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, SEQ ID NO: 7-8, 13, 14-15, 24, 29-30, 39, 44-45, and 54. in the reply filed on 1/20/26 is acknowledged.
Improper Markush Grouping
Claims 1-4, 7-12, 14-19, and 21 are rejected on the basis that it contains 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 grouping of primers or probes identified by SEQ ID NO: alternatives (for example any one of SEQ ID NO: 1-8) is 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 oligonucleotides do not share a common structure.
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 claims 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 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 19 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 19 requires that “each probe is flanked by complementary sequences” but it does not say what the sequences must be complementary to. “Complementary” is a relative term that only has meaning when the partner sequence is known.
Claim Rejections - 35 USC § 103
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) 1, 4, 7, 8, 10, 12, 16, 17, 18, is/are rejected under 35 U.S.C. 103 as being unpatentable over Nakajima et al. (WO 2015/190107 A1) in view of GenBank JN188465, GenBank AY742213, GenBank AY044109 and Buck (BioTechniques (1999) 27(3): 528-536).
A translation of the Nakajima WO document’s specification is provided with this Office action. Page numbering in the rejection refers to the page numbering at the bottom of the translated pages.
Nakajima teaches a multiplex PCR amplification assay followed by detection using an oligonucleotide probe for V. parahaemolyticus which targets toxR, tdh, and trh genes of B. parahaemolyticus (See p. 3, bottom paragraph and following). The reference teaches that the assay highly specific for simultaneously detecting V. parahaemolyticus including non-pathogenic ones and V. parahaemolyticus that cause food poisoning (p. 4, last paragraph).
Regarding claim 4, Nakajima teaches testing the biological sample: namely DNA extracted from V. parahaemolyticus, see at least p. 13. Furthermore, the reference teaches that it is important to accurately test for V. parahaemolyticus in the environment (p. 2 first full paragraph), and teaches that there is a pathogenic Vibrio that lives many in seawater (p. 6, last paragraph), though the reference doesn’t expressly mention an environmental sample. It would have been obvious, following the direct suggestion to test for V. parahaemolyticus in environmental samples. One would have been motivated to do so in order to screen for the illness causing bacteria. Regarding claim 7, it is noted that the claim reads on when an environmental sample is tested, and thus the claim is rejected with this rejection. The claim does not require the sample is a biological sample, it merely further defines the biological sample.
Thus, regarding claim 1, Nakajima teaches contacting a sample with a plurality of pairs of primers, wherein the plurality of pairs of primer comprise a primer pair capable of hybridizing to the toxR gene of V. parahaemolyticus, at least one primer pair capable of hybridizing to the trh gene of V. parahaemolyticus, and at least one primer pair capable of hybridizing to the tdh gene of V. parahaemolyticus, generating amplicons of the three genes, or any combination thereof if the sample comprises the targets and determining the presence of one or more amplicons as an indication of the presence of V. parahaemolyticus in the sample. Furthermore, with regard to claims 16-18, the reference teaches determining the presence of one or more amplicons by contacting the amplicons with a plurality of probes having target sequences within the amplified portions. The primers used for amplification are given in figure 2 of the reference, and the probes for detection are given in Figure 5. The complement of probe identified as SEQ ID NO: 19, targeting trh1 is instant SEQ ID NO: 15, indicating that these two probes hybridize to the same target on opposite strands of the amplicon.
Nakajima does not teach the primers and probes elected for examination in the insant claims, namely SEQ ID NO: 7-8, 13-15, 24, 29-30, and 39.
The sequences of each of the relevant target genes were known, and the claimed primers had 100% identity to known sequences.
The sequence of the toxR gene was taught in JN188465, and instant SEQ ID NO: 7 was identical to nucleotides 337-361, and instant SEQ ID NO: 8 was identical to the complement of nucleotides 453-430. The primers produce an amplicon that is within the amplicon taught by Nakajima, which amplifies from nucleotides 515-829 of the GenBank sequence. The probe instant SEQ ID NO: 13 is identical to nucleotides 364-396 of the GenBank sequence.
The sequence of the trh gene had been taught in Genbank AY742213. Instant SEQ ID NO: 14 and 15 are fragments of this gene, see nucleotides 630-649 (complement of SEQ ID NO: 14) and nucleotides 514-537 (of SEQ ID NO: 15). The primers produce an amplicon that is within the amplicon taught by Nakajima, which amplifies from nucleotides 444-717 of the GenBank sequence. The probe instant SEQ ID NO: 24 is identical to the complement of nucleotides 594-625 of the GenBank sequence.
The sequence of the tdh gene was known in AY044109, and instant SEQ ID NO: 29 is identical to nucleotides 339-362 of the known sequence, and instant SEQ ID NO: 30 is the complement of nucleotides 419-439. The probe instant SEQ ID NO: 39 is identical to the complement of nucleotides 390-417 of the GenBank sequence.
Further, before the invention was made, it was known that most primers from a target sequence could function to amplify the target. Buck analyzed the effect of primer design strategy on the performance of DNA sequencing primers. Specifically, Buck invited primer submissions from a number of labs (39) (page 532, column 3), with 69 different primers being submitted (see page 530, column 1). Buck also tested 95 primers spaced at 3 nucleotide intervals along the entire sequence at issue, thereby testing more than 1/3 of all possible 18 mer primers on the 300 base pair sequence (see page 530, Page 11 column 1). When Buck tested each of the primers selected by the methods of the different labs, Buck found that every single primer worked (see page 533, column 1). Only one primer ever failed, No. 8, and that primer functioned when repeated. Further, every single control primer functioned as well (see page 533, column 1). Buck expressly states “The results of the empirical sequencing analysis were surprising in that nearly all of the primers yielded data of extremely high quality (page 535, column 2).” Therefore, Buck provides direct evidence that all primers would be expected to function, and in particular, all primers selected according to the ordinary criteria, however different, used by 39 different laboratories. It is particularly striking that all 95 control primers functioned, which represent 1/3 of all possible primers in the target region. This clearly shows that the selection and use of primers in primer extension methods yields predictable results.
