DETAILED ACTION
Applicant’s response filed 05/06/2026 has been fully considered. The following rejections and/or objections are either reiterated or newly applied.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 05/06/2026 has been entered.
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
Claim 2 is cancelled by Applicant.
Claims 1 and 3-18 are currently pending.
Claims 7-18 are withdrawn as discussed in section Restriction Election in Office action mailed 10/10/2025.
Claims 1 and 3-6 are herein under examination.
Claims 1 and 3-6 are rejected.
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. As such, the effective filing date for claims 1 and 3-6 is 02/20/2019.
Drawings
The drawings filed 05/06/2026 are objected to for failing to comply with 37 CFR 1.84(l) and (p) because the characters in the axes of Figures 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's arguments filed 05/06/2026 have been fully considered but they are not persuasive.
Applicant argues that replacement drawings for Figures 2A and 2B filed 05/06/2026 overcome the objection (pg. 6, para. 3 of Applicant’s remarks). Applicant’s argument is not persuasive because the replacement sheets filed 05/06/2026 suffer from the same defects as the original drawings because the axes are still illegible in Figures 2A and 2B.
Withdrawn Rejections
35 USC 112(b)
The rejection of claims 1-6 under 35 USC 112(b) is withdrawn in view of claim amendments.
35 USC 101
The rejection of claims 1 and 3-6 under 35 USC 101 is withdrawn in view of claim amendment.
35 USC 103
The rejection of claim 2 under 35 USC 103 is withdrawn in view of claim cancellation.
Claim Objections
The objection to claims 1 and 5-6 are withdrawn in view of claim amendment.
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 and 5-6 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).
Any newly recited portions herein are 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 subject 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] caused by 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 a “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 determining 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 generates 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 performs the analysis (disease characterization model) [37-38] [47]. At S150, a microbiome sample is collected from a collection site of a subject which may be from genitals or other sites [27] [73-74]. Therefore, a positive output indicating an STD caused by HPV from a genital microbiome sample indicates that the genitals contain the HPV associated STD (a region of the subject’s body affected by the cancer related condition associated with the HPV infection). The output indicates health status of the collection site [71].
administering a treatment based on aminolevulinic acid (ALA) or an analog thereof in the affected region, wherein administering the treatment further comprises irradiating the region after a set time during which ALA or the analog thereof transforms into a fluorescent compound, the irradiating being characterized by production of reactive oxygen species in the irradiated region.
Apte generates a therapy recommendation based on a detected set of microbiome targets, wherein the therapy is tailored to the detected STD induced by HPV [76-78]. The method may also implement the therapy [22] [91].
However, Apte does not administer ALA or an analog thereof to a region affected by the HPV-induced STD to then irradiate the region thereby transforming the ALA or analog thereof into a fluorescent compound, resulting in production of reactive oxygen species.
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). Shanghai teaches “[t]he 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 recites “[t]he 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).
It would have been obvious to have modified the method of Apte for detecting HPV-associated STDs and generating therapy recommendations based on the detection by topically administering 5-ALA to the site of HPV infection and irradiating the region to produce reactive oxygen species, as taught by Shanghai. One of ordinary skill would have been motivated to use the HPV treatment method of Shanghai in Apte because Apte is directed toward treating HPV based diseases and because administering treatment is a standard practice in medicine. There would have been 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 5-6:
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 maintained from the previous Office Action.
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 “[t]he 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 “[t]he 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 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 103
Applicant's arguments filed 05/06/2026 have been fully considered but they are not persuasive.
Applicant argues that Apte in view of Shanghai does not teach a disease characterization model trained on HPV-associated population microbiome data to determine if a subject has an HPV-associated cancer related condition in a specific region or administering ALA-based photodynamic therapy to the region (pg. 7, last para. – pg. 8, para. 1). Applicant argues that one of skill would not use the treatment method of Shanghai based on the HPV output of Apte (pg. 8, para. 2). Applicant’s argument is not persuasive because:
Applicant appears to argue against the references individually. However, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). The rejection is based on Apte in view of Shanghai.
Apte discloses a sample handling network that may be a machine learning algorithm trained on microbiome features from a group of individuals [81] [99]. The features are generated from a microbiome sample containing STD features associated with high-risk HPV strains [15] [38] [89] (Figure 1). The microbiome sample is derived from a collection site, which is associated with genitals, rectum, mouth, etc. (abstract) [27]. A diagnostic output indicates whether the collection site is positive or negative for an HPV associated condition based on the microbiome features associated with a collection site [88-89] (Figures 1 and 7). A therapy recommendation is promoted based on the output [91].
