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 .
Status of Claims
Applicant' s amendment filed 03/24/2026 is acknowledged. Claims 1-2, 4-11, and 18 have been amended. Claims 12-17 were previously withdrawn. Claims 1-2 and 4-18 are pending in the instant application and claims 1-2, 4-11, and 18 are the subject of this final office action.
All the amendments and arguments have been reviewed and considered. Any rejections or objections not reiterated herein have been withdrawn in light of amendments to the claims or as discussed in this office action.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Previous Rejection
Status of Prior Rejections/Objections:
The objection to the specification regarding the references to the additional figures and sequencing listings is withdrawn.
The 112(b) rejections to claim(s) 1-2, 4-11, and 18 is/are withdrawn in view of the amendments to the claims.
112(a) written description and enablement rejections are withdrawn in view of the arguments and amendments to the claims. See Response to Arguments.
The 101 rejection is maintained, clarified, and modified as necessary in view of the amendments.
The double patenting rejection over copending application 18023598 is maintained.
New Ground(s) of Rejections
The new ground(s) of rejections were necessitated by applicant’s amendment of the claims.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Drawings/Specification Notes
Applicant was notified of the references to Fig. 21-32 in the previous Office Action and has submitted an amended specification cancelling all references to the omitted drawing figure(s). The submitted additional drawings are referenced as “Annex A” in the Remarks dated 03/24/2026 (pg. 23).
Accordingly, it is interpreted that the Applicant is accepting the application without all the drawing figure(s) referenced in the specification, according to MPEP 601.01(g)(II)(A).
If Applicant intended entry of the additional drawings, a petition under 37 CFR 1.182 and corresponding fee requesting the date of submission of the omitted drawing figure(s) as the application filing date or alleging that that the figures(s) were deposited with the USPTO with the application, including any/all evidence, is required as described in MPEP 601.01(g)(II)(A).
Claim Rejections - 35 USC § 101
Claims 1-2, 4-11, and 18 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception(s) without significantly more. The claim(s) recite abstract ideas/natural phenomena. This judicial exception is not integrated into a practical application. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
The following three inquiries are used to determine whether a claim is drawn to patent-eligible subject matter:
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter?
Yes, the claims are directed to a process/method.
Step 2A, prong 1. Does the claim recite a law of nature, a natural phenomenon, or an abstract idea (recognized judicial exceptions)?
Regarding claims 1 and 2, the claims recite determining a gene expression profile for each of five or more immune defense response genes selected from five or more of a group of 14, wherein the profiles are determined in a biological sample from a subject and determining a prediction of radiotherapy response based on the gene expression profiles of the immune defense response genes.
The step of determining the prediction of radiotherapy response based on a gene expression profile encompasses mental processes (e.g., forming a judgement, evaluation, and/or opinion based on values). Thus, the claims are directed to abstract ideas.
For claim 2, it is noted that the courts do not distinguish between claims that recite mental processes performed by humans and claims that recite mental processes performed on a computer, as discussed in MPEP 2106.04(a)(2)(III) and MPEP 2106.04(a)(2)(III)(c).
Regarding claim 18, the claim recites using a gene expression profile for each of five or more immune defense response genes selected from a group of 14 and determining, using a processor, a prediction of radiotherapy response based on the gene expression profiles of the immune defense response genes.
As above in claims 1 and 2, the claim is directed to the same abstract idea for the same reasons.
Step 2A, prong 2. Is the judicial exception(s) integrated into a practical application?
Regarding claim 1, claim 1 as amended, recites determining from a biological sample obtained from the subject … a gene expression profile for each of five or more immune defense genes. This determination, under the broadest reasonable interpretation, encompasses no more than insignificant extra-solution activity, namely mere data gathering for the subsequent abstract idea. Thus, the limitation fails to integrate the judicial exception into a practical application.
Regarding claims 4-6, the claims recite, respectively, six, nine, or twelve, genes. As such, they merely alter the judicial exceptions and thus fail to integrate the claims.
