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 .
Claim Status
Claims 1, 3-8, 10, 12-15, 18, 32-33, and 57-61 are pending.
Claims 1, 3-8, 10, 12-15, and 18 are withdrawn.
Claims 32-33 and 57-61 are under examination.
Claims 32-33 and 57-61 are rejected.
Claims 32 and 59 are objected to.
Claim 32 is independent.
Claims 57-61 are new.
Office Action Outline
Rejections applied
Abbreviations
112/b Indefiniteness
PHOSITA
"a Person Having Ordinary Skill In The Art before the effective filing date of the claimed invention"
112/b "Means for"
BRI
Broadest Reasonable Interpretation
112/a Enablement,
Written description
CRM
"Computer-Readable Media" and equivalent language
112 Other
IDS
Information Disclosure Statement
x
102, 103
JE
Judicial Exception
x
101 JE(s)
112/a
35 USC 112(a) and similarly for 112/b, etc.
101 Other
N:N
page:line
x
Double Patenting
MM/DD/YYYY
date format
Priority
As detailed in the 12/12/2023 filing receipt, this application is a 371 of PCT/US2022/013449, filed 01/24/2022, which claims benefit to Provisional Application No. 63/140,574, filed 01/22/2021.
Overview of Withdrawal/Revision of Objections/Rejections
In view of the amendment and remarks received 07/15/2026:
• The objection to the drawings is withdrawn.
• The objection to the specification is withdrawn.
• The objection to claim 32 is withdrawn. New claim objections are applied.
• The 101 rejection is maintained with revision.
• The 103 rejection is maintained with revision.
• The non-statutory double patenting rejection is maintained with revision.
Claim Objections
Claims 32 and 59 are objected to because of the following informalities:
Claim 32 step (d) recites "the anti-microbial or -cytokine signature" which should be amended to "the antimicrobial or anticytokine signature" to be consistent with the language recited in step (c).
Claim 59 recites "the differentially expressed genes," which should be amended to "the DEGs" to reflect the abbreviation recited in claim 32 step (b).
Claim 59 recites "using Wald test" which should be amended to "using a Wald test."
Appropriate correction is required.
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.
Response to Applicant Arguments - 35 USC § 101
Applicant's 7/15/2026 arguments have been fully considered, but they are not yet persuasive.
Referring to 101 analysis as drawn from case law and organized in MPEP 2106, it is not clear which step of the analysis Applicant's remarks address. Prosecution, examination and generally communication regarding 101 can be facilitated by focusing on particular, identified steps of the analysis. This is because each step has its own particular rules derived from case law. Also, "significantly more," like "patent eligibility" and even "allowability," is a conclusion best argued by analyzing the interpretations and rules captured in the MPEP, e.g. the particular analysis steps and their particularly associated rules, and leading to the conclusion of "significantly more." For example, regarding "significantly more," the MPEP provides particular "considerations" in Step 2A, 2nd prong (five considerations listed in the rejection below with citation to the MPEP) and other rules regarding what is conventional in Step 2B.
Possibly the remarks below regarding "significantly more" refer to Step 2A, 1st consideration regarding an improvement over the previous state of the technology field, at least because the remarks include "[enabling]... new... targets" as a possible, "more efficient" improvement. The MPEP presents the 2nd prong considerations as causing claims to be interpreted as directed to a practical application and to significantly more than any judicial exception..
Applicant asserts:
• "Applicant submits that the claimed methods result in something significantly more." (Remarks, p.11, ¶ 2.)
• "The order of the steps and how the steps are integrated...provides a unique compound priority list. ... the entire workflow is far greater than the sum of its individual components" (Remarks, p.11, ¶ 3.)
• "The focus on host targets enables a new series of previously unrecognized targets with the potential for inhibition of SARS-CoV-2 infections. This approach can be more efficient than traditional screening approaches." (Remarks, p.12, ¶ 4.)
• "Applicant submits that the claimed methods result in something significantly more." (Remarks, p.11, ¶ 2.)
