DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Response to Amendment
Regarding the Office action mailed 01/02/2026, the double-patenting rejection over U.S. Patent 12,054,792 is withdrawn in view of the terminal disclaimer filed 04/01/2026. The rejections under 35 USC 103 are maintained and reiterated below. Applicant’s remarks will be addressed following the rejections.
Claim Rejections - 35 USC § 103
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 1, 8, 9 and 20 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over De Backer et al. (BMC Microbiology 7:115; 19 December 2007, IDS reference) in view of Zozaya-Hinchliffe et al. (App. Env. Micro. 74(5):1656-1659 (2008)), Marras et al. (Clinica Chimica Acta 363:48-60 (2006), IDS reference) and Reed (US 7,608,399, IDS reference).
De Backer disclosed primer pairs for quantitative determination of four vaginal lactobacillus species (L. crispatus, L. gasseri, L. iners, and L. jensenii), Atopobium vaginae, and Gardnerella vaginalis (see title, table 4 on page 4). The primers were specific for the 16S rRNA gene (see table 4).
Of bacterial vaginosis (BV), De Backer disclosed that both G. vaginalis and A. vaginae were associated with this disorder (page 2, second paragraph under “Background”). De Backer disclosed that the authors “developed real-time PCR primers for L. iners, L. jensenii and A. vaginae and used these, together with described real-time PCR formats of L. crispatus, L. gasseri and G. vaginalis, in an attempt to quantify some of the important bacterial species in the normal and disturbed vaginal microflora” (page 2, right column, last paragraph under “Background”).
De Backer did not disclose that the primers were detectably labeled with a fluorescent label as recited in instant claims 1 and 8. De Backer did not disclose probes with detectable fluorescent labels as recited in claims 9 and 20. Instead of using labeled primers or probes, De Backer’s real-time quantitative PCR was based on the use of SYBR Green I (a dye that binds to double-stranded DNA, upon which it becomes fluorescent, which fluorescent signal increases as PCR product accumulates; see page 11, “Real-time PCR”). De Backer did not disclose primers and probes for Megasphaera as recited in claims. De Backer did not disclose putting the primers and probes into a “master mix”.
Zozaya-Hinchliffe disclosed quantitative PCR targeting the 16S rRNA gene for two types of Megasphaera and found these to be present in higher concentrations in women with bacterial vaginosis (Abstract). Like De Backer, Zozaya-Hinchliffe’s assay used SYBR Green as the signaling mechanism (page 1656, right column, first paragraph).
Marras disclosed alternatives to SYBR Green-based real-time assays in which fluorescently labeled probes (Figure 1A-D) or primers (Figure 1E-F) were used. Marras disclosed (“Conclusions” section of Abstract) that the assays “can be combined with nucleic acid amplification, enabling the detection of rare target nucleic acids. These assays can be followed in real time, providing quantitative determination of target nucleic acids over a broad range of concentrations.” Marras disclosed (in discussing the “Molecular Beacon” type probes of Figure 1A): “Molecular beacons can possess differently colored fluorophores, enabling assays to be carried out that simultaneously detect different targets in the same reaction” (page 52, left column, 2nd full paragraph). Similarly, in discussing “Amplifluor primers” of the type shown in Figure 1F, Marras noted (page 57, right column, lines 3-5, citation omitted): “Recently, a multiplex real-time PCR assay, utilizing amplifluor primers, was reported.” Marras remarked (page 58, left column, last paragraph preceding “Acknowledgements”): “In order to develop high-throughput assays, it is desirable to perform multiplex assays, where more than one target nucleic acid can be identified in the same solution.”
Reed disclosed putting primers and probes for 16S ribosomal RNA gene targets into a master mix (column 18, lines 11-16).
