DETAILED ACTION
Applicant’s response filed 01/05/2026 has been fully considered. The following rejections and/or objections are either reiterated or newly applied.
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 .
Claim Status
Claims 1-18 are currently pending.
Claims 7-18 are withdrawn as discussed in section Restriction Election in Office action mailed 10/10/2025.
Claims 1-6 are herein under examination.
Claims 1-6 are rejected.
Claims 1 and 5-6 are objected.
Priority
The instant application claims domestic benefit as a 371 filing of international application PCT/US2020/019028 filed 02/20/2020, which claims domestic benefit to the following U.S. Provisional Applications: 62/807,761 filed on 02/20/2019; 62/807,760 filed on 02/20/2019; and 62/808,304 filed on 02/21/2019. The claims to domestic benefit are acknowledged for claims 1-6. As such, the effective filing date for claims 1-6 is 02/20/2019.
Information Disclosure Statement
The IDS filed 10/08/2025 follows the provisions of 37 CFR 1.97 and has been considered in full. A signed copy of the list of references cited from this IDS is included with this Office Action.
Drawings
The drawings are objected to for failing to comply with 37 CFR 1.84(l) and (p) because the characters in the axes of Figure 2A and 2B are illegible.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Response to Arguments under Drawings
Applicant has filed replacement sheets for Figures 2A and 2B (pg. 6, para. 3-4 of Applicant’s remarks). However, the replacement sheets suffer from the same defects as the original because the axes are illegible.
Withdrawn Rejections
35 USC 112(b)
The rejection of claim 2 under 35 USC 112(b) is withdrawn in view of claim amendments.
35 USC 101
The rejection of claim 2 under 35 USC 101 is withdrawn in view of claim amendment.
35 USC 102
The rejection of claims 1-6 under 35 USC 102(a)(1) and 102(a)(2) as being anticipated by Apte is withdrawn in view of claim amendments.
Claim Objections
The objection to claims 1 and 6 are withdrawn in view of claim amendment.
Claims 1 and 5-6 are objected to because of the following informalities:
Claim 1, line 14, recites the phrase “and a region of the subject’s body” which should be changed to something similar to “and determining that a region of the subject’s body” to clarify the phrase.
Claim 5 recites “wherein identifying the HPV-associated condition” which should be “wherein determining the subject has the cancer related condition associated with HPV infection” to properly refer to the phrase in claim 1, lines 13-14.
Claim 6 recites “14 (high risk HPV) hrHPV and 5 (low risk HPV) lrHPV strains” which should be “14 high risk HPV (hrHPV) and 5 low risk HPV (lrHPV) strains”
Appropriate correction is required.
Claim Rejections - 35 USC § 112
35 USC 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-6 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. This rejection is newly recited and is necessitated by claim amendment.
Claim 1, line 8, recites the phrase “the individual” which lacks antecedent basis. To overcome the rejection, change the phrase to “the subject”. Claim 5 also recites “the individual” and is indefinite for the same reason.
Claims 2-4 and 6 are also rejected because they depend on claim 1, which is rejected, and because they do not resolve the issue of indefiniteness.
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 and 3-6 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea and a natural phenomenon without significantly more.
Any newly recited portions herein are necessitated by claim amendment.
Step 2A, Prong 1:
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomena (Step 2A, Prong 1). In the instant application, claims 1 and 3-6 recite a method. The instant claims recite the following limitations that equate to one or more categories of judicial exception:
Claim 1 recites “generating a disease characterization model by analyzing one or more microbiome features obtained from microbiome samples from a population having the HPV- associated condition; … to generate one or more microbiome datasets based on the microbiome sample from the individual and extracting a set of microbiome features from the one or more microbiome datasets, wherein the one or more datasets comprise at least one of: a microbiome taxonomic composition dataset, a microbiome function dataset, a microbiome composition diversity dataset, and a microbiome functional diversity dataset; determining that the subject has the cancer related condition associated with HPV infection, and a region of the subject's body affected by the cancer related condition associated with the HPV infection based on the set of microbiome features and the disease characterization model;”
Claim 3 recites “further comprising characterizing the HPV- associated condition following the administration of the treatment based on ALA to determine whether a follow-on ALA based treatment is required.”
Claim 5 recites “wherein identifying the HPV-associated condition comprises analyzing predetermined bacterial targets and HPV strains in the microbiome sample from the individual.”
Claim 6 recites “wherein the HPV strains are selected from the group consisting of 14 (high risk HPV) hrHPV and 5 (low risk HPV) lrHPV strains.”
Limitations reciting a mental process.
The above cited limitations in claims 1, 3 and 5-6 are recited at such a high level of generality that they equate to a mental process because they are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), which the courts have identified as concepts that can be practically performed in the human mind. The paragraphs below discuss the limitations in these claims that recite a mental process under their broadest reasonable interpretation (BRI).
Regarding claim 1, the BRI of generating a disease characterization model includes analyzing genomic data using a regression model or decision tree, as stated in the specification in para. [29]. A human can practically perform the operations of a regression model or decision tree. The BRI of extracting microbiome features from a microbiome dataset includes searching through a database of microorganism specific RNA expression and collecting genes that are specific to a microorganism. The BRI of determining a subject has the HPV-associated condition at a region on the subject’s body based on the microbiome features and the disease characterization model includes inputting the individual’s microorganism specific features into the regression model and determining whether the individual has the condition based on regression analysis.
