DETAILED ACTION
Applicant's response, filed 15 July 2025, has been fully considered. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 the Claims
Claims 1-3 and 5-11 are pending.
Claim 4 is cancelled.
Claims 1-3 and 5-11 are rejected.
Claims 2-3 are objected to.
Priority
The effective filing date of the claimed invention is 17 July 2020.
Information Disclosure Statement
An information disclosure statement (IDS) has not been submitted for the examiner to consider.
Specification
The objection to the specification is withdrawn in view of the amendment to the specification, filed 15 July 2025.
Claim Objections
The objection to claim 4 has been withdrawn in view of the cancellation of the claim.
The objection to claim 1 has been withdrawn in view of the amendment; however, new ground for objection was necessitated by the amendments to the claims, filed 15 July 2025. Claim 1 is objected to because of the following minor informality:
Step (G) of claim 1 should end with a semicolon (“;”).
The objections to claims 2 and 3 are maintained. Claims 2-3 are objected to for the following minor informalities:
Claim 2 recites an inappropriate step identifier (i.e.,
G
1
);
Claim 3 recites inappropriate step identifiers (i.e.,
G
2
,
G
3
).
According to the MPEP, “Where a claim sets forth a plurality of elements or steps, each element or step of the claim should be separated by a line indentation, 37 CFR 1.75(i).” See MPEP § 608.01(m).
To overcome the objections to claims 2-3, the Examiner suggests amending the claims by either using Roman numeral step identifiers (e.g. (I), (II), (III), or (i), (ii), (iii), etc.) or by omitting the step identifiers and instead using line indentations.
An example of how claim 2 could be amended to overcome this objection is as follows:
“The method of claim 1, wherein identifying a mutation based on a difference between the DNA sequence of the test sample and the DNA sequence of the control sample, further comprises:
determining whether the mutation is within predetermined requirements.”
Appropriate correction is required.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier.
In claim 8, “configured to” is the generic placeholder for “means for” and is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Specifically, claim 8 uses the phrases “an identification system configured to: receive…; compare…; and identify.” Claim 8 also uses the phrases “a machine learning system configured to: receive…; compare…; and return.” Claim 8 does recite sufficient structure to perform the functional language as disclosed in these claim limitations.
This application includes one or more claim limitations that use the word “means” or “step” or equivalent but are nonetheless not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph because the claim limitation recites sufficient structure, materials, or acts to entirely perform the recited function. Such claim limitations are: “an identification system configured to: receive…; compare…; and identify” and “a machine learning system configured to: receive…; compare…; and return.” in claim 8.
Because these claim limitations are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it is not being interpreted to cover only the corresponding structure, material, or acts described in the specification as performing the claimed function, and equivalents thereof.
If applicant intends to have these limitations interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitations to remove the structure, materials, or acts that performs the claimed function; or (2) present a sufficient showing that the claim limitations do not recite sufficient structure, materials, or acts to perform the claimed function.
Response to Arguments
Regarding 35 USC § 112(d): Applicant’s arguments (see pages 1-2, Section: Rejection under 35 U.S.C. § 112), filed 15 July 2025, with respect to claims 4 and 10 have been fully considered and are persuasive. The rejection of the claims under 35 USC § 112(d) has been withdrawn in view of the amendments to the claims, filed 15 July 2025.
Regarding 35 USC § 101: Applicant’s arguments (see page 3, Section: Rejection under 35 U.S.C. § 101), filed 15 July 2025, with respect to claims 1-3 and 5-7 have been fully considered but are not persuasive. The rejection of the claims under 35 USC § 101 has been maintained in view of the amendments to the claims, filed 15 July 2025. The additional element of treating the test portion of the tissue using the treatment (administration step) of claim 1 is not particular, and is instead merely instructions to "apply" the exception in a generic way. Thus, the administration step does not integrate the abstract idea into a practical application [see MPEP § 2106.04(d)(2)(a)]. The treatment or prophylaxis limitation must be "particular," i.e., specifically identified so that it does not encompass all applications of the judicial exception(s). For example, consider a claim that recites mentally analyzing information to identify if a patient has a genotype associated with poor metabolism of beta blocker medications. This falls within the mental process grouping of abstract ideas enumerated in MPEP § 2106.04(a). The claim also recites "administering a lower than normal dosage of a beta blocker medication to a patient identified as having the poor metabolizer genotype." This administration step is particular, and it integrates the mental analysis step into a practical application. Conversely, consider a claim that recites the same abstract idea and "administering a suitable medication to a patient." This administration step is not particular, and is instead merely instructions to "apply" the exception in a generic way. Thus, the administration step does not integrate the mental analysis step into a practical application. [MPEP § 2106.04(d)(2)(a)].
