DETAILED ACTION
Claims 1-15 are currently pending and have been examined.
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 .
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 1-15 are rejected under 35 U.S.C. §101 because the claimed invention is directed to an abstract idea without significantly more.
Subject Matter Eligibility Criteria - Step 1:
Claims 1-15 are directed to a method (i.e., a process). Accordingly, claims 1-15 are all within at least one of the four statutory categories.
Subject Matter Eligibility Criteria - Alice/Mayo Test: Step 2A - Prong One:
Regarding Prong One of Step 2A, the claim limitations are to be analyzed to determine whether, under their broadest reasonable interpretation, they “recite” a judicial exception or in other words whether a judicial exception is “set forth” or “described” in the claims. MPEP 2106.04(II)(A)(1). An “abstract idea” judicial exception is subject matter that falls within at least one of the following groupings: a) certain methods of organizing human activity, b) mental processes, and/or c) mathematical concepts. MPEP 2106.04(a).
Representative independent claim 1 includes limitations that recite at least one abstract idea. Specifically, independent claim 1 recites:
1. A computer-implemented method for the diagnostic classification of cancer, the method comprising:
classifying a cancer using a classification algorithm trained using at least data pertaining to biological states of all gene sites in Table 1 (SEQ ID No. 1 to SEQ ID No. 688), wherein the biological states are derived from classified cancer types, wherein classifying the cancer comprises applying the classification algorithm to data pertaining to biological states of a set of gene sites of a cancer sample, wherein the set of gene sites comprises at least 3 gene sites of the cancer sample genome selected from the gene sites in Table 1 (SEQ ID No. 1 to SEQ ID No. 688).
The identified claim limitations fall into one of the enumerated groups of "mathematical concepts", "mental processes", and/or "certain methods of organizing human activity" for the following reasons. In this case, the above "classifying" steps (including the full limitation and not just the verb) are directed to activities that broadly encompass mental processes because it requires organization or analysis that can be reasonably performed by the human mind. It is important to note that "Claims that recite performing information analysis as well as the collection and manipulation of information related to such analysis, have been determined by our reviewing court to be an abstract concept that is not patent eligible. See SAP, 898 F.3d, 1165, 1167, 1168 (Claims reciting "[a] method for providing statistical analysis" (id. at 1165) were determined to be "directed to an abstract idea" (id. at 1168)); see also Content Extraction & Transmission LLC V. Wells Fargo Bank, Nat'l Ass 'n, 776 F.3d 1343, 1345, 1347 (Fed. Cir. 2014).
With regards to applying the classification algorithm to data pertaining to biological states of a set of gene sites of a cancer sample, this step is recited
at a high level of generality (without any technological details or rules directed to how they are performed or the structure of the classification algorithm). Moreover, the classification algorithm is based upon data pertaining to biological states of a set of gene sites of a cancer sample which amounts to a mathematical correlation. It is important to note that a mathematical concept need not be expressed in mathematical symbols, because "[w]ords used in a claim operating on data to solve a problem can serve the same purpose as a formula." In re Grams, 888 F.2d 835, 837 and n.1, 12 USPQ2d 1824, 1826 and n.1 (Fed. Cir. 1989). As such, this step encompasses a mathematical concept of manipulating information through mathematical correlations or calculations. MPEP 2106.04(a)(2).
Accordingly, independent claim 1 recite at least one abstract idea.
Furthermore, dependent claims 2-15 further narrow the abstract idea described in the independent claims. Claim 2 recites the classification algorithm, Claims 3-4 & 7-9 recite determining biological state and patterns, Claims 5-6 & 13 recites the set of gene sites, Claim 10-11 recites a cancer type, Claim 12 recites correlating a biological state. These limitations only serve to further limit the abstract idea and hence, are directed towards fundamentally the same abstract idea as independent claim 1, even when considered individually and as an ordered combination.