Regarding claims 3 and 5-6, the BRI of claim 3 includes analyzing test results to determine if another round of treatment is required. The BRI of claims 5-6 includes analyzing levels of genomic markers specific to bacterial targets and HPV strains.
Limitations reciting a mathematical concept.
Limitations in claim 1 equate to a mathematical concept because they are similar to the concepts of organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)), which the courts have identified as mathematical concepts. The BRI of generating a disease characterization model includes performing calculations using a regression function, as discussed in specification para. [27]. The BRI of generating a microbiome dataset based on a microbiome sample includes calculating relative abundance. The BRI of determining that an individual has the HPV-associated condition by using the microbiome features and the disease characterization model includes using gene expression data as input into a regression function and outputting a numerical result.
Limitations reciting a natural phenomenon.
The above cited limitation in claim 1 of “determining whether the individual has the HPV-associated condition based on the set of microbiome features and the disease characterization model” equates to a natural phenomenon because these limitations are similar to the concept of
a correlation between the presence of myeloperoxidase in a bodily sample (such as blood or plasma) and cardiovascular disease risk, Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1361, 123 USPQ2d 1081, 1087 (Fed. Cir. 2017), which the courts have established as a natural phenomenon. This limitation detects a cancer related condition associated with HPV based on microorganism features which includes genomic data under its BRI. Connecting genetic information to a disease is a natural phenomenon.
As such, claims 1 and 3-6 recite an abstract idea and a natural phenomenon (Step 2A, Prong 1: Yes).
Step 2A, Prong 2:
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exception is not integrated into a practical application because the claims do not recite additional elements that reflect an improvement to a computer, technology, or technical field (MPEP § 2106.04(d)(1) and 2106.5(a)), require a particular treatment or prophylaxis for a disease or medical condition (MPEP § 2106.04(d)(2)), implement the recited judicial exception with a particular machine that is integral to the claim (MPEP § 2106.05(b)), effect a transformation or reduction of a particular article to a different state or thing (MPEP § 2106.05(c)), nor provide some other meaningful limitation (MPEP § 2106.05(e)). Rather, the claims include limitations that equate to an equivalent of the words “apply it” and/or to instructions to implement an abstract idea on a computer (MPEP § 2106.05(f)) and to insignificant extra-solution activity (MPEP § 2106.05(g)). The instant claims recite the following additional elements:
Claim 1 recites “collecting a microbiome sample from the subject; performing culture-independent sequencing … and administering a treatment based on aminolevulinic acid (ALA) or an analog thereof in the affected region.”
Claim 4 recites “wherein upon a determination that a follow-on ALA based treatment is required, administering a second dose of ALA or the analog thereof in the region after a predefined period and irradiating the region after a set time during which the ALA or the analog thereof transforms into a fluorescent compound, the irradiating being characterized by production of reactive oxygen species in the irradiated region.”
The following limitations in claim 1 equate to insignificant, extra-solution activity of necessary data gathering: “collecting a microbiome sample from the subject; performing culture-independent sequencing”. These limitations gather data necessary to perform the judicial exception in claim 1 of “determining that the subject has the cancer related condition associated with HPV infection, and a region of the subject's body affected by the cancer related condition associated with the HPV infection based on the set of microbiome features and the disease characterization model”.
The limitation in claim 1 of “administering a treatment based on aminolevulinic acid (ALA) or an analog thereof in the affected region” does not recite a particular treatment because it has an insignificant relationship to the exception (MPEP 2106.04(d)(2)(b)). ALA alone is not known to treat a cancer related condition associated to HPV infection. Rather, ALA in combination with, for example, photodynamic therapy is known to treat HPV. As such, this limitation equates to insignificant, extra-solution activity because it does not impose meaningful limits on the claim such that it is not nominally or tangentially related to the invention (MPEP 2106.05(g)(2)).
Claim 4 is a contingent limitation. MPEP § 2111.04(II) recites “The broadest reasonable interpretation of a method (or process) claim having contingent limitations requires only those steps that must be performed and does not include steps that are not required to be performed because the condition(s) precedent are not met.” In claim 4, there is an instance where a determination is that made that follow-on ALA based treatment is not required. Thus claim 4 is not required to be performed.
As such, claims 1 and 3-6 are directed to an abstract idea and a natural phenomenon (Step 2A, Prong 2: No).
Step 2B:
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). These claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because these claims recite additional elements that equate to instructions to apply the recited exception in a generic way and/or in a generic computing environment (MPEP § 2106.05(f)) and to well-understood, routine and conventional (WURC) limitations (MPEP § 2106.05(d)). The instant claims recite the following additional elements:
Claim 1 recites “collecting a microbiome sample from the subject; performing culture-independent sequencing … and administering a treatment based on aminolevulinic acid (ALA) or an analog thereof in the affected region.”
