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 1-20 are pending.
Claims 1-20 are rejected.
Claims 3-4, 7, and 10 are objected to.
Priority
Applicant’s claim for the benefit of a prior-filed application, PCT/CN2019/104005 filed 02 Sept. 2019 under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Accordingly, the effective filing date of the claimed invention is 02 Sept. 2019.
Information Disclosure Statement
The information disclosure statement(s) (IDS) submitted on 02 March 2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the list of cited references was considered in full by the examiner.
Drawings
The drawings were received on 02 March 2022. These drawings are accepted.
Specification
The amendments to the specification filed 02 March 2022 have been entered.
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
The abstract of the disclosure is objected to because:
The disclosure recites “The present application disclosed a method…”, which is a phrase that can be implied, and furthermore, is grammatically incorrect.
A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Claim Objections
Claims 3-4, 7, and 10 are objected to because of the following informalities:
Claims 3-4 and 7 recite “…the concerted effect burden data…”, which should recite “the concerted effect burden parameter data” to use consistent language with claim 1 in each instance.
Claim 4 recites “…comparing the concerted effect…with preset threshold…” at lines 6-7, which is a grammatical error and should recite “with the preset threshold…”.
Claim 10 recites “An electronic apparatus…, and when the processor executes the program, a method for automatically predicting treatment management factor characteristics of a disease as claimed is implemented…”, which is redundant and “as claimed” should be removed.
Appropriate correction is required.
Claim Interpretation
Claim 3 recites “…a survival model label” in the last line of the claim. Applicant’s specification at pg. 22, lines 8-11 disclose the survival model label may include, but is not limited to, data (such a 1) indicating long survival period or data (such as 0) indicating short survival period, and/or data including survival years and corresponding survival probability, and/or confidence coefficient parameter prediction results, etc. Therefore, the broadest reasonable interpretation of a “survival model label” in light of the specification is any data labeling survival information (not limited to survival labels relating to a statistical “mode”).
Claim 5 recites “…wherein the preset threshold of the concreted effect burden-survival model model of the disease is determined based on concerted effect burden data…”. The limitation regarding how the preset threshold was determined is interpreted to be a product by process limitation that describes how the preset threshold was previously determined. However, the claim does not require a step of determining the preset threshold. See MPEP 2113 I, stating "[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process." In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985).
Claim 6 recites “…wherein the several modeling samples are from…”, which further limits the process in which the preset threshold was previously determined, and thus is part of the product by process limitation of claim 5.
Claim Rejections - 35 USC § 112(b)
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.
Claims 7-20 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 7 is indefinite for recitation of “the predetermined treatment management factor characteristics” in lines 5 and 7. Claim 7 previously recites “…wherein the step of outputting predictive data of at least one treatment management factor characteristic” and claim 1 similarly recites “outputting…data of at least one treatment management factor characteristics” in the body of the claim. Claim 1 also recites “A method for…predicting treatment management factor characteristics” in the preamble, but these are not required to be outputted in claim 1. Therefore, it is unclear if “the predetermined treatment management factor characteristics” are referring to the ”at least one treatment management factor” recited in claim 1, the “treatment management factor characteristics” in the preamble of claim 1, or both the at least one treatment management factor and the treatment management factor characteristics. For purpose of examination, claim 7 is interpreted to mean outputting relative to the at least one predetermined treatment management factor characteristics.
Claim 8 is indefinite for recitation “of the concerted effect parameters” in each of lines 7, 8, 9, 10, and 11. Claim 8 previously recites “of “…wherein the concerted effect burden parameter…” in line 2 and claim 1, from which claim 8 depends, recites “acquiring…concerted effect burden parameter data”. Therefore there is insufficient antecedent basis for “the concerted effect parameters”, given claims 1 and 8 only previously recite “concerted effect burden parameter data” and “the concerted effect burden parameter”, but not multiple parameters. Furthermore, it is unclear if the recitation of “the concerted effect burden parameter” in line 2 is referring to the “concerted effect burden parameter data” or if the concerted effect burden parameter is an element of the concerted effect burden parameter data, in which there is insufficient antecedent basis for “the concerted effect burden parameter”. For purpose of examination, claim 8 is interpreted to mean “wherein the concerted effect burden parameter data….comprises” and each recitation of “the concerted effect parameters” is interpreted to refer to “concerted effect burden parameters” to correct the antecedent basis.