Regarding 35 USC § 102: Applicant’s arguments (see pages 3-4, Section: Rejection under 35 U.S.C. § 102), filed 15 July 2025, with respect to claims 1-2 and 5-6 have been fully considered but are not persuasive. The rejection of the claims under 35 USC § 102 has been maintained in view of the amendments to the claims, filed 15 July 2025. Applicant respectfully submits that the amendments to independent claim 1 introduce limitations that are not disclosed or suggested by the cited reference. Von Hoff et al. teaches all of the previously presented limitations and teaches the newly added limitations as presented in the amendments to the claims, filed 15 July 2025. Regarding independent claim 1, Von Hoff et al. teaches biological samples, "…obtained from diseased patients by taking a biopsy of a tumor, conducting minimally invasive surgery if no recent tumor is available, obtaining a sample of the patient's blood, or a sample of any other biological fluid including, but not limited to, cell extracts, nuclear extracts, cell lysates or biological products or substances of biological origin such as excretions, blood, sera, plasma, urine, sputum, tears, feces, saliva, membrane extracts, and the like" (pg. 170 of 182, paragraph [0255]). Von Hoff et al. teaches a biological sample that "… typically comes from an individual with a suspected or known disease or disorder, such as, but not limited to, a biopsy sample from a cancer patient” (pg. 99-100 of 182, paragraph [0051]). Von Hoff et al. further teaches a control sample as “The control can include similar cells to the sample but without the disease. The control can be derived from the same patient, e.g., a normal adjacent portion of the same organ as the diseased cells...." (pg.100 of 182, paragraph [0052]). The biological sample and control of Von Hoff et al. read on “A method of testing tissues comprising: selecting a test portion of a tissue; selecting a control portion of the tissue; extracting a test sample from the test portion; extracting a control sample from the control portion.”
Von Hoff et al. further teaches sequencing the test and control samples as “Molecular profiling of the sample can also be performed by any number of techniques that assess the amount or state of a biological factor, such as a DNA sequence, an mRNA sequence or a protein. Such techniques include… various types of sequencing (Sanger, pyrosequencing, etc), comparative genomic hybridization (CGH), NextGen sequencing, …and any other appropriate technique under development to assay the presence or quantity of a biological molecule of interest” (pg.100 of 182, paragraph [0052]) which reads on “sequencing DNA of the test sample; sequencing DNA of the control sample.”
Von Hoff et al. further teaches the comparison of the DNA sequences of the test and control samples as "…comparing two different nucleic acid or polypeptide sequences, one sequence (test sequence) may be described to be a specific percentage identical to another sequence (comparison sequence)" (pg. 103 of 182, paragraph [0079]). Von Hoff et al. further teaches comparing the DNA sequences of the test and control samples and identifying the differences as the “Percent identity of two sequences is calculated by aligning a test sequence with a comparison sequence using BLAST, determining the number of amino acids or nucleotides in the aligned test sequence that are identical to amino acids or nucleotides in the same position of the comparison sequence, and dividing the number of identical amino acids or nucleotides by the number of amino acids or nucleotides in the comparison sequence" (pg. 103 of 182, paragraph [0079]); the percentage of cancer in a sample can be determined by methods known to those of skill in the art, e.g., using pathology techniques… A sample may be required to have a certain threshold of cancer cells before it is used for molecular profiling... The threshold can be at least about 5, 10, 20, 30, 40, 50 60, 70, 80, 90 or 95% cancer cells… the diseased sample is compared to a normal sample taken from the same patient, e.g., adjacent but non-cancer tissue (pg. 27 of 182, paragraph [0203]); and “… a determination is made as to whether one or more of the targets that were tested for in… exhibit a change in expression compared to a normal reference for that particular target” (pg.170 of 182, paragraph [0256]) which read on “identifying a mutation based on a difference between the DNA sequence of the test sample and the DNA sequence of the control sample.”
