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 .
1. The Amendment filed January 20, 2026 in response to the Office Action of July 17, 2025, is acknowledged and has been entered. Claims 1, 2, 5, 12, 13, 15-17, 19, 20, 22, 23, 40, 63-67, 69, and 70 are pending. Claims 3, 4, 6-11, 14, 18, 21, 24-39, 41-62, and 68 are canceled. Claims 1, 16, 40 are amended. Claims 69 and 70 are new. Claims 19, 63-67 remain withdrawn. Claims 1, 2, 5, 13, 15-17, 20, 22, 23, 40, 69 and 70 are currently being examined.
Claims 1 and 16 have been amended and altered in scope to recite different criteria for identifying and selecting a neoepitope for producing a personalized vaccine, necessitating new rejections set forth below.
New Rejections
(necessitated by amendments)
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.
2. Claims 1, 2, 5, 13, 15-17, 20, 22, 23, 40, 69 and 70 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.
A. Claim 1 recites “(A) identifying, in a sample comprising cancer cells from the subject, a neoepitope that results from a cancer-specific mutation in an allele of a gene….wherein…
(c) the cancer-specific mutation is identified in 100% of alleles of the gene in the cancer cell”.
There is insufficient antecedent basis for the limitation of “the cancer cell” in the claim because no single cell has been previously identified. Dependent claims are rejected for encompassing the rejected limitation of claim 1.
B. Claim 16 recites “(A) identifying, in a sample comprising cancer cells from the subject, a plurality of neoepitopes each resulting from a cancer-specific mutation in an allele of a gene, wherein
(a) the cancer-specific mutation is a single nucleotide variation, indel, or gene-fusion event;
(b) the cancer-specific mutation is identified in 100% of alleles of the gene in the cancer cell; and
(c) the gene is an essential gene”.
There is insufficient antecedent basis for the limitation of “the cancer cell” in the claim 16 part (b) because no single cell has been previously identified.
Claim 16 recites identifying a plurality of neoepitopes each resulting from a cancer-specific mutation in an allele of a gene, indicating there could are multiple neoepitopes that could result from different cancer-specific mutations on different alleles of different genes, however, the claim subsequently refers to a singular “the cancer-specific mutation” and “the gene,” indicating there is only one cancer-specific mutation and it can only result from one of a single nucleotide variation, indel or gene-fusion event, and indicating there is only one gene and it has to be an essential gene. The claim is unclear with regard to whether there can be multiple neoepitopes that could result from different cancer-specific mutations on different alleles of different genes, or if there are multiple neoepitopes resulting from only one cancer-specific mutation on one allele of one gene. The metes and bounds of the claimed invention cannot be determined.
Dependent claims are rejected for encompassing the rejected limitation of claim 16.
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.
3. Claim(s) 1, 2, 5, 13, 15-17, 20, 22, 40, 69, and 70 are rejected under 35 U.S.C. 103 as being unpatentable over US Patent Application Publication 2017/0199961, Yelensky et al, claiming priority to December 2015; as evidenced by Database of Essential Genes, KRAS (printed March 2026) and The Human Protein Atlas, KRAS (printed March 2026); in view of US Patent Application Publication 2016/0101170, Hacohen et al claiming priority to August 2013; US Patent Application Publication 2019/0247435, Velculescu et al, claiming priority to June 29, 2016; US Patent Application Publication 2011/0229504, Fritsche et al, published 2011; Soh et al (PLoS ONE, 2009, 4:e7464, internet pages 1-13); Feldhahn, M. (2013). Computational methods for personalized cancer therapy based on genomics data (Doctoral dissertation, Universitätsbibliothek Tübingen); Modrek et al (Molecular Cancer Research, 2009, 7(8):1244-1252); Kramer et al (Cellular Oncology, 2009, 31:161-167); Chaft et al (Clinical Lung Cancer, 2014, 15:405-410).
