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 of Group I and the species of A) SEQ ID NO: 5 in the reply filed on 02/12/2025 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 26, 27, and 32-37 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim.
Claims 23-25 and 28-31 are examined here upon their merits.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. The instant application is a 371 of PCT/EP2020/064893 filed 05/28/2020 which claims the benefit of foreign application EPO 19177444.7 filed 05/29/2019. All claims examined here on their merits are given the benefit of EPO 19177444.7 and are granted a filing date of 05/29/2019.
Information Disclosure Statement
The information disclosure statement(s) (IDS) submitted on 04/28/2022, 07/18/2024, and 03/11/2025 follow the provisions of 27 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
The listing of references in 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, they have not been considered.
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 23-25 and 28-31 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 claims contain 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.
The instant claims 23-25 and 28-31 encompass variants of a peptide comprising a fragment of SEQ ID NO: 8 wherein the fragment comprises at least 8 consecutive amino acids of SEQ ID NO: 8 including at least one of 121 and 135 of SEQ ID NO: 8. Positions 121 and 135 of SEQ ID NO: 8 are any amino acid except cysteine. The claimed variants of fragments of SEQ ID NO: 8 requires no conserved sequence or structure. The claims thus encompass variants comprising SEQ ID NO: 8 that vary between 8 and an unlimited number of amino acids in length and a substitution of any amino acid except cysteine at one or two positions. Claim 23 recites that the claimed peptide is capable of inducing an immune response against a TGFβR2-1a frameshift mutant protein. Applicant has described the using of peptides consisting of fsp2 (SEQ ID NO: 5), fsp4 (SEQ ID NO: 7), fsp1 (SEQ ID NO: 4), and fsp5 (SEQ ID NO: 3), in order to stimulate the induction of an immune response against a TGFβR2-1a frameshift mutant specific T cells. The described peptides range from positions 120-152 of SEQ ID NO: 8 or SEQ ID NO: 2 and therefore retain the sequence between positions of 133 and 143 of SEQ ID NO: 8 or SEQ ID NO: 2, SS(C/G)VPVALMSA wherein (C/G) is either cysteine (C) or glycine (G). However, the claims encompass variants of SEQ ID NO: 8 that could vary substantially in length and also in sequence with no requirement for any particular structural feature to retain the desired activity. The disclosure of the use of SEQ ID NO: 3, 4, 5, and 7 in order to induce an immune response against a TGFβR2-1a frameshift mutant protein does not adequately describe the scope of the genus of the encompassed variants of SEQ ID NO: 8 that maintain the desired activity of inducing an immune response against a TGFβR2-1a frameshift mutant protein.
To provide adequate written description and evidence of possession of a recited genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, methods of making the claimed product, or any combination thereof. In this case, the only factor present in the claims is the disclosure of a small variety of sequences of variants of SEQ ID NO: 8 and the desired activity of inducing an immune response against a TGFβR2-1a frameshift mutant protein. There is no identification of any particular sequence portion of the variant SEQ ID NO: 8 peptide that must be conserved in order to retain the desired activity of inducing an immune response against a TGFβR2-1a frameshift mutant protein.
Vas-Cath Inc. v. Mahurkar, 19USPQ2d 1111, clearly states that “applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed.” (See page 1117.) The specification does not “clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed.” (See Vas-Cath at page 1116). As discussed above, the skilled artisan cannot envision the detailed chemical structure of the encompassed genus of peptides comprised of SEQ ID NO: 8 variants and fragments, and therefore conception is not achieved until reduction to practice has occurred, regardless of the complexity or simplicity of the method of isolation. Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method of isolating it. The compound itself is required. See Fiers v. Revel, 25 USPQ2d 1601 at 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016. One cannot describe what one has not conceived. See Fiddes v. Baird, 30 USPQ2d 1481 at 1483. In Fiddes, claims directed to mammalian FGF’s were found to be unpatentable due to lack of written description for that broad class as the specification provided only the bovine sequence.