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to modify the method of De Backer for quantifying important bacterial species in normal and disturbed vaginal microflora by including primers for Megasphaera, since Zozaya-Hinchliffe demonstrated that Megasphaera species were also associated with bacterial vaginosis. Furthermore, it would have been obvious to modify the method by using fluorescently-labeled primers or probes, instead of SYBR Green, since Marras disclosed these formats as alternatives to the use of SYBR Green. As discussed in MPEP 2144.06, it is prima facie obvious to substitute equivalents known for the same purpose. Here, the cited art clearly demonstrates that SYBR Green, labeled primers, and labeled probes were alternative formats for carrying out real-time quantitative PCR. Moreover, labeled primers or probes would have provided an ability to detect multiple targets in the same reaction, which Marras noted was desirable for the purpose of developing high-throughput assays. It would not have escaped the ordinary skilled worker that the multiplexing capability described by Marras for Molecular Beacons (Marras Figure 1A) and Amplifluor Primers (Marras Figure 1F) would have been equally true for any of the other formats shown in Marras’ Figure 1, as it is simply based on using different fluorescent labels on different primers or probes. Finally, it would have been obvious to put the primers and probes into a master mix as disclosed by Reed, as Reed demonstrates this was known to do when setting up PCR assays.
Claims 2 and 10 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over De Backer et al. (BMC Microbiology 7:115; 19 December 2007, IDS reference) in view of Zozaya-Hinchliffe et al. (App. Env. Micro. 74(5):1656-1659 (2008)), Marras et al. (Clinica Chimica Acta 363:48-60 (2006), IDS reference) and Reed (US 7,608,399, IDS reference) as applied to claims 1, 8, 9 and 20 above, and further in view of Polansky (US 2004/0023207, IDS reference).
The teachings of De Backer, Zozaya-Hinchliffe, Marras and Reed have been discussed. It is noted that De Backer collected samples with swabs (page 10, “Samples”).
These references did not discuss putting the primers, probes and swabs into a “kit”.
Polansky disclosed (paragraph [0919]): “Well known advantages of commercial kits include convenience and reproducibility due to manufacturing standardization, quality control and validation procedures.”
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to put the primers, probes and swabs into a kit in order to obtain the benefits of kits disclosed by Polansky.
Claims 3, 11 and 12 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over De Backer et al. (BMC Microbiology 7:115; 19 December 2007, IDS reference) in view of Zozaya-Hinchliffe et al. (App. Env. Micro. 74(5):1656-1659 (2008)), Marras et al. (Clinica Chimica Acta 363:48-60 (2006), IDS reference) and Reed (US 7,608,399, IDS reference) as applied to claims 1, 8, 9 and 20 above, and further in view of AF325325.1 (submitted 2003, IDS reference).
The disclosures of De Backer, Zozaya-Hinchliffe, Marras and Reed have been discussed. De Backer also disclosed how primers were selected based on aligning the target sequence to closely related sequences and selecting primers based on specificity to the target sequence, using publicly available algorithms to create alignments and to check for primer specificity (page 11, “Primers”). These references did not disclose the sequences of the primers and probes recited in claims 3, 11 and 12.
AF325325.1 discloses the 16S rRNA gene from an Atopobium vaginae clone. SEQ ID. NO: 11 matches this sequence from bases 722 to 741. SEQ ID NO: 12 matches the complement of bases 877-858. SEQ ID NO: 13 matches bases 784-808.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to select alternate sequences for primers and probes based on the known sequence for the A. vaginae 16S rRNA gene by following the routine practice disclosed by De Backer for choosing specific sequences based on aligning a target sequence with related sequences using an algorithm such as CLUSTAL, selecting regions where differences occur, and checking those regions for specificity using an algorithm such as BLAST. Even Applicant’s specification admits: “A number of computer programs, such as Primer Express (Applied Biosystems, Foster City, Calif.), can be used to rapidly obtain optimal primer/probe sets.” One of ordinary skill in the art would have merely regarded the claimed primers and probes as equivalent to the primers/probes suggested by the prior art for the purpose of detecting and quantifying these bacteria. Thus, one of ordinary skill would have had a reasonable expectation of success in arriving at the claimed primers as alternatives to those used by De Backer or probes as suggested by Marras.