Yelensky teaches an optimized method of making a personalized neoepitope vaccine targeting cancer and generating an immune response against tumor neoantigens or neoepitopes comprising assessing several variables for neoepitope selection for the vaccine, the method comprising:
i) identifying neoepitopes that result from cancer-specific somatic mutations in an allele of a gene through sequencing, wherein the cancer-specific mutations are a single nucleotide variance (SNV), wherein the neoepitope somatic mutation is identified by genomic sequencing of tumor cells and comparing to normal cells ([143-146]; [181]; [185-195]; [260-294]; claims 1, 34, 47, 48, 51);
ii) determining the copy number of the mutated allele (“source gene”) comprising the cancer-specific somatic mutation, wherein neoepitope peptides (comprising the somatic mutation) encoded by genes that are subject to homozygous deletion in tumor cells can be assigned a probability of zero for peptide presentation by the immune system (an “allele non-interacting variable”; [145]; [336]; [379]; claim 50m);
wherein the source gene includes known cancer driver genes such as EGFR and KRAS (claim 50; [145]; [339]); wherein the tumor mutation includes KRAS G12D point mutation ([382]);
iii) determining the expression level of the mutated allele or “source gene” encoding the neoepitope peptide, wherein neoepitope peptides from more highly expressed genes are more likely to be presented to the immune system, and peptides from genes with undetectable levels of expression can be excluded from consideration (an “allele non-interacting variable”; [327]; [329]; [349]; [376]; claim 13, claim 50f, g);
iii) determining MHC/HLA binding affinity and likelihood of presentation for the neoepitope and selecting a neoepitope that has high binding affinity and likelihood of presentation to induce a neoepitope-specific T cell response (an “allele-interacting variable” [137-139]; [144]; [149-153]; [174-175]; [201]; [219]; [301-319]; [366-371]; claims 1-5 and 54);
iii) selecting neoepitope sequences for inclusion in the personalized neoepitope vaccine with priority given to neoepitopes that: (1) have a high probability of immunogenicity and elicit a T cell response; (2) have a higher probability of MHC presentation; (3) have higher gene expression; (4) cover a larger number of the patient’s HLA molecules involved in presentation of the neoantigen to reduce probability that tumor will escape immune attack ([238]; claim 54);
vi) producing a vaccine that comprises an RNA encoding a peptide or polypeptide comprising the selected neoepitopes ([199-220]; [252]; [257-259]; claims 33-46 and 53);
wherein the gene harboring the somatic mutation is a known cancer driver gene ([145]; [261]; [339]; [349]; claim 50p);
wherein the cancer is lung, breast, ovarian and several other solid tumors ([147]; [197]; [240]; claim 52);
wherein the neoepitopes included in the vaccine can be “truncal peptides” that are prioritized as being presented by all or most tumor subclones in order to maximize the number of tumor subclones covered by the vaccine ([231]); and
administering the vaccine to the patient ([148]; [239-256]; claim 33).
As evidenced by the Database of Essential Genes (DEG), KRAS is listed an essential gene, therefore Yelensky teaches essential gene KRAS.
As evidenced by The Human Protein Atlas, KRAS is a gene inherently expressed in a plurality of different tissues.
Yelensky teaches prioritizing inclusion of truncal peptide neoepitopes in the vaccine that are presented by all or most tumor subclones in the tumor cell population in order to maximize the number of tumor subclones covered by the vaccine, but does not teach the mutations are homozygous where 100% of alleles of the gene contain the mutation (claims 1 and 16).
Although Yelensky teaches selecting neoepitopes that have higher expression levels and have detectable copy numbers for inclusion in the vaccine, Yelensky does not teach the “source genes” comprising the selected neoepitopes have a copy number greater than 2 or 10 in a cancer cell or in all cancer cells (claims 1, 5, 22, and 69).
Although Yelensky teaches neoepitopes included in the vaccine can be “truncal peptides” that are prioritized as being presented by all or most tumor subclones in order to maximize the number of tumor subclones covered by the vaccine, Yelensky does not teach the selected truncal neoepitope has a copy number greater than 2 in at least half the cancer cells of the sample (claim 20).
Hacohen teaches a method of making a personalized neoepitope vaccine targeting cancer that results from cancer-specific mutation in an allele of a gene, the method comprising:
(i) determining in a tumor cell sample from a cancer patient, the presence of a somatic mutation by whole exome sequencing, wherein the somatic mutation is not present in normal cells (neoepitope), and wherein the mutation is a single nucleotide variation (Figures 1, 4A, and 10; [8-16]; Example 23; [108-111]; [120-132]; [280]; claims 1, 2, 20);
(ii) maximizing likelihood the immune system will generate an attack against the tumor of the patient by the vaccine by:
(a) determining that the somatic mutation is expressed in the tumor ([279]; [413]; Examples 7, 18, [453], and 23, [478], [494-495]; Figure 10);
(b) selecting neoepitope peptides comprising somatic mutations that bind to the patient’s particular MHC/HLA molecules and with high affinity ([112-114]; [280]; Examples 7, 15, 16, and 23, [491]; claims 1, 3, 4, 9, 10, 21, 27, 28; Figures 8 and 10);
(c) selecting neoepitope peptides that have higher expression levels ([413]; Examples 7 and 15);
(d) selecting neoepitope peptides from oncodriver genes such as EGFR and KRAS ([121]; [140]; Example 7, [412], [415]; [480]; Table 34);
(iii) producing the personalized neoepitope vaccine comprising RNA encoding the selected neoepitope peptides ([13]; [24]; [149]; [152-165]; [172-174]; [277-281]; [315-326]; claims 1, 8);
(iv) administering the vaccine to the cancer patient to treat cancer, wherein the vaccine elicits a specific cytotoxic T cell (CTL) response against the cancer cells expressing the neoepitope (Figures 1, 5-7 and 10; [18]; [28-29]; [104]; [172-180]; [315-319]; Example 6, 10 and 11; claims 1, 2, 19-38).
Hacohen teaches further characterizing the somatic mutations by utilizing the ABSOLUTE algorithm (Carter et al, 2012) to estimate tumor purity, ploidy, absolute copy numbers, and clonality of the neoepitope mutation. Hacohen et al teach probability density distributions of allelic fractions of the mutation can be generated followed by conversion to cancer cell fractions (CFFs) of the mutation. Mutations can be classified as clonal or subclonal based on whether the posterior probability of their CCF exceeds 0.95 is greater or less than 0.5 respectively. Hacohen teaches that “clonal” mutations are those that are found in all cancer cells within a tumor. Hacohen suggests that clonal mutations may be prioritized in the design of neoepitope vaccines ([392-393]; Example 22; [470-477]). Hacohen et al suggest that when detecting cancer mutations, tumor samples should have more DNA copy number variation than matched normal tissue ([381]).
