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 .
If the IFW search notes say we did a google search, we should have some notes for it.
Response to Amendment
The amendment filed December 17th, 2025 is acknowledged. Regarding the Office Action mailed September 18th, 2025:
The objections to the claims are withdrawn in view of the amendments.
The rejection set forth under 35 U.S.C. 112(b) is withdrawn in view of the amendments.
The rejection set forth under 35 U.S.C. 112(a) is withdrawn in view of the amendments.
Maintained or modified rejections are set forth below, as necessitated by the amendments. Responses to arguments, if necessary, follow their respective rejection sections.
Claim Summary
Claims 35, 37-44, and 46-47 have been amended. Claims 1-27, 29-32, 34, and 36 have been canceled. Claims 28, 33, 35, and 37-53 are pending. Claims 28 and 33 are withdrawn from consideration as being drawn to a non-elected invention/species. Claims 35 and 37-53 are under examination and discussed in this Office action.
Claim Interpretation – New – Necessitated by Amendment
Claim 52 as currently written has multiple interpretations, depending on the intended order of the method steps. One interpretation is that mutations are determined, and then a patient is classified as a responder to immunotherapy. This interpretation is problematic as there is currently no clear nexus between detecting the mutations in claim 35 and what they mean in terms of classifying a responder to immunotherapy. However, another interpretation may be that the patient is classified as a responder to immunotherapy before mutations are detected, which would then make it a known fact about the patient that does not need to relate to the mutations. This second interpretation is the one used for examination here. If the Applicant intended for there to be a different interpretation, this should be made clear in the response.
Claim Rejections - 35 USC § 101 – Modified – Necessitated by Amendment and Further Considerations
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 52 and 53 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. While the claims are directed to a process, and therefore meet step 1 of the subject matter eligibility test (see MPEP 2106.03), the claims recite the abstract idea of classifying a patient as a responder to immunotherapy. This is an abstract idea because the classifying step can reasonably be performed in the human mind through just looking at data, and is therefore a mental process. While the treatment step of claim 53 recites specific treatments, these are routine and well-known.
Step 2A of the subject matter eligibility test requires a two-pronged analysis. Prong One asks: does the claim recite an abstract idea, law of nature or natural phenomenon? As discussed in MPEP 2106.04(II)(A)(1), the meaning of “recites” is “set forth” or “describes”. That is, a claim recites a judicial exception when the judicial exception is “set forth” or “described” in the claim. In the instant case, the claims describe: the abstract idea of classifying a patient as a responder to immunotherapy.
Prong Two of the analysis under step 2A asks: do the claims recite additional elements that integrate the judicial exception into a practical application of the judicial exception? As discussed in MPEP 2106.04(II)(A)(2), “Because a judicial exception is not eligible subject matter, Bilski, 561 U.S. at 601, 95 USPQ2d at 1005-06 (quoting Chakrabarty, 447 U.S. at 309, 206 USPQ at 197 (1980)), if there are no additional claim elements besides the judicial exception, or if the additional claim elements merely recite another judicial exception, that is insufficient to integrate the judicial exception into a practical application. See, e.g., RecogniCorp, LLC v. Nintendo Co., 855 F.3d 1322, 1327, 122 USPQ2d 1377 (Fed. Cir. 2017) ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016) (eligibility "cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself."). For a claim reciting a judicial exception to be eligible, the additional elements (if any) in the claim must "transform the nature of the claim" into a patent-eligible application of the judicial exception, Alice Corp., 573 U.S. at 217, 110 USPQ2d at 1981, either at Prong Two or in Step 2B.” The considerations to be used are set forth at MPEP 2106.05(a) through (c) and (e) through (h). Turning to those sections of the MPEP:
MPEP 2106.05(a) has to do with improvements to the functioning of a computer or to any other technology or technical field. The claims at issue do not improve the functioning of a computer or other technology. While the instant claims recite contacting a nucleic acid sample obtained from a patient with a composition comprising primer pairs configured for amplification of a plurality of target sequences in the sample, specific target sequences of interest, amplifying the target sequences, detecting specific mutations in the specific target sequences of interest, the sample being from an endometrial tumor, classifying the patient as a responder to immunotherapy, and treating with an antibody, the claims do not improve upon testing methods for detecting changes at genomic sites, detecting specific mutations, or classifying patients. The claims merely use existing methods for these steps. Note that MPEP 2106.05(a) indicates that “[u]sing well-known standard laboratory techniques to detect enzyme levels in a bodily sample” is an example that the courts have indicated may not be sufficient to show an improvement to technology.
