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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 the papers filed April 13, 2026. Currently, claims 1-20 are pending. Claims 7-10, 12-14, 16-17 have been withdrawn as drawn to non-elected subject matter.
Election/Restrictions
Applicant's election without traverse of Chlamydia trachomatis, species a, Claims 1-6, 11, 15, 18-20 in the paper filed April 13, 2026 is acknowledged.
The examiner called Applicant on April 29, 2026 to elect a primer pair. Applicant elected SEQ ID NO: 14, 35, and 44 for initial examination.
The requirement is still deemed proper and is therefore made FINAL.
Priority
This application claims priority to
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Drawings
The drawings are acceptable.
Improper Markush Rejection
Claims 1-4, 10-14, 18-20 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.
A Markush claim contains an “improper Markush grouping” if:
(1) the species of the Markush group do not share a “single structural similarity,” or (2) the species do not share a common use. Members of a Markush group share a “single structural similarity” when they belong to the same recognized physical or chemical class or to the same art-recognized class. Members of a Markush group share a common use when they are disclosed in the specification or known in the art to be functionally equivalent. See MPEP § 2117.
Here each species is considered to each of the target nucleic acid sequences, namely Chlamydia, Neisseria and Trichomonas.
The recited alternative species in the groups set forth here do not share a single structural similarity, as each different bacteria has a separate genome and has its own structure. The bacterial targets recited in the instant claims, do not share a single structural similarity since each consists of a different nucleotide sequences. The only structural similarity present is that all detected positions are part of nucleic acid molecules. The fact that the markers comprise nucleotides per se does not support a conclusion that they have a common single structural similarity because the structure of comprising a nucleotide alone is not essential to the common activity of sexual health conditions. Accordingly, the different bacteria do not share a single structural similarity.
MPEP 2117 (II)(A) provides the following guidance as to what constitutes a physical, chemical, or art recognized class:
A recognized physical class, a recognized chemical class, or an art-recognized class is a class wherein “there is an expectation from the knowledge in the art that members of the class will behave in the same way in the context of the claimed invention. In other words, each member could be substituted one for the other, with the expectation that the same intended result would be achieved”
The recited bacteria do not belong to a recognized chemical class because there is no expectation from the knowledge in the art that the bacteria will behave in the same manner and can be substituted for one another. The different bacteria cause different diseases that are treated differently. In other words, there is no expectation from the knowledge in the art that each of the recited bacteria would function in the same way in the claimed method; it is only in the context of this specification that it was disclosed that all members of this group may behave in the same way in the context of the claimed invention. Further there is no evidence of record to establish that it is clear from their very nature that each of the recited genes possess a common property .
MPEP 2117 (II) further states the following:
Where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the compounds do not appear to be members of a recognized physical or chemical class or members of an art-recognized class, the members are considered to share a "single structural similarity" and common use when the alternatively usable compounds share a substantial structural feature that is essential to a common use. Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984).
The recited alternative species do not share a substantial common structure just because they all have a sugar phosphate backbone. The sugar phosphate backbone of a nucleic acid chain is not considered to be a substantial common structural feature to the group of genes being claimed because it is shared by ALL nucleic acids. Further, the fact that the genes all have a sugar phosphate backbone does not support a conclusion that they have a common single structural similarity because the structure of comprising a sugar phosphate backbone alone is not essential to the asserted common use.
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.
Following this analysis, the claims are rejected as containing an improper Markush grouping.
Claim Rejections - 35 USC § 101
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 1-6, 11, 18-20 are rejected under 35 U.S.C. 101 because the claimed invention is not directed to patent eligible subject matter. Based upon an analysis with respect to the claim as a whole, the rejected claim(s) do not recite something significantly different than a judicial exception. The rationale for this determination is explained below:
Briefly, 1-6, 11, 18-20 are rejected because these claims are drawn to a nucleic acid molecules, namely primers that bind specifically to a target nucleic acid sequence from Chlamydia trachomatis in a kit. Additional claims are directed to extraction buffers, and particular primer sequences.
Claims 1, 15 are directed to nucleic acid fragments from the Chlamydia trachomatis sequence, i.e. known naturally occurring nucleic acids. Such isolated nucleic acid molecules, that are identical to fragments of naturally occurring nucleic acid molecules are not patent eligible subject matter, i.e. they are judicial exceptions to patentable subject matter.
