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 .
Continued Examination Under 37 CFR 1.114
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 07/01/2025 has been entered.
Status of the Applications, Amendments and/or Claims
This action is written in response to applicant's correspondence submitted 07/01/2025. In the paper of 07/01/2025, Applicant amended claim 8 and submitted a new Declaration under 37 C.F.R. 1.132, filed by Koh Amano. Claims 1-10 are still pending.
Response to Arguments
Withdrawn Rejection(s)
The rejection of claim 8 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for reasons as stated in paragraphs 11-13 on page 8 of the Final Office action of 01/03/2025 is withdrawn based on claim amendments.
Maintained Rejection(s)
The rejection of claims 1-10 under 35 U.S.C. 103 as being unpatentable over Kwon et al. (2012, Tuberculosis and Respiratory Diseases, 72(3), pp.293-301) as evidenced by the iQTM SuperMix bulletin by Biorad (2012) in view of GenBank Accession No. EU790488 (submitted June 03, 2008, retrieved on July 10, 2024 from http://www.ncbi.nlm.nih.gov/nuccore/EU790488) and/or GenBank Accession No. AY786579 (submitted Oct 2004, retrieved on July 10, 2024 from http://www.ncbi.nlm.nih.gov/nuccore/AY786579), and An et al. (US2003/0050470), and Santa Lucia et al. (2007, PCR Primer Design. Humana Press: pp 3-33) is maintained as Applicant’s arguments and affidavit were not found sufficient to overcome the rejection.
Response to Amendment
The declaration under 37 CFR 1.132 filed by Dr. Koh Amano on 07/01/2025 is insufficient to overcome the rejection of claims 1-10 under 35 U.S.C. 103 as set forth in the last Office action because of the following.
This affidavit filed 07/01/2025 expands on the results of PCR assays that were previously reported in the affidavit of 11/12/2024 filed by Dr. Koh Amano, (see “PCR assay 1” and “PCR assay 2” as termed by the Examiner in the affidavit of 11/12/2024).
In the affidavit of 11/12/2024, PCR assay 1 and 2 disclose assay results obtained using primer pair 1 (SEQ ID NOS: 6,10), primer pair 2 (SEQ ID NOS: 6,12), primer pair 3 (SEQ ID NOS: 1,8), primer pair 4 (SEQ ID NOS: 1, 9) and control primer pair (SEQ ID NOS: 13, 14) in combination with template DNA at 60 copies per 20 µl (PCR assay 1), and template DNA at 6000 copies per 20 µl (PCR assay 2), respectively.
Applicant’s findings for PCR assay 1 and PCR assay 2 from the affidavit of 11/12/2024 were deemed insufficient to overcome the rejection of claims 1-10 under 35 U.S.C. 103 for a number of reasons in the Final rejection of 01/03/2025. The statements below include summaries of the evidence of unexpected/superior performance disclosed by Declarant in the affidavit of 11/12/2024.
It is noted here that the evidence provided in the instant affidavit filed 07/01/2025 will be addressed and reasons provided for why the current affidavit also does not overcome the current rejection under 35 U.S.C 103.
The affidavit of 11/12/2024
The declarant submitted illustrations for the PCR assays in the prior affidavit of 11/12/2024 which were illegible so the Office could only rely on Applicant’s summary of the data collected for the PCR assays.
Furthermore, the comparative data results presented in the declaration of 11/12/2024 reveals that the PCR cycling conditions applied to both Kwon’s primer pair and the five claimed primer pairs consisting of SEQ ID NOS: 6,10; SEQ ID NOS: 6,12; SEQ ID NOS: 1,8; SEQ ID NOS: 1,9; AND SEQ ID NOS: 13,14 is not optimal to establish a comparison since neither one of Applicant’s PCR assays using Kwon’s primer pair in combination with template DNA at 60 copies per 20 µl, or template DNA at 6000 copies per 20 µl respectively, that was cycled under Applicant’s PCR conditions yielded any amplification for the prior art primers.
The current affidavit filed 07/01/2025
In the Remarks of 07/01/2025, the declarant have filed new illustrations submitted in the affidavit of 07/01/2025 that are legible. The declarant have disclosed amplification profiles for the instant primer pairs in color relative to Kwon’s primer pair i.e.
