicial exception into a practical application. The claims disclose contacting the sample with antibiotic to obtain expression value, quantitative detection of expression, a mental process of comparing treated/untreated expression values, and from this determining whether there was a downshift in expression. Claim 55 articulates that the untreated maker expression value is a control expression value, obtained without antibiotic, and claim 56 repeats the procedural steps of claim 53 inclusive of the same form of quantitative detection, here with the steps relevant to the control sample. Claim 57, 58 recite normalization, a known, conventional step for RNA transcript analysis (see Nieto described below).
The claimed methods constitute routine lab steps with conventional detection, without a particular and novel use of lab equipment or technology, and without a particular technical improvement in technique (see Qin and Suzuki, described below).
Re: Step 2B, the claims represent well-understood, routine, conventional methods such as contacting bacteria with antibiotic, measuring transcript expression, and comparing treatments and controls (here untreated).
Nieto et al (BMC Mol Biol, 2009, 10:63) addressed gene expression and transcriptome analysis (Pg 1 para 1) and the need for normalization (Abstract), including through the use of one or more other genes and relative expression comparisons (Pg 2 right col, 2nd and 3rd full para, Pg 5, left col, final para, and throughout).
Qin (Sci Reports, 23 Feb 2018, 8:3515) had previously disclosed quantitative comparisons, including gene expression and transcriptomes, that were used to identify bacterial drug-resistance, and drug-related genes, in antibiotic-treatment and control (no antibiotic) environments (Pg 5 final para; Pg 6 first full para, final para; Pg 7 first full para).
Suzuki (2014, Nature Comms 5:5792) used gene expression profiles to identify antibiotic resistance in bacteria and pointed to the value of transcriptome and genomic data in evaluating drug resistance (Abstract).
The claims are directed to a law of nature and as such are patent ineligible.
Response to Remarks:
Pg “2-3”, comments addressing “the 2025 restriction” have been addressed, given this restriction is withdrawn. Notably, the prior restriction (“2023”) species election remains valid.
Pg “4”, 8. -11, regarding species election and Markush Groups and an Interview of April 9, 2025, Applicant asserts that the amended group is acceptable regarding Markush groups. It is noted that in the Examiner’s interview summary, the examiner indicated that their position was maintained regarding the improper Markush group rejection. The examiner used examples to explain differences in structural similarity during the interview to try to articulate why the recitations differ. Agreement was reached on Ms. Bruno indicating that she would communicate to her client regarding the possibility of narrowing down a large group to a subset of species in an effort to move toward allowance. However, the amendments provide a suite of alternatives that do not comply with a proper Markush grouping and thus the rejection is maintained for reasons set forth in the rejection above.
Pg ”5”-’”7” rejoinder 12-14. Per the “2023” restriction, claims 53 and 125 are generic.
Conclusion
All claims rejected. Any inquiry concerning this communication or earlier communications from the examiner should be directed to Lisa Horth whose telephone number is (703)756-4557. The examiner can normally be reached Monday-Friday 8-4 EST.
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/LISA HORTH/Examiner, Art Unit 1681
/GARY BENZION/Supervisory Patent Examiner, Art Unit 1681
1 This may result in further restriction to one patentably distinct invention.