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 .
Claims Status
Claim(s) 1-16 is/are currently pending and presented for examination on the merits.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (e.g., “github.com/FRED-2/OptiType”; para 0185). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The use of trade name(s) or mark(s) used in commerce (e.g., Bachem, BD Biosciences, Tree Star, GraphPad, SPSS) has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
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.
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(s) 10 is/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.
Claim 10 recites the limitation "the negatively charged amino acid" in line 1. There is insufficient antecedent basis for this limitation in the claim. Specifically, claim 10 depends from claims 1 and 8, and claim 8 recites “wherein the radical substitution consists of a positively charged amino acid”. Therefore, claim 10 doesn’t have antecedent basis for the negatively charged amino acid recitation. For the purposes of compact prosecution, claim 10 is considered to depend from claim 9, which recites “wherein the negatively charged amino acid is glutamic acid or aspartic acid”. This rejection may be overcome by amending claim 10 to depend from claim 7 or 9.
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 (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 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(s) 1-5 and 12-16 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by US 2019/0307868 A1 (hereinafter “US868”).
Regarding instant claim(s) 1-3, US868 teaches a method for treating cancer comprising the administration of APCs, and further teaches the APCs are autologous (e.g., obtained from subject) dendritic cells that have been pulsed with a 9mer (e.g., nonamer) neoantigen (e.g., a neopeptide associated with the cancer) [e.g., title; abstract; ¶ 0003, 0010, 0012, 0045, 0168, 0036, 0039, 0064, 0082, 0531, 0233, 0362-0363, 0429, 0481, 0562, 0563, 0656, 0612; Tables 1-2]. US868 further teaches the neoantigen(s) may comprise a secondary anchor (e.g., second position) substitution, and that substitutions may be non-conservative (e.g., radical) at the second position [e.g., ¶ 0104, 0135; 183-184, 0191, 0292-0294].
Regarding instant claim(s) 4-5, 14, US868 further teaches a nucleic acid encoding the neoantigen peptide and that the polynucleotide may be derived from the native sequence (e.g., from sequencing subject’s biological sample) such as a tumor-associated antigen [e.g., ¶ 0122, 0124, 0360, 0423, 0481-0483, 0575]. US868 further teaches the tumor antigen is selected from a tumor biopsy, homogenate, or lysate biological specimen [e.g., ¶ 0004, 0014, 0057].
Regarding instant claim(s) 12, US868 further teaches the cancer is NSCLC [e.g., ¶ 0036, 0040, 0066, 0073-0074, 0076].
Regarding instant claim(s) 13, US868 further teaches the cancer is melanoma [e.g., ¶ 0036, 0040, 0065, 0068, 0073-0076, 0530, 0534, 0537].
Regarding instant claim(s) 16, US868 further teaches the administration of a PD-1 inhibitor [e.g., ¶ 0032, 0036-0039, 0082].
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) 6-11 is/are rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0307868 A1 (hereinafter “US868”) as applied to claim(s) 1 above, and further in view of US 2007/0055049 A1 (hereinafter “US049”).
The teachings of US868 as recited above apply for claim 1.
US868 further teaches commonly expressed HLA alleles include HLA-B alleles [e.g., ¶ 0612; tables 1-2].
US868 does not expressly teach that the subject expresses HLA-B supertype (1) B44 and the radical substitution consists of glutamic acid, and/or (2) B27 and the radical substitution is histidine, lysine, or arginine.
Regarding instant claim(s) 6-7, 9-10, US049 teaches pulsed dendritic cells/APCs, HLA binding motifs, peptides, and their uses in cancer therapy and/or diagnosis [e.g., title; abstract; ¶ 0013, 0089, 0113, 0346, 0958-0959, 0961, 0987, 1000, 1026-1027]. US049 teaches that because human population groups have distinct patterns of distribution of specific HLA alleles and it is important to identify peptides capable of interacting with and/or across alleles to achieve sufficient coverage of all population groups [e.g., ¶ 0025]. US049 further teaches the invention defines positions within a motif enabling the selectin of peptides that will bind efficiently to HLA-B alleles; that the peptides are 9 residues (e.g., nonamers); that the HLA-B supertype is B44; and that the HLA-B44 supermotif is characterized by the presence of a negatively charged glutamic acid or aspartic acid residue in position 2 of the peptide ligands (e.g., a neoantigen) [e.g., ¶ 0089, 0091, 0113, 0046].