Claims 4, 13 and 14 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over De Backer et al. (BMC Microbiology 7:115; 19 December 2007, IDS reference) in view of Zozaya-Hinchliffe et al. (App. Env. Micro. 74(5):1656-1659 (2008)), Marras et al. (Clinica Chimica Acta 363:48-60 (2006), IDS reference) and Reed (US 7,608,399, IDS reference) as applied to claims 1, 8, 9 and 20 above, and further in view of AY271950.1 (submitted 2004, IDS reference).
The disclosures of De Backer, Zozaya-Hinchliffe, Marras and Reed have been discussed. De Backer also disclosed how primers were selected based on aligning the target sequence to closely related sequences and selecting primers based on specificity to the target sequence, using publicly available algorithms to create alignments and to check for primer specificity (page 11, “Primers”). These references did not disclose the sequences of the primers and probes recited in claims 4, 13 and 14.
AY271950.1 teaches the 16s rRNA gene from a Megashaera sp. clone. SEQ ID. NO: 14 matches this sequence from bases 307-326. SEQ ID NO: 15 matches the complement of bases 547-528. SEQ ID NO: 16 matches bases 478-502.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to select alternate sequences for primers and probes based on the known sequence for the Megasphaera 16S rRNA gene by following the routine practice disclosed by De Backer for choosing specific sequences based on aligning a target sequence with related sequences using an algorithm such as CLUSTAL, selecting regions where differences occur, and checking those regions for specificity using an algorithm such as BLAST. Even Applicant’s specification admits: “A number of computer programs, such as Primer Express (Applied Biosystems, Foster City, Calif.), can be used to rapidly obtain optimal primer/probe sets.” One of ordinary skill in the art would have merely regarded the claimed primers and probes as equivalent to the primers/probes suggested by the prior art for the purpose of detecting and quantifying these bacteria. Thus, one of ordinary skill would have had a reasonable expectation of success in arriving at the claimed primers as alternatives to those used by Zozaya-Hinchliffe or probes as suggested by Marras.
Claims 7 and 19 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over De Backer et al. (BMC Microbiology 7:115; 19 December 2007, IDS reference) in view of Zozaya-Hinchliffe et al. (App. Env. Micro. 74(5):1656-1659 (2008)), Marras et al. (Clinica Chimica Acta 363:48-60 (2006), IDS reference) and Reed (US 7,608,399, IDS reference) as applied to claims 1, 8, 9 and 20 above, and further in view of AF325325.1 (submitted 2003, IDS reference) and AY271950.1 (submitted 2004, IDS reference).
The disclosures of De Backer, Zozaya-Hinchliffe, Marras and Reed have been discussed. De Backer also disclosed how primers were selected based on aligning the target sequence to closely related sequences and selecting primers based on specificity to the target sequence, using publicly available algorithms to create alignments and to check for primer specificity (page 11, “Primers”). These references did not disclose the sequences of the primers and probes recited in claims 7 and 19.
AF325325.1 discloses the 16S rRNA gene from an Atopobium vaginae clone. SEQ ID. NO: 11 matches this sequence from bases 722 to 741. SEQ ID NO: 12 matches the complement of bases 877-858. SEQ ID NO: 13 matches bases 784-808.
AY271950.1 teaches the 16s rRNA gene from a Megashaera sp. clone. SEQ ID. NO: 14 matches this sequence from bases 307-326. SEQ ID NO: 15 matches the complement of bases 547-528. SEQ ID NO: 16 matches bases 478-502.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to select alternate sequences for primers and probes based on the known sequence for the Atopobium vaginae and Megasphaera 16S rRNA genes by following the routine practice disclosed by De Backer for choosing specific sequences based on aligning a target sequence with related sequences using an algorithm such as CLUSTAL, selecting regions where differences occur, and checking those regions for specificity using an algorithm such as BLAST. Even Applicant’s specification admits: “A number of computer programs, such as Primer Express (Applied Biosystems, Foster City, Calif.), can be used to rapidly obtain optimal primer/probe sets.” One of ordinary skill in the art would have merely regarded the claimed primers and probes as equivalent to the primers/probes suggested by the prior art for the purpose of detecting and quantifying these bacteria. Thus, one of ordinary skill would have had a reasonable expectation of success in arriving at the claimed primers as alternatives to those used by Zozaya-Hinchliffe or probes as suggested by Marras.