For Figs. 1A and 1C
primer pair 1 (SEQ ID NOS: 6,10: see Fig. 1A: 6000 copies/20 µl template DNA, and Fig. 1C: 20 copies/20 µl template DNA: COLOR ORANGE);
primer pair 2 (SEQ ID NOS: 6,12: see Fig. 1A: 6000 copies/20 µl template DNA, and Fig. 1C: 20 copies/20 µl template DNA: COLOR PURPLE);
primer pair 3 (SEQ ID NOS: 1, 8: see Fig. 1A: 6000 copies/20 µl template DNA, and Fig. 1C: 20 copies/20 µl template DNA: COLOR YELLOW GREEN);
primer pair 4 (SEQ ID NOS: 1, 9: see Fig. 1A: 6000 copies/20 µl template DNA, and Fig. 1C: 20 copies/20 µl template DNA: COLOR BLUE), and
CONTROL primer pair 5 (SEQ ID NOS: 13, 14: see Fig. 1A: 6000 copies/20 µl template DNA, and Fig. 1C: 20 copies/20 µl template DNA: COLOR RED).
Kwon’s primer pair (mecA, see Fig. 1A: 6000 copies/20 µl template DNA, and Fig. 1C: 20 copies/20 µl template DNA: COLOR BLACK).
For Figs. 1B and 1D
primer pair 6 (SEQ ID NOS: 3, 7: see Fig. 1B: 6000 copies/20 µl template DNA, and Fig. 1D: 20 copies/20 µl template DNA: COLOR ORANGE);
primer pair 7 (SEQ ID NOS: 2, 9: see Fig. 1B: 6000 copies/20 µl template DNA, and Fig. 1D: 20 copies/20 µl template DNA: COLOR PURPLE);
primer pair 8 (SEQ ID NOS: 4, 11: see Fig. 1B: 6000 copies/20 µl template DNA, and Fig. 1D: 20 copies/20 µl template DNA: COLOR YELLOW GREEN); and
primer pair 9 (SEQ ID NOS: 5, 12: see Fig. 1B: 6000 copies/20 µl template DNA, and Fig. 1D: 20 copies/20 µl template DNA: COLOR BLUE).
However, the illustrations are not actually in color despite declarant labeling them as such. The Office can only still rely on Applicant’s interpretation and summary of the comparative data/amplification profiles collected for the assays. These illustrations cannot be utilized to make any assertions on the amplification and/or detection sensitivity for the instant primer pairs 1-4 and the instant primer pairs 6-9 versus Kwon’s primer pair (closest prior art primer pair) or versus the control primer pair, SEQ ID NOS: 13-14 (i.e. primer pair 5).
The declarant’s has concluded that because amplification of the target DNA occurred with the claimed primer pairs at both concentrations of target DNA (20 copies and 6000 copies) while no amplification occurred at all and the presence of target DNA could not be detected by Kwon’s primer pair is the reason the claimed primer pairs can be seen as superior to that of the primer pair of Kwon at least under the conditions of the experiment (see Remarks of 07/01/2025, pg 6, last three paragraphs) and that the claimed primer pairs have a much higher sensitivity compared to Kwon’s primer pair (Affidavit of 07/01/2025, pg 8, 3rd and 4th para).
The declarant further discloses Kwon’s primer pair show undetectable amplification and speculate that the undetectable amplification may be due to the use of non-optimal annealing temperature as high as 65 ºC for their assays, while Kwon provided annealing at 57 ºC and reported their detection limit at 30 copies (see Remarks of 07/01/2025, pg 7, 1st para).
The Examiner’s response
The conclusion that the instant primer pairs provide superior detection limit relative to Kwon’s primers cannot be taken as evidence of superior performance if optimal conditions are not selected to test both the primers of the prior art along with the instant primers.
Further, the superior detection limit observed with the instant primers is not currently commensurate in scope with the instant claims as the instant claims fail to limit detection of mecA as requiring an annealing temperature ≥ 65 ºC. The declarant’s conclusion of superior performance of the claimed primer pairs is not persuasive to the Examiner because the claims do not also include/recite the conditions of the experiment which is presumed to give the superior observation.
Further, the instant SEQ ID NOS: 13-14 which should provide amplification of a nucleotide sequence (nucleotides 308-429 of Genbank AY786579) positioned near that of Kwon’s primer pair (nucleotides 279-393 of Genbank AY786579), also showed no stable amplification at 20 copies/reaction (see Remarks of 07/01/2025, pg 6, last para and affidavit, pg 7, 1st para).
