DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of Group I in the reply filed on 3/23/2026 is acknowledged.
Claims 1-20 are pending. Claims 12-20 are withdrawn as being drawn to a nonelected invention.
An action on the merits for claims 1-11 is set forth below.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-11 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims are drawn to method for screening, detecting and/or preventing any type of oral disease in any non-human mammalian animals based upon a microbial profile comprising any microbial species and any quantity of abundance.
The genus of the claims includes detection, screening or preventing any oral diseases in any non-human mammalian animal based upon the measurement of the quantity or abundance any or any combination of microbial species based upon correlations.
In analyzing whether the written description requirement is met for genus claims, it is first determined whether a representative number of species have been described by their complete structure.
The instant specification has not provided the critical structures required to functionally predict detection, screening or preventing any oral disease in any non-human mammalian animal. Oral disease encompasses a myriad of diseases including, but not limited to, gingivitis, dental caries, and gum disease. The specification in table 2 diseases microbes for periodontal disease, tooth resorption and halitosis (para 125). As provided by the table different microbial species presence functionally is associated with individual types of oral disease, however, the specification has not provided any one microbial species that functionally detects, screens or prevents any oral disease.
Further, the claims are drawn to the presence or abundance of one or more microbial species, however, such measurements and functionality is population and species dependent (see art below). The specification appears to provide particular diseases base on the measurement of particular microbial species in cats (though it is unclear if the specificaoin is drawn to domesticated cats or the genus of cats). These descriptions does not provide for the critical structures for the overall genus that is claimed.
The specification provides measurement of risk scores, however, the specification has not provided the critical guidance as to determining which risk scores would functionally provide data for screening, detecting and/or preventing oral disease based upon one more microbial species.
Further, the art does not provide guidance to sufficiently describe relevant identifying characteristics or functional attributes that would distinguish different members of the claimed genus. Rather, the art teaches that changes in the structure of nucleic acids between species can have an effect on expression. Enard et al. (Science 2002 Vol 296 p. 340) teaches that even between closely related species gene expression patterns differ (abstract). Enard et al. teaches that mRNA expression levels are different between humans, chimpanzees, orangutans and rhesus marcques (p. 340 1st column last sentence-2nd column 1st paragraph). Enard et al. teaches that there are a large number of quantitative differences in gene expression in closely related mammals (p. 342 2nd column last paragraph).
Further, the specification has not provided any guidance that the expression of levels of bacteria taxa is similar across tissue types. The art of Cobb et al (Crit Care Med 2002 Vol. 30 p. 2711) teaches the unpredictability in analysis of gene expression in spleen and liver sample from septic mice. Notably, the reference teaches that, when compared to a non-septic sample, the relevant expression profiles of the septic mouse spleen and the septic mouse liver contain different nucleic acids at different levels (Table 1; p.2714, middle col., lns.2-8). As such the art teaches that expression levels of the same nucleic acids in different samples differ.
In the instant case the specification does not provide the skilled artisan with an adequate written description of particular nucleic acids suitable for performing the claimed method as generically encompassed in the claims.
In analysis of the claims for compliance with the written description requirement of 35 U.S.C. 112, first paragraph, the written description guidelines note regarding genus/species situations that "Satisfactory disclosure of a ``representative number'' depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features of the elements possessed by the members of the genus in view of the species disclosed." (See: 'Written Description" Requirement, Federal Register, Vol. 66, No. 4, pages 1099-1111, Friday January 5, 2001.) In the instant case, the specification fails to teach the necessary common attributes or features of the transcripts consistently detected across array platforms in view of the species disclosed. As such, one of skill in the art would not recognize that applicant was in possession of the genus of transcripts, encompassed by the broadly claimed invention.
Claim Rejections - 35 USC § 112
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 1-11 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.
Claims 1-11 are indefinite over “quantity or abundance” in the obtaining step of claim 1. In particular it is not clear the difference between the two terms and as such it is not clear when infringement would occur s it is not clear the scope of the two terms. Further for the comparing step it is not clear if the claim intends to compare the profile or two compare the quantity of abundance.
Further, these claims are unclear over the “generating a risk core”. The claim appears to require the generation based upon the comparison hover it is not clear how a match would be correlative to a risk score. It is not clear therefore how to perform the methodology as these risk scorers are based upon comprising profiles but does not require any data analysis of these scores.
The claims are drawn to a preamble of screening, detecting and or preventing, however, the last active step of claim 1 is categorizing. It is not clear the nexus between this categorizing and screening, detecting or providing.
Claim 3and 6 are drawn to steps of obtaining oral microbial provide based upon obtaining nucleic acid sequence data, analyzing, and generating the profile (claim 3). However, it is not clear how this obtaining profile is used to determine quantity or abundance.
