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 .
Status of Claims
Claims 1-17 pending and examined on the merits.
Priority
The instant application filed on 1/23/2023 is a 371 national stage entry of PCT/US21/42787 having an international filing date of 7/22/2021, and claims the benefit of priority to provisional U.S. Application No. 63/055,234 filed on 7/22/2020. Thus, the effective filing date of the claims is 7/22/2020.
The applicant is reminded that amendments to the claims and specification must comply with 35 U.S.C. § 120 and 37 C.F.R. § 1.121 to maintain priority to an earlier-filed application. Claim amendments may impact the effective filing date if new subject matter is introduced that lacks support in the originally filed disclosure. If an amendment adds limitations that were not adequately described in the parent application, the claim may no longer be entitled to the priority date of the earlier filing.
Information Disclosure Statement
The information disclosure statement (IDS) filed on 1/23/2023 has been entered and considered. A signed copy of the corresponding 1449 form has been included with this Office action.
Claim Objections
Claim 10 lines 8-9, "create an output set based the performance of" should read "create an output set based on the performance of".
Claim 12 line 2 "transcriptiomics " should read "transcriptomics".
Appropriate correction is required.
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.
Claims 1-9 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 "comparing a measured performance of the representation of the mutated species with a measured performance of the representation of the initial species based on associated outcome data". It is unclear if the measurement data (the "associated outcome data") is actively being measured as part of the claimed method, or if the data is simply received. To further prosecution, the limitation is interpreted as have a prior step of "measuring performance of the mutated species and the initial species" before the comparison step.
Claims 2-9 depend from independent claim 1, therefore are also rejected as being indefinite.
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 1-17 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea of a mental process, a mathematical concept, organizing human activity, or a law of nature or natural phenomenon without significantly more. In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1: YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claim 1: “comparing a measured performance of the representation of the mutated species with a measured performance of the representation of the initial species based on associated outcome data” provides a comparison (comparing performance metrics) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
“selecting one of the representation of the mutated species and the representation of the initial species based on the results of the comparing to serve as the representation of the initial species in a next iteration of the generating and comparing” provides an evaluation (selecting based on a result) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
Claim 10: “extracting an identification (ID) for each entry of the biological data set a set of IDs” and “generating an initial data set from the biological data set, wherein the initial data set is a subset of the biological data set” provides for organizing information (extracting IDs and generating subsets of data involves sorting or structuring data) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
“selecting one of the mutated data set or the initial data set to create an output set based the performance of each respective data set” provides an evaluation (selecting based on a result) that may be performed in the human mind and is therefore considered a mental process, which is an abstract idea.
These recitations are similar to the concepts of collecting information, analyzing it, and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or are mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. As such, claims 1-17 recite an abstract idea (Step 2A, Prong 1: YES).
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). The judicial exceptions listed above are not integrated into a practical application because the claims do not recite an additional element or elements that reflects an improvement to technology. Specifically, the claims recite the following additional elements:
Claim 1: “generating a representation of a mutated species from a representation of an initial species comprising biological signature data” provides insignificant extra-solution activities (generating data is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
“measuring performance of the mutated species and the initial species” (as interpreted above) provides insignificant extra-solution activities (generating measurement data is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
“outputting a representation of a super species based on a final mutated species, the representation of the super species comprising a set of biological signature features predictive of the outcome” provides insignificant extra-solution activities (outputting data is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
Claim 10: “receiving a biological data set” provides insignificant extra-solution activities (receiving data is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
“generating a mutated data set from the initial data set” provides insignificant extra-solution activities (generating data is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
“measuring performance of the mutated data set and the initial data set” provides insignificant extra-solution activities (generating measurement data is a pre-solution activity involving data gathering and manipulation steps) that do not serve to integrate the judicial exceptions into a practical application.
The steps for receiving, generating, measuring, and outputting data are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application because they are pre- and post-solution activities involving data gathering, data manipulation, and sample manipulation steps (see MPEP 2106.04(d)(2)). Therefore, claims 1-17 are directed to an abstract idea (Step 2A, Prong 2: NO).
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application, or equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment.
The limitations for receiving, generating, measuring, and outputting data are insignificant extra-solution activities that do not serve to integrate the recited judicial exceptions into a practical application. Furthermore, no inventive concept is claimed by these limitations as they are well-understood, routine, and conventional.