It remains unclear to the Office why amplification was observed (shown as a red-colored PCR profile in Fig. 1A on pg 4, affidavit of 07/01/2025) for the PCR assay using the instant SEQ ID NOS: 13-14 and target DNA at 6000 copies/reaction, but no amplification was observed using Kwon’s primer pairs and target DNA at 6000 copies/reaction.
Both the declaration and the Remarks omit an important comparative disclosure for the amplification that uses the instant SEQ ID NOS: 13-14 with target DNA at 6000 copies/reaction relative to that of the other claimed primer pairs with target DNA at 6000 copies/reaction, and relative to the primer pair of Kwon.
It also is unclear to the Office why the declaration of 07/01/2025 omits in the comparative PCR Profile designated as Figure 1B on page 5, the amplification profile observed for the instant SEQ ID NOS: 13-14 in combination with target DNA at 6000 copies/reaction where the profile of other claimed primer pairs (SEQ ID NOS: 2,9; and SEQ ID NOS: 3,7; and SEQ ID NOS: 4,11; and SEQ ID NOS: 5,12) are provided.
Claim Objections
Claim 8 is objected to because of the following informalities: Claim 8 recites the limitation “The detection method according to claim 2, a container, a pipette, pipette tip(s), a microtube, clean bench, or a centrifuge are provided for performing the PCR” omits the limitation “wherein”.
Amendment of claim 8 to a limitation, “The detection method according to claim 2, wherein a container, a pipette, pipette tip(s), a microtube, clean bench, or a centrifuge are provided for performing the PCR” is suggested. Appropriate correction is required.
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 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.
Claims 1-10 are rejected under 35 U.S.C. 103 as being unpatentable over Kwon et al. (2012, Tuberculosis and Respiratory Diseases, 72(3), pp.293-301) as evidenced by the iQTM SuperMix bulletin by Biorad (2012) in view of GenBank Accession No. EU790488 (submitted June 03, 2008, retrieved on July 10, 2024 from http://www.ncbi.nlm.nih.gov/nuccore/EU790488) and/or GenBank Accession No. AY786579 (submitted Oct 2004, retrieved on July 10, 2024 from http://www.ncbi.nlm.nih.gov/nuccore/AY786579), and An et al. (US2003/0050470), and Santa Lucia et al. (2007, PCR Primer Design. Humana Press: pp 3-33).
Claim 1 is construed as being directed to a method of detecting a mecA gene sequence in a sample comprising performing PCR to generate an amplification product using DNA prepared from the sample and one or more primer pairs and detecting the mecA gene sequence in the amplification product, or by analyzing the amplification product,
wherein the primer pair is selected from the group consisting of
a primer pair consisting of SEQ ID NO:3 and SEQ ID NO:7,
a primer pair consisting of SEQ ID NO:2 and SEQ ID NO:9,
a primer pair consisting of SEQ ID NO: 1 and SEQ ID NO:8,
a primer pair consisting of SEQ ID NO: 1 and SEQ ID NO:9,
a primer pair consisting of SEQ ID NO:4 and SEQ ID NO: 11,
a primer pair consisting of SEQ ID NO:5 and SEQ ID NO: 12,
a primer pair consisting of SEQ ID NO:6 and SEQ ID NO: 10, and
a primer pair consisting of SEQ ID NO:6 and SEQ ID NO: 12.
Kwon et al. (claims 1 and 3-8)
Regarding claim 1, Kwon et al. teach a detection method for a mecA gene sequence in a sample, comprising:
a step of performing PCR using DNA prepared from the sample and a primer pair for amplifying the DNA (see Kwon et al., pg 295, right col., text of section 6, “Quantitative PCR” and pg 296, Table 2, wherein Kwon et al. teach a qPCR assay that uses mecA forward primer (F mecA) 5’- ACGAGTAGATGCTCAATA-‘3 and mecA reverse primer (R mecA) 5’-GACGCTATGATCCCAATC-‘3); and a step of detecting the mecA gene sequence in an amplification product obtained by the PCR step using the mecA probe (P mecA) 5’-CalRed610-AACTACGGTAACATTGATCGCAACG-BHQ2) (pg 296, Table 2).
