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 .
Election/Restrictions
Applicant’s election without traverse of claims 1-7 in the reply filed on June 9, 2026 is acknowledged.
Applicant elects the following without traverse: Species I - the first barcoded index primer of SEQ ID NO: 204; Species II - the second barcoded index primer of SEQ ID NO: 234; Species III - the barcode sequence of SEQ ID NO: 4; and Species IV - the linker sequence of SEQ ID NO: 104. Species I, II, and III read on elected claims.
Claims 1-7 are pending and examined herein.
Drawings
The drawings are objected to because:
Figure 2 shows barcodes F and R, but the specification does not disclose barcodes F and R. Additionally, figure 2 shows universal sequences U1 and U2, but the claims recite universal sequences A and B.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claims 2-4 are objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Claim 4 recites “barcode sequences set forth in Table 1”. SEQ ID NOs of the barcode sequences of Table 1 should be included in the claim.
Appropriate correction is required.
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 7 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for the composition of claims 1-6, does not reasonably provide enablement for a composition of claim 7, wherein an identifying nucleotide
sequence is attached to an affinity reagent by a linker comprising (a) a cleavable protein
photocrosslinker; or (b) a fluorescent moiety.
The invention of parent claim 1 is directed to a composition of a nucleotide sequence attached to an affinity reagent and used for identification of proteins. The identification of a target protein is achieved by amplification of a part of the nucleotide sequence using primers corresponding to the affinity reagent with specificity to the target protein.
Claim 7 adds additional limitations of a cleavable protein photocrosslinker or a fluorescent moiety as parts of the linker.
The art of DNA amplification for detection purposes is very mature. However, prior art is silent on using cleavable protein photocrosslinkers and fluorescent moieties together with detection by DNA amplification. Prior art is also silent on problems that could be solved by using cleavable protein photocrosslinkers and fluorescent moieties in the disclosed composition.
The specification fails to disclose how one of ordinary skill in the art should use cleavable protein photocrosslinkers and fluorescent moieties of instant invention. The only example disclosed in the specification ([0055]-[0060]) fails to mention cleavable protein photocrosslinkers and fluorescent moieties.
Based on the above findings, one of ordinary skill in the art would conclude that the specification fails to teach the skilled artisan how to use the claimed invention.
Claim Rejections - 35 USC § 102
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 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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim 1 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Brofelth et al. (IDS; Commun Biol. 2020 Jul 3;3(1):339).
Regarding claim 1, Brofelth teaches a composition for multiplex identification and quantification of target molecules in a plurality of samples (Abstract; pg. 2, col. 2, par. 2-3; pg. 3, col. 1, par. 1). The affinity reagents are scFv antibodies with specificity to 17 different target antigens (Table 1 and pg. 2, col. 2, par. 2). Fig. 3 demonstrates a unique identifying nucleotide sequence attached to a scFv (barcode oligo) and two primers (primer 1 and index primer). The 8 bp region in the middle of the barcode oligo is a scFv-specific tag, which is the unique identifying nucleotide sequence relative to other affinity reagents of claim 1.
The identifying nucleotide sequence is flanked by a first amplifying nucleotide sequence and a second amplifying nucleotide sequence (20 bp boxes in the barcoded oligo).
The first barcoded index primer (index primer of Fig. 3) comprises a P7 sequence (universal sequence A) and a 20 bp sequence configured to anneal to the first amplifying nucleotide sequence of the barcode oligo.
The second barcoded index sequence (the primer 1 of Fig. 3) comprises a P5 sequence (universal sequence B) and a 20 bp sequence configured to anneal to the second amplifying nucleotide sequence.
Regarding claim 5, Brofelth teaches affinity reagents are antibodies. Specifically, the reference teaches 17 scFv antibodies (pg. 2, col. 2, par. 2).
Claim Rejections - 35 USC § 103
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 set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
Determining the scope and contents of the prior art.
Ascertaining the differences between the prior art and the claims at issue.
Resolving the level of ordinary skill in the pertinent art.
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 6 is rejected under 35 U.S.C. 103 as being unpatentable over Brofelth in view of Groff et al. (Biotechnol Adv. 2015 Dec;33(8):1787-98).
The teachings of Brofelth have been set forth above.
Regarding claim 6, Brofelth fails to teach the affinity reagents of the plurality are peptide aptamers or nucleic acid aptamers.
Regarding claim 6, Groff teaches Modern affinity reagents: Recombinant antibodies and aptamers (Title). Specifically, Groff teaches aptamers as alternative affinity reagents that are similar to antibodies in that they can bind to proteins (pg. 1791, col. 1, last par.) and can be used to detect and characterize their targets (pg. 1791, col. 2, par. 2).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have modified the composition of Brofelth, by employing nucleic acid aptamers as taught by Groff, as affinity reagents for detection of protein targets, as an obvious matter of simple substitution of one known affinity reagent (aptamers) for another (antibodies) to obtain predictable results.
One having ordinary skill in the art would have had a reasonable expectation of success in combining the prior art references because aptamers are known in the art as alternative affinity reagents to antibodies for detection of protein targets (Groff, pg. 1791, col. 1, last par. and col. 2, par. 2).
Subject Matter Free of the Prior Art
Claims 2-4 and 7 are free of the prior art.
The prior art neither teaches nor suggests: a primer of SEQ ID NO:204 (claim 2); a primer of SEQ ID NO:234 (claim 3); an identifying nucleotide sequence of SEQ ID NO:1 and a barcode sequence of SEQ ID NO:4 (claim 4); and an identifying nucleotide sequence attached to an affinity reagent by a linker comprising a cleavable protein photocrosslinker or a fluorescent moiety (claim 7).
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Alexander Volkov whose telephone number is (571) 272-1899. The examiner can normally be reached M-F 9:00AM-5:00PM (EST).
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bao-Thuy Nguyen can be reached on (571) 272-0824. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ALEXANDER ALEXANDROVIC VOLKOV/
Examiner, Art Unit 1677
/REBECCA M GIERE/Primary Examiner, Art Unit 1677
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