Claim 4 recites “wherein upon a determination that a follow-on ALA based treatment is required, administering a second dose of ALA or the analog thereof in the region after a predefined period and irradiating the region after a set time during which the ALA or the analog thereof transforms into a fluorescent compound, the irradiating being characterized by production of reactive oxygen species in the irradiated region.”
As discussed in Step 2A, Prong 2, claim 4 is being interpreted as a contingent limitation and is thus not required to be performed.
The above cited limitations in claim 1 are WURC as taught below by Wargo et al. (“Wargo”; WO 2018/064165 A2; newly cited), Gallo et al. (“Gallo”; WO 2018/183288 A1; newly cited), and Raymond et al. (“Raymond”; US 2016/0053301 A1; newly cited).
Wargo disclose methods for treating cancer (abstract). A gut microbiome sample is analyzed from a patient by 16S ribosomal sequencing or metagenomics whole genome sequencing (claims 126 and 128). A microbial profile derived from the microbiome sample indicates high-alpha diversity or high abundance of butyrate-producing bacteria (claim 121). A chemotherapeutic agent such as aminolevulinic acid is administered directly to an ear that contains cancer of a patient [170] [176].
Gallo collects a microbiome sample of a cancer patient as well as whole-genome sequencing of M034 strains from human skin which were used for metagenomic analysis such as detecting frequencies of strains [187]. Chemotherapeutics may be administered directly to an area containing cancer in a patient [91], which include aminolevulinic acid [139-140].
Raymond discloses sequencing target DNA for microbiome profiling in patients [95] [214] [221]. Anti-cancer drugs such as aminolevulinic acid can be administered to a patient [216-217]
When these additional elements are considered individually and in combination, they do not provide an inventive concept because they are WURC limitations of performing microbiome sequencing and administering aminolevulinic acid, as taught above by Wargo, Gallo, and Raymond. Therefore, these additional elements do not transform the claimed judicial exception into a patent-eligible application of the judicial exception and do not amount to significantly more than the judicial exception itself (Step 2B: No).
As such, claims 1 and 3-6 are not patent eligible.
Response to Arguments under 35 USC 101
Applicant's arguments filed 01/05/2025 have been fully considered but they are persuasive only in part.
Applicant argues that “performing culture-independent sequencing to generate one or more microbiome datasets” cannot be performed in the mind (pg. 7, para. 2 of Applicant’s remarks). Examiner agrees in part for the following reasons:
The sequencing step itself is an additional element. However, using sequencing data to generate a microbiome dataset includes mathematical concepts such as calculating relative abundance.
Applicant argues that “generating a disease characterization model” does not recite math and refers to Diamond v. Diehr (pg. 7, para. 2 of Applicant’s remarks). Applicant’s argument is not persuasive for the following reasons:
MPEP 2106.04(a)(2)(I)(b) recites that a mathematical concept may be recited in a claim as a textual replacement for a particular equation or formula. The limitation “generation a disease characterization model” is a textual replacement for training or fitting a logistic regression or other suitable model. This interpretation is evidenced by specification para. [29].
Regarding Applicant’s comment on Diamond v. Diehr, the claim in Diamond v. Diehr did recite a mathematical concept (i.e., Arrhenius equation). However, the claim as a whole was not directed to a mathematical concept because of the practical application of molding rubber products conferred by additional elements.
Applicant argues that claim 1 does not recite a natural phenomenon because the microbiome features are not naturally occurring but are rather extracted from a microbiome dataset (pg. 7, para. 3 of Applicant’s remarks). Applicant’s argument is not persuasive for the following reasons:
The BRI of a microbiome feature, extracted from a microbiome dataset derived from a microbiome sample of a subject, includes the microbiome feature being an abundance of a bacterial or viral population. Although the microbiome feature is obtained computationally, it is reflective of the real microbial/viral abundance within the subject. Therefore, determining that a patient has a condition associated with HPV infection based on microbiome features recites a natural phenomenon.
Applicant appears to argue that claim 1 recites a particular treatment (pg. 7, para. 4 of Applicant’s remarks). Applicant’s argument is not persuasive for the following reasons:
As discussed in the rejection above, administering a treatment based on ALA does not recite a particular treatment. This is because ALA alone does not treat conditions associated with HPV. Rather, ALA in combination with, for example, photodynamic therapy is known to treat HPV associated conditions. This is why claim 2 was found to recite a particular treatment because it requires both ALA and photodynamic therapy.
Applicant argues that the invention recites an inventive concept (pg. 8, para. 1 of Applicant’s remarks). Applicant’s argument is not persuasive because the additional elements in claim 1 have been taught to be WURC by Wargo, Raymond, and Gallo.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 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 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 1-6 are rejected under 35 U.S.C. 103 as being unpatentable over Apte et al. (“Apte”; FOR ref. 2 on IDS filed 01/11/2023; WO 2017/004379 A1; published 5 January 2017; previously cited) in view of Shanghai et al. (“Shanghai”; CN 101874795 A; published 03/11/2010; previously cited on PTO892 mailed 10/10/2025).
This rejection is newly recited as necessitated by claim amendment.
The bold and italicized text below are the limitations of the instant claims, and the italicized text serves to map the prior art onto the instant claims.