Hacohen suggests detecting a somatic cancer mutation in KRAS or EGFR oncogenic-driver (cancer-driver) gene as a neoepitope (Table 34) and that oncogenic driver genes represent a high priority group for inclusion in the vaccine ([121]; [140]; Example 7, [412], [415]). Hacohen teaches because clonal evolution is a fundamental feature of cancer, it has been posited that immunologic targeting of cancer drivers would have the advantage of minimal antigenic drift, given their essentiality in tumor function that would require them to be maintained in the face of selective pressure ([480]). Hacohen further teaches their results demonstrate that targeting truncal (“trunk”) or clonal mutations is impactful from an immunological standpoint, regardless of mutation being a passenger or driver mutation. Hacohen demonstrated that mutations that were both passenger mutations (not driver mutations) and clonal (truncal), affected the bulk of the cancer mass and should be prioritized for vaccine selection (Example 22; [480]).
Velculescu teaches a method of making a personalized neoepitope vaccine targeting cancer that results from cancer-specific mutation in an allele of a gene, the method comprising:
(i) determining in a tumor cell sample from a cancer patient, the presence of somatic mutations and copy number alterations by whole exome sequencing that are not present in normal cells, wherein the somatic mutations encompass single base and amino acid substitutions, wherein the mutations are detected by whole exome sequencing, wherein the mutations were found in cancer driver genes;
(ii) assessing or predicting the immunogenicity of the somatic mutations by evaluating binding of epitopes comprising the somatic mutation to the patient’s MHC class I haplotype in order to identify epitopes that will stimulate an epitope-specific T cell response;
(iii) assessing expression levels of the mutations in coded proteins;
(iv) determining gene copy number of the allele comprising the mutation, including copy numbers greater than 2;
(v) assessing allelic imbalance by: (a) determining mutant allele frequency, tumor purity and ploidy to provide “mutation cellularity” that is the fraction of cancer cells in the sample harboring the somatic mutation; (b) identifying mutations as clonal (“truncal”) or subclonal, wherein a cellularity of >75% differentiates truncal from subclonal mutations;
(vi) verifying and selecting neoepitopes comprising the somatic mutations that are expressed by the tumor and have high MHC affinity and high cellularity;
(vii) formulating a personalized vaccine comprising a neoepitope peptide that has a high HLA haplotype binding affinity and a high cellularity (a high fraction of tumor cells comprising the neoepitope mutation, “truncal” or clonal); and
(viii) administering the vaccine to the cancer patient to treat cancer (abstract; Figures 1 and 3; [12-16]; [15-23]; [80]; Examples 2-6; claims 1-57).
Fritsche teaches making a peptide vaccine to treat a patient having cancer, comprising selecting and administering an immunogenic epitope overexpressed by the patient’s cancer, wherein the immunogenic epitope is present in high concentrations in the tumor by increased gene copy number/cell, wherein the immunogenic epitope is recognized by the patient’s cytotoxic T cells and able to bind the patient’s MHC ([19-23]; [61]; [73]). Fritsche teaches the importance of the immunogenic epitope having high copy numbers in tumor cells and not normal cells in order to prevent an undesired autoimmune reaction against normal cells in the patient when the immunogenic epitope vaccine is administered ([73]). Fritsche teaches tumor-specific and tumor-associated antigens used in their vaccine are often derived from proteins directly involved in transformation of a normal cell to a tumor cell ([19]). Fritsche identified immunogenic HLA-binding KRAS epitopes for vaccine production and administration ([179]; Table 2; [212]; [213]).
Feldhahn teaches selecting neoepitopes for producing personalized peptide vaccine therapy. Feldhahn teaches identifying somatic mutations in tumors (particularly SNVs), generating peptides containing the mutation, determining HLA-binding efficacy to patient’s HLA type, and selecting them for peptide vaccine production (section 5.4; p. 73-75). Feldhahn teaches the mutations can be heterozygous or homozygous (100% alleles contain the mutation) (p. 75, step 4). Feldhahn teaches this approach is individualized with respect to the patient’s tumor and immune system, in order to identify effective T-cell epitopes derived from somatic mutations for production of an epitope-based vaccine (p. 57). Further, Feldhahn recognizes that next generation sequencing is used to identify cancer-associated genes altered by SNVs or indels, changes in copy number that can result upregulation of gene, and gene expression levels (chapter 3).
Soh recognizes that mutant allele specific imbalance (MASI) is a characteristic of activating mutations contributing to tumorigenesis. Soh determined that 1) mutational status; 2) copy number gains (CNGs), and 3) relative ratio between mutant and wild type alleles of KRAS, EGFR, BRAF, and PIK3CA by direct sequencing of tumor cell lines, human tumors, and xenograft tumors identified homozygous mutations of the oncogenes were frequent. Soh determined that there are two major forms of MASI: 1) MASI with copy number gains (CNGs), and 2) MASI without CNG due to complete loss of wild-type allele (UPD) (abstract; Figure 1; Discussion p. 9). MASI was a frequent event in KRAS and EGFR genes (abstract). Soh concludes that MASI is frequently present in mutant EGFR and KRAS tumor cells, and is associated with increased allele transcription (increased expression) and increased gene activity (abstract). Soh identified EGFR and KRAS mutations existing as homozygous in cancer cells (Figure 1; Table 1) and teach homozygous mutations (complete MASI) of oncogenes are frequent in tumor cells (Results, p. 5-6; Table 1). Soh determines allelic imbalance (AI) of CNGs of KRAS and EGFR genes using SNP data, and determined MASI with CNG occurs frequently in EGFR and KRAS (p. 6, col. 2; Figure 3 and 5; Table 2).