The F mecA forward primer of Kwon et al. hybridizes nucleotides 234-251 of Staphylococcus aureus subsp. aureus strain HM1 MecA gene having the GenBank Accession No. EU790488 while the R MecA reverse primer of Kwon et al. hybridizes nucleotides 348-331 of Staphylococcus aureus subsp. aureus strain HM1 MecA gene having the GenBank Accession No. EU790488.
The mecA (P mecA) probe of Kwon et al. hybridizes nucleotides 265-289 of Staphylococcus aureus subsp. aureus strain HM1 MecA gene having the GenBank Accession No. EU790488.
The primer pair of Kwon et al. amplify nucleotides 234-348 of Staphylococcus aureus subsp. aureus strain HM1 MecA gene having the GenBank Accession No. EU790488.
Regarding claims 3-5, Kwon et al. teach an iQTM SuperMix which contains antibody-mediated hotstart iTaq DNA polymerase which is a thermostable DNA polymerase enzyme derived from a thermostable organism (claim 3), or a thermophile, or hyperthermophile (claim 4). The antibody-mediated hotstart iTaq DNA polymerase of the iQ SuperMix of Kwon et al. is derived from Thermus aquaticus (see section of the iQ SuperMix Bulletin from BioRad entitled Kit Contents).
Regarding claim 6, Kwon et al. teach an iQTM SuperMix which comprise dNTP, Mg source, an antibody-mediated hotstart iTaq DNA polymerase i.e. an enzyme for PCR, and pH buffer solution, or sterile water (see Kwon et al., pg 295, right col. section 6; and see section of the iQ SuperMix Bulletin from BioRad entitled Kit Contents).
Regarding claim 7, Kwon et al. teach P mecA probe comprising Cal610Red and BHQ2 labeling substances. The CalRed610 is a fluorescent dye (see Kwon et al., pg 296, Table 2).
Regarding claim 8, Kwon et al. teach use of a container, pipette, pipette tip, microtube, clean bench for the PCR step (pg 296, right col., section 3, pg 295, right col., section 6).
Regarding claims 9-10, Kwon et al. teach the mecA primer pair having a detection limit of 100 fg, or 30 copies (pg 296, right col., section 2 and see pg 298, Figure 1).
Omitted from Kwon et al. (claims 1-2, 9-10)
Regarding claim 1, Kwon et al. do not teach the primer pair consisting:
(SEQ ID NOS: 1, 8) for amplifying nucleotides 1043-1329 of Staphylococcus aureus subsp. aureus strain HM1 MecA gene having the GenBank Accession No. EU790488,
(SEQ ID NOS: 1, 9) for amplifying nucleotides 1043-1332 of Staphylococcus aureus subsp. aureus strain HM1 MecA gene having the GenBank Accession No. EU790488,
(SEQ ID NOS: 2, 9) for amplifying nucleotides 1042-1332 of Staphylococcus aureus subsp. aureus strain HM1 MecA gene having the GenBank Accession No. EU790488,
(SEQ ID NOS: 3, 7) for amplifying nucleotides 880-1191 of Staphylococcus aureus subsp. aureus strain HM1 MecA gene having the GenBank Accession No. EU790488,
(SEQ ID NOS: 4, 11) for amplifying nucleotides 1308-1849 of Staphylococcus aureus subsp. aureus strain HM1 MecA gene having the GenBank Accession No. EU790488,
(SEQ ID NOS: 5, 12) for amplifying nucleotides 1409-1799 of Staphylococcus aureus subsp. aureus strain HM1 MecA gene having the GenBank Accession No. EU790488,
or
(SEQ ID NOS: 6, 12) for amplifying nucleotides 1542-1799 of Staphylococcus aureus subsp. aureus strain HM1 MecA gene having the GenBank Accession No. EU790488.
Regarding claims 1-2, Kwon et al. do not teach primer pair consisting (SEQ ID NOS: 6, 10) for amplifying nucleotides 1542-1944 of Staphylococcus aureus subsp. aureus strain HM1 MecA gene having the GenBank Accession No. EU790488.
Regarding claims 9-10, Kwon et al. do not teach the primer pair has a detection limit of 10.4 copies to 2.6 copies, or 5.2 to 2.6 copies.
GenBank
Genbank teach a 1944 bp Staphylococcus aureus subsp. aureus strain HM1 MecA oligonucleotide having the GenBank Accession No. EU790488 which is identical to and indistinguishable from the instant SEQ ID NOS: 1-12 (see % homology to GenBank Accession No. EU790488 as stated in the claim interpretations provided above).