Therefore, applicant has not disclosed sufficient species or common structural features such that one skilled in the art would conclude that applicant was in possession of the claimed genus of peptides comprising SEQ ID NO: 8 (including variants and fragments thereof). Therefore, only the administration of variants of SEQ ID NO: 8 or SEQ ID NO: 2 peptides consisting of SEQ ID NO: 3, 4, 5, and 7, but not the full breadth of the claims meets the written description provision of 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AlA), first paragraph.
Applicant is reminded that Vas-Cath makes clear that the written description provision of 35 U.S.C. §112 is severable from its enablement provision (see page 1115).
Claims 23-25 and 28-31 are 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 peptides consisting of the following SEQ ID NOs: 3, 4, 5, and 7, it does not reasonably provide enablement for a peptide comprising a fragment of SEQ ID NO: 8 wherein the fragment comprises at least 8 consecutive amino acids of SEQ ID NO: 8 including at least one of positions 121 and 135 and is capable of inducing an immune response against a TGFβR2-1a frameshift mutant protein. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make the invention commensurate in scope with these claims.
Claim 23 is drawn towards a peptide comprising a fragment of SEQ ID NO: 8 wherein the fragment comprises at least 8 consecutive amino acids of SEQ ID NO: 8 including at least one of positions 121 and 135 of SEQ ID NO: 8. Claims 24 and 25 provide further limitations of the fragment comprising at least 9 and 12 consecutive amino acids of SEQ ID NO: 8, respectively. SEQ ID NO: 8 is 161 amino acids long and therefore dozens of fragments of SEQ ID NO: 8 meet the length and position criteria of claims 23, 24, and 25. Furthermore, the positions of 121 and 135 of SEQ ID NO: 8 are inclusive of any amino acid except for cysteine. Thus, the instant claims encompass dozens of peptides which range widely in length, sequence, and structure. The instant specification teaches that peptides consisting of the following SEQ ID NOs can be used to stimulate induction of TGFβR2 frameshift mutant specific T-cells: 3, 4, 5, and 7 (instant specification page 42). Thus, the specification enables peptides consisting of the following SEQ ID NOs: 3, 4, 5, and 7. However, the claims encompass variants of SEQ ID NO: 8 that may vary substantially in length and composition with no requirement for any particular feature beyond the inclusion of at least one of positions 121 and 135 of SEQ ID NO: 8. The feature of requiring at least one of positions of 121 and 135 of SEQ ID NO: 8 does not confer the requirement of a conserved structure because two non-overlapping sequences may both satisfy the requirement.
The disclosure of the administration of peptides consisting of the following SEQ ID NOs: 3, 4, 5, and 7 does not enable the scope of the genus of the encompassed variants of SEQ ID NO: 8. Moreover, Applicants have not taught all of the encompassed variants of SEQ ID NO: 8 that would maintain the desired activity of inducing an immune response against a TGFβR2-1 frameshift mutant protein. While recombinant techniques are available, it is not routine in the art to screen large numbers of polypeptides that might potentially retain the desired activity, because the expectation of obtaining similar activity is unpredictable. Thus, one of skill in the art would require additional guidance, such as information as to what structural features would result in the variants or fragments of the claimed peptide which retain the desired activity. Thus, to practice the invention commensurate with the scope of the claims would result in undue experimentation.