Soh teaches KRAS mutations or KRAS CNGs were significantly associated with increase ras GTPase activity, and the two molecular changes were synergistic (abstract). Soh teaches that while mutations, CNGs, and allelic imbalance of mutations may all contribute to tumorigenesis, combinations of the three events may be more effective than any single event. Evidence for this concept was provided by their finding that the combination of mutation and CNGs acted synergistically to enhance ras GTPase activity. Soh concludes their study demonstrates evidence that the combination of KRAS mutations and CNGs act synergistically (p. 11, col. 2). Soh teaches that understanding CNG and MASI occurring together in tumor cells may contribute to the development of rational targeted therapies (p. 11, col. 2).
Modrek teaches and successfully demonstrates detecting both copy number gain and allelic frequency of KRAS and EGFR mutations, and identified tumor cells that were homozygous for 215G>T (G12C) KRAS mutant allele (p. 1249, col. 2 to p. 1250, col. 1; Table 1; Materials and Methods). Modrek determined mutant KRAS copy number gains are correlated to increase mutant KRAS expression, including copy number gains greater than 2. Modrek demonstrates the correlation between KRAS mutation copy number gain and expression level is linear, wherein copy number gains of greater than 10 are expected to have increased expression levels (p. 1245, col. 2; Figures 1-3). Modrek observed somatic tumor mutations in KRAS gene including G12C, G12D, G12A, G12V, and G13C (p. 1249, col. 2).
Kramer teaches and successfully demonstrates detecting allelic frequency of KRAS somatic mutations in tumor cells, and identified KRAS G12C mutation as homozygous (present in 100% of alleles) in both a tumor cell line and a patient NSCLC tumor sample (Figure 1; p. 164, col. 1-2; p. 165, col. 1). Kramer detected the allelic frequency of KRAS somatic mutations G12C, G12D, G12A, G12S, G12V, G13C, and G13D in tumor cells and NSCLC and CRC patient tumor samples (Tables 2 and 3).
Chaft demonstrates successfully treating NSCLC patients identified as having KRAS G12A, G12V, G12C, and/or G12D somatic mutations by administering to the patients a peptide vaccine (GI-4000) comprising the somatic mutation that their tumor expresses (Table 1 and 3; p. 406, col. 2 to p. 407 col. 1, Patent Selection, Study Design and Intervention; p. 407 Results). Chaft teaches the vaccine successfully induced a T cell immune response to the mutant epitopes and increased overall survival (abstract; Figures 1 and 2; p. 408, col. 1-2). Chaft teaches G1-4000 vaccine has been administered clinically to KRAS-mutant malignancies including pancreatic cancer and colorectal cancer with success (p. 409, col. 1-2).
Selecting a neoepitope mutation that is homozygous in cancer cells:
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was filed to select neoepitopes that have copy numbers greater than 2 or 10 and are homozygous, in the optimized method of making the personalized neoepitope vaccine taught by Yelensky. One would have been motivated to because: (1) Yelensky, Hacohen, Velculescu, Feldhahn, and Chaft all teach the goal of producing the personalized vaccine is to select and make immunogenic neoantigen epitopes that are expressed by the patient’s tumor and will bind to the patient’s MHC to induce an effective neoantigen-specific T cell immune response against the tumor; (2) Yelensky, Hacohen, Velculescu, and Feldhahn all teach selecting neoepitopes for personalized vaccine production from cancer-driver genes, such as KRAS, and teach assessing mutant gene copy number, mutant allele frequency, expression levels, and binding affinity to the patient’s MHC during selection; (3) Yelensky teaches and recognizes including neoepitope mutations in the vaccine that are present on an allele in the patient’s cancer cell, and excluding neoepitope mutations with two deleted copies because those are not likely to be presented to the immune system; and Feldhahn also teaches selecting neoepitopes for personalize vaccine that can either be present on one (heterozygous) or both alleles (homozygous); and (3) Soh teaches homozygosity of somatic mutations is common in cancer and a frequent event for EGFR and KRAS somatic tumor mutations. One of ordinary skill in the art would have a reasonable expectation of success to select somatic mutation neoepitopes that are homozygous in cancer cells because: (1) the cited references teach and demonstrate that methods for detecting allelic frequency (heterozygosity or homozygosity) are well established and utilized for characterizing SNV mutations in tumors and in EGFR and KRAS oncodriver gene, and these methods are utilized for identification of therapeutically targetable tumor genes and selection of neoepitopes in personalized vaccines; (2) Chaft teaches and demonstrates cancers identified as expressing KRAS mutations are successfully treated with personalized peptide vaccines comprising their somatic tumor mutations and the vaccines elicit a neoepitope-specific T cell immune response; and (3) Soh, Modrek, and Kramer all demonstrate the KRAS mutations comprised in the successful personalized vaccine of Chaft occur in tumor cells as homozygous and are expressed by the tumor cells.