The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 1-17 are not patent eligible.
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.
Claims 1-17 rejected under 35 U.S.C. 103 as being unpatentable over Bonyhadi et al. (US-20190345543).
Regarding claims 1 and 10, Bonyhadi teaches extracting an identification (ID) for each entry of the biological data set a set of IDs (claim 10) (Para.0147 "In some embodiments, the methods involve identification, alignment, filtering, processing, mapping and/or analysis of the sequences obtained from one or more steps of the methods provided herein").
Bonyhadi also teaches generating a representation of a mutated species from a representation of an initial species comprising biological signature data (Para.0164 "In other embodiments, the output contains coordinates or a string describing one or more mutations in the subject nucleic acid relative to the reference genome" and para.0494 "For example, in some cases, a wild-type TCR can be used as a template for producing mutagenized TCRs in which in one or more residues of the CDRs are mutated, and mutants with an desired altered property, such as higher affinity for a desired target antigen, are selected").
Bonyhadi also teaches: measuring performance of the mutated species and the initial species; and comparing a measured performance of the representation of the mutated species with a measured performance of the representation of the initial species based on associated outcome data (claim 1) (Para.0012 "Provided herein are methods for determining or identifying an epigenetic property associated with an attribute or feature of a cell composition, the method comprising: (a) determining or measuring a level or degree or relative level or degree of an epigenetic property of one or more genomic regions for a cell or a population of cells comprised in a first cell composition; (b) determining or measuring a level or degree or relative level or degree of said epigenetic property of the one or more genomic regions for a cell or a population of cells comprised in a second cell composition; and (c) comparing the level or degree in (a) and the level or degree in (b), wherein a difference, optionally a significant difference, in the level or degree of the epigenetic property of the one or more of the genomic regions identifies or determines the presence of an epigenetic property indicative of or that correlates with an attribute or feature present in cells of one but not the other of the first and second composition").
Bonyhadi also teaches: selecting one of the representation of the mutated species and the representation of the initial species based on the results of the comparing to serve as the representation of the initial species in a next iteration of the generating and comparing; and outputting a representation of a super species based on a final mutated species, the representation of the super species comprising a set of biological signature features predictive of the outcome (Para.0050 "the method includes if the comparison indicates that the cell composition is or is likely to have the phenotype or function, selecting the one or more test agent or condition for culturing the cells. In some embodiments, the method includes if the comparison indicates that the cell composition is or is likely not to have the phenotype or function, repeating steps (a) and (b) with one or more further test agent or condition").
It is recognized that the citations and evidence provided above are derived from potentially different embodiments of a single reference. Nevertheless, it 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 to employ combinations and sub-combinations of these complementary embodiments, because Bonyhadi et al. explicitly motivates doing so (at least in para.0119 "In some embodiments, various changes may be made and equivalents may be substituted in the various embodiments. In addition, many modifications may be made to adapt a particular situation, material, composition of matter, process, process act(s) or step(s) to the objective(s), spirit or scope of the various embodiments. In some embodiments, each of the individual variations described and illustrated herein has discrete components and features that may be readily separated from or combined with the features of any of the other several embodiments without departing from the scope or spirit of the various embodiments. All such modifications are intended to be within the scope of claims associated with this disclosure") and otherwise motivating experimentation and optimization. Additionally, doing so merely combines prior art elements according to known methods to yield predictable results.
Regarding claims 2 and 11, Bonyhadi teaches the methods of Claims 1 and 10 on which this claim depends/these claims depend, respectively. Bonyhadi also teaches the measured performance is an area under a receiver operating characteristic curve determined from at least one classification threshold (Para.0933 "A receiver operating characteristic (ROC) curve was generated by plotting the true positive rate against the false positive rate, and the area under the curve (AUC) was determined").
Regarding claims 3 and 12-15, Bonyhadi teaches the methods of Claims 1 and 10 on which this claim depends/these claims depend, respectively. Bonyhadi also teaches the biological signature data comprises proteomic data, bulk transcriptome data, single-cell transcriptome data, genomic data (SNP data), metabolomic data, microbiotomic data, or any combination thereof (Para.0270 "the epigenetic and/or epigenomic analysis can be used in combination with other detection and/or analysis methods, such as transcription analysis, transcriptome analysis, transcription factor occupancy assays, RNAseq, protein expression, proteomic analysis, protein modification analysis, functional activity assays, flow cytometry and/or intracellular cytokine staining").