Shanghai is not solely directed to treating noncancerous warts. Shanghai states that 5-ALA treats high-risk HPV viruses which are associated with cervical cancer and precancerous lesions (pg. 1, sec. background, para. 2) (pg. 2, sec. summary of invention, para. 1). Photodynamic therapy is applied to HPV associated lesions by topically applying 5-ALA and irradiating the region to produce reactive oxygen species (pg. 3, para. 5 and 7) (pg. 2, para. 7).
One of ordinary skill would have recognized that the HPV associated STD detection output based on microbiome features from a collection site of Apte could be used to implement a treatment regime. This is because Apte directly states that the detection output is used to implement a treatment (Figure 1) [91]. One of skill would be motivated to use the output of Apte to implement the therapy of Shanghai. This is because the treatment of Shanghai uses 5-ALA photodynamic therapy to treat HPV associated precancerous lesions or HPV caused cervical cancer. Apte detects disease associated with high-risk HPV strains and recommends therapy while Shanghai teaches a therapy that directly treats lesions associated with high-risk HPV strains. There would have been a reasonable expectation of success to treat the HPV related cancer condition in Apte using the treatment of Shanghai because Shanghai teaches that lesions associated with high-risk HPV strains can be treated with 5-ALA photodynamic therapy and is safe to use (pg. 3, last para.).
Applicant argues that Wang does not cure the deficiencies of Apte and Shanghai (pg. 8, last para. – pg. 9, para. 1). Applicant’s argument is not persuasive because, as discussed in the responses and rejection above, Apte in view of Shanghai disclose microbiome profiling, a disease characterization model, and identification of HPV-associated cancer related conditions in body regions through microbial analysis. Wang is not relied upon for the method of instant claim 1.
Applicant argues that claim 3 requires using the microbiome-based analytical framework of claim 1 to characterize the HPV-condition after treatment (pg. 9, para. 1). Applicant’s argument is not persuasive because:
Claim 3 does not require using the microbiome-based framework of claim 1. Rather, the BRI of claim 3 requires determining if a follow-on treatment is required based on characterizing the HPV-associated condition after initial treatment. Wang teaches this limitation by reciting “PDT was repeated at 2-week intervals if lesion and HPV infection remained” (abstract). This necessitates inspection of lesions and HPV infection in order to repeat treatment.
Applicant argues that both rejections under 35 USC 103 use hindsight reasoning because Examiner uses knowledge of the invention to reconstruct the instant claims using the prior art (pg. 9, last para.). Applicant’s argument is not persuasive because:
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). Examiner has only relied upon the knowledge of one of ordinary skill in the art before the effective filing date of the instant invention. Examiner has provided obviousness rationales for each combination.
Applicant argues that the motivation to combine rational of “because Apte is directed towards treating HPV based diseases and because administering treatment is a standard practice in medicine” is so broadly stated that is applies to any combination of HPV diagnostic reference and any HPV treatment reference, which demonstrates hindsight reasoning (pg. 10, para 1). Applicant’s argument is not persuasive because:
Applicant has not viewed the motivation to combine in context. Specifically, Shanghai discloses a method to treat high-risk HPV associated precancerous lesions using photodynamic therapy and 5-ALA (pg. 1, sec. background, para. 2) (pg. 2, sec. summary of invention, para. 1) (pg. 3, para. 5 and 7) (pg. 2, para. 7). Apte detects STDs associated with high-risk HPV strains in specific body regions and outputs therapy recommendations (abstract) [15] [27] [38] [81] [88-89] [91] [99] (Figures 1 and 7). One of ordinary skill would have been motivated to use Shanghai’s therapy regime specific to HPV associated lesions in Apte because it would have treated the HPV associated lesions. It would have been prima facie obvious to one of ordinary skill in the art to apply a known treatment to a known disease.
Applicant appears to argue that claim 1 is nonobvious because no single cited reference teaches all the limitations of claim 1 (pg. 10, para. 1). Applicant’s argument is not persuasive because:
35 USC 103 is directed towards combinations of references to arrive at the claimed invention. MPEP 2141 recites “[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.” As discussed above, Examiner has reached a legal conclusion of obviousness on the basis of facts gleaned from the prior art as demonstrated by the prima facie case of obviousness.
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.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Double Patenting over US 11,001,900 B2
Claims 1 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 subject 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, wherein administering the treatment further comprises irradiating the region after a set time during which ALA or the analog thereof transforms into a fluorescent compound, the irradiating being characterized by production of reactive oxygen species in the irradiated 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). 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.
Claims 3-4 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), as applied above to instant 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 in view of further consideration of the claims.
The limitations of claim 1 have been taught in the rejection above by Patent ‘900 and Shanghai.
Claim 3:
Patent ‘900 facilitates treatment for an HPV related condition in claims 1-2. 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, Patent ‘900 and Shanghai do not 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 “[t]he 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 “[t]he 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, Patent ‘900 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 have modified the method of Shanghai and Patent ‘900 for treating HPV associated disease 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.