Claim 4-5 is unclear as the step of “isolating the microbial nucleic acid” is optional. It is not clear how one sequencings microbial nucleic acid from an oral sample without isolating.
Claim 6 is unclear over the phrase “do not suffer” and “suffer”. These terms are unclear as it is not clear the metes and bounds. In particular it is not clear if “suffer” is intending to evoke having and oral disease, having a particular level of oral disease, or have particular clinical embodiments of the disease to make the subject “suffer”. As such it is not clear how the term is intending to modify and limit the abundance patterns. Further the steps is towards “compositional abundance patterns” wherein the claims are drawn to “abundance” as such it is not clear if the claim is intending a different measurement than the breadth of the term “abundance” in claim 1.
Claim 8 is drawn to “presence of one or more predictive microbial species”. The claims do not encompass what the microbial species is predictive of. As such it is not clear which microbial species would be considered “predictive” as the term is considered a relative term.
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 1-11 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial expectation of a natural phenomenon and an abstract idea without significantly more. The claim recite(s) screening, detecting and preventing oral disease based upon the presence or absence of microbial species (natural phenomenon) and generating risk scores and categorizing (abstract ideas).
This judicial exception is not integrated into a practical application because the steps of obtaining, an oral profile are considered routine and conventional steps. The steps of comparing, generating and categorizing are abstract steps. Further, the steps do not add a meaningful limitations to the methods as they are insignificant extra solution activity. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception the steps have been reviewed and are considered routine and conventional.
These judicial exceptions are not integrated into a practical application because the claims only recite the natural correlation and abstract ideas, wherein the step of obtaining does not integrate the judicial expectation. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the steps are considered general and routine knowledge in the prior art as exemplified by the specification (as discussed below).
According to the 2019 Patent Eligibility Guidance an initial two step analysis is required for determining statutory eligibility.
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter? In the instant case the Step 1 requirement is satisfied as the claims are directed towards a process.
Step 2A Prong one. Does the claim recite a law of nature, a natural phenomenon or an abstract idea? Yes, a natural phenomenon and an abstract idea.
. The steps of comparing, generating and categorizing are abstract steps These steps are considered an abstract idea or mental step. (UNIVERSITY OF UTAH RESEARCH v. AMBRY GENETICS CORPORATION).
Step 2A prong two. Does the claim recite additional elements that integrate the judicial exception into a practical application? The answer is no as the steps require only routine and convention steps and does not integrate the judicial exception to a practical application.
Step 2B. Does the claim recite additional elements that are significantly more than the judicial exceptions? No as the claims do not require any elements that integrate the judicial exception.
The steps that are not considered judicial expectations is obtaining an oral profile. As noted, Cutcliffe et al. (WO2019/046646 March 7, 2019) teaches a method of obtaining an oral microbial profile from a subject (para 183-186). Cutcliffe et al. teaches that the subject can include laboratory animals, livestock and household pets (para 131). Cutcliffe et al. teaches comparison to the information in a database with weighted correlations (para 108-11). Cutcliffe et al. teaches correlations with oral disease (para 289). Cutcliffe et al teaches generating of a risk score to determine matches and categorizing based upon risk scores that meet a threshold for a disease (para 211-217).
. Claim 2and 11 are drawn to administering a therapeutic treatment, however, this does not integrate the judicial exception as this treatment is drawn to general treatments and is not specific. CLiams 3-4, 6-8, 10 are drawn to abstract steps of modifying sequencing data. Claim5 is considered a general method of isolating that is known in the prior art. Claim 9 limits the diseases to a known naturally occurring disease.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1-4, 7-11 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Cutcliffe et al. (WO2019/046646 March 7, 2019),
With regard to claim 1, Cutcliffe et al. teaches a method of obtaining an oral microbial profile from a subject (para 183-186). Cutcliffe et al. teaches that the subject can include laboratory animals, livestock and household pets (para 131). Cutcliffe et al. teaches comparison to the information in a database with weighted correlations (para 108-11). Cutcliffe et al. teaches correlations with oral disease (para 289). Cutcliffe et al teaches generating of a risk score to determine matches and categorizing based upon risk scores that meet a threshold for a disease (para 211-217).
With regard to claim 2, Cutcliffe et al teaches a method of administering treatment protocols (para 439-449).
With regard to claim 3, Cutcliffe et al. teaches a method of obtaining an oral microbial profile from a subject (para 183-186). Cutcliffe et al. teaches that the subject can include laboratory animals, livestock and household pets (para 131). Cutcliffe et al. teaches comparison to the information in a database with weighted correlations (para 108-11). Cutcliffe et al. teaches correlations with oral disease (para 289). Cutcliffe et al teaches generating of a risk score to determine matches and categorizing based upon risk scores that meet a threshold for a disease (para 211-217). Cutcliffe et al. teaches analyzing sequence data to generate profiles (para 203-205).
