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 II, further electing the gene set TPR, DNAJB1, PDCD10, PSMB7, MERTK, AFTPH, BCOR, RASSF5, SNX11, and ANP32B0 in the reply filed on 9/8/25 is acknowledged.
Newly added claims 21-23 are drawn to non-elected inventions since applicant elected a set of 10 genes when given the opportunity to elect any set of 10 or more. Rejoinder will be considered upon the finding of allowable subject matter for the elected invention.
Claim Objections
Claim 15 is objected to because of the following informalities: the conjunction “and” should be added between MTCH1 and TUBB. Appropriate correction is required.
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 19-20 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.
Claim 19 and claim 20 recite “the specificity” and “the accuracy” but do not state what must have the claimed specificity and accuracy for. There is no required step in claim 15 that classifies, diagnosis, or other wise labels the sample, and it is not clear what the specificity and accuracy refer to. Since the independent claim does not set forth a complete diagnostic method and since claims 19 and 20 do not refer to what must have specificity and sensitivity, the claims are indefinite.
Improper Markush Grouping
Claims 15-20 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of “said genes selected from the genes of Table 1” is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: The different sets of genes encompassed by the alternative language are not joined by any common structure. There are at least 56 different groups of “ten” in which none of the genes overlap at all.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
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 15-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a law of nature and an abstract idea without significantly more. The claim(s) recite(s) the naturally occurring relationship between gene expression and the presence of lung cancer, as well as “detecting,” “evaluating,” “identifying changes,” and “comparing, ” which are mental process abstract idea exceptions. The claims further set forth the relationship between naturally occurring changes in expression levels of at least 10 of the 10 or more genes in the sample from those of the reference with a detection or evaluation of lung cancer. The relationship between gene expression levels and lung cancer is a natural phenomenon law of nature.
This judicial exception is not integrated into a practical application because the claims in addition to the judicial exceptions, the claims only recite or require contacting a sample with molecules that hybridize to one or more genes in the sample, which is a data gathering step that does not apply or use the judicial exceptions in any way.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims only recite or require contacting a sample with molecules that hybridize to one or more genes in the sample, which is a data gathering step that is presolution activity that only gathers data necessary to practice the judicial exceptions and employs any of a variety of well-known assay techniques. See specification p. 33, line 1 and following.
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.
Claim(s) 15-17 and 19-20 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zhang et al. (Cell. Mol. Live Sci. (2012) 69:3341-3350)).
Zhang et al. teach a method including the steps of identifying the changes in the expression set TPR, DNAJB1, PDCD10, PSMB7, MERTK, AFTPH, BCOR, RASSF5, SNX11, and ANP32B0 in a sample from a subject and comparing said subject’s gene expression levels with the levels of the same genes in a reference control.
Namely, Zhang et al. teach obtaining saliva samples from recently diagnosed lung cancer patients and matched cancer-free controls, and using the Affymetrix Human Genome U133 array to assay gene expression at the genes on the array. Each of the elected genes has probes for determining gene expression on the array, as was confirmed by reviewing the U133 platform data table (GPL570) at https://www.ncbi.nlm.nih.gov/geo/. Zhang et al. does not specifically enumerate results for any of the elected set TPR, DNAJB1, PDCD10, PSMB7, MERTK, AFTPH, BCOR, RASSF5, SNX11, and ANP32B0, but the instant claim requires only clearly requires comparing the sample gene expression to a control, and the method taught by Zhang et al. does that.
Insofar as the preamble recites “a method for detecting or evaluating a lung cancer” and claim 16 further modifies the preamble, this is a statement of intended use and the measuring and comparing taught by the reference could be used in this way. It is inherent to the gene expression that the changes correlate with diagnosis or evaluation of cancer.
Insofar as the claims recite “wherein changes in expression levels of at least 10 of the 10 or more genes in the sample from those of the reference correlates with a detection of or evaluation of lung cancer,” this limitation states an inherent relationship between the expression and lung cancer, but does not require any further positive process step that distinguishes from the activity of the reference.
With regard to claim 17, the microarray assay teaches identifying upregulation and downregulation. Here it is noted that the claim does not require upregulation or downregulation of any particular amount, that is be statistically different, or that particular genes are upregulated rather than down regulated and vice versa. By comparing the levels between cases and controls it is inherent that some level of difference would be observed, even if very small.
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.
Claim(s) 18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. in view of Gierada et al. (JNCI J Natl Cancer Inst (2014) 106(11); pages 1-7).
The teachings of Zhang et al. are given previously in this Office action and are fully incorporated here. Zhang et al. does not teach measuring the size of lung nodules.