Double Patenting over US 11,572,555 B2
Claims 1 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 subject 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 determining 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, wherein administering the treatment further comprises irradiating the region after a set time during which ALA or the analog thereof transforms into a fluorescent compound, the irradiating being characterized by production of reactive oxygen species in the irradiated 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 determining a region of the subject’s body affected by the HPV infection or administering aminolevulinic acid to a region affected by the HPV condition.
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). The lesions are associated with specific regions of a body such as cervical or mount and are related to specific HPV strains (pg. 1, sec. background, para. 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 obvious to have modified the method of Patent ‘555 for detecting and treating a microorganism-related condition by detecting an STD caused by specific trains of HPV associated to particular regions of a body 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.
Claims 3-4 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), as applied above to instant 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 in view of further consideration of the claims.
The limitations of claim 1 have been taught in the rejection above by Patent ‘555 and Shanghai.
Claim 3:
Patent ‘555 provides therapy to a patient with an HPV related condition in claims 1-2 and 4. 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, Patent ‘555 and Shanghai do not 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 “[t]he 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 “[t]he 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, Patent ‘555 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 have modified the method of Shanghai and Patent ‘555 for treating HPV associated disease 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.
Double Patenting over US 10,787,714 B2
Claims 1 and 3-4 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, wherein administering the treatment further comprises irradiating the region after a set time during which ALA or the analog thereof transforms into a fluorescent compound, the irradiating being characterized by production of reactive oxygen species in the irradiated 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, identifying a specific region associated with HPV infection, or 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 1 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 obvious 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 specific HPV strains associated with regions of a subject 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.
Claims 5-6 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), as applied above to instant claim 1, and in further view of Apte et al. (“Apte”; FOR ref. 2 on IDS filed 01/11/2023; WO 2017/004379 A1; published 5 January 2017; previously cited).
This rejection is newly recited in view of further consideration of the claims.
The limitations of claim 1 have been taught in the rejection above by Patent ‘714 and Shanghai.
Claims 5-6:
Patent ‘714 detects a health condition associated with a microorganism using microbiome functional features then providing treatment for the condition in claim 1. Shanghai treats HPV with 5-aminolevulinic acid (5-ALA) (title). However, Patent ‘714 and Shanghai do not analyzed predetermined bacterial targets and HPV strains in a microbiome sample or teach 14 high risk and 5 low risk HPV strains.
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].
It would have been prima facie obvious to have detected HPV associated conditions using microbiome data as taught by Apte in Patent ‘714 because an HPV associated condition is a microorganism associated health condition identified in Patent ‘714 using microbiome features. There would have been a reasonable expectation of success because the microbiome features used to detect the condition in Patent ‘714 can be used to detect the HPV associated condition in Apte.
Response to Arguments under Double Patenting
Applicant's arguments filed 05/06/2025 have been fully considered but are not persuasive.
Applicant argues that there is no motivation to combine Shanghai with the US Patents (pg. 10, para. 3 – pg. 12, para. 1). Applicant’s arguments are not persuasive because:
Shanghai treats warts and precancerous lesions caused by HPV infection (pg. 1, sec. background, para. 2) (pg. 2, sec. summary of invention, para. 1). In Shanghai the HPV infection is associated with high-risk HPV strains related to cervical cancer or other regions of a subject’s body such as mouth (a region of the subject’s body) (pg. 1, sec. background, para. 2). Photodynamic therapy is applied to HPV associated lesions by topically applying 5-ALA and irradiating the region to produce reactive oxygen species (pg. 3, para. 5 and 7) (pg. 2, para. 7).
US patent US 11,001,900 B2 is directed to HPV associated conditions in a female reproductive system. US 11,572,555 B2 is directed to detecting HPV associated conditions. US 10,787,714 B2 is directed to detecting micro-organism associated conditions. Thus, one of ordinary skill would have been motivated to use HPV strain features associated with particular regions of a subject’s body in the models of the US Patents to identify regions of patients infected with HPV precancerous lesions to then treat the lesions as taught by Shanghai. The motivation for doing so is to treat HPV associated lesions, which is a microorganism associated condition. There would have been a reasonable expectation of success because specific HPV strains are associated with regions of a subject’s body and because ALA-PDT treats the HPV associated lesions as taught by Shanghai (pg. 1, sec. background, para. 1) (abstract).
Conclusion
No claims are allowed.
Claims 1 and 3-6 are patent eligible under 35 USC 101. Claim 1 recites a particular treatment by administering aminolevulinic acid (ALA) or an analog thereof to a region affected by an HPV infection related cancer condition then irradiating ALA or the analog to produce reactive oxygen species.
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/N.A.A./Examiner, Art Unit 1687
/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685
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