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 .
This action is in response to papers filed 10/10/2025.
Applicant’s election without traverse of Group II in the reply filed on 3/24/2025 is acknowledged.
Claims 1-12 are pending. Claims 1-4 are withdrawn as being drawn to a nonelected invention.
The following rejections are modified (35 USC 103) or newly applied (35 USC 112b and 35 USC 112a) as necessitated by amendment. Response to arguments follows.
This action is FINAL.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. 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. See p. 32
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.
Claims 5-12 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.
The claims have been amended to “exhibit exclusivity for each C candida…” in claim 5 and the newly applied claims 11-12. Further the claims have been newly amended to “set is inclusive of CA clades …”. These appear to constitute new matter. The reply asserts that support is found in Example 2, Table VI, figures 3-4 and 8.
First it is noted that Figures 3-4 and 8 only provided assay results and does not provide the primers and probes that are exclusive or inclusive limitations. Page 10 of the specification states that Figure 3 shows the exclusivity profile of the modified AUR2 assay as described in Example 2. On page 31 the specification describes exclusivity to the assay not to the recited primers and probes. As such this exclusivity is based upon the assay and not the primers and probes. As is known in the art rather or not a primer or probe hybridizes to a particular target is not only the structure of the primer or probe but the assay conditions used. The same issue occurs with regard to “inclusive”. Page 32 describes the inclusivity to the assay and not to the primers and probes claimed.
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 5-12 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 5-8 are indefinite over the phrase “wherein the combination of the forward oligonucleotide primer, the reverse oligonucleotide primer and the fluorescent detectably labeled probe exhibit exclusivity “. The phrase is not clear as it is not clear how the wherein clause alters the claimed structure of a primer comprising SEQ ID No. 13, Seq ID No. 14 and a probe comprising SEQ ID No. 15. As the claim requires particular structures it is not clear how the wherein clause alters the claimed structures. As such it is not clear which primers and probe would be encompassed by the claim language.
Claims 9-12 are indefinite over the wherein limitation of “wherein the detection set detects the ….in the absence of at least one pre-analytic step…”. The claims are drawn to a detection set comprising primers and probe. It is not clear how the wherein clause intends to limit the structure of the primers and probe. Therefore the claims are indefinite as it is not clear how the recitation of the method step alters the structure of the primers.
Claims 10-12 are indefinite over the phrase “wherein the combination of the forward oligonucleotide primer, the reverse oligonucleotide primer and the fluorescent detectably labeled probe exhibit exclusivity “ and the “inclusive of”. The phrases are not clear as it is not clear how the wherein clause alters the claimed structure of a primer comprising SEQ ID No. 13, Seq ID No. 14 and a probe comprising SEQ ID No. 15. As the claim requires particular structures it is not clear how the wherein clause alters the claimed structures. As such it is not clear which primers and probe would be encompassed by the claim language.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
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.
Claim(s) 5-12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Leach et al. (Journal Clinc Microbiology Feb 2018 cited on IDS ) in view of Kordalewska et al (Journal of clinical microbiology 2017 p 2445), Hogan (US patent 6773882 Aug 10, 2004) , Diffenbach (PCR methods and Applications (1993) volume 3, pages S30-S37) and Roux et al (PCR Methods and Applications (1995) volume 4, pages s185-s194).
With regard to claims 5, 9-12 Leach et al. teaches design of primers and probes for RT PCR assay for detecting C. auris for ITS2 gene region (p. 2-3). Therefore Leach et al. teaches primers and probes towards a portion of the targeted region of claim 5. As noted above the claims are indefinite over the effect of the wherein clause or exclusive or inclusive to the structures of the claims. The wherein clause with recitation of the method steps in claim 9 does not appear to alter the claimed structure.
Leach et al. teaches addition of donor and quencher labels for the probe (p. 2 1st 3 paragraphs).
With regard to claim 6, Leach et al. teaches addition of donor and quencher labels for the probe (p. 2 1st 3 paragraphs).
With regard to claim 7-8, Leach teaches nucleoside triphosphates, polymers and buffers to perform PCR using a polymerase (p. 2-3).
However Leach et al. does not teach primers or probes for C. auris 5.8S region.
With regard to claims 5-12, Kordalewska et al. teaches a design of primers and probes for both ITS2 and 5.8S regions (table 1 and p. 2446). Therefore Milena et al. teaches primers and probes that would amplifying the region of the target that the recited primers and probes anneal/hybridize.
