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 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 26, 28-40 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a method for detecting a bacterial infection in a human patient displaying symptoms of infection by directly measuring the mRNA level of ELANE and IFI27 in a bodily fluid sample of the patient, does not reasonably provide for practicing this method based on the gene pair ELANE and IFI44L. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
In the examples (beginning on p. 36), the specification teaches measuring mRNA expression levels of ELANE and IFI44L and show that the ratio of these two genes’ expression is 100% sensitive for suggesting bacterial infection is present, HOWEVER, the disclosure also shows that in 34 out of 64 cases the classifier ALSO identified viral samples as bacterial infections. Since the patients are already required to be symptomatic for infection, the detection of a classifier that indicates “bacterial” infection does not appear to be meaningful when ELANE and IFI44L are used alone. The specification exemplifies that it is highly unpredictable to apply the claimed method to distinguish between a viral and bacterial infection, since the accuracy of the claimed combination was only 56% for distinguishing a viral infection from a bacterial infection. That is the majority of infections, regardless of etiology were identified as bacterial. Therefore, the specificity of detecting bacterial infection compared to healthy control is almost a coin toss (56%).
It would require an extensive experimentation to establish that the instantly claimed invention could identify a bacterial infection as required by part (b) of the claim for the ELANE/IFI44L combination since there is no evidence to support that such a meaningful classifier could be produced.
Thus, having considered all of this, it would require undue experimentation to practice the claimed invention commensurate in scope with the instant claims.
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 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) 26, 28-40 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Griffiths (WO 2017/068347).
The instant claims are rejected in this office action under 112 1st paragraph for scope of enablement. Accordingly, the priority document, which does not disclose more than the instant non-provisional application, does not provide support for the instant claims under 112 1st paragraph, and the instant claims do not enjoy the benefit of priority to that document. Therefore, the effective filing date for the instant claims is the date of the PCT filing, 4/11/2019. As such, the Griffiths 2017 document is available as prior art against the claims under 102(a)(1). If the claims are granted priority to the foreign priority date (4/12/2018) then the Griffiths reference will no longer be available as prior art. When the claims are narrowed to be commensurate in scope with the showing they will enjoy benefit of priority.
The reference discloses also a method of detecting and treating a bacterial infection in a subject, the method comprising:
(a) assaying a body fluid sample obtained from the subject to determine expression of at least the gene pair least the gene pair ELANE and IF127;
(b) determining the presence of a bacterial infection in the subject based on the presence of the expression of the at least gen pair ELANE and IFI27 relative to each other and
(c) treating the subject with a therapeutically effective amount of an antibacterial agent (see. claims 5-29, see especially claims 12-13; page 2, paragraph 3 - page 5, paragraph 1; page 7 - page 8, paragraph 5 and esp. page 8, paragraph 4- page 9, paragraph 3). The disclosure is inclusive of determining the relative abundance of all of the genes recited in the claims.
The reference teaches that the bacterial infection can be caused by Streptococcus pneumoniae or E. coli or Staphylococcus saprophyticus (see p. 7). The infection can be pneumonia (i.e. lower respiratory) or sepsis (p. 7-8).
The reference teaches that the sample is selected from those including, blood, plasma, serum, CSF and synovial fluid (see claim 15, p. 28).
The reference teaches that assaying the body fluid can include using RT-PCR or ELISA, as well as other techniques (see p. 12).
The reference teaches calculating a relative abundance ratio and that a ratio above 1.18 indicates bacterial infection (see Figure 7).
The reference teaches a method that includes obtaining data indicative of additional gene pairs, see claim 5 reciting “at least one gene pair” which is inclusive of multiple gene pairs.
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 26, 28-40 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13 of U.S. Patent No. 11608535. Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are obvious in view of the issued claims.
Claim 8 of the issued patent teaches determining expression of a gene pair ELANE and IFI27 and ELANE and IFI44L within a method of treating a symptomatic infection that also determines gene expression of DUSP1 and IFI27, and claim 10 teaches using the relative abundance ratio of more than one gene pair for determining the presence of bacterial infection. The limitations of the additionally rejected claims are in the additional issued claims of the ‘535 patent and combination of these technique limitations with claim 8 of the issued patent would have been prima facie obvious as these techniques give more detail about how to practice the invention of the independent claim, which claim 8 is a dependent claim of. It would have been obvious to use the disclosed techniques in the dependent claims to practice the method for the benefit of providing methods for detecting and treating bacterial infections.
Response to remarks
Any rejection which is not reiterated was overcome by amendment.
A new rejection under 112a is set forth to address the amended claims. As a consequence, Griffiths remains available as prior art.
The claims are not patentably distinct from the issued patent because the issued patent also discloses combinations. The restriction between the sub combination and combinations was withdrawn in the parent application.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Tang et al. teach that IFI27 discriminates between influenza and bacteria in patients with suspected respiratory infection (Tang et al. Eur Resp J 2017; 49: 1602098, 12 pages). O'Garra et al. (US 2015/0315643) mention both ELANE and IFI27 as being present in blood transcriptional signatures of active pulmonary tuberculosis and sarcidosis, see Table 7, for example, but there is no suggestion to consider the expression level of these two as a ratio of one another. Neither reference teaches determining the presence of a bacterial infection in a symptomatic subject based on the presence of the expression of at least the gene pair ELANE and IFI27 relative to each other. Likewise, neither reference teaches determining the presence of a bacterial infection in a symptomatic subject based on the presence of the expression of at least the gene pair ELANE and IFI44L relative to each other.
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 Juliet Switzer whose telephone number is (571)272-0753. The examiner can normally be reached Monday to Thursday, 8:00 AM-3:30 PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Winston Shen can be reached on (571)-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Juliet Switzer
Primary Examiner
Art Unit 1682
/JULIET C SWITZER/Primary Examiner, Art Unit 1682