Claims 17-20 are indefinite for recitation of “the concerted effect burden parameter” in line 1 and “the concerted effect parameters” throughout the claims for the same reasons discussed above for claim 18.
Claims 8 and 17-20 recite “…meets a preset conditions…” in line 5. It is unclear if claims 8 and 17-20 intend to require the number of genes meets a preset condition or meets preset conditions, due to the grammatical error in claims 8 and 17-20 that uses the singular article “a” with a plural “conditions”. Clarification is requested via claim amendment. For purpose of examination, claims 8 and 17-20 are interpreted to mean “meets a preset condition”.
Claims 8 and 17-20 are indefinite for recitation of “…a sum of absolute values, a median, a maximum value, and/or a variant, etc….” because it is unclear what value(s) are encompassed by “etc.”. Clarification is requested. For purpose of examination, the concerted effect burden parameter is interpreted to comprise (as an option), a sum of absolute values, a median, a maximum value, and/or a variant, and/or any statistical value.
Claims 8 and 17-20 are indefinite for recitation of “…at least two simple data of the concerted effect parameters…” in each of lines 1 and 4 of the last limitation of the claim. The term “simple” in claims 8 and 17-20 is a relative term which renders the claim indefinite. The term “simple” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. For purpose of examination, claims 8 and 17-20 is interpreted to mean “acquiring at least two data of concerted effect burden parameters for describing…”.
Claims 9 and 11-16 are indefinite for recitation of “…wherein the step of acquiring concerted effect burden parameter data…comprises: for the genes in the predetermined genome, acquiring concerted effect parameter data of the several mutant genes on the expression activity of each gene….; performing noise reduction processing on the concerted effect parameter data…; acquiring the concerted effect burden parameter data…based on a result of performing the noise reduction”. The claims refer to “concerted effect parameter data” for both the acquired data prior to performing noise reduction processing (i.e. not the acquired data of claim 1) and also for the processed concerted effect burden parameter data. As a result, it is unclear if “the concerted effect burden parameter data” in the last limitation of claims 9 and 11-16 is referring to the acquired concerted affect burden parameter data of claim 1, referenced in the preamble of claims 9 and 11-16, or referring to the acquired concerted effect parameter data in the first and second limitations (without noise reduction processing) of claims 9 and 11-16. It is suggested Applicant use different terminology for the unprocessed acquired data and the acquired data after noise reduction processing. For purpose of examination, the claims will be interpreted to mean initial concerted effect parameter data is acquired in the first limitation, the initial concerted effect parameter data is processed with the noise reduction processing, and the concerted effect burden parameter data (i.e. of claim 1) is acquired based on a result of performing the noise reduction on the initial data.
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea and law of nature without significantly more.
The Supreme Court has established a two-step framework for this analysis, wherein a claim does not satisfy § 101 if (1) it is “directed to” a patent-ineligible concept, i.e., a law of nature, natural phenomenon, or abstract idea, and (2), if so, the particular elements of the claim, considered “both individually and as an ordered combination,” do not add enough to “transform the nature of the claim into a patent-eligible application.” Elec. Power Grp., LLC v. Alstom S.A., 830 F.3d 1350, 1353 (Fed. Cir. 2016) (quoting Alice, 134 S. Ct. at 2355). Applicant is also directed to MPEP 2106.
Step 1: The instantly claimed invention (claims 1 and 10 being representative) is directed to a method and system. Therefore, the instantly claimed invention falls into one of the four statutory categories. [Step 1: YES]
Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in in Prong Two if the recited judicial exception is integrated into a practical application of that exception.
Step 2A, Prong 1: Under the MPEP § 2106.04, the Step 2A (Prong 1) analysis requires determining whether a claim recites an abstract idea, law of nature, or natural phenomenon.
Claims 1 and 10 recite the following steps which fall under the mental processes groupings of abstract ideas:
acquiring…concerted effect burden parameter data of several mutant genes of a tested sample of a target object on expression activity of each gene in a predetermined genome, wherein the predetermined genome corresponds to the disease;
outputting…predictive data of at least one treatment management factor characteristic of the target object relative to the disease based on the concerted effect burden parameter data.