With regard to claims 5-12, Diffenbach and Roux et al. teach constraints to designing oligonucleotides. Diffenbach teaches parameters and principles of promoter design include primer length, terminal nucleotide, GC content, melting temperature, PCR product length, and placement of target sequence (s30-s34). Diffenbach teaches PCR software was known (s35).
Roux teaches optimization of PCR by the presence of enhancing agents, Mg2+, annealing temperature, primer design, cycle number, hot start PCR (s185-s194).
The art of making probes from known target regions is well known in the art. Hogan et al. teaches the use of specific probes to amplify the 16S region of bacteria.
Hogan et al. provides guidance for the selection of probes.
"Once the variable regions are identified, the sequences are aligned to reveal areas of maximum homology or 'match'. At this point, the sequences are examined to identify potential probe regions. Two important objectives in designing a probe are to maximize homology to the target sequence(s) (greater than 90% homology is recommended) and to minimize homology to non-target sequence(s) (less than 90% homology to non-targets is recommended). We have identified the following useful guidelines for designing probes with the desired characteristics.
Fist, probes should be positioned so as to minimize the stability of the probe: nontarget nucleic acid hybrid. This may be accomplished by minimizing the length of perfect complementarily to non-target organisms, avoiding G and C rich regions of homology to non-target sequences, and by positioning the probe to span as many destabilizing mismatches as possible (for example, dG:rU base pairs are less destabilizing than some others). Second, the stability of the probe: target nucleic acid hybrid should be maximized. This may be accomplished by avoiding long A and T rich sequences, by terminating the hybrids with G: C base pairs and by designing the probe with an appropriate Tm. The beginning and end points of the probe should be chosen so that the length and %G and %C result in a Tm about 2-10 ºC higher than the temperature at which the final assay will be performed. The importance and effect of various assay conditions will be explained further herein. Third, regions of the rRNA which are known to form strong structure inhibitory to hybridization are less preferred. Finally probes with extensive self complementarity should be avoided." (See Column 6 lines 66-67 and Column 7 lines 1-29).
Hogan et al. teaches, "while oligonucleotide probes of different lengths and base composition may be used, oligonucleotide probes preferred in this invention are between about 15 and about 50 bases in length" (see Column 10, lines 13-15). Hogan et al teaches labels that fluoresce can be used (column 12 lines 20-40).
Designing oligonucleotides to hybridize to specific targets, which are equivalents to those taught in the art is routine experimentation. The prior art teaches the parameters and objectives involved in the selection of oligonucleotides that function as primers, see Diffenbach and Roux and Hogan who teach selection of oligonucleotides that function as probes. The prior art is replete with guidance and information necessary to permit the ordinary artisan in the field of nucleic acid detection to design primers and probes. As discussed above, the ordinary artisan would be motivated to have designed and tested oligonucleotides from the ITS and 5.8 rRNA regions taught by Leach et al and Milena et al. to obtain additional oligonucleotides that function to detect C. Aureus and identify oligonucleotides with improved properties for such detection. Thus, for the reasons provided above, the ordinary artisan would have designed additional oligonucleotides using the teachings in the art at the time the invention was made including oligonucleotides that comprise the recited sequences. As such the recited oligonucleotides are obvious over the cited prior art, absent secondary considerations.
Response to arguments
The reply traverses the rejection. A summary of the arguments is provided below with response to arguments following. The reply asserts that the unique feature of the claimed primers and probes is the inclusivity and exclusivity for the intended targets (p. 2). The reply asserts that these are highly sensitive and exclusive primers and probes (p. 2-3). The reply asserts that claim 9 requires a detection set that detects the nucleic acid of CA in the absence of at least one preanalytical step (p. 4). The reply pointes to example 2 and asserts that these provide significantly less hands on processing and no preanalytical step (p. 4).
These arguetmsn have been reviewed but have not been found persuasive.
The reply appears to be asserting unexpected results with “highly sensitive and exclusive” primers and probes, however, the primers and probe in example 2 are not the same scope as the claimed primers and probe as the recited structure is “comprising” and as such can include structures more than the primers and probe consisting of in example 2. The recitation of “inclusivity” and “exclusivity” are directed towards the assays in the specificaoin. It is not clear how these alter or modify the claimed structure of the primers and probe and how these would different from any primers and probe comprising the recited sequences.
Conclusion
No claims are allowed.
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 KATHERINE D SALMON whose telephone number is (571)272-3316. The examiner can normally be reached 9-530.
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/KATHERINE D SALMON/ Primary Examiner, Art Unit 1682