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 claims dated 12/23/2025 are under consideration.
The amendments and arguments presented in the papers filed 12/23/2025 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 9/23/2025 listed below have been reconsidered as indicated.
a) The amendments to the specification are acknowledged.
b) The objections of claims 1, 28, and 38 are withdrawn in view of the amendments to the claims.
c) The rejections of claims 1, 2, 6, 7, 8, 11 and 13 under 35 U.S.C. 101 are withdrawn because the claimed composition is substantially different than a natural product.
d) The rejections of claims 28, 29, 30, 31 and 32 under 35 U.S.C. 101 because the amount of sequencing data to be considered and analyzed cannot be feasibly considered in the human mind alone or with the aid of pen and paper.
e) The rejections of claims 38 and 39 under 35 U.S.C. 101 are withdrawn because the claimed composition is substantially different than a natural product.
f) The rejections of claims 1-2, 6, 7, 8, 11, 12, 13, 28, 29, 30, 31, 32 and 38 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, are withdrawn in view of the amendments to the claims.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The restriction requirement between Groups I, II and IV was withdrawn.
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Once a restriction requirement is withdrawn, the provisions of 35 U.S.C. 121 are no longer applicable.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.
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 Objections
Claim 1 is objected to because of the following informalities: the claim recites “a 5’ translated region (5’ UTR) and a 3’ untranslated region (3’ UTR); a 5’ UTR that beings with a contiguous sequence of at least 300 bases; and a 3’ UTR that terminates in a contiguous sequence of at least 300 bases” rather than “a 5’ translated region (5’ UTR) and a 3’ untranslated region (3’ UTR); a 5’ UTR that beings with a contiguous sequence of at least 300 bases; or a 3’ UTR that terminates in a contiguous sequence of at least 300 bases”.
Appropriate correction is required.
Claim 1 is objected to because of the following informalities: the claim recites:
wherein the plurality of first DNA probes, first RNA probes, or both first DNA probes and first RNA probes and the plurality of second DNA probes, second RNA probes, or both second DNA probes and second RNA probes are coupled to the at least one surface of the substrate or plurality of substrates by being at least one of: biotinylated, attached to digoxigenin, modified with a single terminal amine group that reacts with N-hydroxysuccinimide modified PEG, 5'- succinylated, 5'-disulfide modified, crosslinked with phenyldiisothiocyanate, crosslinked with maleic anhydride, or reacted with 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide.
While the Examiner is able to determine the scope of the attachment of the probes to the substrate or plurality of substrates using one of the recited couplings, the language is objected to based on the bolded language. The options appear to include a mixture of: by how the elements are coupled; and the coupling being at least one of. It is suggested that the claim either recite: 1) “coupled to the at least one surface of the substrate or plurality of substrates by” and amending the claim to recite interactions or reactions that result in coupling; or 2) “probes coupling to the at least one surface of the substrate or plurality of substrates being at least one of” and amending the claim to recite interactions or reactions that result in coupling.
Appropriate correction is required.
Claim 28 is objected to because of the following informalities: the claim recites “a 5' untranslated region (5'UTR) and a 3' untranslated region (3'UTR); a 5'UTR that begins with a contiguous sequence of at least 300 bases; or a 3'UTR that terminates in a contiguous sequence of at least 300 bases” rather than “a 5’ translated region (5’ UTR) and a 3’ untranslated region (3’ UTR); the 5’ UTR that beings with a contiguous sequence of at least 300 bases; and the 3’ UTR that terminates in a contiguous sequence of at least 300 bases” (emphasis added).
Appropriate correction is required.
Claim 28 is objected to because of the following informalities: the claim recites the word “and” between some steps and not others. It is suggested that “and” consistently be used between steps or only between the last two recited steps.
Appropriate correction is required.
Claim 28 is objected to because of the following informalities: the claim recites “said supports” in line 1 of step (e), presumably in reference to a “solid support”. It is suggested a single term consistently be used when referring to a particular claim element.
Appropriate correction is required.
Claim 38 is objected to because of the following informalities: the claim recites:
probes that are coupled to the at least one surface of the substrate or plurality of substrates by being at least one of: biotinylated, attached to digoxigenin, modified with a single terminal amine group that reacts with N-hydroxysuccinimide modified PEG, 5'- succinylated, 5'-disulfide modified, crosslinked with phenyldiisothiocyanate, crosslinked with maleic anhydride, or reacted with 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide.
While the Examiner is able to determine the scope of the attachment of the probes to the substrate or plurality of substrates using one of the recited couplings, the language is objected to based on the bolded language. The options appear to include a mixture of: by how the elements are coupled; and the coupling being at least one of. It is suggested that the claim either recite: 1) “coupled to the at least one surface of the substrate or plurality of substrates by” and amending the claim to recite interactions or reactions that result in coupling; or 2) “probes coupling to the at least one surface of the substrate or plurality of substrates being at least one of” and amending the claim to recite interactions or reactions that result in coupling.
Appropriate correction is required.
Claim Interpretation
The claims use the term “about” in reference to the length of nuclei acids. The term is interpreted in view of the instant specification as meaning plus or minus 25 bps (para. 36).
The DNA probes and/or RNA probes of claim 1 are interpreted as having a length of about 200 to about 1,000 bases and are complementary to the location of a known pL1 insertion site for each of the pL1 insertion sites listed in Table 2 as set forth in the claim. The insertion site complementary region may be at the 5’ or 3’ end of the probe or located in the interior of the probe.
Claim 13 requires “third DNA probes, RNA probes or both”. The probes have a length of about 200 to about 1000 bases and are complementary to the location of fixed L1 insertion points associated with cancer. The insertion site complementary region may be at the 5’ or 3’ end of the probes or located in the interior of the probe.
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.
Claim 12 is 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 following are new rejections necessitated by the amendments to the claims.
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 12 comprises two “attachments”: one defined in claim 1; and a second defined in claim 12. Claim 12 states the composition of claim 1 “further comprising an attachment”, and broadly encompasses a “further” attachment in addition to that of claim 1. The instant specification only contemplates a single attachment of a probe to a substrate or a plurality of substrates (see, e.g., p. 3 and 29).
Claim 12 constitutes new matter.
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.
Claim 28 is 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 claim 28, the claim is amended to require using a “bioinformatics program” that “identifies and records in the memory”, whether two scenarios are present. Each scenario (i.e., (1) and (2)), includes an “indicating” clause. It is unclear if the clause is setting forth an active method step performed by the “bioinformatics program” or if it is describing an “indication” associated with the presence of the described sequences.
Conclusion
Claims 12 and 28 would be allowable if rewritten to overcome the rejection(s) under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), 2nd paragraph, set forth in this Office action and to include all of the limitations of the base claim and any intervening claims.
Regarding claims 1, 28 and 38, Applicant's reply must either comply with all formal requirements objected to as described above or specifically traverse each requirement not complied with. See 37 CFR 1.111(b) and MPEP § 707.07(a).
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