Claim 1:
A method of treating a subject having a cancer related condition associated with human papillomavirus (HPV) infection, the method comprising:
Apte teaches diagnostic testing that “can diagnose and/or provide information regarding STDs including: viral infections e.g., human papillomavirus” (abstract) [15] [66]. An STD caused by HPV can turn into cancer. A patient is treated after diagnosis [22].
generating a disease characterization model by analyzing one or more microbiome features obtained from microbiome samples from a population having the HPV-associated condition;
Apte shows in Figure 1 at S130 that a sample handling network (disease characterization model) generates a microbiome sequence dataset of microorganisms contained in a human sample S110. The sample handling network may be various types of models [99]. The microorganisms can be associated with STDs such as those acquired from HPV (HPV-associated condition) [38]. The microbiome dataset that targets HPV is derived from selected features of ranked primers and/or targets and amplicons (microbiome features) [38]. Method 100 in Figure 1 can be modified to include samples from multiple subjects (a population) [68] [93].
collecting a microbiome sample from the subject;
Apte shows in Figure 1 at steps S110 and S130 collecting samples from subjects to generate a microbiome sequence dataset by sequencing nucleic acid content of a microorganisms in the samples.
performing culture-independent sequencing to generate one or more microbiome datasets based on the microbiome sample from the individual and extracting a set of microbiome features from the one or more microbiome datasets;
Apte shows in Figure 1 at steps S110, S130 and S140 generating a microbiome sequence dataset from a human microbiome sample to detect presence of a set of microbiome targets, wherein the targets are associated with STDs [60], particularly HPV [38] [81]. This analysis can be performed on multiple microbiome sequence datasets simultaneously [67].
wherein the one or more datasets comprise at least one of: a microbiome taxonomic composition dataset, a microbiome function dataset, a microbiome composition diversity dataset, and a microbiome functional diversity dataset;
Apte shows in Figure at step S145 that a microbiome functional diversity dataset can be generated from the microbiome sample [63]. Alternatively, the method can generate “sample distribution of taxonomic groups of microorganisms present in the sample and/or functions of the microbiome” [87].
determining that the subject has the cancer related condition associated with HPV infection, and a region of the subject's body affected by the cancer related condition associated with the HPV infection based on the set of microbiome features and the disease characterization model; and
Apte teaches generating a diagnostic analysis S150 based on detecting presence of a set of microbiome targets in the microbiome sequence dataset S140. The diagnostic analysis indicates a positive or negative test result for each of a set of diseases of interest based on the sequences in the microbiome sequence dataset [88]. The diseases of interest are STDs associated with HPV [89]. The sample handling network (disease characterization model) is used to perform this [37-38] [47]. At S150, a microbiome sample can be collected from a subject’s genitals (a region of the subject’s body affected by the cancer related condition) [73-74].
administering a treatment based on aminolevulinic acid (ALA) or an analog thereof in the affected region.
Apte teaches generating a therapy recommendation based on a detected set of microbiome targets, wherein the therapy is tailored to the detected STD, which may be induced by HPV [76-78]. The method may also implement the therapy [22] [91].
However, Apte does not teach administering aminolevulinic acid to a region affected by the HPV-induced STD.
Shanghai uses 5-aminolevulinic acid (5-ALA) as a treatment for HPV (title). 5-ALA is applied topically to a site of a lesion (pg. 3, para. 5), wherein a lesion is a result of the HPV infection (pg. 1, para. 2 under Background technique).
Claim 2:
Apte generates a therapy recommendation tailored to the detected HPV-induced STD [76-78]. However, Apte does not teach administering ALA or irradiating the ALA.
Shanghai teaches “The 5-aminolevulinic acid according to the present invention is a commonly used compound with photodynamic therapeutic effect. After entering the human body, it is converted into hematoporphyrin (PpIX) and retained in the body. After being irradiated with a specific wavelength, active oxygen such as single line is generated. Oxygen and other free radicals kill pathogenic cells (cancer cells, HPV and HSV infected cells), while neighboring normal tissue cells are not affected” (pg. 2, para. 7). Shanghai also teaches “The lesion is irradiated with light with a wavelength of 500 to 700 nm. The treatment spot should completely cover the lesion, the irradiation energy density should be ≥60 J / cm2, and the irradiation time should be 5 to 60 minutes” (pg. 3, para. 7). Irradiation should occur 2 to 6 hours after applying 5-ALA (pg. 3, para. 6).
Prima facie case for combining Shanghai to Apte for claims 1-2:
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the instant invention to have modified the method of Apte for detecting HPV-associated STDs and generating therapy recommendations by topically administering 5-ALA to the site of HPV infection and irradiating the applied region, as taught by Shanghai. This is because Apte is directed towards treating HPV based diseases and because administering treatment is a standard practice in medicine. One of ordinary skill in the art would have had a reasonable expectation of success for topically treating HPV infections with 5-ALA because Shanghai states that 5-ALA treats HPV infections and is safe to use (pg. 3, last para). Shanghai also states that 5-ALA can treat high risk HPV patients with persistent infection (pg. 2, para. 5).
