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, (1) selecting the subject for a therapy with a platinum-based agent if (i) the tumor sample has a wild-type BRCA1/2 gene mutational status and an immune signature above a threshold level, or (ii) the tumor sample has a mutated BRCA1/2 gene mutational status; (2) designating the subject as a good responder to a therapy with a platinum-based agent based on the BRCA1/2 gene mutational status of the tumor sample; (3) the subject is designated as a good responder if the tumor sample has a mutated BRCA1/2 gene mutational status; (4) the immune signature is a M1 macrophage immune signature generated using an algorithm capable of estimating abundances of member cell types in a mixed cell population using
gene expression data; and (5) cisplatin. in the reply filed on 1/15/2026 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Claims 22-23 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 1/15/2026.
Priority
The instant application was filed 07/13/2023 and is a National Stage entry of PCT/US2022/011767 with an international filing date: 01/10/2022 and claims priority from provisional application 63232907 , filed 08/13/2021 and claims priority from provisional application 63137853 , filed 01/15/2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 12/13/2023 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 Objections
Claim 1-6, 9-11, 14-20 and 34 is objected to because of the following informalities:
Claim 1 recites, “a method.” Claims are clearer and more concise when the preamble sets forth the intended outcome of the claim.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-6, 9-11, 14-20 and 34 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 claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Independent claim 1 is drawn to “A method comprising: assaying a tumor sample from a subject for a wild-type BRCA1 and BRCA2 (BRCA1/2) gene mutational status; and assaying for an immune signature in the tumor sample.”
Thus the claims encompass any tumor sample from any subject from any species. This is an enormous genus of subject and cancers.
Further the claim 1 encompasses any which can be considered by immune signature by any standard. This is an enormous genus.
Dependent claims provide limitations requiring selecting treatment basis on the immune signature being above or below a threshold. Thus immune signature thus requires a calculation. While the specification teaches, “An immune signature may be assessed using one or more of a variety of different assays and algorithms known or later developed. For example, an immune signature may be generated using an algorithm capable of estimating abundances of member cell types in a mixed cell population using gene expression data (e.g., RNA-SEQ data). The output of such an algorithm is an abundance score for member cell types. The abundance score may be based on all immune cell types or a subset of immune cell subtypes, for example. In some embodiments, the algorithm used to estimate abundance of member cell types in a mixed cell population is trained on all immune cell subtypes (e.g., lymphoid cells and/or myeloid cells). In some embodiments, the algorithm used to estimate abundance of member cell types in a mixed cell population is trained on a subset of immune cell subtypes. Non-limiting examples of algorithms that could be used are associated with the following computational tools: the Microenvironment Cell Populations-Counter (MCP-counter) (Becht et al., 2016, incorporated by reference herein), the University of San Francisco xCell webtool, the Tumor Immune Estimation Resource (TIMER), and CIBERSORT (Chen et al. 2018, incorporated by reference herein).”The specification does not provide specific guidance on how an immune signature is calculated or how to select or provide a threshold.
Burgin (Journal of Mammalogy, 99(1):1–14, 2018) teaches, “We found 6,495
species of currently recognized mammals.”
Modrek (Nucleic Acid Research (2001) volume 29, pages 2850-2859) teaches they assayed more than 2.1 million mRNA and EST transcripts.
Thus while the claims encompass an enormous genus of species, cancers, mRNA, immune signature, etc. the teachings of the specification are limited to humans with triple negative breast cancer or ovarian cancer. The specification does not specifically disclose what is required of immune signature or how to calculate. Thus the claims lack adequate written description for the genus of the independent claims.
Claims 2-4, 6 provide limitations with respect to a threshold. The specification provides no specific guidance on how to determine the threshold level. In one instance the specification teaches threshold level (i.e. media). However, the claims are drawn to a single subject, thus the specification does not provide written description of how to determine a threshold based on a single sample.