MPEP 2106.04(b)(II) discusses products of nature. The MPEP specifically discusses DNA, primers and probes. The isolated DNA of Myriad and the primers of Ambry Genetics were described as products of nature by the courts. Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 133 S. Ct. 2107, 2116-17, 106 USPQ2d 1972, 1979 (2013); University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 758-59, 113 USPQ2d 1241, 1243 (Fed. Cir. 2014). The MPEP further states the “product of nature exceptions include both naturally occurring products and non-naturally occurring products that lack markedly different characteristics from any naturally occurring counterpart. See, e.g., Ambry Genetics, 774 F.3d at 760, 113 USPQ2d at 1244 ("Contrary to Myriad's argument, it makes no difference that the identified gene sequences are synthetically replicated. As the Supreme Court made clear, neither naturally occurring compositions of matter, nor synthetically created compositions that are structurally identical to the naturally occurring compositions, are patent eligible.").” The Federal Circuit in Ambry Genetics reviewed “[t]he Supreme Court held ineligible claims directed to segments as short as 15 nucleotides, the same length as the primer claims at issue here, suggesting that even short strands identical to those found in nature are not patent eligible. Compare ’492 patent col. 170 ll. 32–38, with ’282 patent col. 153 ll. 66–67.”
In the instant case, the claims, embrace probes and primers that are identical to naturally occurring gene fragments and clearly read on nature-based products that themselves do not exhibit markedly different characteristics from the naturally occurring gene. See e.g. Myriad in which one claim at issue was drawn to “[a]n isolated DNA having at least 15 nucleotides [an isolated DNA coding for a BRCA1 polypeptide having the amino acid sequence of SEQ ID NO: 2] (Myriad at 2113). The Court recognized that this claim, if valid, would have given Myriad exclusive right to isolate any strand of 15 or more nucleotides of an individual’s BRCA1 gene (paragraph bridging 2113 and 2114). This is directly analogous to the instant situation wherein Applicant’s claims cover probe and primer molecules that are fragments of a naturally occurring Chlamydia trachomatis genome sequence. The Court held that “[a] naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated”, and that “Myriad’s claims are not saved by the fact that isolating DNA from the human genome severs the chemical bonds that bind gene molecules together” (page 2118). The Court found that while Myriad had located and sequenced an important gene, Myriad had not created anything, and that “separating that gene from its surrounding genetic material is not an act of invention” (page 2118). Consistent with the findings of the Court in Myriad, the Office finds that the primers and probe molecules embraced by the instant clams are not patent eligible compositions of matter regardless of whether or not they are isolated from the genome. The Guidelines indicate that a change in biological function or activity maybe a characteristic of an isolated product that can provide a marked difference sufficient to distinguish over a naturally occurring product. However, in this case, as in the Ambry case, the function of the nucleic acids is the same function as the relevant portion of the naturally occurring sequence. Just as in nature, primers and probes utilize the innate ability of DNA to bind to itself.
Having established that the claims include a naturally occurring product that is a judicial exception, it must now be determined whether or not the claims recite an element or combination of elements that amount to significantly more than that exception, and whether those additional elements also amount to significantly more for the other claimed exception(s), which ensures that the claim does not have a preemptive effect with respect to any of the recited exceptions. To determine whether a claim that includes a nature-based product limitation recites a “product of nature” exception, an analysis is performed in which it is first determined if a claim includes a nature-based product that has markedly different characteristics from the corresponding naturally occurring product, and if it does not, then it is determined whether or not other elements of the claim are sufficient to ensure that the claim as a whole amounts to significantly more than the exception itself (see the Interim Guidance on Patent Subject Matter Eligibility published 12/16/2014 in the Federal Register at pages 74618-74633). In order to be markedly different the claimed product must possess at least one characteristic that is different from that of the counterpart.
The fact that these natural products are organized into a system or kit with an intended use adds nothing to the judicial exceptions that would distinguish them from the naturally occurring material. The kit must be considered in the context of whether or not the combination can provide some way of ensuring it does not limit the public’s access to the naturally occurring material. That does not occur in this case because the naturally occurring material exists as a distinct entity within the kit, and is not integrated in terms of form or function with any other element of the kit. A claim to a kit in which one of the kit elements is naturally-occurring product that is separate and distinct from the other kit elements would forestall the use of that naturally occurring product.
Therefore, the claims are properly rejected under 35 USC 101 as being drawn to patent-ineligible subject matter.
Claim Rejections - 35 USC § 112- Second Paragraph
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.
Claims 1-6, 11-15, 18-20 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 pre-AIA the applicant regards as the invention.
Claim 1 is indefinite because it claims both product and methods steps for using the products. As the limitations of the claim are drawn to how a user would use the lab analysis kit, not the systems itself, there is confusion as to when direct infringement occurs. Step (c ) is a method step of analyzing the sample using the laboratory analysis kit to detect whether the sexual health condition is present in the use. The claim is directed to a system or product. Correction is required. See MPEP 2173.05(p). Claim 19-20 are further directed to method steps but do not limit the elements in the system/product. Correction is required.