The problem of predicting protein structure from sequence data and in turn utilizing predicted structural determinations to ascertain functional aspects of the protein is extremely complex. While it is known that many amino acid substitutions are generally possible in any given protein the positions within the protein's sequence where such amino acid substitutions can be made with a reasonable expectation of success are limited. Certain positions in the sequence are critical to the protein's structure/function relationship, e.g. such as various sites or regions directly involved in binding, activity and in providing the correct three-dimensional spatial orientation of binding and active sites. These or other regions may also be critical determinants of antigenicity. These regions can tolerate only relatively conservative substitutions or no substitutions. However, Applicants have provided little or no guidance beyond the mere presentation of sequence data to enable one of ordinary skill in the art to determine, without undue experimentation, the positions in the protein which are tolerant to change (e.g. such as by amino acid substitutions or deletions), and the nature and extent of changes that can be made in these positions. Although the specification outlines art-recognized procedures for producing and screening for active muteins, this is not adequate guidance as to the nature of active derivatives that may be constructed, but is merely an invitation to the artisan to use the current invention as a starting point for further experimentation. Even if an active or binding site were identified in the specification, they may not be sufficient, as the ordinary artisan would immediately recognize that an active or binding site must assume the proper three-dimensional configuration to be active, which conformation is dependent upon surrounding residues; therefore substitution of non-essential residues can often destroy activity. The art recognizes that function cannot be predicted from structure alone (Bork, 2000; Skolnick et al., 2000, especially p. 36 at Box 2; instant PTO-892). Tokuriki et al. 2009 (instant PTO-892) also teaches that mutations are generally destabilizing. For instance, Tokuriki teaches at p. 596, right column, last paragraph, that “as mutations accumulate, protein fitness declines exponentially...or even more than exponentially...So by the time an average protein accumulates, on average, five mutations, its fitness will decline to <20%.” Further, at p. 598, left column, last paragraph, Tokuriki notes that 50% of mutations are destabilizing, and >15% of mutations are highly destabilizing, and of the about 5% of mutations that are stabilizing values... many of these mutations result in inactive protein. Tokuriki concludes that “a more comprehensive understanding of how mutations affect protein fitness within living cells is needed, including their combined effects on function, thermodynamic and kinetic stability, and clearance through aggregation and degradation” (see p. 602, left column, 2nd paragraph), thus underscoring the lack of predictability with regard to the effects of mutation on protein function in vivo. In conclusion, Tokuriki teaches that “mutations, and mutations that alter protein function (new-function mutations), in particular, are generally destabilizing, and can reduce protein and organismal fitness.” (See p. 602, left column, 2nd paragraph).
The criteria set forth in Ex parte Forman (230 USPQ 546 (Bd. Pat. App. & Int. 1986), and reiterated in In re Wands (858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988)), which include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art and (8) the breadth of the claims, is the basis for determining undue extermination. In the instant case, one skilled in the art would not be able to predict which peptides comprising variants of SEQ ID NO: 8 would maintain the desired activity of inducing an immune response against a TGFβR2-1a frameshift mutant protein. Finally, due to the large quantity of experimentation necessary to generate the large number of peptides comprising SEQ ID NO: 8, including fragments thereof, recited in the claims and screen the same for activity; the lack of direction/guidance presented in the specification regarding which structural features are required to provide activity for the claimed variants; the complex nature of the invention; and the state of the prior art which establishes the unpredictability of the effects of mutation on protein structure and function, the skilled artisan would not know how to make and use the invention recited in claims 23-25 and 28-31 in its full scope.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 30 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 30 depends upon claim 29. Claim 29 recites a peptide according to claim 23, wherein the peptide comprises an amino acid sequence selected from the group consisting of SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 28, and SEQ ID NO: 30. Claim 30 recites the peptide according to claim 29, wherein the peptide is selected from the group consisting of SEQ ID NO: 5, SEQ ID NO: 7, SEQ ID NO: 28, and SEQ ID NO: 30. As claim 30 recites the peptide according to claim 29, the peptide of claim 30 and 29 are identical. Furthermore, the group of claim 30 is identical to the group of claim 29. Claim 30 therefore fails to further limit the subject matter of claim 29, upon which it depends.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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.
Claims 23-25 and 28-31 are rejected under 35 U.S.C. 103 as being obvious over Eriksen WO9958552 (hereafter Eriksen; instant PTO-892).
The applied reference has a common inventor with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2).
The instant claims are drawn to a peptide comprising a fragment of a variant of a TGFβR2-1a frameshift mutant.