With regard to claim 4, Cutcliffe et al. teaches that the sequence data is sequencing microbial nucleic acid from an oral sample (para 126-28).
With regard to claim 7, Cutcliffe et al. teaches calculating abundance, identifying species and comparison to a microbiome (para 163-213).
With regard to claim 8, Cutcliffe et al. teaches generating a risk score that have similarities between abundance indicates the presence of a microbial biome and disease (paras 215-217). As it is not clear the metes and bounds of “compositional” it would be encompassed by any recitation of abundance.
With regard to claim 9, Cutcliffe et al. teaches that the disease can include halitosis (para 236).
With regard to claim 10, Cutcliffe et al teaches generating a report that includes risk scores, disease and administration (e.g. timing practices) (para 176-180 and 237-240).
With regard to claim 11, Cutcliffe et al. teaches a method wherein the treatment is intended to alter the oral microbial profile (para 22-25).
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.
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.
Claim(s) 5 is/are rejected under 35 U.S.C. 103 as being unpatentable over Cutcliffe et al. (WO2019/046646 March 7, 2019) in view of Blainey et al. (WO 2017/136751 August 10 2017)
Cutcliffe et al. teaches a method of obtaining an oral microbial profile from a subject (para 183-186). Cutcliffe et al. teaches that the subject can include laboratory animals, livestock and household pets (para 131). Cutcliffe et al. teaches comparison to the information in a database with weighted correlations (para 108-11). Cutcliffe et al. teaches correlations with oral disease (para 289). Cutcliffe et al teaches generating of a risk score to determine matches and categorizing based upon risk scores that meet a threshold for a disease (para 211-217).
However, Cutcliffe et al. does not teach performing heat treatment, performing magnetic SPRI beads for isolating the microbial nucleic acid.
With regard to claim 5, Blainey et al. teaches isolation from a heterogeneous population including bacterial samples (para 106). Blainey et al. teaches isolation by performing heat treatment, performing magnetic SPRI beads for isolating the microbial nucleic acid (para 137).
Therefore it would be prima facie obvious to one of ordinary skill in the art at the time of the effective filing date to modify the method of Cutcliffe et al. to use the isolation process of Blainey et al. in order to isolate the nucleic acid for sequencing. The ordinary artisan would be motivated to modify the method as Blainey et al. teaches isolation of nucleic acid from heterogeneous samples such as the ones used by Cutcliffe et al.
Claim(s) 5-6 is/are rejected under 35 U.S.C. 103 as being unpatentable over Cutcliffe et al. (WO2019/046646 March 7, 2019) in view of Miller et al. (US Patent Application Publication 2020/0131485 April 30, 2020)
Cutcliffe et al. teaches a method of obtaining an oral microbial profile from a subject (para 183-186). Cutcliffe et al. teaches that the subject can include laboratory animals, livestock and household pets (para 131). Cutcliffe et al. teaches comparison to the information in a database with weighted correlations (para 108-11). Cutcliffe et al. teaches correlations with oral disease (para 289). Cutcliffe et al teaches generating of a risk score to determine matches and categorizing based upon risk scores that meet a threshold for a disease (para 211-217). Cutcliffe et al. teaches analyzing sequence data to generate profiles (para 203-205).
However, Cutcliffe et al. does not teach the steps of sequencing data comprising demultiplexing, trimming and mapping.
With regard to claim 5, Miller et al. teaches isolation by performing heat treatment, performing magnetic SPRI beads for isolating the microbial nucleic acid (para 179).
With regard to claim 6, Miller et al. teaches microbial nucleic acid sequence data analysis that comprises sequencing reads that are demultiplexed, trimmed and mapping (para 179).
Therefore it would it would be prima facie obvious to one of ordinary skill at the time of the effective filing date to modify the method of Cutcliffe et al. to use on of the finite number of sequencing protocols for read analysis including the method of Miller et al. The ordinary artisan would be motivated to use the sequence read analysis of Miller et al. as Miller et al. teaches read analysis for microbial genomes with an exception of analysis of data information from the sequences.
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.
Claims 1-11 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1, 3-10 of copending Application No. 18578291 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the copending application steps used in the method of obtaining an oral microbial profile and generating a risk score would be encompassed by the instant claims recitation of non-human mammalian subjects. Although the copending case is towards “dermatologic diseases” , these would encompass particular oral diseases including oral lichen, lupus, candidiasis, for example.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KATHERINE D SALMON whose telephone number is (571)272-3316. The examiner can normally be reached 9-530.
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/KATHERINE D SALMON/ Primary Examiner, Art Unit 1682
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