The arguments are not yet persuasive because when analyzing the claims at Step 2A, 2nd prong regarding an explanation of improvement over the previous state of the technology field.
It is not yet sufficiently clear what is an improvement in the context of these claims, noting that any improvement should be to the technology field and should lead to a practical application. Thus, a "unique compound priority list" may differ from the previous state of the field but is not itself clearly an improvement. It may be a means by which the claims deliver an improvement. The above-asserted "new series of previously unrecognized targets" may be the basis for an improvement, but further explanation would be helpful as to the relevance of the practical application. Also, any asserted increase in efficiency may be further explained as to efficiency in what sense, with respect to what process parameters, and as to how PHOSITA would gauge and recognize such an increase in efficiency.
Not to exclude arguments relying on other steps of 101 analysis, but if Step 2A, 2nd prong, 1st consideration explanation if improvement over the previous state of the technology field is to be the basis for a 101 argument, then the following Examiner suggestions may help.
Step 2A, 2nd prong, 1st consideration: explanation of improvement over the previous state of the technology field (MPEP 2106.04(d) and (d)(1)) -- An explanation of a technical improvement may help to overcome a 101 rejection, as discussed at Step 2A/2nd Prong, 1st consideration of the 101 analysis in MPEP 2106.04(d) and (d)(1). Such an improvement requires detailed explanation applicable to all embodiments reasonably within the claim scope. In particular, such an explanation of improvement over the previous state of the technology field may include:
identification of the technology field,
the particular improvement, as particular as possible identification of any asserted improvement(s),
explanation of a clear difference from the technology field (since there can be no improvement without a difference),
explanation that reasonably all embodiments within the claim scope will result in the asserted improvement, and
finally, extension of the explanation as far as possible to include the result of an identified practical application in order to persuasively demonstrate integration of the identified judicial exception(s) (JEs), i.e. nexus between improvement associated with a JE and a practical application.
As further examples, argument may clearly and adequately explain cause and effect leading to improvement or, for example when such cause and effect explanation is not possible, then may include evidence (e.g. experimental data) comparing a claimed result to conventional results.
Also, arguments and evidence may be extrinsic to the original disclosure, including references available after the priority date, as long as it is clear that an argument applies to all embodiments of a properly supported claim.
Applicant is encouraged to request an interview to discuss 101 and any other issues.
Claims 32-33 and 57-61 are rejected under 35 U.S.C. 101 because the claimed invention is directed to one or more judicial exceptions without significantly more.
MPEP 2106 details the following framework to analyze Subject Matter Eligibility:
• Step 1: Are the claims directed to a category of statutory subject matter (a process, machine, manufacture, or composition of matter)? (see MPEP § 2106.03)
• Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. an abstract idea, a law of nature, or a natural phenomenon? (see MPEP § 2106.04(a), 2106.04(a)(2), and 2106.04(b))
• Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application? (see MPEP § 2106.04(d))
• Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept? (see MPEP § 2106.05)
Step 1:
Claims 32-33 and 57-61 are directed to a 101 process, here a method, and therefore to a category of statutory subject matter. (See MPEP § 2106.03). (Step 1: Yes.)
Step 2A, Prong One:
The claims recite abstract ideas as follows:
Independent claim 32 recites mental processes and mathematical concepts of:
• (b) identifying differentially expressed genes (DEGs)
• (c) characterizing host-targeted antimicrobial or anticytokine signature
• (d) identifying compounds that stimulate the anti-microbial or -cytokine signature
• (e) identifying compounds identified in (d) whose targets are known or predictable
• (f) constructing an infection host response protein-protein interaction (PPI) network and modules
• (g) prioritizing compounds identified in (e) based on network proximity analysis using the PPI network and modules of (f)
• (h) clustering of prioritized compounds associated with selected disease modules,
• (i) selecting representative compounds from each cluster for in vitro assays
• (j) analyzing the results to identify the compound for treating or preventing the infection with an infectious microbe.