Regarding claims 7 and 8, the claims, as amended, recite that the determining is performed with particular mathematical calculations (regression and sum functions, respectively). As such the determining remains directed to an abstract idea, including a mathematical calculation, including those that may be accomplished by the human mind (i.e., both a mental process and a mathematical calculation). As such, the claims fail to integrate the judicial exception(s) into a practical application by further limiting the abstract idea(s) of the claims.
Regarding claims 9-10, the claims recite particular timing of biological samples or radiotherapy. As such, they are directed to either a selection of samples (insignificant extra-solution activity) or a variation in the abstract ideas (i.e., the natural phenomenon and/or mathematical calculations). Thus, the claims fail to integrate the judicial exception(s) into a practical application.
Regarding claim 11, the claim, as amended, recites recommendation of a therapy. A recommendation is not sufficient to integrate the claim as it does not actually require administration of said therapy, as discussed in MPEP 2106.04(2).
It is further noted, for the sake of compact prosecution, it is noted that at least “an alternative therapy” alone would not be considered particular to the judicial exception.
Regarding claims 2 and 18, These claims fall for the same reasons as claim 1. It is also noted for clarity that receipt of data is mere data gathering. Additionally, the claims recite “determining, by a processor, the prediction”. The term “processor” is a generic computer component. While a “particular machine” can integrate an abstract idea into a practical application, the Courts are clear that a generically recited computer component merely used to implement an abstract idea, such as an idea that could be done by a human analog, does not. See MPEP 2106.05(b) and 2106.05(d)(II). See also MPEP 2106.05(h), which discusses field of use and technological environments, particularly (iv) relating to execution of an abstract on a generic computer.
Step 2B. Does the claim amount to significantly more?
No claims amount to significantly more.
MPEP 2106.05(I) discusses the search for the inventive concept, which must be furnished beyond the judicial exceptions(s). In the instant case, the claims encompass only abstract ideas and generically recited insignificant extra-solution activity, as discussed above. Taken together, no claim is sufficient to amount to significantly more than the judicial exception.
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 1-2, 4-7, 9-11, and 18 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1-18 of copending Application No. 18/023,598 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because of the following. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Both sets of claims are directed to a set of genes encompassing 5 or more of the immune defense response genes AIM2, APOBEC3A, CIAO1, DDX58, DHX9, IFI16, IFIH1, IFIT1, IFIT3, LRRFIP1, MYD88, OAS1, TLR8, and ZBP, obtaining a gene expression profile for each of the selected genes determined in a biological sample obtained from a prostate cancer subject and determining a prediction of a therapy response based on a set of expression profiles including said immune defense response genes (claim 1), wherein the [predicted] therapy may be radiotherapy (claims 9 and 10).
Boths sets of claims also teach a processor adapted to perform the method (claim 12), wherein it would be obvious to utilize such an apparatus in the method of claim 1 of ‘598 motivated by the desire to make the method simpler to use in the clinical setting.
Both sets of claims teach a prediction using a regression function derived from a population of prostate cancer patients (claim 3), obtaining the same before the start of therapy (claim 8), that the radiotherapy may be radical or salvage (claim 9), that the prediction is negative or positive and the set of recommended therapies of instant claim 11 (claim 10).
Any additional limitations of the ‘598 claims are encompassed by the open claim language “comprising” and/or ”based on” found in the instant claims.
Therefore, the claims are deemed to be patentably indistinct.
Response to Arguments
Applicant’s arguments, see pg. 18-28, filed 03/24/2026, with respect to the 112(a) written description rejection of claims 1-2, 4-11, and 18 have been fully considered and are persuasive In particular, the arguments that there would be a reasonable overlap within the selection of at least 5 marker genes listed in Table 3 such that it would be reasonably predictable are deemed to be persuasive such that the skilled artisan would have concluded that the invention was in possession of the claimed invention at the time of filing. Therefore, the rejection of claims 1-2, 4-11, and 18 has been withdrawn.