It would have been prima facie obvious for one of ordinary skill in the art before the effective filing date to design primers for multiplex analysis of toxR, trh, and tdh by designing any set of primer pairs and oligonucleotide probes designed from the known sequences to detect the presence of V. parahaemolyticus in a biological sample using the multiplex PCR methods taught by Nakajima. An ordinary artisan would have been motivated to do so with a reasonable expectation of success, since: (i) Nakajima taught useful oligonucleotide primers and probes the same gene targets , (ii) the complete toxR, trh, and tdh sequences were known in the art at the time of the invention, and (iii) Buck establishes that essentially all primers designed from a known sequence are reasonably capable of functioning in nucleic acid amplification methods. Thus, absent any unexpected results with respect to the particular primers and probes recited in the claims, they are prima facie obvious in view of the combined teachings of the cited references.
Attention is also directed to KSR Int’l Co. v. Teleflex Inc. (550 U.S.____ , 127 S. Ct. 1727 (2007)) where the Supreme Court determined that “a person of ordinary skill has good reason to pursue the known options within his or her technical grasp. If this leads to the anticipated success, it is likely the product not of innovation but of ordinary skill and common sense. In that instance the fact that a combination was obvious to try might show that it was obvious under § 103 (KSR, 550 U.S. at____ , 82 USPQ2d at 1397).”
In the instant case, as discussed above, an ordinary artisan would have been motivated to design oligonucleotide primers and probes from the known toxR, trh, and tdh sequences for the detection of P. parahaemolyticus in a biological sample based on the teachings of Nakajima. The complete nucleotide sequence of the toxR, trh, and tdh genes, which is disclosed in the cited GenBank records, presented the ordinary artisan with a finite number of possible primers and probes for amplification and hybridization, respectively. Then, since Buck taught that a large number of primers designed to detect the same target functioned reasonably well, an ordinary artisan would have expected predictable results, and thus would have had a reasonable expectation of success, when testing the finite number of possible amplification primers and probes suggested by the GenBank records. Thus, the methods are prima facie obvious in view of the combined teachings of the cited references.
Claim(s) 14, 19, and 21 is/are rejected under 35 U.S.C. 103 as being unpatentable over Nakajima et al. (WO 2015/190107 A1) in view of GenBank JN188465, GenBank AY742213, GenBank AY044109 and Buck (BioTechniques (1999) 27(3): 528-536) as applied to claims 1, 4, 7, 8, 10, 12, 16, 17, 18, above, and further in view of Gubala et al. (2006. Appl Environ Microbiol 72: 6424-6428).
The teachings of Nakajima, the GenBank records and Buck are given previously in this Office action and are fully incorporated here.
None of Nakajima, the GenBank records or Buck teach quantitative real-time PCR, probe flanked by complementary sequences, or a probe with a fluorescence emitter and a quencher.
Gubala et al teaches multiplexed real-time PCR in which employs PCR and detection with probes labeled with different fluorophores occurs in a single reaction. The probes are molecular beacons which have target sequences flanked by complementary sequences at the 5’ end and the 3’ end wherein each complementary sequence is complementary to the other. See Table 2. Each probe has a fluorescence emitter moiety and a fluorescence quencher moiety attached. The reference teaches that the assay using molecular beacons for the simultaneous detection of four target genes, resulted the specificity and sensitivity that surpassed those of the published PCR assays for the detection of V. cholerae. See p. 2467.
It would have been obvious to have modified the method taught by Nakajima and the additional references so as to have selected probes for detection of amplicons from the known sequences for the detection of amplicons, and to have used a molecular beacon design for multiplex detection. One would have been motivated to do so in order to take advantages of the real-time multiplex molecular beacon PCR method as taught by Gubala et al.
Claim(s) 14, 15 and 21 is/are rejected under 35 U.S.C. 103 as being unpatentable over Nakajima et al. (WO 2015/190107 A1) in view of GenBank JN188465, GenBank AY742213, GenBank AY044109 and Buck (BioTechniques (1999) 27(3): 528-536) as applied to claims 1, 4, 7, 8, 10, 12, 16, 17, 18, above, and further in view of Ward et al. (APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Mar. 2006, p. 2031–2042).
The teachings of Nakajima, the GenBank records and Buck are given previously in this Office action and are fully incorporated here.
None of Nakajima, the GenBank records or Buck teach primers with exogenous sequences.
Ward et al teaches multiplexed real-time PCR in which PCR and detection with a probes labeled with different fluorophores occurs in a single reaction. Each probe has a fluorescence emitter moiety and a fluorescence quencher moiety attached. The assay provides a rapid and reliable alternative to conventional detection methods by reducing the analysis time and obviating the need for multiple assays. See abstract, Table 1, and throughout.
It would have been obvious to have modified the method taught by Nakajima and the additional references so as to have selected probes for detection of amplicons from the known sequences for the detection of amplicons. One would have been motivated to do so in order to take advantages of the real-time PCR method as taught by Ward et al.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Nelapati et al. Veterinary World Vol.3(6): 268-271 teaches detection of total and pathogenic V. parahaemolyticus by PCR using toxR, tdh and trh genes.
Claims 2, 3, 9, and 11 are free of the prior art. The prior art does not teach or suggest amplifying the YaiO gene along with the other targets. The basis for the claims is to the parent application 11/5/2020.
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Juliet Switzer
Primary Examiner
Art Unit 1682
/JULIET C SWITZER/Primary Examiner, Art Unit 1682
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