Claim 4 is directed to a system of “any of claim 1”. This language is unclear whether the claim is intended to depend on more than one claim or whether the language is an artifact from prior amendments.
Claim 11 contains trademark/trade names to buffers. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe buffers and, accordingly, the identification/description is indefinite.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
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.
Claim(s) 1-5, 18-19 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kersh et al. (J. of Clinical Microbiology, Vol. 59, No. 11, pages 1-13, November 2021).
Kersh teaches at home specimen self-collection and self-testing for sexually transmitted infection. Figure 1 illustrates a home sample collection, mail away, lab testing and electronic results (page 4). Kersh teaches the patient ships the specimen to a laboratory that offers a test accepting self-collected specimens and results are reported back to the clinic or directly to the patient (page 3)(a computer readable medium storing code). The system of Kersh comprises a home sample collection, a transport container and a labeled shipping container.
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Kersh teaches the CGC recommends screening for C. trachomatis by nucleic acid amplification tests (NAATs) using or vaginal swabs (page 2)(limitations of Claim 18-19). Amplification methods rely upon primers and reagents. Thus, the system inherently has primers and reaction mixtures.
With respect to Claim 2, Kersh teaches the collection instrument (e.g., a swab or a urine container) and a corresponding test tube with buffers/solutions that stabilize the collected material until testing are included (page 5).
With respect to Claim 3, Kersh teaches nucleic acid analysis.
With respect to Claim 4, Kersh teaches follow up with telemedicine.
With respect to Claim 5, Kersh teaches the bacterial sexually transmitted infection is chlamydia (Chlamydia trachomatis)(abstract).
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.
Claims 6, 11, 15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kersh et al. (J. of Clinical Microbiology, Vol. 59, No. 11, pages 1-13, November 2021) in view of Dean et al. (Emerging Infections Diseases, Vol. 15 No. 9., pages 1385-1394, September 2009) and Eszik et al. (J. of Microbiological Methods, Vol. 120, pages 15-22, January 2016) and further in view of Untergasser et al. (Nucleic acids research, Vol. 40, No. 14, e115, June 2012).
Kersh teaches at home specimen self-collection and self-testing for sexually transmitted infection. Figure 1 illustrates a home sample collection, mail away, lab testing and electronic results (page 4). Kersh teaches the patient ships the specimen to a laboratory that offers a test accepting self-collected specimens and results are reported back to the clinic or directly to the patient (page 3)(a computer readable medium storing code). The system of Kersh comprises a home sample collection, a transport container and a labeled shipping container. Kersh teaches the CGC recommends screening for C. trachomatis by nucleic acid amplification tests (NAATs) using or vaginal swabs (page 2)(limitations of Claim 18-19). Amplification methods rely upon primers and reagents. Thus, the system inherently has primers and reaction mixtures.
Kersh does not teach particular primers or probes for the analysis of Chlamydia trachomatis samples.
However, the prior art teaches numerous primer and probes for pykF gene of Chlamydia trachomatis for detecting sexually transmitted diseases. For example, Dean teaches primers used for PCR of chlamydiceae species and strains of pykF (Table 1). The primers flank the region of the instant primers and amplify a 500bp region of pykF.
Eszik is also directed to PCR analysis of Chlamydia trachomatis using primers in pykF. The primers of Eszik overlap with the instant oligonucleotides. Eszik teaches the same region of amplification to detect Chlamydia trachomatis. Eszik teaches analysis of serovar D (limitations of Claim 6). Eszik teaches use of PBS for extracts buffer (limitations of Claim 11).
The illustration below illustrates the position of SEQ ID NO: 14, 35 and 44 in the pykF gene. The next two alignments are the Eszik pykF primers and the bottom two oligonucleotides are the primers of Dean.