MPEP 2106.05(b) has to do with whether the claims involve the use of a particular machine. In this case, the claims do not involve the use of a particular machine. While the instant claims recite contacting a nucleic acid sample obtained from a patient with a composition comprising primer pairs configured for amplification of a plurality of target sequences in the sample, specific target sequences of interest, amplifying the target sequences, detecting specific mutations in the specific target sequences of interest, the sample being from an endometrial tumor, classifying the patient as a responder to immunotherapy, and treating with an antibody, no such machines are required by the claim, and certainly no particular machines. Even if some conventional machine were recited in the claims, like a PCR machine for amplification, further considerations such as the particularity or generality of the recited machine must be taken into account, as well as whether the involvement of the machine is merely extra-solution activity. MPEP 2106.05(g) describes “extra-solution activity”, noting that “[d]etermining the level of a biomarker in blood” is an example of “mere data gathering” which the courts have found to be insignificant extra-solution activity.
MPEP 2106.05(c) has to do with whether the claims involve a particular transformation. Here, none of the limitations of the claims involve a particular transformation. For example, generic testing of a genomic site does not transform that genomic site into something else.
MPEP 2106.05(e) has to do with “other meaningful limitations”. The additional limitations imposed upon the abstract idea of classifying a patient as a responder to immunotherapy in the instant case have to do with contacting a nucleic acid sample obtained from a patient with a composition comprising primer pairs configured for amplification of a plurality of target sequences in the sample, specific target sequences of interest, amplifying the target sequences, detecting specific mutations in the specific target sequences of interest, the sample being from an endometrial tumor, and treating with an antibody. These limitations are not considered “meaningful limitations”. MPEP 2106.05(e) states: “The phrase "meaningful limitations" has been used by the courts even before Alice and Mayo in various contexts to describe additional elements that provide an inventive concept to the claim as a whole.” In addition, as has been discussed, they represent insignificant extra-solution activity, i.e. “data gathering”.
MPEP 2106.05(f) raises the question as to whether the additional elements recited in the claim represent “mere instructions to apply an exception”. Here, the judicial exception is the abstract idea of classifying a patient as a responder to immunotherapy. The additional elements recited in the claims (i.e. contacting a nucleic acid sample obtained from a patient with a composition comprising primer pairs configured for amplification of a plurality of target sequences in the sample, specific target sequences of interest, amplifying the target sequences, detecting specific mutations in the specific target sequences of interest, the sample being from an endometrial tumor, and treating with an antibody) do amount to mere instructions to apply the judicial exceptions, since testing for genomic changes in endometrium samples to determine specific mutations serves as mere conventional steps taken for the purpose of gathering data about the mutational status of a patient, which any practical use of the judicial exception would require.
MPEP 2106.05(g) has to do with whether the additional elements of the claim amount to insignificant extra-solution activity. MPEP 2106.05(g) notes “[d]etermining the level of a biomarker in blood” is an example of “mere data gathering” which the courts have found to be insignificant extra - solution activity. Likewise, MPEP 2106.05(g) notes that “[p]erforming clinical tests on individuals to obtain input for an equation” also represents insignificant extra-solution activity. This aligns closely with the instant claims, where the additional elements of the claims amount to gathering samples, testing for genomic changes, and treating with an antibody.