Gierada teaches measuring the size of lung nodules as a predictive test to screen for lung cancer (Abstract, throughout).
It would have been prima facie obvious to have modified the method taught by Zhang et al. so as to have also included measuring lung nodules in the lung cancer patients in order to gather another valuable piece of diagnostic information about the cancer of the lung cancer patients.
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 15-20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8 of U.S. Patent No. 11661632. Although the claims at issue are not identical, they are not patentably distinct from each other because Claims 1-8 reagents capable of hybridizing to the gene set TPR, DNAJB1, PDCD10, PSMB7, MERTK, AFTPH, BCOR, RASSF5, SNX11, and ANP32B0 of the reference application recites a pharmaceutical composition comprising compound X.
The reference claim differs from the instant claims because it does not recite a method of using substrate or set of polynucleotides for diagnosing or evaluating lung cancer. (the reference claims are directed to a product, not a method).
However, MPEP 804(II)(B)(1) states that “it is also proper to look at the disclosed utility in the reference disclosure to determine the overall question of obviousness in a nonstatutory double patenting context.” See Sun Pharm. Indus., Ltd. v. Eli Lilly & Co., 611 F.3d 1381, 95 USPQ2d 1797 (Fed. Cir. 2010); Pfizer, Inc. v. Teva Pharm. USA, Inc., 518 F.3d 1353, 86 USPQ2d 1001 (Fed. Cir. 2008); Geneva Pharmaceuticals Inc. v. GlaxoSmithKline PLC, 349 F3d 1373, 1385-86, 68 USPQ2d 1865, 1875 (Fed. Cir. 2003).
Consistent with Sun Pharm., it is permissible to use a product claim to reject a method of use claim where that method of use is disclosed in the specification of the application claiming the compound.
In this case, the specification of the reference patent also discloses that claimed substrate or set of polynucleotides may be used for evaluating or diagnosing lung cancer, page 101 and following.
Accordingly, when the claims of the reference application are properly construed using its accompanying specification, the claimed method of treating graft versus host disease is obvious over the claims to the compound X pharmaceutical composition, since this same utility for compound X is disclosed in the specification of the reference application.
The instant application is a CONTINUATION of the application which was allowed and matured into US 11661632. The continuation application is not shielded from the instant NSDP rejection. This application, which discloses and claims only subject matter disclosed in prior Application No. 16/312036, appears to claim only subject matter directed to an invention that is independent and distinct from that claimed in the prior application, and names the inventor or at least one joint inventor named in the prior application. Accordingly, this application may constitute a divisional application. Should applicant desire to claim the benefit of the filing date of the prior application, attention is directed to 35 U.S.C. 120, 37 CFR 1.78, and MPEP § 211 et seq. The presentation of a benefit claim may result in an additional fee under 37 CFR 1.17(w)(1) or (2) being required, if the earliest filing date for which benefit is claimed under 35 U.S.C. 120, 121, 365(c), or 386(c) and 1.78(d) in the application is more than six years before the actual filing date of the application.
Response to Remarks
Any rejection not reiterated, updated, or otherwise specifically addressed was overcome by amendment to the claims on 3/2/2026.
Applicant argues that the genes in claim 15 are all “informative genes” in which expression changes characteristically in the presence of lung cancer, and as such the skilled artisan would expect each of these genes to “behave” the same way. However, there is no expectation from the prior art and no disclosure from the prior art that these genes behave the same way. Furthermore, one would not consider an “upregulated” gene to “behave” the same way as a “downregulated” gene. Further still, there is no evidence in the specification that each subset of 10 or more genes functions with the same specificity or sensitive as any other for identifying the presence or lung cancer or any of the other functions given in claim 16.
This rejection could be overcome by amending claim 15 to require all ten of the elected genes, and optionally any one or more of the remaining genes. Then each group would require a core “common structure” that could also include additional genes.
The improper Markush rejection is maintained because the members of the Markush group do not share a common structure that is essential to their function.
Applicant argues that the claims do not recite or describe any exception, but the examiner does not agree for the reasons enumerated in the rejection.
Applicant argues that the rejections for 102 are overcome by amendment, but the examiner does not agree for the reasons set forth in the rejection, namely that the “wherein” clause does not distinguish the action of the reference from the claimed method.
Applicant argues that the double patenting is precluded because the claims are patentably distinct from on another. However, the standard for restriction and NSDP differ, and the reasons that NSDP are appropriate are given in the rejection.
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.
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, Winston Shen can be reached at (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
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