Selecting a neoepitope mutation that also has a copy number greater than 2 or 10 in cancer cells:
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was filed to select homozygous neoepitopes that also have copy numbers greater than 2 or 10, in the optimized method of making the personalized neoepitope vaccine taught by Yelensky. One would have been motivated to because: (1) Yelensky, Hacohen, Velculescu, Fritsche, Feldhahn, and Chaft all teach the goal of producing the personalized vaccine is to select and make immunogenic neoantigen epitopes that are expressed by the patient’s tumor and will bind to the patient’s MHC to induce an effective neoantigen-specific T cell immune response against the tumor; (2) Yelensky, Hacohen, Velculescu, Fritsche, and Feldhahn all teach selecting neoepitopes for personalized vaccine production from cancer-driver genes, such as KRAS, and teach assessing mutant gene copy number, mutant allele frequency, expression levels, and binding affinity to the patient’s MHC during selection; (3) the references teach selecting neoepitopes for vaccine production that are cancer driver genes, such as KRAS, having increased expression levels or copy number gains, wherein Soh and Modrek demonstrate a linear relationship between increasing copy numbers of KRAS mutations and increasing KRAS mutation expression levels and activity, confirming increasing copy numbers as a mechanism of increased expression; (4) Fritsche teaches the importance of selecting immunogenic peptides having increased copy numbers in tumor cells because it contributes to targetable tumor overexpression and minimizes autoimmune response to normal cells; and (4) Soh teaches KRAS mutations can occur as MASI complete (homozygous) and have CNG. One of ordinary skill in the art would have a reasonable expectation of success to select somatic cancer-specific mutation neoepitopes that are homozygous and have copy numbers greater than 2 or 10 in cancer cells because: (1) The cited references all teach and demonstrate that methods for detecting all of somatic mutation/SNV, gene copy number, and allelic frequency (homozygosity) are well established and utilized for characterizing SNV mutations in tumors and in KRAS oncodriver gene, and these methods are utilized for identification of therapeutically targetable tumor genes and selection of neoepitopes in personalized vaccines; (2) Chaft teaches and demonstrates cancers identified as expressing KRAS mutations are successfully treated with personalized peptide vaccines comprising their somatic tumor mutations and the vaccines elicit a neoepitope-specific T cell immune response; (3) Soh demonstrates that KRAS mutations occur as homozygous and have CNGs, and teach these features contribute to malignant phenotype; and (4) Soh, Modrek, and Kramer all demonstrate the KRAS mutations comprised in the successful vaccine of Chaft occur in tumor cells as increased in copy numbers greater than 2, increased in expression levels, and homozygous.
Given: (1) the demonstrated success of the personalized KRAS mutation vaccine of Chaft in the treatment of cancers expressing the KRAS mutations and induction of neoepitope-specific T cell immune responses, (2) these KRAS mutations are known to be expressed in tumor cells having increased KRAS gene copy numbers, homozygosity, and increased expression, are known to contribute to malignant phenotype, and are known to be therapeutic targets for cancer treatment, and (3) methods for assessing gene copy number gains and allele frequency of KRAS somatic tumor mutations are routine; it is well within the level of the ordinary skilled artisan to assess gene copy number gains and homozygosity of these KRAS mutations in patient cancer cells, and to select these KRAS mutations for personalized peptide vaccine treatment of cancer patients expressing the KRAS mutations, when the patients are expressing the KRAS mutations as a result of being homozygous and having CNGs greater than 2 or 10, with a reasonable expectation of success.
Copy number of mutated allele is greater than 2 in a clonal fraction of at least 0.5 (50%) of cancer cells:
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was filed to select neoepitopes that have a copy number greater than 2 in at least half the cancer cell of the sample. One would have been motivated to and have a reasonable expectation of success to because: (1) of the reasons stated above for selecting neoepitopes having copy numbers greater than 2; (2) Yelensky suggests neoepitopes included in the vaccine are “truncal peptides” that are prioritized as being presented by all or most tumor subclones in order to maximize the number of tumor subclones covered by the vaccine, therefore the mutant alleles occur at high frequency in the tumor sample; (3) Hacohen suggests determining absolute copy number and the fraction of tumor cells comprising the mutation, and classifying mutations as clonal or subclonal, and Hacohen specifically suggests prioritizing clonal mutations for production of the neoepitope vaccine, wherein at least 50% alleles in the cell sample comprise the mutation for a clonal population; (4) Velculescu teaches motivation to screen for and select neoepitopes comprising somatic mutation for personalized cancer vaccines that are clonal (truncal) and have high gene copy number and high allelic fraction values; (5) Soh established that mutant allele specific imbalance (MASI) is a characteristic of activating mutations contributing to tumorigenesis and Soh demonstrates allelic imbalance (AI) of CNGs occurs frequently in KRAS mutants; (6) Soh, Modrek, and Kramer demonstrate successfully detecting allelic frequency of 100% and copy number gains greater than 2 for KRAS somatic mutations in tumor cells, wherein Kramer successfully identified a patient’s tumor cell sample as being completely homozygous for KRAS mutation G12C; and (7) Soh teaches simultaneous presence of mutation, CNGs, and allelic imbalance all contribute to tumorigenesis synergistically, and should be therapeutically targeted. As stated above, the cited prior art teaches identifying and selecting truncal (highly clonal) mutant peptides for vaccine inclusion, and teaches motivation and expectation of success to select mutations that have copy number gains greater than 2. Given both criteria are readily measurable and identified as criteria for neoepitope vaccine inclusion, it is well within the level of the ordinary skill artisan to include neoepitopes that are both truncal and have CNG greater than 2.