The dependent claims recite mental processes and mathematical concepts of:
• using a Wald test to identify differentially expressed genes (claim 59)
• using manual curation to characterize signatures (claim 60)
• considering additional criteria to identify the compound (claim 61)
Additionally, dependent claim 57 and 58 further limit the selected disease modules of claim 32, and dependent claim 33 further limits the infectious microbe to a coronavirus.
Step 2A Prong One Summary: Claim 32 and 33 recite judicial exceptions of abstract ideas (characterized as mental processes and mathematical concepts). Considering the broadest reasonable interpretation (BRI) of the claims, the mental processes recited in independent claim 32 (e.g., identifying DEGs, characterizing signatures, identifying compounds, evaluating targets, constructing a PPI, etc.) are directed to processes that may be performed in the human mind, or with pen and paper, because there are no limitations recited which would prevent the analysis and generating of results mentally. Additionally, at least the limitations for prioritizing compounds and clustering the prioritized compounds inherently recite mathematical concepts such as those disclosed in Specification [122:17-123:19]. Such analysis performed mentally, or with paper and pencil, may take considerable time and effort, and although a general-purpose computer can perform these calculations at a rate and accuracy that can far exceed the mental performance of a skilled artisan, the nature of the activity is essentially the same, and therefore constitutes an abstract idea.
Therefore, the claims recite elements that constitute a judicial exception in the form of an abstract idea. (Step 2A, Prong One: Yes.)
Step 2A, Prong Two:
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs). Here at Step 2A, Prong Two, any remaining steps and/or elements not identified as JEs are therefore in addition to the identified JE(s), and are considered additional elements. Because the claims have been interpreted as being directed to judicial exceptions (abstract ideas in this instance) then Step 2A, Prong Two provides that the claims be examined further to determine whether the judicial exception is integrated into a practical application [see MPEP § 2106.04(d)]. A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception.
20. MPEP § 2106.04(d)(I) lists the following five example considerations for evaluating whether a judicial exception is integrated into a practical application:
(1) An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a).
(2) Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2).
(3) Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b).
(4) Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c).
(5) Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
The claims recite additional elements as follows:
Additional elements of data gathering: Claim 32 recites the additional element of obtaining data. Data gathering steps are additional elements which perform functions of inputting, collecting, and outputting the data needed to carry out the abstract idea. These steps are considered insignificant extra-solution activity, and are not sufficient to integrate an abstract idea into a practical application as they do not impose any meaningful limitation on the abstract idea or how it is performed, nor do they provide an improvement to technology [see MPEP § 2106.04(d)(I)].
Step 2A Prong Two summary: The claims have been further analyzed with respect to Step 2A, Prong Two, and no additional elements have been found, alone or in combination, that would integrate the judicial exception into a practical application. At this point in examination, it is not yet the case that any of the Step 2A Prong Two considerations enumerated above clearly demonstrates integration of the identified JE(s) into a practical application. Referring to the considerations above, none of: (1) an improvement, (2) a treatment, (3) a particular machine, or (4) a transformation is clear in the record. For example, regarding the first consideration for improvement at MPEP 2106.04(d)(1), the record, including the Specification, does not yet clearly disclose an explanation of improvement over the previous state of the technology field, and the claims do not yet clearly result in such an improvement. (Step 2A, Prong Two: No).
Step 2B:
Because the additional claim elements do not integrate the judicial exceptions (i.e., the abstract ideas) into a practical application, the claims are further examined under Step 2B, which evaluates whether the additional elements, individually and in combination, amount to significantly more than the judicial exception itself by providing an inventive concept. An inventive concept is furnished by an element or combination of elements that is recited in the claim in addition to the judicial exception, and is sufficient to ensure that the claim, as a whole, amounts to significantly more than the judicial exception itself (see MPEP § 2106.05).