Claims 5 and 6:
Apte detects microbiome targets in a set of microbiome targets detected in a microbiome sequence dataset (Figure 1) [67]. The microbiome targets detect HPV, which includes both high and low risk HPV strains [15 [89]. The targets may also be specific for bacteria [14].
Claims 3-4 are rejected under 35 U.S.C. 103 as being unpatentable over Apte et al. (“Apte”; FOR ref. 2 on IDS filed 01/11/2023; WO 2017/004379 A1; published 5 January 2017; previously cited) in view of Shanghai et al. (“Shanghai”; CN 101874795 A; published 03/11/2010; previously cited on PTO892 mailed 10/10/2025;), as applied above to claim 1, and in further view of Wang et al. (“Wang”; Photochemistry and photobiology 88, no. 3 (2012): 565-569; previously cited on PTO892 mailed 10/10/2025).
This rejection is newly recited as necessitated by claim amendment.
The limitations of claim 1 have been taught in the rejection above by Apte and Shanghai.
Claim 3:
Shanghai treats HPV patients with 5-ALA then performs a follow-up after treatment, wherein 46 out of 86 patients changed from HPV positive to HPV negative (pg. 4, Example 3). However, neither Shanghai nor Apte repeat treatment after a follow-up visit.
Wang treats HPV infection-associated cervical acuminata with 5-ALA mediated photodynamic therapy (title). Wang states “PDT was repeated at 2-week intervals if lesion and HPV infection remained” (abstract).
Claim 4:
Shanghai teaches “The 5-aminolevulinic acid according to the present invention is a commonly used compound with photodynamic therapeutic effect. After entering the human body, it is converted into hematoporphyrin (PpIX) and retained in the body. After being irradiated with a specific wavelength, active oxygen such as single line is generated. Oxygen and other free radicals kill pathogenic cells (cancer cells, HPV and HSV infected cells), while neighboring normal tissue cells are not affected” (pg. 2, para. 7). Shanghai also teaches “The lesion is irradiated with light with a wavelength of 500 to 700 nm. The treatment spot should completely cover the lesion, the irradiation energy density should be ≥60 J / cm2, and the irradiation time should be 5 to 60 minutes” (pg. 3, para. 7). Irradiation should occur 2 to 6 hours after applying 5-ALA (pg. 3, para. 6).
However, Apte and Shanghai do not determine that a follow-on treatment is required, which includes applying a second dose of a therapy.
Wang states “PDT was repeated at 2-week intervals if lesion and HPV infection remained” (abstract).
It would have been prima facie obvious to one of ordinary skill in the art to have modified the method of Shanghai and Apte for treating HPV associated diseases with 5-ALA and performing follow-ups by administering another round of 5-ALA photodynamic therapy to patients who still show signs of HPV infection at the follow-up, as taught by Wang. The motivation for doing so is to treat the HPV-infection if it persists even after treatment, as taught by Wang (abstract). One of ordinary skill in the art would have had a reasonable expectation of success for repeating 5-ALA treatment because 5-ALA treats HPV, as taught in Shanghai and Wang.
Response to Arguments under 35 USC 102
Applicant's arguments filed 01/05/2026 have been fully considered but they are not persuasive.
Applicant argues that Apt does not teach administering aminolevulinic acid (pg. 8 of Applicant’s remarks). Applicant’s argument is not persuasive because the Shanghai reference is relied upon to teach the administrating step, not Apte, in the new grounds of rejection.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Double Patenting over US 11,001,900 B2
Claims 1-2 and 5-6 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2 and 16-17 of U.S. Patent No. US 11,001,900 B2 (hereinafter “Patent ‘900”) in view of Shanghai et al. (“Shanghai”; CN 101874795 A; published 03/11/2010; previously cited on PTO892 mailed 10/10/2025).
Any newly recited portions herein are necessitated by claim amendment.
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are an obvious variation of the claims in Patent ‘900. The following table shows claims in Patent ‘900 that read on the limitations of the instant claims:
Instant Application
Patent ‘900
Claims
Limitations
Claims
Limitations
1
generating a disease characterization model by analyzing one or more microbiome features obtained from microbiome samples from a population having the HPV-associated condition;
1
generating a female reproductive system-related characterization model based on the supplementary data and the set of microbiome composition features, wherein the female reproductive system-related characterization model is associated with the at least one female reproductive system-related condition;
2
wherein the at least one female reproductive system-related condition further comprises an HPV infection.
1
collecting a microbiome sample from the subject;
1
collecting, for the set of subjects, supplementary data associated with the at least one female reproductive system-related condition;
1
performing culture-independent sequencing to generate one or more microbiome datasets based on the microbiome sample from the individual and extracting a set of microbiome features from the one or more microbiome datasets, wherein the one or more datasets comprise at least one of: a microbiome taxonomic composition dataset, a microbiome function dataset, a microbiome composition diversity dataset, and a microbiome functional diversity dataset;
1
determining a microorganism sequence dataset associated with a set of subjects based on microorganism nucleic acids from samples associated with the set of subjects, wherein the microorganism sequence dataset is usable for identifying microbiome features and the samples comprise at least one sample associated with the at least one female reproductive system-related condition; determining a set of microbiome composition features based on the microorganism sequence dataset
16
wherein the user microbiome features comprise at least one ratio of sequencing reads between the HPV targets and the set of synthetic dsDNA spike molecules;
17
determining first alignment data based on alignment of the first set of processed sequence reads to 16S rRNA gene sequences associated with the bacterial targets; determining second alignment data based on alignment of the second set of processed sequence reads to HPV sequences associated with the HPV targets; and determining the user microbiome features based on the first and the second alignment data.
