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 invention I in the reply filed on 10/24/25 is acknowledged.
Claims 2, 4 and 6 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 10/24/25.
Claims 1, 3 and 5 are examined on the merits.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 1/17/23, 12/11/24 and 10/24/25 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
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, 3 and 5 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, 3 and 5 recite "a genome of interest". The scope of this recitation is critical for performing the claimed method because it determines the mapped reads and un-mapped reads. Since the claim does not specify the genome of interest the scope of aligning is unclear because depending on the genome of interest the number of un-mapped reads would change. Moreover, while the claims do recite that bacterial RNA are a focus of assaying, the genome of interest is not specified as being that of bacteria.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1 and 5 are rejected under 35 U.S.C. 102a1 as being anticipated by Mergemeier (US PGPub 20170204452), as evidenced by Chikuie et al. (Kansenshogaku Zasshi, 2008, Vol. 82, No. 5, pages 455-460, abstract provided herein).
The claimed invention is drawn to a method of treatment of sepsis, comprising the steps of: (a) identifying the sepsis patient to be treated using a diagnostic step, the diagnostic step comprising:
(1) obtaining a body sample from the patient;
(2) assaying the sample for bacterial RNA reads that identify bacteria causing sepsis; and
(3) identifying the bacteria causing sepsis by aligning the RNA reads to a genome of interest; and
(b) treating the identified sepsis patient with a treatment for sepsis.
The claimed method is also drawn to a method of treatment of acute respiratory distress syndrome (ARDS), comprising the steps of: (a) identifying the ARDS patient to be treated using a diagnostic step, the diagnostic step comprising:
(1) obtaining a body sample from the patient;
(2) assaying the sample for bacterial RNA reads that identify the patient as having ARDS; and
(3) identifying the patient as having ARDS by aligning the RNA reads to a genome of interest; and
(b) treating the identified ARDS patient with a treatment for ARDS.
The claimed methods are directed to treating sepsis or ARDS by assaying a body sample for bacterial RNA reads, which indicate the patient has sepsis or ARDS. The patient is identified as having sepsis or ARDS by aligning the RNA reads to a genome of interest, followed by treating the identified sepsis or ARDS patient with a sepsis or ARDS treatment.
Since the diagnosis of these patients only involves assaying for bacterial RNA reads and aligning the RNA with a genome of interest, if the prior art teaches assaying a body sample for bacterial RNA of a patient suspected having sepsis or ARDS, aligning the bacterial RNA with a genome of interest and treating the subject for sepsis or ARDS.
The Prior Art
Mergemeier teach the screening of samples from humans suspected of having a human pathogen or genetic material thereof and comparing any detect genetic material with a known sequence. [see abstract and paragraphs ] Mergemeier also teach that samples obtained from a subject exhibiting one or more symptoms of sepsis, or septic shock are screened for genetic detection of bacteria and subsequence identification of the bacteria. [see paragraphs 30, 38 and 41] One example of detection is using RT-PCR to detect and amplify the 16S rRNA of a bacterial pathogen and binding the sequence with a reference sequence from E. coli 16S. [see paragraphs 33 and 36] Therefore, Mergemeier teach aligning RNA reads of bacteria with a genome of interest. Following detection and diagnosis of the causative pathogen of sepsis, Mergemeier teach prescribing an appropriate medicament during treatment, such as antibiotics. [see paragraphs 41, 42 and 65] The administration of these treatments would also be treating any sepsis induced ARDS, as evidenced by Chikuie et al., since they teach that treating a patient with antibiotics for E. coli induced septic shock, which led to ARDS. [see abstract of Chikuie et al.]
Therefore, these teachings of Mergemeier, as evidenced by Chikuie et al., anticipate the instant invention.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim 3 is rejected under 35 U.S.C. 103 as being obvious over Mergemeier (supra) as evidenced by Chikuie et al., and Monaghan et al. (WO 2021/163692).
The applied reference has common inventors and assignee with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2).
This rejection under 35 U.S.C. 103 might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C.102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B); or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement. See generally MPEP § 717.02.
The claimed invention is also drawn to a method of treatment of sepsis, comprising the steps of: (a) identifying the sepsis patient to be treated using a diagnostic step, the diagnostic step comprising:
(1) obtaining a body sample from the patient;
(2) assaying the sample for RNA reads that identify bacteria causing sepsis using Principal Component Analysis of RNA splicing entropy to identify sepsis; the patient as having ARDS; and
(3) identifying the patient as having sepsis by aligning the RNA reads to a genome of interest; and
(b) treating the identified sepsis patient with a treatment for sepsis.
The Prior Art
The teachings of Mergemeier, as evidenced by Chikuie et al., are summarized above, however, they do not teach the use of Principal Component Analysis of RNA splicing entropy to identify sepsis.
Monaghan et al. teach the use of Principal Component Analysis of RNA splicing entropy to identify sepsis. [see paragraph 12 and example 4] They obtain a body sample from a subject suspected of having sepsis and screen for bacterial RNA reads and compare those reads with a genome of interest, followed by identifying the bacteria that caused sepsis. This assay can also use PCA to identify sepsis in the subject. [see claims 1 and 4]
It would have been obvious to one of ordinary skill in the art to modify the methods taught by Mergemeier in order to employ another RNA sequence analysis technique, such as Principal Component Analysis of RNA splicing entropy, to identify sepsis. One would have been motivated to do so, given the suggestion by Mergemeier that the RNA sequencing of body samples can be used to detect bacterial induced sepsis. There would have been a reasonable expectation of success, given the knowledge that Principal Component Analysis of RNA splicing entropy was previously taught in the identification of bacterial induced sepsis, as taught by Monaghan et al. Thus the invention as a whole was clearly prima facie obvious to one of ordinary skill in the art at the time the invention was made.
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.
Claim 1, 3 and 5 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4 and 10 of copending Application No. 17760490 in view of Mergemeier (supra) and Chikuie et al. (supra).
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant invention screens a body sample from a patient for bacterial RNA reads which is indicative of sepsis or ARDS. In order to do this, the bacterial RNA reads are compared to a genome of interest, and the patient is then treated for sepsis or ARDS. The method also utilizes PCA to identify the sepsis. The claimed invention of ‘490 is also drawn to a method of screening for bacterial RNA in a body sample from a patient that is suspected of having sepsis by comparing detected RNA with bacterial genomes and if bacteria are identified, treatment for sepsis is conducted by using antibiotics affective against the identified organism. ‘490 also claims the use of PCA for identifying sepsis in a body sample. However, ‘490 does not teach treating a patient for ARDS following detection of bacterial RNA in a body sample. As summarized above, the teachings of Mergemeier and Chikuie et al. render obvious the detection of bacterial RNA in a patient suspected of having sepsis and resulting treatment of said patient, which also includes the treatment of ARDS caused by septic shock. Therefore, the invention of the copending application in view of the teachings of Mergemeier and Chikuie et al. render obvious the instant invention.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BENJAMIN P BLUMEL whose telephone number is (571)272-4960. The examiner can normally be reached M-F 8-5 EST.
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, Michael Allen can be reached at (571) 270-3497. 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.
/BENJAMIN P BLUMEL/Primary Examiner, Art Unit 1671
Prosecution Insights