Von Hoff et al. further teaches comparing the identified sequence differences to at least one database as “…performing DNA sequencing on the sample to determine a sequencing mutation profile on at least one gene; and comparing …the sequencing mutation profile against a rules database, wherein the rules database comprises a mapping of treatments whose biological activity is known against diseased cells that: … have zero or more mutations in one or more genes included in the sequencing mutation profile; and identifying the treatment if the comparison against the rules database indicates that the treatment should have biological activity against the diseased cells; and the comparison against the rules database does not contraindicate the treatment for treating the diseased cells" (pg. 118 of 182, paragraph [0191]). Von Hoff also teaches databases with a plurality of known conditions as “Various databases used herein may include: …biological sample data, prior treatment and protocol data, patient clinical data, molecular profiling data of biological samples, data on therapeutic drug agents and/or investigative drugs, a gene library, a disease library, a drug library…” (pg. 166 of 182, paragraph [0221]). Von Hoff et al. further teaches the present invention provides methods and system for molecular profiling, using the results from molecular profiling to identify treatments for individuals (paragraph [0007]); the rules database comprises a mapping of treatments whose biological activity is known against cancer cells that: i) overexpress or underexpress one or more proteins included in the IHC expression profile; ii) overexpress or underexpress one or more genes included in the microarray expression profile; iii) have no mutations, or one or more mutations in one or more genes included in the FISH mutation profile; and/or iv) have no mutations, or one or more mutations in one or more genes included in the sequencing mutation profile; the candidate treatment is identified if: i) the comparison step indicates that the treatment should have biological activity against the cancer; and ii) the comparison step does not contraindicate the treatment for treating the cancer (paragraph [0013]); and the candidate treatment comprises administration of one or more candidate therapeutic agents (paragraph [0023]) which read on “comparing the mutation against a database comprising a plurality of known conditions each of which having a known DNA mutation associated therewith”; “identifying a condition based on a similarity between the mutation and the known DNA mutation associated with said condition”; “reporting a treatment for the condition”; and “treating the test portion of the tissue using the treatment.”
Regarding 35 USC § 103: Applicant’s arguments (see pages 4-5, Section: Rejection under 35 U.S.C. § 103), filed 15 July 2025, with respect to claims 1-3 and 7-11 have been fully considered but are not persuasive. The rejection of the claims under 35 USC § 103 has been maintained in view of the amendments to the claims, filed 15 July 2025. Applicant respectfully submits that the amended claims now recite limitations that are not disclosed, taught, or suggested by the cited references, either individually or in any combination. Regarding independent claim 1, Von Hoff et al. teaches all of the previously presented limitations and teaches the newly added limitations as presented in the amendments to the claims, filed 15 July 2025 (see above). Regarding independent claim 8, Von Hoff et al. teaches a microarray expression analysis system for the analysis of DNA sequences and mutations as "Microarray expression analysis comprises identifying whether a gene or gene product is up-regulated or downregulated relative to a reference. The identification can be performed using a statistical test to determine statistical significance of any differential expression observed. In some embodiments, statistical significance is determined using a parametric statistical test." (pg.106 of 182, paragraph [0108]). Von Hoff further teaches using databases with a plurality of known conditions as “Various databases used herein may include: …biological sample data, prior treatment and protocol data, patient clinical data, molecular profiling data of biological samples, data on therapeutic drug agents and/or investigative drugs, a gene library, a disease library, a drug library…” (pg. 166 of 182, paragraph [0221]).
Von Hoff et al. further teaches a system of analysis, data warehouse, clinical information management system, and clinical decision support system as "A user interacts with the system by entering data into the system via form-based entry/upload of data sets, formulating queries and executing data analysis jobs, and acquiring and evaluating representations of output data. The data warehouse in the web based system is where data is extracted, transformed, and loaded from various database systems. The data warehouse is also where common formats, mapping and transformation occurs. The web based system also includes datamarts which are created based on data views of interest” (pg 171 of 182, paragraph [0260]) and "… an exemplary clinical decision support system of the information-based personalized medicine drug discovery system and method of the present invention is shown in FIG. 7. The clinical information management system includes the laboratory information management system and the medical information contained in the data warehouses and databases includes medical information libraries, such as drug libraries, gene libraries, and disease libraries, in addition to literature text mining. Both the information management systems relating to particular patients and the medical information databases and data warehouses come together at a data junction center where diagnostic information and therapeutic options can be obtained" (pg.171 of 182, paragraph [0261]).
Von Hoff et al. demonstrates the systems of analysis, data warehouse, clinical information management system, and clinical decision support system in Figures 6 and 7 (pgs. 10-11 of 182) which reads on A system for analysis of differences between a test DNA sequence and a control DNA sequence comprising: a database comprising: information about a plurality of tissue conditions; an identification system configured to: receive the test DNA sequence and the control DNA sequence; compare the test DNA sequence to the control DNA sequence; and identify differences between the test DNA sequence and the control DNA sequence.
Von Hoff et al. teaches a system of analysis comprising databases and an identification system but does not explicitly name a machine learning system, neural network, or artificial intelligence system.
Abraham et al. teaches systems of analysis and prediction using machine learning models trained to predict cancerous tissue origins as “… perform NGS of genomic DNA, RNA sequencing, and IHC analysis on the tumor specimen. A molecular profile is generated for the sample... The machine learning models described… are used to predict the primary site of the tumor…The molecular profiling results are included in the report... The report is provided to the oncologist. The oncologist uses the information provided in the report to assist in determining a treatment regimen for the patient” (pg. 365 of 462, lines 1-10).