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Therefore, it would have been prima facie obvious to one having ordinary skill in the art before effective filing date of the claimed inventio to apply familiar primer design parameters to yield the primers of elected SEQ ID NO: 14, 35, 44 with a reasonable expectation of success. The prior art is replete with teachings of the Chlamydia trachomatis pykF gene. The prior art, see Dean and Esik designed primers to the same region of pykF to detect C. trachomatis. The prior art demonstrates an interest in developing primers in the same regions as the instant primers as illustrated above. A skilled artisan would have applied familiar primer design parameters programmed into familiar, freely available primer design tools in order to yield primers to try such as SEQ ID NOS: 14, 35, and 44. The skilled artisan at the time of filing would have designed primers and probes to known sequences (such as the sequences disclosed in the above references) with a high expectation of success. To design such primers constituted routine and conventional optimization at the time of filing. See In re Aller, 220 F.2d 454, at 456 (CCAP 1955) (“where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.”). Numerous references describe how to design and optimize primers and probes for PCR applications. For example, Untergasser teach how to design primers and probes from known sequences using known online primer/probe design programs for use in PCR assays. Untergasser teaches how to use Primer3Plus online program to design primers and probes to known sequences (Untergasser at pgs. W71-74). Untergasser provides specific guidance and parameters to optimize primer, probe and PCR assay design to yield optimal results; thus, designing PCR assays for particular applications constitutes well-known routine optimization. Optimization parameters are explicitly recognized in Untergasser. As noted in In re Aller, 105 USPQ 233 at 235, where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation. Routine optimization is not considered inventive and no evidence has been presented that the primer selection performed was other than routine, that the products resulting from the optimization have any unexpected properties, or that the results should be considered unexpected in any way as compared to the closest prior art.
The instant sequences are functional homologues of the above similar primers based on the known HBV sequence. This is supported by In Re Deuel, 34 USPQ 2d 1210 (Fed. Cir. 1995), in which the Court of Appeals for the Federal Circuit stated that (emphasis added),
Normally, a prima facie case of obviousness is based upon structural similarity, i.e., an established structural relationship between a prior art compound and the claimed compound. Structural relationships may provide the requisite motivation or suggestion to modify known compounds to obtain new compounds. For example, a prior art compound may suggest its homologs because homologs often have similar properties and therefore chemists of ordinary skill would ordinarily contemplate making them to try to obtain compounds with improved properties.
One of ordinary skill in the art is not selecting a particular DNA sequence from among a large number of degenerate variants, but rather selecting particular DNA sequences (primers) having particular art-recognized parameters, e.g., nucleotide length, GC content, melting temperature, and homology both within and without the particular DNA sequence. The claimed sequences were structural homologs of the sequences disclosed in the prior art, and concerning which a biochemist of ordinary skill would attempt to obtain alternate compounds with improved properties. Therefore, the claimed sequences are prima facie obvious over the cited references in the absence of secondary considerations.
The ordinary artisan would have had a reasonable expectation of success that such primers generated using known sequences as taught by Dean and Esik to detect the same Chlamydia trachomatis because the claimed probes are functional equivalents of the sequences. The ordinary artisan would have been motivated to generate a number of said primers to the same HBV sequence to provide flexibility and optimize experimentation (see Untergasser). Selection of specific oligonucleotides for specific Tm represents routine optimization with regard to sequence, length and composition of the oligonucleotide. Such optimization parameters are explicitly recognized in Untergasser. As noted in In re Aller, 105 USPQ 233 at 235, where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation. Routine optimization is not considered inventive and no evidence has been presented that the primer selection performed was other than routine, that the products resulting from the optimization have any unexpected properties, or that the results should be considered unexpected in any way as compared to the closest prior art.
In sum, the claimed primers are prima facie obvious because there was clear motivation to design PCR primers to detect the same pykF sequence; and designing and optimizing such primers constitutes a well-known, routine and conventional technique which would yield the claimed primers with a reasonable expectation of success. Applicants should submit secondary evidence of non-obviousness in line with MPEP §§ 716.01-716.02 (e.g. unexpected results evidence).
Claim 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kersh et al. (J. of Clinical Microbiology, Vol. 59, No. 11, pages 1-13, November 2021) in view of UK Health Security Agency, Blog, October 5, 2022.
Kersh does not teach a kit for sampling a combination of samples.
However, UK Health Security teaches testing for STI using sampling kits. UK teaches sampling kits will include a combination of sampling tools in a self-sampling kit. The kits may include a combination of urine, blood samples, anal, vaginal and throat swabs. UK teaches the kit will also come with instructions explaining how to best take the samples and video guides online. UK teaches sample results will be returned by text-message usually with in a few days.
Therefore, it would have been prima facie obvious prior to the effective filing date of the claimed invention to have modified the sampling kits of Kersh to analyze multiple samples in the same kit. The ordinary artisan would have been motivated to have tested and analyzed multiple samples in one test to save on shipping costs and reagents.
Conclusion
No claims allowable over the art.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEANINE ANNE GOLDBERG whose telephone number is (571)272-0743. The examiner can normally be reached Monday-Friday 6am-3:30pm.
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, Wu-Cheng Winston Shen can be reached on (571)272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JEANINE A GOLDBERG/Primary Examiner, Art Unit 1682
June 8, 2026
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