Claims 5, 15 and 16 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over De Backer et al. (BMC Microbiology 7:115; 19 December 2007, IDS reference) in view of Zozaya-Hinchliffe et al. (App. Env. Micro. 74(5):1656-1659 (2008)), Marras et al. (Clinica Chimica Acta 363:48-60 (2006), IDS reference) and Reed (US 7,608,399, IDS reference) as applied to claims 1, 8, 9 and 20 above, and further in view of AY262350.1 (submitted 2003, IDS reference).
The disclosures of De Backer, Zozaya-Hinchliffe, Marras and Reed have been discussed. De Backer also disclosed how primers were selected based on aligning the target sequence to closely related sequences and selecting primers based on specificity to the target sequence, using publicly available algorithms to create alignments and to check for primer specificity (page 11, “Primers”). These references did not disclose the sequences of the primers and probes recited in claims 5, 15 and 16.
AY262350.1 teaches the 16s rRNA gene from a Lactobacillus jensenii clone. SEQ ID. NO: 4 matches this sequence from bases 100-119. SEQ ID NO: 5 matches the complement of bases 227-208. SEQ ID NO: 6 matches bases 160-184.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to select alternate sequences for primers and probes based on the known sequence for the L. jensenii 16S rRNA gene by following the routine practice disclosed by De Backer for choosing specific sequences based on aligning a target sequence with related sequences using an algorithm such as CLUSTAL, selecting regions where differences occur, and checking those regions for specificity using an algorithm such as BLAST. Even Applicant’s specification admits: “A number of computer programs, such as Primer Express (Applied Biosystems, Foster City, Calif.), can be used to rapidly obtain optimal primer/probe sets.” One of ordinary skill in the art would have merely regarded the claimed primers and probes as equivalent to the primers/probes suggested by the prior art for the purpose of detecting and quantifying these bacteria. Thus, one of ordinary skill would have had a reasonable expectation of success in arriving at the claimed primers as alternatives to those used by De Backer or probes as suggested by Marras.
Response to Arguments
Applicant's arguments filed 04/01/2026 have been fully considered but they are not persuasive.
Applicant argues: “…this rejection relies on impermissible hindsight and fails to establish that a person of ordinary skill in the art (PHOSITA) would have had a reasonable expectation of success in formulating the claimed multiplex master mix.”
In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
Regarding “reasonable expectation of success”, Applicant further argues: “A POSITA understands that multiplex PCR is notoriously unpredictable. Combining multiple primer pairs and probes into a single master mix frequently results in competitive inhibition, primer-dimer formation, cross-reactivity, and divergent amplification efficiencies. Reed’s generalized disclosure that multiplexing is possible does not teach how to overcome the specific thermodynamic and kinetic hurdles of co-amplifying these specific three targets simultaneously…Without a convincing line of reasoning based on established scientific principles demonstrating that these specific assays could be successfully combined without cross-reactivity, a POSITA would have had no reasonable expectation of success.”
This argument is not persuasive. It is to be noted that a “reasonable expectation of success” does not require an absolute guarantee of success. It is also to be noted that most of Applicant’s claims do not limit to specific primer and probe sequences combined with other specific primer and probe sequences in the claimed master mix or reaction mixture. The examiner did not reject these broad claims under the enablement prong of 35 USC 112(a) because it was well within the skill of the ordinary artisan in the field of PCR analysis to obtain primers and probes for a given set of targets that function in multiplex PCR.
Conclusion
THIS ACTION IS MADE FINAL. 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 SAMUEL C WOOLWINE whose telephone number is (571)272-1144. The examiner can normally be reached 9am-5:30pm.
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/SAMUEL C WOOLWINE/ Primary Examiner, Art Unit 1681
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