Subject Matter Eligibility Criteria - Alice/Mayo Test: Step 2A - Prong Two:
Regarding Prong Two of Step 2A of the Alice/Mayo test, it must be determined whether the claim as a whole integrates the abstract idea into a practical application. As noted at MPEP §2106.04(II)(A)(2), it must be determined whether any additional elements in the claim beyond the abstract idea integrate the exception into a practical application in a manner that imposes a meaningful limit on the judicial exception. The courts have indicated that additional elements merely using a computer to implement an abstract idea, adding insignificant extra solution activity, or generally linking use of a judicial exception to a particular technological environment or field of use do not integrate a judicial exception into a “practical application.” MPEP §2106.05(I)(A).
In the present case, the additional limitations beyond the above-noted at least one abstract idea recited in the claim are as follows (where the bolded portions are the “additional limitations” while the underlined portions continue to represent the at least one “abstract idea”):
1. A computer-implemented method for the diagnostic classification of cancer, the method comprising:
classifying a cancer using a classification algorithm trained using at least data pertaining to biological states of all gene sites in Table 1 (SEQ ID No. 1 to SEQ ID No. 688), wherein the biological states are derived from classified cancer types, wherein classifying the cancer comprises applying the classification algorithm to data pertaining to biological states of a set of gene sites of a cancer sample, wherein the set of gene sites comprises at least 3 gene sites of the cancer sample genome selected from the gene sites in Table 1 (SEQ ID No. 1 to SEQ ID No. 688).
For the following reasons, the Examiner submits that the above identified additional limitations do not integrate the above-noted at least one abstract idea into a practical application.
Regarding the additional limitations of the computer; the Examiner submits that these limitations amount to merely using computers as tools to perform the above-noted at least one abstract idea (see MPEP § 2106.05(f)).
Thus, taken alone, the additional elements do not integrate the at least one abstract idea into a practical application.
Looking at the additional limitations as an ordered combination adds nothing that is not already present when looking at the elements taken individually. For instance, there is no indication that the additional elements, when considered as a whole with the abstract idea, reflect an improvement in the functioning of a computer or an improvement to another technology or technical field, apply or use the above-noted judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, implement/use the above-noted judicial exception with a particular machine or manufacture that is integral to the claim, effect a transformation or reduction of a particular article to a different state or thing, or apply or use the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole does not integrate the abstract idea into a practical application of the abstract idea. MPEP §2106.05(I)(A) and §2106.04(II)(A)(2).
For these reasons, representative independent claim 1 does not recite additional elements that integrate the judicial exception into a practical application.
Accordingly, the claims recites at least one abstract idea.
The remaining dependent claim limitations not addressed above fail to integrate the abstract idea into a practical application as set forth below:
Claims 14-15: These claims recite a computer with processor and memory which amount to merely using computers as tools to perform the above-noted at least one abstract idea (see MPEP § 2106.05(f)).
Thus, taken alone, any additional elements do not integrate the at least one abstract idea into a practical application. Therefore, the claims are directed to at least one abstract idea.
Subject Matter Eligibility Criteria - Alice/Mayo Test: Step 2B:
Regarding Step 2B of the Alice/Mayo test, representative independent claim 1 does not include additional elements (considered both individually and as an ordered combination) that are sufficient to amount to significantly more than the judicial exception for reasons the same as those discussed above with respect to determining that the claim does not integrate the abstract idea into a practical application.
Regarding the additional limitations of the computer; the Examiner submits that these limitations amount to merely using computers as tools to perform the above-noted at least one abstract idea (see MPEP § 2106.05(f)).
The dependent claims also do not include additional elements (considered both individually and as an ordered combination) that are sufficient to amount to significantly more than the judicial exception for the same reasons to those discussed above with respect to determining that the dependent claims do not integrate the at least one abstract idea into a practical application.
Therefore, claims 1-15 are ineligible under 35 USC §101.
Claim Objections
Claims 4-13 are objected to under 37 CFR 1.75(c) as being in improper form because a multiple dependent claim should refer to other claims in the alternative only and cannot depend from any other multiple dependent claim. See MPEP § 608.01(n). Accordingly, the claims 4-13 not been further treated on the merits.