Further claims 10 and 11 provide limitations provide limitations with respect to algorithm capable of estimating abundance of member cell types or capable of calculating separate enrichment scores. While the specification provides specific programs for this, it does not teach how the programs are trained or analysis is done. Thus the claims lack adequate written description.
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.
Claims 1-6, 9-11, 14-20 and 34 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 1 recites, “wild-type BRCA1 and BRCA2 (BRCA1/2) gene mutational status.” The recitation is confusing as it is self-contradictory. It is unclear what is required as it recite wildtype and mutational status. Further it is unclear as wild-type and mutation are relative terms. Further BRCA exchange (https://brcaexchange.org/about/variation, downloaded 7/29/2026) teaches, “Benign variants are not associated with any markedly increased risk of disease. Variants of uncertain significance (VUS) are those for which the evidence of disease risk is not clear yet, sometimes because there is not yet enough evidence to classify them as either pathogenic or benign.” Thus the metes and bounds are unclear how benign variants affect selecting therapy.
Further claim 1 recites, “assaying for an immune signature in the tumor sample.” Thus the claim appears to require a wet step or assaying however dependent claims require comparison to a threshold, thus suggesting a calculation. Further the specification teaches, “An immune signature may be assessed using one or more of a variety of different assays and algorithms known or later developed. For example, an immune signature may be generated using an algorithm capable of estimating abundances of member cell types in a mixed cell population using gene expression data (e.g., RNA-SEQ data). The output of such an algorithm is an abundance score for member cell types. The abundance score may be based on all immune cell types or a subset of immune cell subtypes, for example. In some embodiments, the algorithm used to estimate abundance of member cell types in a mixed cell population is trained on all immune cell subtypes (e.g., lymphoid cells and/or myeloid cells). In some embodiments, the algorithm used to estimate abundance of member cell types in a mixed cell population is trained on a subset of immune cell subtypes. Non-limiting examples of algorithms that could be used are associated with the following computational tools: the Microenvironment Cell Populations-Counter (MCP-counter) (Becht et al., 2016, incorporated by reference herein), the University of San Francisco xCell webtool, the Tumor Immune Estimation Resource (TIMER), and CIBERSORT (Chen et al. 2018, incorporated by reference herein). In some embodiments, an immune signature of a tumor sample can be assayed by generating a tumor sample CIBERSORT score of a (at least one) immune cell-specific gene expression profile. In some embodiments, one immune cell-specific expression profile is used to generate a CIBERSORT score of a tumor sample. In some embodiments, two immune cell-specific expression profiles are used to generate two CIBERSORT scores of a tumor sample and the two CIBERSORT scores are considered together. In some embodiments, a CIBERSORT score is a M1 macrophage signal in a tumor sample.” Thus it is unclear what assay provides a numerical data as encompassed by the claim.
Claim 11 recites, “algorithm capable of estimating abundances of member cell types.” The recitation suggests there are algorithms in capable of estimating abundances of member cell types.” The specification and claims provide no standard to differentiate algorithm capable of estimating abundances of member cell types from algorithm in-capable of estimating abundances of member cell types. Thus the metes and bounds are unclear.
Claim 12 recites, “immune cell-specific enrichment score generated using an algorithm capable of calculating separate enrichment scores for each pairing of a sample and gene set.” The recitation suggests there algorithm incapable of calculating separate enrichment scores for each pairing of a sample and gene set. The specification and claims do not provide a basis to differentiate algorithm incapable of calculating separate enrichment scores for each pairing of a sample and gene set from algorithm capable of calculating separate enrichment scores for each pairing of a sample and gene set. Thus the metes and bounds are unclear.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-6, 9-11, 14-20 and 34 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural correlation and mental step without significantly more. The claim(s) recite(s) the abstract idea or mental step of assaying an immune signature which based on dependent claims and the specification encompasses a calculation. Further assaying of wildtype BRCA1 and BRCA2 can broadly encompass reading a report. Further the claims provide selecting therapy, designate a good or bad responder, etc. based the immune signature and/or BRCA1/2 status . This judicial exception is not integrated into a practical application because the independent claim provide no steps which specifically depend from or otherwise integrate the judicial exception. Dependent claims which require treatment are not specific treatments. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because The claims provide no specific reagents or steps which provide for significantly more. .