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that are well-understood, routine, and conventional. Those additional elements are as follows:
Additional elements of data gathering: The additional element of obtaining data in claim 32 does not cause the claims to rise to the level of significantly more than the judicial exception. The courts have recognized receiving or transmitting data over a network; storing and retrieving information in memory; using polymerase chain reaction to amplify and detect DNA; detecting DNA or enzymes in a sample; analyzing DNA to provide sequence information or detect allelic variants; and amplifying and sequencing nucleic acid sequences, [see MPEP§2106.05(d)(II)], as well-understood, routine, conventional activity when they are claimed in a merely generic manner (e.g., at a high level of generality) or as extra-solution activity.
Therefore the additional elements of data gathering are shown to be routine, well-understood, and conventional in the art, and do not provide an inventive concept needed to amount to significantly more than the judicial exception.
All limitations of claims 32-33 have been analyzed with respect to Step 2B, and none provides a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception, and thus do not transform the judicial exception into a patent eligible application of the exceptions. Step2B: NO.
Therefore, claims 32 and 33, when the limitations are considered individually and as a whole, are rejected under 35 U.S.C. § 101 as being directed to non patent-eligible subject matter.
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.
Response to Applicant Arguments - 35 USC § 103
Applicant's 7/15/2026 arguments have been fully considered, but they are not yet persuasive.
Applicant asserts:
• "Applicant amends claim 32 herein to recite a method of identifying a compound for treating or preventing an infection with an infectious microbe in a subject in need thereof, the method comprising, in the following order"... (Remarks, p.14, ¶ 5).
• "...Of note is the work of Zhou et al., where repurposable drugs against SARSCo
V-2 were identified by evaluating the proximity of targets of known
drugs to human proteins engaged in the human-CoV-host cell interactome
(Zhou Yet al. Cell Discov. 2020, 6, 14). This type of network proximity
analysis ... is also used here, but in a different context, mainly for
prioritizing the candidate compounds/drugs that have been already
identified from the DEG patterns of SARS-CoV-2 infected cells and
corresponding Cmap signatures. In contrast, Zhou et al. used gene set
enrichment data (from MERS-CoV and SARS-CoV-infected cells) and
Cmap gene-drug signatures for validating their predicted drugs (Zhou Y et
al. Cell Discov. 2020, 6, 14). Another important component unique to this
analysis is the use of the interface QuartataWeb that allows for identifying
drug-target associations, and for evaluating and classifying the pathways
implicated in the disease modules deduced from the SARS-CoV-2-specific
virus-host interactome ... and assessing the mechanisms of action.
Quartata Web was further used to cluster the selected compounds based on
their mechanisms of action... Thus, this study differs from that of Zhou et al. ...in the overall design of the computational protocol, the types of data used as
input, as well as the output analyses for compound selection, prioritization, and validation, while both studies utilize state-of-the-art methods (network proximity analysis) and resources (e.g., Cmap library) at different steps of the workflow." (Remarks, p.15, ¶ 3).
The arguments are not persuasive because there are embodiments of the instant claims upon which Zhou reads as applied in the 103 rejection below. Additionally, the claims do not recite either the above-asserted Cmap or Quartata Web, and as such these arguments are not yet persuasive. Therefore the 103 rejections are maintained below.
103-1 (of 2):
Claims 32-33, 57-58, and 60-61 are rejected under 35 U.S.C. 103 as being unpatentable over Zhou (Cell discovery, vol. 6(1):14, pp. 1-18 (2020); cited in the 09/26/2023 IDS).
Regarding obtaining transcriptomic data from cell infected with an infectious microbe, and identifying differentially expressed genes (DEGs) of claim 32 steps a) and b), and wherein the microbe is coronavirus of claim 33, Zhou shows collecting three differential gene expression data sets of hosts infected by human coronaviruses (HCoVs), two transcriptome data sets were SARSCoV-infected samples from patient’s peripheral blood (GSE1739) and one from Calu-3 cells (GSE33267) (p.15, col.2, ¶2).