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 1-15 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 training a classification algorithm using "data pertaining to biological states of all gene sites in Table 1" but "pertaining to" does not have a clear definition, leaving ambiguous whether this means all genes in Table 1, only genes in Table 1, or other possible meanings. For the purposes of this examination, in accordance with the language later in the claim "at least 3 gene sites", the interpretation has been made that the training data set must consist of three or more gene sites chosen from the list appearing in Table 1. Dependent claims 2-15 are also rejected due to their dependency from Claim 1.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claim(s) 1-3 & 14-15 are rejected under 35 U.S.C. 103 as being unpatentable over Pfister (US20180066317) in view of in view of the publication entitled "Loss of ABAT-Mediated GABAergic System Promotes Basal-Like Breast Cancer Progression by Activating Ca2+ -NFAT1 Axis" by Xingyu Chen et al. (hereinafter "Chen"), and further in view of the publication entitled "Association Between BM/ and DNA Methylation in Blood or Normal Adult Breast Tissue: A Systematic Review" by Dzevka Dragic et al. (hereinafter "Dragic") and the publication entitled "ABR, a novel inducer of transcription factor C/EBP-alpha, contributes to myeloid differentiation and is a favorable prognostic factor in acute myeloid leukemia" by Carolina Yaeko Namasu et al. (hereinafter " Namasu ").
As per claim 1, Pfister teaches a computer-implemented method for the diagnostic classification of cancer, the method comprising:
classifying a cancer using a classification algorithm (claim 10: generating a classification-rule for aiding the classification of tumor samples in cancer) trained using at least data pertaining to biological states (para. 9-11: training data pre-determined methylation data derived from multitude of pre-classified tumor species) wherein the biological states are derived from classified cancer types, wherein classifying the cancer comprises applying the classification algorithm to data pertaining to biological states of a set of gene sites of a cancer sample (para. 6-11: wherein the classification-rule is obtained by random forest analysis of a training-data-set, the training-data-set comprising pre-determined methylation data derived from multitude of pre-classified tumor species, wherein said pre-determined methylation data comprises the methylation status of said CpG positions in the genome of each of said pre-classified tumor species)
Pfister does not expressly teach training data pertaining to biological states of all gene sites in Table 1 (SEQ ID No. 1 to SEQ ID No. 688), wherein the set of gene sites comprises at least 3 gene sites of the cancer sample genome selected from the gene sites in Table 1 (SEQ ID No. 1 to SEQ ID No. 688).
Chen teaches SEQ ID No. 1 (ABAT (SEQ ID No. 1 of the instant application). Wherein loss of ABAT-mediated GABAergic system promotes breast cancer progression; title; abstract).
It would have been obvious to one of ordinary skill in the art at the time of the invention to modify the Pfister invention to provide wherein the set of gene sites comprises gene sites of the cancer sample genome selected from the gene sites of SEQ ID No. 1, as taught by CHEN, in order to provide a computer classifying system that recognizes a classifying gene site that is a known indicator of cancer (CHEN reference, title; abstract).
Dragic teaches SEQ ID No. 2 (ABLIM2 (SEQ ID No. 2 of the instant application) gene is known in its potential role in lung cancer metastasis; page 1804, first column, last paragraph).
It would have been obvious to one of ordinary skill in the art at the time of the invention to modify the Pfister invention to provide wherein the set of gene sites comprises gene sites of the cancer sample genome selected from the gene sites of SEQ ID No. 2, as taught by Dragic, in order to provide a computer classifying system that recognizes a classifying gene site that is a known indicator of metastasis (Dragic reference, page 1804,.first column, last paragraph).