1
determining that the subject has the cancer related condition associated with HPV infection, and a region of the subject's body affected by the cancer related condition associated with the HPV infection based on the set of microbiome features and the disease characterization model;
1
determining a female reproductive system-related characterization for the user for the at least one female reproductive system-related condition based on the user microbiome features;
1
administering a treatment based on aminolevulinic acid (ALA) or an analog thereof in the affected region.
1
and facilitating a therapy for the user for the at least one female reproductive system-related condition, the therapy being determined based on a therapy model and the user microbiome features.
5
wherein identifying the HPV-associated condition comprises analyzing predetermined bacterial targets and HPV strains in the microbiome sample from the individual.
2
wherein the set of microbiome composition features further comprises microbiome features associated with a set of HPV targets; wherein the set of bacterial targets comprises at least one of Aerococcus (genus), Aerococcus christensenii (species), Atopobium (genus), Atopobium vaginae (species), Chlamydia trachomatis (species), Dialister micraerophilus (species), Fusobacterium (genus), Fusobacterium nucleatum (species), Gardnerella (genus), Gardnerella vaginalis (species), Gemella (genus), Lactobacillus (genus), Lactobacillus iners (species), Lactobacillus jensenii (species), Megasphaera (genus), Mobiluncus (genus), Mobiluncus curtisii (species), Mobiluncus mulieris (species), Mycoplasma genitalium (species), Neisseria gonorrhoeae (species), Papillibacter (genus), Parvimonas (genus), Peptoniphilus (genus), Peptostreptococcus (genus), Porphyromonas (genus), Prevotella (genus), Prevotella amnii (species), Prevotella timonensis (species), Sneathia (genus), Staphylococcus aureus (species), Streptococcus agalactiae (species), and Treponema pallidum (species); and
6
wherein the HPV strains are selected from the group consisting of 14 hrHPV and 5 lrHPV strains.
2
wherein the set of HPV targets comprises at least one of HPV types 6, 11, 42, 43, 44, 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 66, and 68.
Regarding claim 1, Patent ‘900 does not teach administering aminolevulinic acid to a region affected by the HPV condition.
Shanghai teaches using 5-aminolevulinic acid (5-ALA) as a treatment for HPV (title). 5-ALA is applied topically to a site of a lesion (pg. 3, para. 5), wherein a lesion is a result of the HPV infection (pg. 1, para. 2 under Background technique).
Regarding claim 2, Shanghai teaches “The 5-aminoketovaleric acid according to the present invention is a commonly used compound with photodynamic therapeutic effect. After entering the human body, it is converted into hematoporphyrin (PpIX) and retained in the body. After being irradiated with a specific wavelength, active oxygen such as single line is generated. Oxygen and other free radicals kill pathogenic cells (cancer cells, HPV and HSV infected cells), while neighboring normal tissue cells are not affected” (pg. 2, para. 7). Shanghai also teaches “The lesion is irradiated with light with a wavelength of 500 to 700 nm. The treatment spot should completely cover the lesion, the irradiation energy density should be ≥60 J / cm2, and the irradiation time should be 5 to 60 minutes” (pg. 3, para. 7).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the instant invention to have modified the method of Patent ‘900 for detecting and treating a female reproductive system-related condition associated with microorganisms by detecting an STD caused by HPV to then topically administer 5-ALA to the site of HPV infection, as taught by Shanghai, because an HPV-induced STD is a microorganism-related condition and 5-ALA would treat the HPV. One of ordinary skill in the art would have had a reasonable expectation of success for the combination because the user microbiome features of Patent ‘900 could be used to detect HPV and because 5-ALA treats HPV.
Double Patenting over US 11,572,555 B2
Claims 1-2 and 5-6 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 2-4 of U.S. Patent No. US 11,572,555 B2 (“Patent ‘555”) in view of Shanghai et al. (“Shanghai”; CN 101874795 A; published 03/11/2010; previously cited on PTO892 mailed 10/10/2025).
Any newly recited portions herein are necessitated by claim amendment.