Regarding characterizing host-targeted antimicrobial or anticytokine signatures, identifying compounds that stimulate those signatures, and evaluating targets of the identified compounds of claim 32 steps c), d), and e), Zhou shows the three datasets were used as HCoV–host signatures to evaluate the treatment effects of drugs.
Regarding constructing an infection host response protein-protein interaction (PPI) network and modules, prioritizing compounds based on network proximity analysis, and clustering of prioritized compounds associated with selected disease modules of claim 32 steps f), g), and h) Zhou shows the interplay between the virus–host interactome and drug targets in the human PPI network (p.3, fig.1); drug-target network analysis of the HCoV–host interactome (p.6, fig.3); and a discovered drug-HCoV network, including network proximity (Z-score) between drug targets and the HCoV-associated proteins in the human interactome network (p.7, fig.4). Additionally, it would have been obvious to use clustering on prioritized compounds.
Regarding selecting representative compounds from each cluster for in vitro assays, and analyzing the results of the previous steps to identify the compound for treating or preventing the infection of claim 32 step i) and j), Zhou shows based on comprehensive evaluation, the prioritization of 16 candidate repurposable drugs (see Fig. 5, p.8-9) and three potential drug combinations (see Fig. 6, p.12) for targeting 2019-nCoV/SARS-CoV-2 (p.13, col.1, ¶2).
Regarding the disease modules comprise: viral entry; viral replication and translation; host cell regulation and signaling; immune response of claims 57 and 58, Zhou shows viral process, transport of virus, positive regulation of viral life cycle (interpreted to corresponding to viral entry, replication, translation) (p.6, fig. 3c); and NF-kappa B signaling pathway, apoptosis/phagosome (corresponding to host regulation/signaling and immune response) (p.6, fig. 3b).
Regarding using manual curation of gene ontology (GO) enrichment results corresponding to the DEGs of claim 60, Zhou shows network predicted repurposable drugs with literature derived (interpreted as manually curated) anti-viral evidence (p.10, Table 10).
Regarding the additional criteria such as drug development status, side effects, mechanism of action (MOA), and antiviral activities of claim 61, Zhou shows mechanism-of-action networks for four selected drugs (p.8, Fig 5b-e; see text top of p.9).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use the drug repurposing method of Zhou with clustering for the prioritized compounds, as clustering is a widely known statistical technique for grouping data. One of ordinary skill would have had a reasonable expectation of success, as Zhou shows a network-based methodology for systematic identification of putative repurposable drugs and drug combinations for potential treatment of 2019-nCoV/SARS-CoV-2, and based on comprehensive evaluation of Zhou, 16 candidate repurposable drugs were prioritized.
103-2 (of 2):
Claim 59 is rejected under 35 U.S.C. 103 as being unpatentable over Zhou as applied to claims 32-33, 57-58, and 60-61 above, and further in view of Wu (Proceedings of the National Academy of Sciences, vol. 117(45), pp.28336-28343; cited on the attached form PTO-892).
Zhou does not show a Wald test of claim 59.
Regarding using the Wald test with false discovery rate of claim 59, Wu shows use of the Wald test with an adjusted P value of 0.05 in transcriptional profiling in enriching of pathways in Covid-19 cases (Wu, p. 28338-28340, Figs.2-4).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the drug repurposing method of Zhou with the Wald test of Wu. One of ordinary skill would have had a reasonable expectation of success in modifying Zhou with Wu, as the Wald test of Wu can provide useful statistical analysis of transcriptional data, and such the modification would have been obvious.
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.
Response to Applicant Arguments - Double Patenting
Applicant's arguments filed 07/15/2026 have been fully considered but they are not persuasive.
Applicant lists (p.16-17) the elements of pending claim 32 (from the instant application) followed by the elements of copending claim 1 (from reference application 18/686,925) and then asserts "Applicant submits that the instant claims are distinct from those of U.S. Application 18/686,925 and therefore requests withdrawal of the double patenting rejection."
