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 .
The preliminary amended claims dated 4/18/2024 are under consideration.
Election/Restrictions
Applicant’s election without traverse of a fusion nucleic acid molecule and a MYO5C-ROS1 fusion molecule in the reply filed on 7/27/2026 is acknowledged.
Claim 50 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 7/27/2026. The breakpoint 1 and 2 of Table 3 do not describe the elected fusion molecule of MYO5C-ROS1.
Priority
The present application is a 371 national stage entry of PCT/US2022/078934 (filed 10/25/2022), which claims benefit of US provisional application 63/273,794 (filed 10/29/2021).
Priority is recognized.
Information Disclosure Statement
The listing of references in the specification or the citation of references throughout 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 or on a submitted IDS, they have not been considered.
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.
Claim 8 is rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exceptions without significantly more.
The claims are drawn to methods, one of the four statutory categories.
The claim(s) recite(s):
“acquiring knowledge of a fusion nucleic acid molecule, or a fusion polypeptide encoded by the fusion nucleic acid molecule, in a sample from an individual having a cancer” (claim 8).
The above step is an abstract idea that coordinates human behavior, e.g., one party obtaining information from another party. Alternatively, the step broadly encompasses an abstract idea in the form of a mental process that may be performed by reading a report or lab results.
The judicial exceptions are not integrated into a practical application because the claims do not involve:
improvements to the functioning of a computer or to any other technology or technical field;
applying or using the judicial exceptions to effect a particular treatment or prophylaxis for a disease or medical condition;
applying the judicial exception with, or by use of, a particular machine; or
effecting a transformation or reduction of a particular article to a different state or thing.
The claimed limitations add insignificant extra-solution activity to the judicial exceptions. The steps are mere data gathering steps. See MPEP 2106.05(g).
While claim 8 further comprises “administering to the individual an effective amount of a treatment that comprises an anti-cancer therapy”, the treatment is not a particular treatment. Thus, there is no nexus between the above judicial exceptions and the treating step of claim 8, despite the step being done “responsive to said knowledge”. The claim broadly encompasses simply treating the patient for a cancer and does not specify in which way the acquired knowledge is implemented in the context of the “administering” step. There is no guidance in the specification or in the claim as to how the treatment is administered “responsive to said knowledge”. The step is a mere direction to apply a treatment in the same manner a doctor would to a patient having cancer.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims encompass the use of well-known assays and performed in a conventional manner as described in paragraph 59 of the instant specification.
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 8, 9, 49, 50, 54, 58, 320, 322, 326, 330, 332, 335, 362, 363, 364, 368, 370, 371, 375, 384, 414 and 415 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.
Regarding claims 8, 9, 49, 50, 54, 58 and 320, the claims each reference at least one Table, each of which sets forth a variety of fusion molecules. The claims are incomplete based on the reference to incorporate the multiple tables recited in each of the claims. Claims are to be complete in themselves, and incorporation by reference of a table is a necessity doctrine and not one of convenience. See MPEP 2173.05(s).
The remainder of the claims depend from the above claims and are rejected for the same reason.
Regarding claim 8, it is unclear if the individual is administered an “anti-cancer therapy” regardless of the knowledge that is acquired in step (a). For example, it is unclear if the individual is administered a treatment if knowledge indicating the absence of a fusion molecule is acquired but not if knowledge of the presence is acquired.
Claim Rejections - 35 USC § 103
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 (i.e., changing from AIA to pre-AIA ) 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 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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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(s) 8, 9, 49, 54, 58, 320, 322, 330, 332, 335, 362, 364, 368, 371, 384, 414 and 415 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ou (Lung Cancer. 2019. 130: 201-207).
Regarding claim 8, Ou demonstrates that acquiring knowledge of ROS1 fusion nucleic acids was known, including a MYO5C-ROS1 fusion (Table 1).
Ou further demonstrates that non-small cell lung cancer cells having ROS1 fusion nucleic acids (ROS1+ NSCLC) are treated with TKIs, including crizotinib (p. 202). Ou further describes that patients with non-CD74-ROS1 fusion, e.g., MYO5C-ROS1, had a higher ORR as compared to those with a CD74-ROS1 fusion when treated with crizotinib.
Based on Ou, it would have been prima facie obvious to the ordinary artisan to have analyzed patient samples for ROS1 fusion nucleic acids and responsive to the knowledge of a MYO5C-ROS1 fusion nucleic acid being present to have treated the patient with crizotinib.