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are an obvious variation of the claims in Patent ‘555. The following table shows claims in Patent ‘555 that read on the limitations of the instant claims:
Instant Application
Patent ‘555
Claims
Limitations
Claims
Limitations
1
generating a disease characterization model by analyzing one or more microbiome features obtained from microbiome samples from a population having the HPV-associated condition;
2
generating the sequenced set of targets with reduced amplification bias in accordance with the method of Claim 1; generating at least one of a microbiome composition diversity dataset and a microbiome functional diversity dataset based on the sequenced set of targets; receiving a supplementary dataset, associated with at least a subset of the population of subjects, wherein the supplementary dataset is informative of the microorganism-related condition
4
wherein the set of taxa corresponding to the set of targets comprises at least one of: HPV 3 (virus variant), HPV 6 (virus variant), HPV 16 (virus variant), HPV 18 (virus variant), HPV 31 (virus variant), HPV 33 (virus variant), HPV 35 (virus variant), HPV 39 (virus variant), HPV 43 (virus variant), HPV 45 (virus variant), HPV 51 (virus variant), HPV 52 (virus variant) HPV 53 (virus variant), HPV 54 (virus variant), HPV 56 (virus variant), HPV 58 (virus variant), HPV 59 (virus variant), HPV 66 (virus variant), HPV 68 (virus variant), HPV (virus), and HPV (multiple type) (virus).
1
collecting a microbiome sample from the subject;
2
collecting a user sample from a user, wherein the user sample comprises user sample nucleic acid material sharing target sequences with the set of targets;
1
performing culture-independent sequencing to generate one or more microbiome datasets based on the microbiome sample from the individual and extracting a set of microbiome features from the one or more microbiome datasets, wherein the one or more datasets comprise at least one of: a microbiome taxonomic composition dataset, a microbiome function dataset, a microbiome composition diversity dataset, and a microbiome functional diversity dataset;
2
generating a user microbiome dataset by sequencing the user sample nucleic acid material based on user-associated gRNA complexes sharing sequences with the proteins and the gRNAs, user-associated adapters sharing the adapter sequence, and user-associated primers sharing the primer sequence;
1
determining that the subject has the cancer related condition associated with HPV infection, and a region of the subject's body affected by the cancer related condition associated with the HPV infection based on the set of microbiome features and the disease characterization model;
2
determining a microbiome-associated characterization for the user for the microorganism- related condition based on the user microbiome dataset and the characterization model
1
administering a treatment based on aminolevulinic acid (ALA) or an analog thereof in the affected region.
2
dataset and the characterization model; and providing a therapy to the user with the microorganism-related condition based on the of microbiome-associated characterization and a therapy model, wherein the therapy modulates user microbiome composition to improve a state of the microorganism-related condition.
5
wherein identifying the HPV-associated condition comprises analyzing predetermined bacterial targets and HPV strains in the microbiome sample from the individual.
3
wherein the set of taxa corresponding to the set of targets comprises at least one of: Escherichia (genus), Finegoldia (genus), HPV 3 (virus variant), HPV 6 (virus variant)
6
wherein the HPV strains are selected from the group consisting of 14 hrHPV and 5 lrHPV strains.
2
wherein the set of taxa corresponding to the set of targets comprises at least one of: HPV 3 (virus variant), HPV 6 (virus variant), HPV 16 (virus variant), HPV 18 (virus variant), HPV 31 (virus variant), HPV 33 (virus variant), HPV 35 (virus variant), HPV 39 (virus variant), HPV 43 (virus variant), HPV 45 (virus variant), HPV 51 (virus variant), HPV 52 (virus variant) HPV 53 (virus variant), HPV 54 (virus variant), HPV 56 (virus variant), HPV 58 (virus variant), HPV 59 (virus variant), HPV 66 (virus variant), HPV 68 (virus variant), HPV (virus), and HPV (multiple type) (virus).
Regarding claim 1, Patent ‘555 does not teach administering aminolevulinic acid to a region affected by the HPV condition.
Shanghai teaches using 5-aminolevulinic acid (5-ALA) as a treatment for HPV (title). 5-ALA is applied topically to a site of a lesion (pg. 3, para. 5), wherein a lesion is a result of the HPV infection (pg. 1, para. 2 under Background technique).
Regarding claim 2, Shanghai teaches “The 5-aminoketovaleric acid according to the present invention is a commonly used compound with photodynamic therapeutic effect. After entering the human body, it is converted into hematoporphyrin (PpIX) and retained in the body. After being irradiated with a specific wavelength, active oxygen such as single line is generated. Oxygen and other free radicals kill pathogenic cells (cancer cells, HPV and HSV infected cells), while neighboring normal tissue cells are not affected” (pg. 2, para. 7). Shanghai also teaches “The lesion is irradiated with light with a wavelength of 500 to 700 nm. The treatment spot should completely cover the lesion, the irradiation energy density should be ≥60 J / cm2, and the irradiation time should be 5 to 60 minutes” (pg. 3, para. 7).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the instant invention to have modified the method of Patent ‘555 for detecting and treating a microorganism-related condition by detecting an STD caused by HPV to then topically administer 5-ALA to the site of HPV infection, as taught by Shanghai, because an HPV-induced STD is a microorganism-related condition and 5-ALA would treat the HPV. One of ordinary skill in the art would have had a reasonable expectation of success for the combination because the user microbiome dataset of Patent ‘555 could be used to detect HPV and because 5-ALA treats HPV.
Double Patenting over US 10,787,714 B2
Claims 1-4 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 9-10 of U.S. Patent No. US 10,787,714 B2 (hereinafter “Patent ‘714”) in view of Shanghai et al. (“Shanghai”; CN 101874795 A; published 03/11/2010; previously cited on PTO892 mailed 10/10/2025).