Namasu teaches SEQ ID No. 3 (ABR (SEQ ID No. 3 of the instant application) is a favorable prognostic factor in acute myeloid leukemia; title; abstract). It would have
been obvious to one of ordinary skill in the art at the time of the invention to modify the Pfister invention to provide wherein the set of gene sites comprises gene sites of the cancer sample genome selected from the gene sites of SEQ ID No. 3, as taught by Namasu, in order to provide a computer classifying system that recognizes prognostic cancer genes (Namasu reference, title; abstract).
As per claim 2, Pfister, Chen, Dragic, and Namasu, in combination, disclose the computer-implemented method of claim 1.
Pfister further discloses wherein the classification algorithm is based on at least one of: discriminant analysis, discriminant functional analysis, a kernel method, multidimensional scaling (multidimensional scaling (MDS) scaling of 107 medulloblastoma samples of molecular subtypes; paragraph [0056]; Fig. 4), a nonparametric method, Partial Least Squares, a tree-based method (RF classification trees used; paragraph [0072]), a generalized linear model, a principal components based method, a generalized additive model, a fuzzy logic based method, a neural network, and a genetic algorithm based method.
As per claim 3, Pfister, CHEN, DRAG IC, and NAMASU, in combination, disclose the computer-implemented method of claim 1 or 2. Pfister further comprises: determining a biological state pertaining to the cancer sample genome (classification includes
determining different biological states in induvial tumor species or classes; paragraph [0026]); and determining a biological state pattern
based on the determined biological states (classification includes determining different biological states in induvial tumor species or
classes. Where distinguishable DNA methylation patterns are determined for cancer prognosis; paragraphs [0003]-[0004], [0026], [0077]).
Pfister does not disclose each of the at least 3 gene sites.
Chen teaches SEQ ID No. 1 (ABAT (SEQ ID No. 1 of the instant application). Wherein loss of ABAT-mediated GABAergic system promotes breast cancer progression; title; abstract).
It would have been obvious to one of ordinary skill in the art at the time of the invention to modify the Pfister invention to provide wherein the set of gene sites comprises gene sites of the cancer sample genome selected from the gene sites of SEQ ID No. 1, as taught by Chen, in order to provide a computer classifying system that recognizes a classifying gene site that is a known indicator of cancer (Chen reference, title; abstract).
Dragic teaches SEQ ID No. 2 (ABLIM2 (SEQ ID No. 2 of the instant application) gene is known in its potential role in lung cancer metastasis; page 1804, first column, last paragraph).
It would have been obvious to one of ordinary skill in the art at the time of the invention to modify the Pfister invention to provide wherein the set of gene sites comprises gene sites of the cancer sample genome selected from the gene sites of SEQ ID No. 2, as taught by Dragic, in order to provide a computer classifying system that recognizes a classifying gene site that is a known indicator of metastasis (Dragic reference, page 1804,.first column, last paragraph).
Namasu teaches SEQ ID No. 3 (ABR (SEQ ID No. 3 of the instant application) is a favorable prognostic factor in acute myeloid leukemia; title; abstract).
It would have been obvious to one of ordinary skill in the art at the time of the invention to modify the Pfister invention to provide wherein the set of gene sites comprises gene sites of the cancer sample genome selected from the gene sites of SEQ ID No. 3, as taught by Namasu, in order to provide a computer classifying system that recognizes prognostic cancer genes (Namasu reference, title; abstract).
Claims 14-15 recite substantially similar limitations as those already addressed in claim 1, and, as such, are rejected for similar reasons as given above.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Grail (US 20190287649 A1) teaches to selecting and analyzing biological data of high dimensionality, in particular, nucleic acid sequencing data obtained using next-generation sequencing technologies.
Burwinkel (US 20180245159 A1) teaches to panels of methylation and miRNA marker as well as their use in the prognosing, diagnosing and/or treatment of cancer, means for detecting said marker, kits comprising said means, and devices for analysing the marker panel.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Jonathan K Ng whose telephone number is (571)270-7941. The examiner can normally be reached M-F 8 AM - 5 PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anita Coupe can be reached at 571-270-7949. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Jonathan Ng/ Primary Examiner, Art Unit 3619
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