The identified claim limitations falls into one of the groups of abstract ideas of mental processes for the following reasons. First, acquiring effect burden parameter data of mutant genes on expression activity of genes involves analyzing expression data of genes in a genome and determining how the expression level changes in these genes in the presence of the several mutant genes compared to in the presence of unmutated genes, which is a mental process of performing data comparisons. Furthermore, outputting predictive data of a treatment management factor based on the concerted effect burden parameter data can be practically performed in the mind by comparing the concerted effect burden parameter data of a target object with a control concerted effect burden survival mode model of a disease, as recited in claim 3, to determine a survival of the target object based on the burden parameter data. Overall, the claims analogous to a claim to "collecting information, analyzing it, and displaying certain results of the collection and analysis," where the data analysis steps are recited at a high level of generality such that they could practically be performed in the human mind, Electric Power Group v. Alstom, S.A., 830 F.3d 1350, 1353-54, 119 USPQ2d 1739, 1741-42 (Fed. Cir. 2016). Other than reciting the steps are carried out by an electronic apparatus, nothing in the claims precludes the steps from being practically performed in the mind. See MPEP 2106.04(a)(2) III.
Dependent claims 2-9 and 11-20 further recite an abstract idea and/or are part of the abstract idea identified above. Dependent claims 9 and 11-16 further limit the mental process of acquiring concerted effect parameter data to comprise acquiring concerted effect parameter data, performing noise reduction processing on the data, and acquiring the data as a result of performing the noise reduction processing. Dependent claim 2 further limits the step of outputting predictive data of at least one treatment management factor characteristic to comprise survival characteristics, pathophysiological characteristics and/or clinical intervention effects. Dependent claim 3 further limits the mental process of outputting the predictive data to comprise performing data comparisons between the concerted effect burden data with a preset concerted effect burden-survival mode model of the disease, and acquiring and outputting a survival model label. Furthermore, the comparison using a survival mode model (e.g. a Cox proportional hazards model) of the disease further recites a mathematical concept in light of Applicant’s specification at pg. 23, lines 23 to 30. Dependent claim 4 further limits the abstract idea of the concerted effect burden-survival mode model to comprise a first and second survival model label and a preset threshold, and further limits the comparing to comprise assigning the first label or the second label depending on whether the concerted effect burden data reaches or is less than the preset threshold, respectively. Dependent claims 5-6 further limit the process in which the preset threshold was previously determined and thus are part of the abstract idea of claim 4 discussed above. Dependent claim 7 further limits the mental process of outputting of predictive data to be based on the concerted effect burden parameter data of the target object, concerted effect burden data of pre-acquired modeling samples, and measured data. Dependent claims 8 and 17-20 further limit the mental process of acquiring concerted effect burden parameter data to involve determining a number of genes with influenced expression and/or a sum of absolute values, a median, a maximum value, and/or a statistical value (also reciting a mathematical concept) and/or acquiring composite data of parameters based on simple data of the concerted effect parameters. Dependent claims 9 and 11-16 also further recite a mathematical concept of performing noise reduction processing (i.e. normalization) in light of Applicant’s specification at pg. 16, lines 4-11.
The claims further recite a law of nature of a natural correlation between expression levels of mutated genes and treatment outcomes for a disease, analogous to the natural relationship between a patient’s CYP2D6 metabolizer genotype and the risk that the patient will suffer QTc prolongation after administration of a medication called iloperidone, Vanda Pharmaceuticals Inc. v. West-Ward Pharmaceuticals, 887 F.3d 1117, 1135-36, 126 USPQ2d 1266, 1281 (Fed. Cir. 2018). See MPEP 2106.04(b) I.
Therefore, claims 1-20 recite an abstract idea and law of nature. [Step 2A, Prong 1: YES]
Step 2A: Prong 2: Under the MPEP § 2106.04, the Step 2A, Prong 2 analysis requires identifying whether there are any additional elements recited in the claim beyond the judicial exception(s), and evaluating those additional elements to determine whether they integrate the exception into a practical application of the exception. This judicial exception is not integrated into a practical application for the following reasons.