Claim analysis
The instant claim 1 is directed towards a method comprising: assaying a tumor sample from a subject for a wild-type BRCA1 and BRCA2 (BRCA1/2) gene mutational status; and assaying for an immune signature in the tumor sample
The specification teaches, “The experimental data provided herein was generated using (a) a detailed analysis of whole genome sequence (WGS) data, (b) treatment response studies from three cohorts of patients having triple negative breast cancer (TNBC) or ovarian cancer“. Further the specification teaches, “An immune signature may be assessed using one or more of a variety of different assays and algorithms known or later developed. For example, an immune signature may be generated using an algorithm capable of estimating abundances of member cell types in a mixed cell population using gene expression data (e.g., RNA-SEQ data). The output of such an algorithm is an abundance score for member cell types. The abundance score may be based on all immune cell types or a subset of immune cell subtypes, for example. In some embodiments, the algorithm used to estimate abundance of member cell types in a mixed cell population is trained on all immune cell subtypes (e.g., lymphoid cells and/or myeloid cells). In some embodiments, the algorithm used to estimate abundance of member cell types in a mixed cell population is trained on a subset of immune cell subtypes. Non-limiting examples of algorithms that could be used are associated with the following computational tools: the Microenvironment Cell Populations-Counter (MCP-counter) (Becht et al., 2016, incorporated by reference herein), the University of San Francisco xCell webtool, the Tumor Immune Estimation Resource (TIMER), and CIBERSORT (Chen et al. 2018, incorporated by reference herein). In some embodiments, an immune signature of a tumor sample can be assayed by generating a tumor sample CIBERSORT score of a (at least one) immune cell-specific gene expression profile. In some embodiments, one immune cell-specific expression profile is used to generate a CIBERSORT score of a tumor sample. In some embodiments, two immune cell-specific expression profiles are used to generate two CIBERSORT scores of a tumor sample and the two CIBERSORT scores are considered together. In some embodiments, a CIBERSORT score is a M1 macrophage signal in a tumor sample.” Thus the assaying steps can broadly be interpreted to encompass reading reports or calculating scores, which are mental steps.
Claims 2-4 provide for selecting therapy, which is a mental step.
Claims 5-6 and 9 require designating good or poor responders. This is a mental step or abstract idea.
Claim 10 and 11 provide for the use of algorithm or calculations. Thus these are abstract ideas or mental steps.
Claim 13 provides the immune signature is based on measurement of one or more immune gene sets.
Claims 13, 14, 34 limit the claims to a specific cancer.
Claims 16-20 provide for the treatments.
According to the 2019 Patent Eligibility Guidance an initial two step analysis is required for determining statutory eligibility.
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter? In the instant case the Step 1 requirement is satisfied as the claims are directed towards a process.
Step 2A Prong one. Does the claim recite a law of nature, a natural phenomenon or an abstract idea? Yes, the independent claims encompass reading reports and/or calculating in view of the specification which are mental steps or abstract ideas.
Dependent claims as detailed above provide correlating naturally occurring immune signatures or BRCA1/BRCA2 status with response to treatment, selecting treatment or generally applying the natural correlation.
Step 2A prong two. Does the claim recite additional elements that integrate the judicial exception into a practical application? The answer is no as the claims provide no steps which integrate the claim with more than a high level of generality.