Eriksen teaches a peptide which is a fragment of a TGFβR2 frameshift mutant (Eriksen claim 10) that induces a T cell response (Eriksen claim 1). Eriksen teaches peptides which are fragments of a TGFβR2-1a frameshift mutant and range from 9 to 44 amino acids (see Eriksen table 8). Eriksen further teaches a peptide which is comprised of the naturally-occurring sequence of instant SEQ ID NO: 5 (i.e., instant SEQ ID NO: 4) (Eriksen SEQ ID NO: 14). The aforementioned sequences of Eriksen are silent with regard to the mutation of cysteine to either any amino acid other than cysteine (instant claims 23-25) or to glycine (instant claims 28-30).
Instant claims 28-30 are drawn towards the peptide described supra having a glycine at position corresponding to a position corresponding to position 121 or 135 of SEQ ID NO: 8 such as in instant SEQ ID NO: 5. Information on evidence of nonobviousness can be found in MPEP §716.02.
In the instant disclosure, Applicants described the process of developing consensus sequences and variants thereof predicted to be immunogenic (instant examples 1, 2, and 3). These sequences include the pairs of SEQ ID NO: 4-SEQ ID NO: 5 and SEQ ID NO: 6-SEQ ID NO: 7. SEQ ID NO: 4 and SEQ ID NO: 5 and are identical save for the cysteine at position 2 of SEQ ID NO: 4 which is changed to a glycine in SEQ ID NO: 5 and SEQ ID NO: 6 and SEQ ID NO: 7 are identical save for the cysteine at position 3 of SEQ ID NO: 6 which is changed to a glycine in SEQ ID NO: 7. Example 6 demonstrates that peptides consisting of both the naturally-occurring cysteine residue, SEQ ID NO: 4 and SEQ ID NO: 6 as well as the mutated SEQ ID NO: 5 and SEQ ID NO: 7, respectively can be produced equally effectively (instant specification page 38, lines 21-24). In fact, each of these sequences were produced at a purity above 90% with no advantage given to either the naturally-occurring or mutated sequences. Example 7 demonstrates that both the modified peptides, SEQ ID NO: 5 and SEQ ID NO: 7, and unmodified peptides, SEQ ID NO: 4 and SEQ ID NO: 6, can both be used to stimulate induction of the cells (instant specification page 42, lines 11-18). Applicants have not demonstrated that the mutation of the cytosine at position 2 of SEQ ID NO: 4 or position 3 of SEQ ID NO: 6 to a glycine as in SEQ ID NO: 5 or SEQ ID NO: 7 produce an unexpectedly effective results, either in effectiveness of production or in immunogenicity. In fact, Applicants have not demonstrated that SEQ ID NO: 5 or SEQ ID NO: 7 are more effective in either production or in immunogenicity that SEQ ID NO: 4 or SEQ ID NO: 6. SEQ ID NO: 5 and SEQ ID NO: 7 are therefore obvious variants of SEQ ID NO: 4 and SEQ ID NO: 6 and Eriksen reads on instant claims 23-25 and 28-30.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 23-25 and 28-31 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 26 of copending Application No. 17927544 (hereafter ‘544).
Although the instant claims are not identical to the claims of ‘544, they are not patentably distinct from each other because the claims of ‘544 encompass the instant invention. ‘544 claim 26 recites a peptide mixture wherein the second peptide may be a peptide capable of inducing an immune response against a TGFβR2-1a frameshift mutant protein comprising an immunogenic fragment selected from at least 8 consecutive amino acids of ‘544 SEQ ID NO: 3 including at least one of positions 121 and 135. ‘544 SEQ ID NO: 3 is identical to instant SEQ ID NO: 8 and therefore, the claims of ‘544 encompass instant claims 23-25 and 28-31.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KATRINA J CAMPBELL whose telephone number is (703)756-1326. The examiner can normally be reached Monday - Thursday 7:30 - 5 (ET), Every other Friday 7:30 - 4 (ET).
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/KATRINA J. CAMPBELL/Examiner, Art Unit 1675
/JEFFREY STUCKER/Supervisory Patent Examiner, Art Unit 1675