Dependent claims 2-9 and 11-20 do not recite any elements in addition to the judicial exception and thus are part of the judicial exception.
The additional elements of claims 1 and 10 include:
an electronic apparatus (i.e. a computer);
a processor (claim 10); and
a memory (claim 10).
The additional elements of a computer comprising a processor and memory are generic computer components merely used to carry out the abstract idea. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not integrate a judicial exception into a practical application. See MPEP 2106.05(f).
Therefore, the additionally recited elements merely invoke computers as a tool to perform the abstract idea, as such, the claims as a whole do no integrate the abstract idea into practical application. Thus, claims 1-20 are directed to an abstract idea and law of nature. [Step 2A, Prong 2: NO]
Step 2B: In the second step it is determined whether the claimed subject matter includes additional elements that amount to significantly more than the judicial exception. See MPEP § 2106.05.
The claims do not include any additional steps appended to the judicial exception that are sufficient to amount to significantly more than the judicial exception.
Dependent claims 2-9 and 11-20 do not recite any elements in addition to the judicial exception and thus are part of the judicial exception.
The additional elements of claims 1 and 10 include:
an electronic apparatus (i.e. a computer);
a processor (claim 10); and
a memory (claim 10).
The additional elements of a computer comprising a processor and memory are conventional computer components merely used to carry out the abstract idea. The courts have found the use of a computer or other machinery in its ordinary capacity for economic or other tasks (e.g., to receive, store, or transmit data) or simply adding a general purpose computer or computer components after the fact to an abstract idea (e.g., a fundamental economic practice or mathematical equation) does not provide significantly more. See Affinity Labs v. DirecTV, 838 F.3d 1253, 1262, 120 USPQ2d 1201, 1207 (Fed. Cir. 2016) (cellular telephone); TLI Communications LLC v. AV Auto, LLC, 823 F.3d 607, 613, 118 USPQ2d 1744, 1748 (Fed. Cir. 2016) (computer server and telephone unit).
Therefore, taken alone, the additional elements do not amount to significantly more than the above-identified judicial exception(s). Even when viewed as a combination, the additional elements fail to transform the exception into a patent-eligible application of that exception. Thus, the claims as a whole do not amount to significantly more than the exception itself. [Step 2B: NO]
Therefore, the instantly rejected claims are not drawn to eligible subject matter as they are directed to an abstract idea and law of nature without significantly more. For additional guidance, applicant is directed generally to applicant is directed generally to the MPEP § 2106.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Pongor (2015).
Cited reference: Pongor et al., A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients, 2015, Genome Medicine, 7:104, pg. 1-11.
Regarding claims 1 and 10, Pongor discloses a method for predicting clinical outcome in breast cancer (i.e. a disease) using expression data and mutational status (Abstract), implemented using software stored on a computer, which inherently requires a processor for executing the software and memory storing the software (Abstract, see conclusion), which comprises the following:
Pongor discloses analyzing expression values of each gene of RNAseq and microarray data in breast cancer genomes of samples of cancer patients (i.e. a predetermined genome corresponding to the disease) and acquiring a set of genes whose expression is significantly up- or down-regulated between cohorts of patients having a mutation status in genes (i.e. several mutation genes) (pg. 2, col.2 , para. 3 and pg. 4, col. 1, para. 2, e.g. mutations in multiple genes can be used; Fig. 2, e.g. 3 genes together) compared to patients not having a mutation in the genes (i.e. concerted effect burden parameter data of several mutation genes on expression activity of each gene in the predetermined genome) (pg. 4, col. 1, para. 4-5 and col. 2, para. 1-3 to pg. 5, col. 1, para. 1 and col. 2, para. 3). Pongor refers to this acquired concerted effect burden parameter data as “metagenes” (pg. 5, col. 2, para. 2).
Pongor discloses calculating and outputting a survival curve of probability of survival over time of a breast cancer patient (i.e. predictive data of at least one treatment management characteristic) using the expression data of the identified metagenes (i.e. based on the concerted effect burden parameter data) (pg. 2, col. 2, para. 3, e.g. predict probability of patient survival; pg. 5, col. 2, para. 3-4; FIG. 3, e.g. see survival prediction using expression signature of genes affected by AKT1 mutation; FIG. 2, e.g. survival prediction using signature).