MPEP 2106.05(h) has to do with whether the additional elements amount to more than generally linking the use of a judicial exception to a particular technological environment or field of use. Here, “[t]he field of the invention generally relates to cancer, including methods for diagnosing, prognosing, and treating cancer. In particular, the field of the invention relates to novel signatures of unique sets of point mutations involving a change of a cytosine or a guanidine, and methods, systems, and components thereof based upon the novel signature for identifying tumor samples having increased tumor mutational burden (TMB). Both the signatures and the methods, systems, and components thereof may be utilized for identifying cancer patients, microsatellite stable-cancer patients in particular, who will effectively respond to immune checkpoint blockade therapy. (Page 1 of the instant specification)”. However, as MPEP 2106.05(h) indicates, such limiting to a particular “field of use” does not confer patentability on otherwise ineligible subject matter.
In addition, the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exceptions (as set forth in step 2B of the subject matter eligibility test; see MPEP 2106-III) because it was known in the prior art to look at panels of genes to determine mutations, along with classifying responders to immunotherapy and antibody treatments.
Frampton (US20190085403A1; previously cited) teaches on testing a panel of genes for mutations (Page 22, paragraph [0390]). Frampton teaches on a select list of genes to determine mutations for (Page 22, paragraph [0393]; Table 1). Frampton teaches on determining if a subject will be a responder to immunotherapy, with treatment options of a PD-1 or PD-L1 inhibitor (Page 25, paragraph [0401]). These inhibitors may be antibodies (Page 16, paragraph [0322]). Additional therapies can include CTLA-4 antibodies (Page 17, paragraph [0339]). Frampton also teaches that this can be determined for subjects with endometrial cancer (Page 19, paragraph [0359]).
Having considered the factors discussed in MPEP 2106.05 (a)-(c) and (e)-(h), as well as the prior art of Frampton, it is clear that the additional elements recited in the claims, whether considered individually or as a combination, do not integrate the judicial exceptions into a practical application of those exceptions in such a way as to provide meaningful limits on the use of the judicial exception. Therefore, claims 52 and 53 are rejected here under 35 U.S.C. 101.
Response to Arguments
Applicant's arguments filed December 17th, 2025 have been fully considered but they are not persuasive in regards to claims 52 and 53.
The Applicant first summarizes the Examiner’s rejection from the previous Office Action (Page 11 of the Remarks filed December 17th, 2025). The Applicant then recites the new amendments to claim 35 (Page 11 of the Remarks filed December 17th, 2025). The Applicant states that the newly amended method steps do not possess an abstract idea or mental process (Page 11 of the Remarks filed December 17th, 2025). The Applicant argues that the claims recite additional elements that amount to significantly more than a judicial exception as well, with reference to specific aspects of the instant disclosure that Frampton does not teach (Page 12 of the Remarks filed December 17th, 2025).
In response to these arguments, the Examiner would like to note for the Applicant that claims 35 and 37-51 are no longer considered to contain judicial exceptions as they are directed to an assay. However, claims 52 and 53 are still rejected under 35 U.S.C. 101 because claim 52 recites the mental process of classifying a patient as a responder, which requires no more than looking at patient data and deciding that they are a responder in the human mind, and the treatments of claim 53 are well-known and routine treatments in the prior art. Furthermore, in response to the arguments related to Frampton and its failure to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., aspects related to tumor mutation burden, how this relates to microsatellite-stable tumors, and computational analysis to investigate markers related to tumor mutational burden (see Page 12 of the Remarks filed December 17th, 2025)) are not recited in the rejected claims. Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). Therefore, the rejection under 35 U.S.C. 101 is modified as necessitated by amendment and maintained.
Conclusion
Claims 52 and 53 are rejected. Claims 35 and 37-51 are allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Allison E Schloop whose telephone number is (703)756-4597. The examiner can normally be reached Monday-Friday 8:30-5 ET.
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/ALLISON E SCHLOOP/Examiner, Art Unit 1683
/Robert T. Crow/Primary Examiner, Art Unit 1683