The argument is not persuasive as there are no specific supporting details or reasoning for withdrawal, just a listing of claim elements. Additionally, the double patenting rejection has been revised to better clarify the mapping of the double patenting rejection. As such, the non-statutory double patenting rejection is maintained.
NSDP rejection:
Instant claims 32 and 33 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 7 of reference Application No. 18/686,925 (the '925 application) in view of Gordon (Nature, vol.583(7816), pp.459-468 (2020); cited in the 09/26/2023 IDS). Although the claims at issue are not identical, they are not patentably distinct from each other because:
Obtaining transcriptomic data of instant claim 32 step (a) reads on analyzing RNA-seq data of reference app. '925, claim 1.
Identifying differentially expressed genes (DEGs) of instant claim 32 step (b) reads on identifying differentially expressed genes of reference app. '925, claim 1.
Characterizing a host-targeted antimicrobial or cytokine signature of instant claim 32 step (c) reads on deriving gene expression signatures associated with disease states of the disease using the DEGs and the differentially enriched biological pathways of reference app. '925, claim 1. The host-targeted antimicrobial or cytokine aspect of this element is not specifically shown by the reference app '925, but is shown by Gordon, at least at p.466, col.1, ¶ 3, "Identification of drugs that target host factors").
Identifying compounds that that stimulate the anti-microbial or -cytokine signature of instant claim 32 step (d) reads on identifying, using the computing device, a plurality of drugs predicted to reverse a particular gene expression signature associated with a particular disease state of the disease of reference app. '925, claim 1.
Identifying compounds identified whose targets are known or predictable of instant claim 32 step (e) is not specifically shown by the reference app '925, but reads on "Identification of drugs that target host factors" (Gordon, at least at p.466, col.1, ¶ 3).
Constructing an infection host response protein-protein interaction (PPI) network and modules of instant claim 32 step (f) is not specifically shown by the reference app '925, reads on SARS-CoV-2 protein–protein interaction network. 332 high-confidence interactions between 26 SARS-CoV-2 proteins (red diamonds) and human proteins (Gordon, p.462, Fig. 3).
Prioritizing compounds based on network proximity analysis using the PPI network and modules constructed of instant claim 32 step (g) reads on prioritizing drugs of reference app. '925, claim 1. The PPI network is not specifically shown by the reference app '925, but is shown by Gordon, which shows a PPI network at p.462, Fig. 3, and throughout document.
Clustering of prioritized compounds of instant claim 32 step (h) reads on using a clustering algorithm of reference app. '925, claim 7.
Selecting representative compounds and analyzing results to identify a compound for treating/testing of instant claim 32 step (i) and (j) reads on identifying a plurality of drugs predicted to reverse a particular gene expression signature associated with a particular disease state of the disease; testing...a drug or combination of drugs selected from the drugs predicted to normalize the particular gene expression signature and/or physiological characteristic associated with the particular disease state of the disease of reference app. '925, claim 1.
The infectious microbe is a coronavirus of instant claim 33 is not specifically shown by the reference app '925, but is shown by Gordon, which shows analysis of SARS-COV2-host protein interactions (p.460, and entire document), showing both PPI and a coronavirus.
It would have been obvious to one of ordinary skill in the art to modify the method of reference claims 1 and 7 of the '925 application to include the PPI and coronavirus of Gordon, as the method of Gordon identified PPIs between SARS-CoV-2 protein and human protein, which further led to identification of compounds targeting the interactions. One would have had a reasonable expectation of success in combining, as both Gordon and the '925 application are drawn to related teachings of drug repurposing, and as such, the combination would have been obvious. Accordingly, instant claims 32 and 33 are not patentably distinct from reference claims 1 and 7 of the ‘925 application.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are allowed.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Meredith A Vassell whose telephone number is (571)272-1771. The examiner can normally be reached 8:30 - 4:30.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, KARLHEINZ SKOWRONEK can be reached at (571)272-9047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/M.A.V./Examiner, Art Unit 1687
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686
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