Regarding claim 9, Ou demonstrates that non-small cell lung cancer cells having ROS1 fusion nucleic acids (ROS1+ NSCLC) are treated with TKIs, including crizotinib (p. 202). Ou further describes that patients with a non-CD74-ROS1 fusion, e.g., MYO5C-ROS1, had a higher ORR as compared to those with a CD74-ROS1 fusion when treated with crizotinib.
Ou demonstrates that acquiring knowledge of ROS1 fusion nucleic acids was known, including a MYO5C-ROS1 fusion (Table 1).
Based on Ou, it would have been prima facie obvious to the ordinary artisan to have analyzed patient samples for ROS1 fusion nucleic acids and responsive to the knowledge of a MYO5C-ROS1 fusion nucleic acid being present to have treated the patient with crizotinib.
Regarding claims 49, 54, 58, 320, 330, 332, 335, 384, 414 and 415, Ou demonstrates that detecting ROS1 fusion nucleic acids in NSCLC patient (e.g., human patient) samples was known, including a MYO5C-ROS1 fusion (Table 1).
Ou further demonstrates that non-small cell lung cancer cells having ROS1 fusion nucleic acids (ROS1+ NSCLC) are treated with TKIs, including crizotinib (p. 202). Ou further describes that patients with non-CD74-ROS1 fusion, e.g., MYO5C-ROS1, had a higher ORR as compared to those with a CD74-ROS1 fusion when treated with crizotinib.
Based on Ou, it would have been prima facie obvious to the ordinary artisan to have analyzed patient samples for ROS1 fusion nucleic acids and responsive to the knowledge of ROS1 fusion nucleic acid being present to have treated the patient with crizotinib.
Regarding claim 322, Ou teaches the fusion molecules have kinase activity (p. 202).
Regarding claims 362, 364 and 368, Ou teaches tumor samples, which comprise nucleic acids from cancer cells, are used to identify the presence of fusion nucleic acids (p. 202).
Regarding claim 371, Ou teaches that using PCR to detect ROS1 fusion nucleic acids was known (p. 203).
Claim(s) 363, 370 and 375 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ou (Lung Cancer. 2019. 130: 201-207) as applied to claim 49 above, and in further view of Guibert (Annals of Oncology. 2018. 29:1049-1055).
Regarding claims 363, 370 and 375, Ou renders obvious the elements of claim 49 as described above.
Ou does not teach the additional elements specific to claims 363, 370 and 375.
However, Guibert teaches using primers to enrich for hotspot fragments within cfDNA samples from plasma (p. 1050). The cfDNA from plasma are fragments and in order to detect the fusions present, the fragments include breakpoints.
It would have been prima facie obvious to have modified the method suggested by Ou by using plasma samples to detect the presence of ROS1 fusions, including a MYO5-ROS1 fusion nucleic acid molecule. One would be motivated to do so because cfDNA in plasma represents a non-invasive source of nucleic acids for analysis. The modification has a reasonable expectation of success as ROS1 fusion molecules known to the user were detected using the method.
Claim(s) 326, 363, 370 and 375 is/are rejected under 35 U.S.C. 103 as being unpatentable over Ou (Lung Cancer. 2019. 130: 201-207) and Dagogo-Jack (Journal of Thoracic Oncology. 2019. 14(5):816-824).
Regarding claims 326, 363, 370 and 375, Ou renders obvious the elements of claim 49 as described above.
Ou does not teach the additional elements specific to claims 326, 363, 370 and 375.
However, Dagogo-Jack demonstrates detecting ROS1 fusion molecules in plasma samples using capture probes to enrich nucleic acids and sequencing was known (p. 817, Genetic Assessment). The cfDNA from plasma are fragments and in order to detect fusions in the fragments, the fragments include breakpoints.
Dagogo-Jack further teaches detecting mutations in PIK3CA, which contributes to resistance to crizotinib (p. 820; and Figure 3).
It would have been prima facie obvious to have modified the method suggested by Ou by using plasma samples to detect the presence of ROS1 fusions, including a MYO5-ROS1 fusion nucleic acid molecule. One would be motivated to do so because cfDNA in plasma represents a non-invasive source of nucleic acids for analysis. The modification has a reasonable expectation of success as ROS1 fusion molecules known to the user were detected using the method.
Conclusion
No claims allowed.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOSEPH G DAUNER whose telephone number is (571)270-3574. The examiner can normally be reached 7 am EST to 4:30 EST with second Fridays Off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JOSEPH G. DAUNER/ Primary Examiner, Art Unit 1682