4. Claim(s) 23 is rejected under 35 U.S.C. 103 as being unpatentable over US Patent Application Publication 2017/0199961, Yelensky et al, claiming priority to December 2015; as evidenced by Database of Essential Genes, KRAS (printed March 2026); US Patent Application Publication 2016/0101170, Hacohen et al claiming priority to August 2013; US Patent Application Publication 2019/0247435, Velculescu et al, claiming priority to June 29, 2016; US Patent Application Publication 2011/0229504, Fritsche et al, published 2011; Feldhahn, M. (2013). Computational methods for personalized cancer therapy based on genomics data (Doctoral dissertation, Universitätsbibliothek Tübingen); Modrek et al (Molecular Cancer Research, 2009, 7(8):1244-1252); Kramer et al (Cellular Oncology, 2009, 31:161-167); and Chaft et al (Clinical Lung Cancer, 2014, 15:405-410), as applied to claims 1, 2, 5, 13, 15-17, 20, 22, 40, 69, and 70 above, and further in view of Carter et al (Nature Biotechnology, 2012, 30:413-421 and Online Methods).
Yelensky, Hacohen, Velculescu, Fritsche, Feldhahn, Modrek, Kramer, and Chaft (the combined references) teach a method of making a personalized cancer vaccine for a patient comprising:
(A) identifying in a sample of cancer cells form the subject, a neoepitope resulting from a cancer-specific somatic mutation in an allele of a gene, wherein:
(i) the cancer-specific mutation is an SNV;
(ii) the mutated allele comprising the cancer-specific mutation has a copy number greater than 2; and
(iii) the cancer-specific mutation is identified in 100% of alleles of the gene in the cancer cell (homozygous);
(B) selecting at least one neoepitope that full fills (i)-(iii) as a suitable neoepitope for including in a personalized vaccine for the patient; and
(C) producing the personalized vaccine, wherein the vaccine comprises RNA encoding a peptide or polypeptide comprising the selected neoepitope;
wherein the gene is KRAS which is an essential gene, as set forth above.
As stated above Hacohen suggests determining gene copy numbers comprising the neoepitope mutations based on ABSOLUTE copy numbers.
The combined references do not exemplify utilizing using ABSOLUTE to determine gene copy numbers.
Carter et al teach the method of using ABSOLUTE, referenced by Hacohen et al, to determine somatic mutation absolute gene copy number, tumor purity and ploidy. Carter et al explain the motivation and advantage of using ABSOLUTE to determine copy number:
Pages 413-414:
Measuring somatic copy-number alterations (SCNAs) on a rela-tive basis is straightforward using microarrays or massively paral-lel sequencing technology; it has been the standard approach for copy-number analysis since the development of comparative genomic hybridization (CGH).
The meaning of such measurements is dependent on the tumor’s purity and its overall ploidy; they are hence complicated to inter-pret and compare across samples. Ideally, copy number should be measured in copies per cancer cell. Such measurements are straight-forward to interpret and, for alterations that are fixed in the cancer cell population, are simple integer values. This is considerably more challenging than measuring relative copy number in units of diploid DNA mass in a tumor-derived sample.
Inferring absolute copy number is more difficult for three reasons: (i) cancer cells are nearly always intermixed with an unknown frac-tion of normal cells (tumor purity); (ii) the actual DNA content of the cancer cells (ploidy), resulting from gross numerical and structural chromosomal abnormalities, is unknown; and (iii) the cancer cell population may be heterogeneous, perhaps owing to ongoing subclonal evolution. In principle, one could infer absolute copy numbers by rescaling relative data on the basis of cytological measurements of DNA mass per cancer cell, or by single-cell sequencing approaches. However, such approaches are not suited to support initial large-scale efforts to comprehensively characterize the cancer genome.
We subsequently developed the fully quantitative ABSOLUTE method and applied it to several cancer genome analysis projects, including The Cancer Genome Atlas (TCGA) project. ABSOLUTE provides a foundation for integrative genomic analysis of cancer genome alterations on an absolute (cel-lular) basis. We used these methods to correlate purity and ploidy estimates with expression subtypes and to develop statistical power calculations and use them to select well-powered samples for whole-genome sequencing in several published, and numerous ongoing projects, including breast, prostate and skin cancer genome charac-terization. Recently, we extended ABSOLUTE to infer the multiplicity of somatic point-mutations in integer allelic units per cancer cell.