Regarding instant claim(s) 8, 11, US049 further teaches that the HLA-B supertype is B27, and that the HLA-B27 supermotif is characterized by the presence of a positively charge histidine, lysine, or arginine residue in position 2 of the peptide ligands (e.g., a neoantigen) [e.g., ¶ 0445, 0948].
It would have been prima facie obvious to a person having ordinary skill in the art (PHOSITA) before the effective filing date of the claimed invention to substitute the HLA-B allele expressing APCs within the method of treating cancer comprising administration of dendritic cells pulsed with neoantigen as taught by US868, with the HLA-B44 and/or HLA-B27 supertype expression by APCs as taught by US049, in the context of designing and developing APCs for cancer therapy that more coverage across patient populations (e.g., based on specific HLA allele expression patterns). A PHOSITA would have been motivated to substitute HLA-B allele expressing APCs within the method of treating cancer comprising administration of dendritic cells pulsed with neoantigen as taught by US868, with the HLA-B44 and/or HLA-B27 supertype expression by APCs as taught by US049, because US868 teaches the base method of administering APCs pulsed with neoantigen for cancer therapy and that HLA-B alleles are commonly expressed, US868 and US049 both teach peptide antigen pulsed APCs for cancer therapy and HLA-B expression, and US049 teaches specific HLA-B supertype (e.g., B44 and/or B27) expression for cancer therapy. A PHOSITA would have been further motivated by US049 teaching that HLA alleles differ across populations and that including more alleles is necessary to cover more patient populations. There would have been a reasonable expectation of success for a PHOSITA to substitute the HLA-B allele expressing APCs within the method of treating cancer comprising administration of dendritic cells pulsed with neoantigen as taught by US868, with the HLA-B44 and/or HLA-B27 supertype expression by APCs as taught by US049, because US868 teaches base method of administering APCs pulsed with neoantigen for cancer therapy and that HLA-B alleles are commonly expressed, US868 and US049 both teach peptide antigen pulsed APCs for cancer therapy and HLA-B expression, and US049 teaches specific HLA-B supertype (e.g., B44 and/or B27) expression for cancer therapy. This rationale aligns with the principle of simple substitution of one known element for another to obtain predictable results, supporting a conclusion of obviousness (see MPEP § 2141).
Thus, the invention as a whole is prima facie obvious over the references, especially in the absence of evidence to the contrary.
Claim(s) 15 is/are rejected under 35 U.S.C. 103 as being unpatentable over US 2019/0307868 A1 (hereinafter “US868”) as applied to claim(s) 1 and 4 above, and further in view of Richters et al. (Genome Medicine, (2019) 11:56; hereinafter “Richters”).
The teachings of US868 as recited above apply for claims 1 and 4.
US868 does not expressly teach that the biological sample is ctDNA.
Regarding instant claim(s) 15, Richters teaches best practices for characterization of neoantigens for clinical utility [e.g., title; abstract]. Richters further teaches that neoantigens are identified from a ctDNA biological sample [e.g., pg. 3, col. 2, ¶ 1].
It would have been prima facie obvious to a person having ordinary skill in the art (PHOSITA) before the effective filing date of the claimed invention to substitute the biological sample in the method of treating cancer comprising administration of dendritic cells pulsed with neoantigen as taught by US868, with the ctDNA biological sample as taught by Richters, in the context of designing and developing a neoantigen based cancer therapy that doesn’t require invasive solid tumor biopsies. A PHOSITA would have been motivated to substitute the biological sample in the method of treating cancer comprising administration of dendritic cells pulsed with neoantigen as taught by US868, with the ctDNA biological sample as taught by Richters, because US868 teaches the therapeutic method and Richters teaches best practices for neoantigen characterization, including the use of ctDNA biological samples. There would have been a reasonable expectation of success for a PHOSITA to substitute the biological sample in the method of treating cancer comprising administration of dendritic cells pulsed with neoantigen as taught by US868, with the ctDNA biological sample as taught by Richters, because US868 teaches the therapeutic method and Richters teaches best practices for neoantigen characterization and a ctDNA biological sample. This rationale aligns with the principle of simple substitution of one known element for another to obtain predictable results, supporting a conclusion of obviousness (see MPEP § 2141).
Thus, the invention as a whole is prima facie obvious over the references, especially in the absence of evidence to the contrary.
Conclusion
No claims are currently allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMY M CHATTIN whose telephone number is (571)270-0646. The examiner can normally be reached T-F 0600-1600 PST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Julie Wu can be reached at (571) 272-5205. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/AMY M. CHATTIN/Examiner, Art Unit 1643
/JULIE WU/Supervisory Patent Examiner, Art Unit 1643
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