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 claim amendments dated 6/23/2026 are under consideration.
The amendments and arguments presented in the papers filed 6/23/2026 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 3/27/2026 listed below have been reconsidered as indicated.
a) The amendments to the specification addressing trade name and/or mark usage are acknowledged.
b) Any objections and rejections of claims 12, 32, 33, 38 and 58 are rendered moot by the cancellation of the claims.
c) The rejections of claim 8 under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more are withdrawn in view of the amendments to the claims.
d) The rejections of claim 34 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, are withdrawn in view of the amendments to the claims.
The Examiner’s responses to the Remarks regarding issues not listed above are detailed below in this Office action.
New and modified grounds of rejection necessitated by amendment are detailed below and this action is made FINAL.
Election/Restrictions
The restriction requirement dated 11/18/2025 was withdrawn in its entirety.
In view of the above noted withdrawal of the restriction requirement, applicant is advised that if any claim presented in a divisional application is anticipated by, or includes all the limitations of, a claim that is allowable in the present application, such claim may be subject to provisional statutory and/or nonstatutory double patenting rejections over the claims of the instant application.
Once a restriction requirement is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131-32 (CCPA 1971). See also MPEP § 804.01.
Priority
The present application is a 371 national stage entry of PCT/US2021/065561 (filed 12/29/2021), which claims benefit of: US provisional application 63/243,002 (filed 9/10/2021); and US provisional application 63/132,085 (filed 12/30/2020).
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 cited on a submitted IDS, they have not been considered.
Claim Interpretation
The terms “COL5A2-ALK fusion nucleic acid molecule or polypeptide” and “COL3A1-ALK fusion nucleic acid molecule or polypeptide” are interpreted in view of paragraphs 70 and 82. The elements are required to include portions that are specifically identifiable as a ALK sequence and portions specifically identifiable as a COL5A2 sequence or as a COL3A1 sequence. Some claims, such as claim 46, describe fusion nucleic acids being “at least 95%...identical” to a specific SEQ ID NO. ALK is known to fuse with genes other than COL5A2 or COL3A1, such as EML4. EML4-ALK or NPM1-ALK fusion nucleic acids may be “at least 95%...identical” to COL5A2-ALK or COL3A1-ALK fusion nucleic acids of the present claims. However, those EML4-ALK and NPM1-ALK sequences are outside of the scope of the claim as they do not include specific identifiable sequences from COL5A2 or COL3A1. The fusion polypeptide element of the claims is similarly interpreted.
References to chromosome positions are interpreted in view of the specification to be in reference to hg19.
The COL5A2-ALK or COL3A1-ALK fusions are described as having “kinase activity”. ALK is a kinase, while COL5A2 and COL3A1 are not kinases. The kinase domain of ALK is known and thus, one would recognize which fusions molecules having “kinase activity” are encompassed by the claims.
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 8, 13, 17, 18, 20, 34, 41, 46, 50, 52, 54, 56, 59, 60, 63 and 64 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement.
The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 8 requires “acquiring knowledge of a COL5A2-ALK fusion nucleic acid molecule or polypeptide or a COL3A1-ALK fusion nucleic acid molecule or polypeptide in a sample from the individual”.
Claim 13 requires “detecting a COL5A2-ALK fusion nucleic acid molecule or polypeptide or a COL3Al- ALK fusion nucleic acid molecule or polypeptide in a sample from an individual”.
Claim 18 further limits the types of cancers.
Claim 20 pairs types of cancer with particular fusion molecules.
Claims 46 and 50 broadly encompass several different fusion molecules between COL5A2 and ALK.
Claims 52, 54 and 56 broadly encompass several different fusion molecules between COL3A1 and ALK.
Claim 59 broadly encompasses non-cancerous tissues.
Claim 60 broadly encompasses non-cancerous tissues.
The instant specification provides a limited number of species of fusion molecules identified in the context of 9,969 sarcoma tissue samples. While no specific data is provided regarding the COL5A2-ALK and COL3A1-ALK fusion molecules observed, the instant specification only identifies a limited number of fusion molecules that occurred between specific introns or exons of COL5A2 and ALK and specific introns or exons of COL3A1 and ALK.
There is no evidence that COL5A2-ALK or COL3A1-ALK fusion molecules occur in other types of cancers or within non-cancerous samples. One would not reasonably extrapolate the limited species described in the instant specification to all other types of patient samples as there is no indication that COL5A2-ALK or COL3A1-ALK fusion molecules occur in other types of biological samples or that they would have any impact on the course of a cancer or response to treatment.
While ALK fusions are well-known in the field, the type of fusions varies between cancer types. See Shreevivas (previously cited). Further, it is well established that treatments vary between cancer types and depend on the status of the cancer. See Shreevivas (previously cited). Given the limited species regarding simply detecting the presence of particular COL5A2-ALK or COL3A1-ALK fusion molecules in sarcoma samples from patients, the specification does not provide support for the full scope of the genus of methods presently claimed. There is no guidance for one to reasonably extrapolate the limited data to in the context of sarcoma to embodiments involving other types of cancers and other types of samples.
Response to the traversal of the 112(a) rejections
The Remarks argue the claims have been amended to specify the COL5A2-ALK and COL3A1-ALK fusions and the type of anti-cancer therapy that is administered (p. 15-17).
The arguments have been fully considered. The above rejections have been modified as necessitated by the amendments to the claims. The specification does not adequately describe a representative number of species for the type of samples and the types of cancers to support the full scope of the claims. The claims broadly encompass treating or delaying any type of cancer, while the instant specification only evaluated sarcomas, which are tumors that develop in bone and connective tissue that surrounds bones and joints. Sarcomas are not related to basal cell carcinomas, adenocarcinomas or squamous cell carcinomas, which are broadly encompassed by the generic “cancers” of the claimed method.
Sarcoma tissues were analyzed in the specification. This single species is not representative of the broad scope of the generic “samples” encompassed by the claimed method. Sarcomas tissues are not representative of non-cancerous tissues, or different types of samples of other types of cancers.
Conclusion
No claims 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 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.
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, 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
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