Regarding claim 2, Pongor discloses the at least one treatment management factor characteristics comprises predicted probabilities of survival over time of a patient with breast cancer (i.e. survival characteristics of the target object relative to the disease) (Fig. 3).
Regarding claim 3, Pongor discloses comparing the over-expressed and under-expressed genes of the metagenes (i.e. concerted effect burden data) in a Cox Proportional hazards model of survival in breast cancer that takes the metagene expression data as input (i.e. a preset-concerted effect burden-survival mode model of the disease) (Fig. 3; pg. 5, col. 1, para. 3-4) and outputting probabilities of survival and corresponding survival years for the cancer patient with breast cancer (i.e. a survival model label of the target object relative to the disease) (Fig. 3).
Regarding claim 4, Pongor discloses the concerted effect burden-survival mode model comprises probabilities of survival over time for each of patients exhibiting high expression of up-regulated genes and low expression of up-regulated genes (i.e. a first and second survival model label) (Fig. 3, e.g. two different curves).
Pongor discloses the expressions of the metagenes (i.e. the concerted effect burden data) of each cancer patient (i.e. target object) in the cohort of patients carrying the mutation are compared to a preset threshold representing a median expression level of the cohort for the survival model (pg. 5, col. 1, para. 3), and outputting a “high” survival curve probabilities for patients with concerted effect burden data higher than the median (i.e. reaching the preset threshold), or including the patients in the “low” survival curve probabilities having concerted effect burden data lower than the median (i.e. less than the preset threshold).
Regarding claim 5, Pongor discloses the preset threshold is a median expression of the concerted effect burden data (e.g. metagenes) of a cohort of patients with breast cancer (i.e. the preset threshold Is determined based on concerted effect burden data of modeling samples suffering from the disease) (pg. 5, col. 1, para. 3).
Regarding claim 6, Pongor discloses the modeling samples are from patients with breast cancer as discussed above (pg. 1, col. 1, para. 3). While Pongor does not explicitly state which stage of breast cancer the patients include, as discussed above in claim interpretation, the process in which the preset threshold was previously determined is a product by process limitation. "[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process. See MPEP 2113 I. Here, the preset threshold representing a threshold expression level of the survival model of Pongor is the same product (preset threshold) as in the claims, particularly given claim 6 encompassing the patients having any stage of disease, and thus the preset threshold of Pongor anticipates the threshold of the claims.
Regarding claim 7, Pongor discloses outputting the survival curve based on the concerted burden effect parameter data comprises outputting predicted probabilities of survival at various time points (i.e. predictive data) using expression data of the metagenes of a cohort of patients having breast cancer in a training set with known survival (i.e. concerted effect burden data of pre-acquired modeling samples and measured data of the predetermined treatment management factor characteristics) in a fitted Cox proportional hazards model (pg. 5, col. 1, para. 3-4 and col. 2, para. 2, e.g. survival data for separate large cohort of breast cancer patients).
Regarding claims 8 and 17-20, Pongor discloses the concerted effect burden parameter data comprises a number of genes with statistically significantly increased or decreased expression in patients with mutations in the several mutant genes compared to patients without the mutations (i.e. a number of genes whose expression activity is influenced by the several mutant genes among the genes in the predetermined genome) (pg. 4, col. 2, para. 3 to pg. 5, col. 1, para. 2; Fig. 2, e.g. 3 genes together). Pongor discloses the determination of statistically significant genes uses threshold of 0.01 (i.e. the genes meet a preset condition) (pg. 5, col. 1, para. 5).
Regarding claims 9 and 11-16, Pongor discloses acquiring the metagene data of the mutant genes comprises filtering genes with expression values with a p-value > 0.01 and an AUC less than 0.65, which removes genes with weaker associations with the mutant genes (i.e. noise reduction processing). Thus the acquired concerted effect burden data is based on a result of performing the noise reduction processing.
Therefore, Pongor anticipates the claimed invention.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KAITLYN L MINCHELLA whose telephone number is (571)272-6485. The examiner can normally be reached 7:00 - 4:00 M-Th.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685