Genbank teach a 2007 bp St Staphylococcus aureus mutant PBP2a (mecA) gene having the GenBank Accession No. AY786579 which is identical to and indistinguishable from the instant SEQ ID NOS: 1-12 (see % homology to GenBank Accession No. AY786579 as stated in the claim interpretations provided above).
An et al. (2003)
Regarding primer and/or probe design, An et al. teach at paragraphs [0065]-[0067]:
"Various probes and primers can be designed around the disclosed nucleotide sequences. Primers may be of any length but, typically, are 10-20 bases in length. By assigning numeric values to a sequence, for example, the first residue is 1, the second residue is 2, etc., an algorithm defining all primers can be proposed:
n to n+y
where n is an integer from 1 to the last number of the sequence and y is the length of the primer minus one (9 to 19), where n+y does not exceed the last number of the sequence. Thus, for a 10-mer, the probes correspond to bases 1 to 10, 2 to 11, 3 to 12 . . . and so on. For a 15-mer, the probes correspond to bases 1 to 15, 2 to 16, 3 to 17 . . . and so on. For a 20-mer, the probes correspond to bases 1 to 20, 2 to 21, 3 to 22 . . . and so on."
Therefore, An et al. not only taught designing primers of any length based on a known sequence, but also taught an algorithm for defining all possible primers of a given length based on a known sequence. In this respect, An et al. taught that all possible subsequences of a known sequence could be considered as a primer for that sequence. While An et al. was discussing in particular sequences having to do with prostate, bladder and breast cancer (see Abstract), one of ordinary skill in the art would have recognized that the principles of designing primers and probes based on a disclosed nucleotide sequence would have applied to any nucleotide sequence under study.
SantaLucia et al. (2007)
SantaLucia et al. teach on page 14, “over the last 10 years (1996–2006), I have informally polled scientists who are experts in PCR and asked: “What percentage of the time does a casually designed PCR reaction ‘work’ without any experimental optimization?” In this context, “work” means that the desired amplification product is made in good yield with a minimum of artifact products such as primer dimers, wrong amplicons, or inefficient amplification. By “casually designed,” I mean that typical software tools are used by an experienced molecular biologist. The consensus answer is 70–75%.
If one allows for optimization of the annealing temperature in the thermocycling protocol (e.g., by using temperature gradient optimization), magnesium concentration optimization, and primer concentration optimization, then the consensus percentage increases to 90–95%."
Thus, SantaLucia et al. teach primers casually designed to a target sequence have a reasonable expectation of success at hybridizing, amplifying and detecting a target sequence.
It would have been prima facie obvious to an ordinary skilled artisan, wanting to detect the presence of resistant Staphylococcus aureus subsp. aureus HM1 MecA strain in a sample, before the effective filing date of the instant invention, to provide alternative primers that are functionally equivalent MecA specific primers to the MecA forward and reverse primers taught by Kwon et al.
Based on the teachings of Kwon et al., Genbank Accession No. EU790488 or Genbank Accession No. AY786579 and SantaLucia et al. (2007) and An et al., and particularly concerning primer/probe design, the ordinary skilled artisan would have readily being apprised of how to make and use the instant SEQ ID NOS: 1-12 which are derived from Genbank Accession No. EU790488/ GenBank Accession No. AY786579.
The ordinary skilled artisan would have had a reasonable expectation at making and using the instant SEQ ID NOS: 1-12 as primer(s) and/or probe(s) as SantaLucia et al. elaborates that sequences casually designed for use as primers are generally successfully at hybridizing, amplifying and/or detecting, particularly when further optimized as taught by SantaLucia et al.
The ordinary skilled artisan would have been readily apprised on modifying and testing and optimizing select primer sequences to derive a detection limit of at a specific copy number.
In view of the combined teachings of all of the cited reference(s), the instant claims 1-10 are prima facie obvious.
Conclusion
No claims are currently allowed.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to OLAYINKA A OYEYEMI whose telephone number is (571)270-5956. The examiner can normally be reached Monday -Thursday: 9:00 am - 5:00 pm, EST.
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, GARY Benzion can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
OLAYINKA A. OYEYEMI
Examiner
Art Unit 1681
/OLAYINKA A OYEYEMI/Examiner, Art Unit 1681
/GARY BENZION/Supervisory Patent Examiner, Art Unit 1681