Applicant’s arguments, see pg. 18-28, filed 03/24/2026, with respect to the 112(a) enablement rejection of claims 1-2, 4-11, and 18 have been fully considered and are persuasive. In particular, the arguments that the large-scale/robotics assays would limit the experimentation to only what is reasonable to one of ordinary skill in the art is persuasive. Accordingly, the rejection of claims 1-2, 4-11, and 18 has been withdrawn.
Applicant's arguments filed 03/24/2026 regarding the 101 and double patenting rejections on pg. 36-42 and 12-13, respectively, have been fully considered but they are not persuasive.
Regarding the 101 rejection, Applicant argues that the claims as a whole are not directed to an abstract idea and asserts that the claims “as a whole” are not directed to a mental process, a mathematical calculation, or a natural law. Applicant argues that the claims cannot be performed in the human mind alone and thus cannot be directed to a mental process. Applicant further argues that the claims do not recite a mental process or equation because while the limitation may be based on mathematical concepts, such are not recited in the claims. Applicant recites Subject Matter Eligibility Examples 38, 39, and 41 as evidence and alleges that the Office is bound by these examples. Applicant argues that the claims are not directed to a natural law as the claim as a whole is not directed to the correlation. Applicant also argues that the claims integrate any judicial exception into a practical application under Step 2B by comprising an improvement to the analysis and treatment of prostate cancer.
Regarding Step 2A, Prong One, as recited in the quote of MPEP 2106(II)(A)(I) by the applicant, the requirement is that claims recite the judicial exception rather than merely involve the judicial exception. There is no requirement that the claims “as a whole” be abstract, for example, to recite an abstract idea. Applicant may wish to consult Subject Matter Eligibility Example 49; it recites both a collecting and administering step and is deemed to recite an abstract idea. Example 42 may also be useful to the Applicant. As discussed extensively in the Remarks, the Subject Matter Eligibility Examples provide additional illustration of current Office policy detailed in the MPEP. However, as stated in these documents, such examples are hypothetical and are intended to be illustrative of the patent eligibility guidance.
The 101 analysis has been clarified to focus on the abstract idea(s) recited in the claims. While it is noted the entire claim does not need to be directed to the natural phenomenon to trigger eligibility analysis, upon further consideration, a correlation between gene expression and “radiotherapy response” is sufficiently close to an inability to survive chemotherapy discussed in MPEP 2106.04(b)(I).
The specific mathematical calculations in claims 7-8 (i.e., claim 7: “regression function” and “sum function that sums discretized gene expression profiles”) are noted.
Regarding the analysis under Step 2B, MPEP 2160.05(a)(II) recites: “However, it is important to keep in mind that an improvement in the abstract idea itself (e.g. a recited fundamental economic concept) is not an improvement in technology.” Applicant argues that the determination and prediction, i.e., the abstract idea itself, is the “important improvement”. Applicant has not provided any discussion or evidence of how such improvements differ from the abstract idea(s) of the claims, e.g., “determining … a prediction of radiotherapy response by the prostate cancer subject” (claim 1). Further, MPEP 2106.04(d)(1) directs that “the examiner should not determine the claim improves technology” based on “a bare assertion of an improvement without the detail necessary to be apparent to a person of ordinary skill in the art”.
The claims have been analyzed as a whole under Step 2B and additional limitations require no more than insignificant extra-solution activity. Asserted improvements are directed at the abstract idea(s) of the claims. Thus, the claims remain directed to the abstract idea(s) and are neither integrated into a practical application nor sufficiently more than the judicial exception(s).
Regarding the double patenting rejection, Applicant notes that to the extent necessary upon final approval of the claims, Applicant may submit a terminal disclaimer.
No disclaimer has been submitted, and the double patenting rejection cannot be held in abeyance.
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 Emma R Hoppe whose telephone number is (703)756-5550. The examiner can normally be reached Mon - Fri 11:00 am - 7:00 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, Anne Gussow can be reached at (571) 272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/EMMA R HOPPE/Examiner, Art Unit 1683
/NANCY J LEITH/Primary Examiner, Art Unit 1636
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