Step 2B. Does the claim recite additional elements that are significantly more than the judicial exceptions? No
With regards to claim 1 the claim provide assaying steps, however, the specification teaches, “The experimental data provided herein was generated using (a) a detailed analysis of whole genome sequence (WGS) data, (b) treatment response studies from three cohorts of patients having triple negative breast cancer (TNBC) or ovarian cancer“. Further the specification teaches, “An immune signature may be assessed using one or more of a variety of different assays and algorithms known or later developed. For example, an immune signature may be generated using an algorithm capable of estimating abundances of member cell types in a mixed cell population using gene expression data (e.g., RNA-SEQ data). The output of such an algorithm is an abundance score for member cell types. The abundance score may be based on all immune cell types or a subset of immune cell subtypes, for example. In some embodiments, the algorithm used to estimate abundance of member cell types in a mixed cell population is trained on all immune cell subtypes (e.g., lymphoid cells and/or myeloid cells). In some embodiments, the algorithm used to estimate abundance of member cell types in a mixed cell population is trained on a subset of immune cell subtypes. Non-limiting examples of algorithms that could be used are associated with the following computational tools: the Microenvironment Cell Populations-Counter (MCP-counter) (Becht et al., 2016, incorporated by reference herein), the University of San Francisco xCell webtool, the Tumor Immune Estimation Resource (TIMER), and CIBERSORT (Chen et al. 2018, incorporated by reference herein). In some embodiments, an immune signature of a tumor sample can be assayed by generating a tumor sample CIBERSORT score of a (at least one) immune cell-specific gene expression profile. In some embodiments, one immune cell-specific expression profile is used to generate a CIBERSORT score of a tumor sample. In some embodiments, two immune cell-specific expression profiles are used to generate two CIBERSORT scores of a tumor sample and the two CIBERSORT scores are considered together. In some embodiments, a CIBERSORT score is a M1 macrophage signal in a tumor sample.” Thus the assaying steps can broadly be interpreted to encompass reading reports or calculating scores, which are mental steps.
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.
Claim(s) 1-6, 9-11, 13, 15-18, 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Heindl (NATURE COMMUNICATIONS| (2018) 9:3917 |DOI: 10.1038/s41467-018-06130-3).
The specification provides numerous embodiments encompassed by immune signature, but does not provide a limiting definition. Further dependent claims provides limitations suggesting immune signature provides a value, but the specification provides no limiting definition of what the calculation is done. Thus the broadest reasonable interpretation of immune signature is anything that can be used to evaluate immune status or response to chemotherapies,
With regards to claim 1, Heindl teaches detection of BRCA1 and BRCA2 mutation status (page 4, 1st column, last paragraph). Heindl teaches immune signature detect (page 4, column 2, last paragraph).
With regards to claim 2, 4Heindl teaches, “FANCG is one of the six genes associated with Fanconi anemia that governed the Fanconi anemia-BRCA (FANC-BRCA) pathway together with BRCA1/241.Disruption of this pathway can induce cisplatin resistance.” (page 8, 2nd column)
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to treat subjects with intact Fanconi anemia-BRCA (FANC-BRCA) with cisplatin. The artisan would be motivated as Heindl suggest disruption of Fanconi anemia-BRCA (FANC-BRCA) provides for cisplatin resistance. The artisan would have a reasonable expectation of success as the art suggest the correlation was known.
With regards to claim 3, 4Heindl teaches, “FANCG is one of the six genes associated with Fanconi anemia that governed the Fanconi anemia-BRCA (FANC-BRCA) pathway together with BRCA1/241.Disruption of this pathway can induce cisplatin resistance.” (page 8, 2nd column)
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to treat subjects with disrupted Fanconi anemia-BRCA (FANC-BRCA) with something other than cisplatin. The artisan would be motivated as Heindl suggest disruption of Fanconi anemia-BRCA (FANC-BRCA) provides for cisplatin resistance. The artisan would have a reasonable expectation of success as the art suggest the correlation was known.
With regards to claim 5-6, 9 Heindl teaches, “FANCG is one of the six genes associated with Fanconi anemia that governed the Fanconi anemia-BRCA (FANC-BRCA) pathway together with BRCA1/241.Disruption of this pathway can induce cisplatin resistance.” (page 8, 2nd column)
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to treat subjects with disrupted Fanconi anemia-BRCA (FANC-BRCA) with something other than cisplatin. The artisan would be motivated as Heindl suggest disruption of Fanconi anemia-BRCA (FANC-BRCA) provides for cisplatin resistance. The artisan would have a reasonable expectation of success as the art suggest the correlation was known.