Any newly recited portions herein are necessitated by claim amendment.
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are an obvious variation of the claims in Patent ‘714. The following table shows claims in Patent ‘714 that read on the limitations of the instant claims:
Instant Application
Patent ‘714
Claims
Limitations
Claims
Limitations
1
generating a disease characterization model by analyzing one or more microbiome features obtained from microbiome samples from a population having the
1
generating a characterization model of the health condition based on the microbiome functional feature dataset;
1
generating a microbiome functional feature dataset, including diversity features, for the population of subjects based on the set of microorganism nucleic acid sequences;
1
collecting a microbiome sample from the subject;
1
receiving an aggregate set of samples from the set of sampling kits, the aggregate set of samples comprising at least one sample comprising microorganisms associated with the health condition;
1
performing culture-independent sequencing to generate one or more microbiome datasets based on the microbiome sample from the individual and extracting a set of microbiome features from the one or more microbiome datasets, wherein the one or more datasets comprise at least one of: a microbiome taxonomic composition dataset, a microbiome function dataset, a microbiome composition diversity dataset, and a microbiome functional diversity dataset;
1
selecting a primer for a nucleic acid sequence;
with a next generation sequencing platform of a sample processing system, determining a set of microorganism nucleic acid sequences based on processing the aggregate set of samples with the primer;
generating a microbiome functional feature dataset, including diversity features, for the population of subjects based on the set of microorganism nucleic acid sequences;
1
determining that the subject has the cancer related condition associated with HPV infection, and a region of the subject's body affected by the cancer related condition associated with the HPV infection based on the set of microbiome features and the disease characterization model;
1
processing a sample from the subject with the characterization model, thereby generating a diagnosis of the subject with the health condition based upon at least the subset of functional features;
1
administering a treatment based on aminolevulinic acid (ALA) or an analog thereof in the affected region.
1
determining a therapy for the subject based on the characterization, wherein the therapy is operable to improve a state of the health condition; and providing the therapy to the subject with the health condition, wherein the therapy is operable to modulate microbiome composition to improve the state of the health condition.
3
further comprising characterizing the
9
after providing the therapy, receiving a post-therapy sample from the subject; with the next generation sequencing platform of the sample processing system, processing the post-therapy sample based on the primer; and generating a post-therapy characterization of the subject in relation to the health condition and the therapy based on the processed post-therapy sample.
4
wherein upon a determination that a follow-on ALA based treatment is required, administering a second dose
10
determining post-therapy microbiome functional features associated with the subject, based on the processed post-therapy sample; determining an updated therapy for the subject based on the post-therapy microbiome functional features; and providing the updated therapy to the subject, wherein the updated therapy is operable to modulate microbiome function to improve the state of the health condition.
Regarding claims 1 and 3, Patent ‘714 does not teach that the microorganism associated with the health condition is an HPV associated disease, nor does Patent ‘714 teach treating an HPV associated disease with ALA directly to an infected region.
Shanghai teaches using 5-aminolevulinic acid (5-ALA) as a treatment for HPV (title). 5-ALA is applied topically to a site of a lesion (pg. 3, para. 5), wherein a lesion is a result of the HPV infection (pg. 1, para. 2 under Background technique).
Regarding claims 2 and 4, Patent ‘714 does not teach the HPV associated disease or irradiation using ALA. Shanghai teaches “The 5-aminoketovaleric acid according to the present invention is a commonly used compound with photodynamic therapeutic effect. After entering the human body, it is converted into hematoporphyrin (PpIX) and retained in the body. After being irradiated with a specific wavelength, active oxygen such as single line is generated. Oxygen and other free radicals kill pathogenic cells (cancer cells, HPV and HSV infected cells), while neighboring normal tissue cells are not affected” (pg. 2, para. 7). Shanghai also teaches “The lesion is irradiated with light with a wavelength of 500 to 700 nm. The treatment spot should completely cover the lesion, the irradiation energy density should be ≥60 J / cm2, and the irradiation time should be 5 to 60 minutes” (pg. 3, para. 7).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the instant invention to have modified the method of Patent ‘714 for detecting microorganisms associated with a health condition and generating therapy recommendations by detecting an STD caused by HPV to then topically administer 5-ALA to the site of HPV infection, as taught by Shanghai, because an HPV-induced STD is a microorganism caused health condition and 5-ALA would treat the HPV. One of ordinary skill in the art would have had a reasonable expectation of success for the combination because the functional features of Patent ‘714 could be used to detect HPV and because 5-ALA treats HPV.
Response to Arguments under Double Patenting
Applicant's arguments filed 01/05/2025 have been fully considered. Applicant requests that the Double Patenting rejection be held in abeyance (pg. 8 of Applicant’s remarks).
Conclusion
No claims are allowed.
Claim 2 is patent-eligible under 35 USC 101. Claim 2 recites a particular treatment when viewed in combination with claim 1 limitation “administering a treatment based on aminolevulinic acid (AL) or an analog thereof in the affected region”. ALA and analogs thereof are used in photodynamic therapy to treat HPV related conditions.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/N.A.A./Examiner, Art Unit 1687
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685