We describe three key mathematical features of ABSOLUTE. First, it jointly estimates tumor purity and ploidy directly from observed relative copy profiles (point mutations may also be used, if available). Second, because joint estimation may not be fully determined on a single sample, it uses a large and diverse sample collection to help resolve ambiguous cases. Third, it attempts to account for subclonal copy-number alterations and point mutations, which are expected in heterogeneous cancer samples.
We then describe how estimates of tumor purity and absolute copy number allow us to analyze allelic-fraction values (the fraction of non-reference sequencing reads supporting a mutation) to distin-guish clonal and subclonal point mutations, and to detect macro-scopic subclonal structure in an ovarian cancer sample. Clonal events may be classified as homozygous or heterozygous in the cancer cells, guiding interpretation of their function. In addition, the ability to quantify integer multiplicity of point mutations aids in the relative timing of segmental DNA copy-number gains, as multiplicity values of greater than one imply that the point mutation preceded copy gain of the locus. Controlling for tumor purity and local copy-number allow such timings to be calculated more generally than in the special case of copy-neutral loss of heterozygosity.
The output of ABSOLUTE then provides inferred information on the absolute cel-lular copy number of local DNA segments and, for point mutations, the number of mutated alleles (Fig. 1).
DISCUSSION page 420:
ABSOLUTE provides a tool for the design of studies using genomic sequencing to detect variant alleles in cancer tissue samples, based on calculation of sensitivity to detect mutations as a function of sample purity, local copy number and sequencing depth (Supplementary Fig. 7).
Copy number is absolute copy number:
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was filed to determine absolute copy number as copy number in the method of the combined references. One would have been motivated to and have a reasonable expectation of success to because: (1) Yelensky teaches determining somatic mutation copy numbers in tumor cells and frequency of presence in subclonal tumor cell populations for their method of making a neoepitope vaccine; (2) Velculescu teaches motivation to screen for and select neoepitopes comprising somatic mutation for personalized cancer vaccines that are clonal (truncal) and have high gene copy number and high allelic fraction values; (3) Hacohen suggests determining absolute copy number and the fraction of tumor cells comprising the mutation, and classifying mutations as clonal or subclonal, referencing Carter for methods of doing so, and Hacohen specifically suggests prioritizing clonal mutations for production of the neoepitope vaccine; and (4) Carter delineates known methods for determining absolute gene copy number of somatic mutations in cancer cell populations in order to analyze allelic-fraction values and distin-guish clonal and subclonal point mutations.
Response to Relevant Arguments
5. Applicants submit the Tadmor declaration under 37 CFR 1.132 and argue that the instant invention is directed to selecting neoepitopes based on zygosity and not expression levels. Applicants argue that zygosity and gene expression have different impacts on therapy efficacy, and different orthogonal biological aspects. Applicants present figures calculating probability of therapeutic efficacy of treatment increasing with increasing zygosity. Applicants argue that increasing zygosity decreases probability of tumor escape and therapeutic failure. Applicants argue that gene expression increases slowly linearly with zygosity therefore therapeutic effect achieved by overexpression requires much higher zygosities. Applicants admit that increasing zygosity results in increasing expression, but argue increased gene expression is also achieved by other means that do not have the same therapeutic effect of minimizing tumor escape. Applicants argue that zygosity is prioritized in selecting therapeutic neoepitopes and not gene expression.
6. The arguments have been considered but are not persuasive. A new rejection is set forth above addressing the claim amendments with regards to zygosity. The cited prior art demonstrates that KRAS mutations resulting in neoepitopes are already produced as a personalized vaccine and used to successfully treat cancer patients having tumors expressing the KRAS mutations, including successfully inducing a neoepitope-specific T cell immune response. The cited prior art teaches and demonstrates that KRAS mutation homozygosity in cancer cells is a frequent occurrence, demonstrates KRAS mutation with CNGs results in increased expression and malignant phenotype, teaches the combination of mutation, allelic imbalance, and copy number is expected to contribute to tumorigenesis more than any single event, and suggests therapeutically targeting these events. The cited prior art demonstrates the KRAS mutations of the successful personalized GI-4000 vaccine frequently occur as homozygous and are increased in gene copy number in tumor cells, providing a reasonable expectation of success to select them for making a personalized cancer vaccine when they are homozygous and have CNGs of greater than 2 or 10 in a patient’s tumor cells.
The Tadmor declaration provides a probability model of reducing tumor escape and enhancing therapeutic efficacy by selecting neoepitopes that have higher zygosity, however, the declaration does not demonstrate enhanced selection and therapeutic efficacy for neoepitopes above and beyond what is taught and expected by the cited prior art, particularly for the GI-4000 KRAS vaccine containing KRAS neoepitope mutations that are known to be homozygous, have CNGs, and have increased expression in tumor cells. Although the Tadmor declaration provides a theoretical comparison of the effects of zygosity versus expression level for mutations on likelihood of therapeutic efficacy, the Tadmor declaration does not demonstrate any working data/evidence demonstrating actual production of a personalized vaccine comprising a mutation that exists as homozygous in cancer cells, and does not demonstrate that such a method results in a vaccine that has superior or unexpected properties compared to a vaccine produced utilizing the exact same mutation that exists as overexpressed in a tumor cells. The resulting personalized vaccine would be the same because the same mutation was used to produce the vaccine neopeitope.