The specification provides no definition of what is required of an M1 macrophage immune signature. However, Heindl teaches in figure 5:
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Thus claims 10 and 11 are at least obvious over the teachings of figure 5b.
With regards to claim 13, Heindl teaches, “Molecular data analysis. ESTIMATE62 and ABSOLUTE63 tumor purity data were downloaded from64. ESTIMATE uses gene expression profiles of 141 immune genes and 141 stromal genes to estimate tumor purity, stromal and immune scores (based on TCGA Agilent array-based expression profiles of ovarian cancer n = 417 used for ovarian cancer in the original publication). ABSOLUTE uses somatic copy-number data for inferring tumor purity. Copy number (n = 463), gene expression (n = 455), methylation (n = 433), mutation data and mutation burden as the total number of somatic mutations (n = 297) were obtained from the Broad Institute and cBioportal65,66. Differential gene expression analysis of samples with and without diversification was performed using the R (v3.3.1) package limma67
(v3.28.21) available via Bioconductor68. Gene set enrichment analysis was performed
using the R package HTSanalyzeR (v2.26.0). Multiple testing correction was performed using False Discovery Rate69. Immune cell subset analysis was performed using CIBERSORT32 and the most variable probe for each gene was selected according to standard deviation. Gene expression was then deconvoluted using the LM22 signature matrix32, which contains 547 genes for the identification of 22 hematopoietic cell types. Statistical significance was assessed by generating pvalues from 200 permutations. Only the patient subset with immune abundance greater than the median immune abundance and with internal filtering step p ≤ 0.05 was considered for deconvolution analysis. Hypergeometric test was used for copy number and mutation data analysis to identify specific alterations or mutations enriched in morphologically diverse samples with multiple testing corrections. Only Immunoreactive subtype contained sufficient number of samples after filtering. BRCA1 epigenetically silenced group was derived by clustering BRCA1 expression and methylation data using Gaussian mixture models70 following.”
With regards to claim 15, Heindl teaches ovarian cancer (title).
With regards to claim 16, Heindl teaches cisplatin ((page 8, 2nd column)
With regards to claim 17-18, 20Heindl teaches taxane and cisplatin (page 9, 2nd column last paragraph)
Claim(s) 14, 19, 34 is/are rejected under 35 U.S.C. 103 as being unpatentable over Heindl (NATURE COMMUNICATIONS| (2018) 9:3917 |DOI: 10.1038/s41467-018-06130-3) as applied to claim1-6, 9-11, 13, 15-18, 20 above, and further in view of Hutchinson (Clin Cancer Res (2020) 26 (3): 657–668.)
The teachings of Heindl provide above teach determination of BRCA1/BRCA2 status, immune signatures, treatment with cisplatin and taxanes. However, Heindl does not specifically teach breast cancer, triple negative breast cancer or paclitaxel.
However, Hutchinson teaches determination of BRCA1 and BRCA2 in TNBC (660, 2nd column). Hutchinson teaches immune phenotyping(immune signature) (page 664-665). Further Hutchinson teaches paclitaxel and docetaxel treatment (663, 1st column).
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to examine triple negative breast cancer by determining BRCA1/BRCA2 status, determining immune signature (phenotype) and treating with paclitaxel or docetaxel. The artisan would be motivated as Hutchinson specifically teaches determining BRCA1/BRCA2 status, determining immune signature (phenotype) and treating with paclitaxel or docetaxel in TNBC. The artisan would have a reasonable expectation of success as Hutchinson demonstrates it has been done.
Summary
No claims are allowed.
Conclusion
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/Steven Pohnert/ Primary Examiner, Art Unit 1683
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