Regarding claims 4-7, Bonyhadi teaches the methods of Claim 1 on which these claims depend. Bonyhadi also teaches testing using gene subsets (Para.0273 "In some aspects, any of the analysis methods, including additional, further or downstream analyses, can be performed on one or more selected genomic regions or gene loci. In some aspects, the methods can be performed based on one or more selected genes, such as a subset of genes, panel of genes or module of genes").
Specifically, regarding claims 4-5, Bonyhadi also teaches: the super species comprises a set of genes associated with resistance to a treatment for acute myeloid leukemia (AML); and the super species comprises a set of genes associated with cardiovascular disease risk (Para.0379 "In some examples, cells are separated based on one or more property, such as density, adherent properties, size, sensitivity and/or resistance to particular components", and para.0546 "Among the diseases, conditions, and disorders are tumors, including solid tumors, hematologic malignancies, and melanomas, and including localized and metastatic tumors, infectious diseases, such as infection with a virus or other pathogen, e.g., HIV, HCV, HBV, CMV, HPV, and parasitic disease, and autoimmune and inflammatory diseases. In some embodiments, the disease, disorder or condition is a tumor, cancer, malignancy, neoplasm, or other proliferative disease or disorder. Such diseases include but are not limited to leukemia, lymphoma, e.g., chronic lymphocytic leukemia (CLL), ALL, non-Hodgkin's lymphoma, acute myeloid leukemia, multiple myeloma, refractory follicular lymphoma, mantle cell lymphoma, indolent B cell lymphoma, B cell malignancies, cancers of the colon, lung, liver, breast, prostate, ovarian, skin, melanoma, bone, and brain cancer, ovarian cancer, epithelial cancers, renal cell carcinoma, pancreatic adenocarcinoma, Hodgkin lymphoma, cervical carcinoma, colorectal cancer, glioblastoma, neuroblastoma, Ewing sarcoma, medulloblastoma, osteosarcoma, synovial sarcoma, and/or mesothelioma").
Specifically, regarding claim 6, Bonyhadi also teaches the super species comprises a set of genes associated with cancer relapse (Para.0344 "In some embodiments, the burden of a disease or condition in the subject is detected, assessed, or measured. [. . .]. In some aspects, survival of the subject, survival within a certain time period, extent of survival, presence or duration of event-free or symptom-free survival, or relapse-free survival, is assessed").
Specifically, regarding claim 7, Bonyhadi also teaches the super species comprises a set of genes associated with post-traumatic stress disorder (PTSD) (Para.0545 "The disease or condition that is treated can be any in which expression of an antigen is associated with and/or involved in the etiology of a disease condition or disorder" and para.0549 "In some embodiments, the antigen associated with the disease or disorder is or includes an antigen selected from the group consisting of [. . .] Human leukocyte antigen A1 (HLA-A1), Human leukocyte antigen A2 (HLA-A2)", and PTSD is associated with HLA as evidenced by Katrinli et al. "Association of HLA locus alleles with posttraumatic stress disorder." Brain, behavior, and immunity 81 (2019): 655-658 (page 1 abstract "Immune dysregulation has been widely observed in those with posttraumatic stress disorder (PTSD). An individual’s immune response is shaped, in part, by the highly polymorphic Human Leukocyte Antigen (HLA) locus that is associated with major psychiatric disorders such as schizophrenia, major depression and bipolar disorder [. . .]. Gene expression modules of PTSD-related HLA alleles were enriched in various pathways, including pathways related to immune and neural activity")).
Regarding claims 8-9 and 17, Bonyhadi teaches the methods of Claims 1 and 10 on which this claim depends/these claims depend, respectively. Bonyhadi also teaches using the set of biological signature features to determine an outcome (Abstract "Provided herein are methods of identifying genomic region(s) predictive of an outcome").
Regarding claim 16, Bonyhadi teaches the methods of Claim 10 on which this claim depends/these claims depend, respectively. Bonyhadi also teaches measuring performance of the mutated data set and the initial data set comprises: propagating the mutated data set and the initial data set in parallel multiple times (Para.0147 "In some embodiments, the sequential order of one or more steps can be in any order, or any one or more steps, functions, processes or scripts can be performed in parallel").
Conclusion
No claims are allowed.
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/R.A.P./Examiner, Art Unit 1686
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687
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