With regards to arguments that the method results in a personalized vaccine with enhanced therapeutic efficacy by reducing tumor escape in the subject from which it was made, Applicants are arguing limitations not recited in the claims. Claims 1 and 16 are directed to methods of making a personalized vaccine, and not methods of treatment, and there is no step of administering the vaccine to the subject from which it was made to enhance therapeutic efficacy. MPEP 716.02(d) states:
Whether the unexpected results are the result of unexpectedly improved results or a property not taught by the prior art, the "objective evidence of nonobviousness must be commensurate in scope with the claims which the evidence is offered to support." In other words, the showing of unexpected results must be reviewed to see if the results occur over the entire claimed range.
In the instant case, Applicants are arguing the personalized vaccine produced by the claimed method results in a vaccine having enhance therapeutic efficacy by reducing tumor escape in a subject whose cancer cells express a cancer-specific mutation that is homozygous, resulted in a neoepitope, and the neoepitope is comprised by the vaccine. However, the advantageous therapeutic effects argued by Applicants and the Tadmor declaration are relative according to who the vaccine is administered to, and no administration or therapeutic effect is required in claims 1 and 16. Therefore, Applicant’s arguments and declaration data are not commensurate in scope with the claimed invention.
With regards to claims 2 and 17 that do require administering the vaccine to the subject expressing the mutation homozygously, the Tadmor declaration does not provide persuasive evidence that the vaccine produced by the claimed method comprises superior or unexpected properties above and beyond those taught and demonstrated by the cited prior art. The declaration does not demonstrate any non-obvious advantages or enhanced therapeutic efficacy in subjects from which the vaccine was produced. Applicants admit that homozygous mutations result in enhanced expression levels, and the art teaches the advantages of selecting mutations for a personalized vaccine that have increased expression levels. Claims 2 and 17 do not exclude mutations that are both homozygous and overexpressed in the subject’s cancer cells. Additionally, the cited prior art teaches that activating somatic tumor mutations occur frequently as homozygous, particularly in EGFR and KRAS genes, and demonstrate a personalized KRAS neoepitope vaccine successfully treats and induces a neoepitope-specific T cell immune response in patients having cancer expressing the KRAS mutation resulting in the neoepitope. The cited prior art also demonstrates that the mutations utilized to make the KRAS neoepitope personalized vaccine frequently occur as homozygous, increased in copy numbers, and increased in expression levels in cancer cells. Therefore, the cited prior art provides a reasonable expectation of success for therapeutic efficacy of personalized vaccines comprising neoepitopes resulting from somatic mutations in the patient’s cancer cells and that exist as homozygous and having CNGs to any extent.
Further, the Tadmor declaration fails to demonstrate that a tumor-specific mutation expressed as homozygous in a cancer cell is the sole and critical inventive factor responsible for the vaccine to have enhanced therapeutic efficacy. All of Yelensky, Hacohen, Velculescu, Fritsche, Feldhahn, and Chaft teach the criticality of selecting neoepitopes that can be recognize, bound, and presented by the patient’s HLA/MHC so that an effective T-cell immune response can be mounted against the tumor. Hacohen teaches “driver mutations may not necessarily generate immunogenic peptides” ([480]). Fritsche teaches: “However, the identification of genes over-expressed in tumor tissues or human tumor cell lines, or selectively expressed in such tissues or cell lines, does not provide precise information as to the use of the antigens being transcribed from these genes in an immune therapy. This is because only an individual subpopulation of epitopes of these antigens are suitable for such an application since a T cell with a corresponding TCR has to be present and immunological tolerance for this particular epitope needs to be absent or minimal. It is therefore important to select only those peptides from over-expressed or selectively expressed proteins that are presented in connection with MHC molecules against which a functional T cell can be found. Such a functional T cell is defined as a T cell which upon stimulation with a specific antigen can be clonally expanded and is able to execute effector functions (“effector T cell”)” ([22]).
The cited references teach that identifying a cancer-specific mutation, regardless of zygosity and expression levels, provides no information on its ability to induce an effective immune response and to function as a personalized vaccine. Testing is required to identify which mutations result in immunogenic epitopes that bind to a patient’s HLA/MHC. All of Yelensky, Hacohen, Velculescu, Fritsche, and Feldhahn, demonstrate, after identifying neoepitopes resulting from somatic tumor-specific mutations, making different peptides comprising the mutations and testing their ability to bind to a MHC and induce a neoepitope-specific T cell response (in silico or actual), where they vary greatly in their potential for inducing an immune response and therapeutic efficacy. Therefore, identifying and selecting a cancer-specific mutation that is homozygous in a tumor cell and making a peptide comprising the mutation does not necessitate, nor reasonably extrapolate to, a peptide having any predictably enhanced therapeutic efficacy or even functioning as a personalized cancer vaccine. The Tadmor declaration does not provide persuasive evidence that homozygous mutations utilized for production of a peptide vaccine predictably induce an immune response or have therapeutic improvements/properties non-obvious or superior to the therapeutic efficacy of the personalized vaccines taught and made by the cited prior art.
7. All other rejections recited in the Office Action mailed July 17, 2025 are hereby withdrawn in view of amendments.
8. Conclusion: No claim is allowed.
Conclusion
9. 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.
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/Laura B Goddard/Primary Examiner, 1642