Von Hoff et al. in view of Abraham et al. which describes a machine learning system, teaches the distribution and communication among all components of the systems described above as "Communication among the parties may be accomplished through any suitable communication channels… The various system components may be independently, separately or collectively suitably coupled to the network via data links…" (pg.166 of 182, paragraphs [0222-0223]) which reads on wherein one or more of the database, the identification system, and the machine learning system are distributed and are communicably connected via a communications network.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified Von Hoff et al. to incorporate the teachings of Abraham et al. to aid in the automation of the system of analysis and to add a machine learning model or neural network to aid in the receiving of DNA differences, comparing the differences to a database, and returning information of identified tissue conditions. Doing so allows for more efficient, comprehensive, and accurate molecular profiling as recognized by Abraham et al.
Von Hoff et al. in view of Abraham et al. does not explicitly teach an artificial intelligence system.
Chang et al. (i) show that artificial intelligence can robustly recognize genomic patterns within imaging, (ii) advance noninvasive characterization of gliomas, and (iii) demonstrate the potential of algorithmic tools within the clinic to aid clinical decision making (Abstract). Chang et al. further teaches a deep learning algorithm can achieve high accuracy in predicting IDH mutation in gliomas; and Chang et al. trained a deep learning algorithm to noninvasively predict IDH status within a multi-institutional data set of low and high-grade gliomas (pg. 1074, column 2, paragraph 1). Chang et al. further teaches a technique to noninvasively predict IDH genotype in grade II–IV glioma using conventional MR imaging; …their deep learning model does not require preengineered features… and may have the potential to serve as a noninvasive tool that
complements invasive tissue sampling, guiding patient management at an earlier stage of disease and in follow-up (pg. 1079, column 2, paragraph 2).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified Von Hoff et al. in view of Abraham et al. with the artificial intelligence system for predicting mutations in tumors of Chang et al. Chang et al. teaches their deep learning system improves current cancer diagnosis techniques by serving as “a noninvasive tool that complements invasive tissue sampling, guiding patient management at an earlier stage of disease and in follow-up.” This modification would have had reasonable expectation of success because both Von Hoff et al. in view of Abraham et al. and Chang et al. are directed to identifying cancer based on genetic differences in tissue sample 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 1-3 and 5-11 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract ideas without significantly more.
Framework with which to analyze Subject Matter Eligibility:
Step 1: Are the claims directed to a category of statutory subject matter (a process, machine, manufacture, or composition of matter? (see MPEP § 2106.03)
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e. an abstract idea, a law of nature, or a natural phenomenon? (see MPEP § 2106.04(a))
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application? (see MPEP § 2106.04(d))
Step 2B: If the claims do not integrate the judicial exception, do the claims provide an inventive concept? (see MPEP § 2106.05)
Framework Analysis as pertains to the Instant Claims 1-3 and 5-11:
Step 1: Yes, the claims are directed to statutory subject matter, specifically: methods (claims 1-3 and 5-7) and systems (claims 8-11). (See MPEP § 2106.03).
Step 2A, Prong One: The claims recite abstract ideas. The MPEP at 2106.04(a)(2) further explains that abstract ideas are defined as:
mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations);
certain methods of organizing human activity (fundamental economic practices or principles, managing personal behavior or relationships or interactions between people); and/or
mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information).
The MPEP at 2106.04(b) defines natural law/ natural phenomena as:
naturally occurring principles/ relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature.
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims are found herein to recite abstract ideas that fall into the grouping of mathematical concepts and mental processes.
Abstract ideas in the form of mathematical concepts and/or mental processes are recited in the following claims:
Independent claim 1: selecting test and control portions of tissue and comparing the test and control sequences (mental processes); identifying a mutation and comparing the mutation against a database (mental processes); identifying a condition associated with the mutation (mental processes);
Dependent claims 2-3 and 5-7: determining whether the mutation is within predetermined requirements (mental process); considering moving the location to collect test tissue responsive to a negative determination (mental process); determining that a test tissue contains a characteristic that the control tissue does not (mental process), determining the margin of tissue having atypical DNA characteristics (mental process);
Independent claim 8: an identification system and an artificial intelligence system for identifying and comparing DNA sequence differences (math/statistical processes; in addition, the identification system of claim 8 can also be considered a mental process of identifying and comparing);
Dependent claims 9-10: further limit the “artificial intelligence system” of claim 8 (math/statistical processes);
Dependent claim 11: further limits the “system for analysis” of claim 8 (math/statistical processes).
Therefore, the claims recite elements that constitute a judicial exception in the form of an abstract idea. (Step 2A, Prong One: Yes).
Step 2A, Prong Two analysis: Because the claims do recite judicial exceptions, direction under Step 2A, Prong Two provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application. A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The Step 2A, Prong Two analysis is performed by analyzing the additional elements of the claim, alone or in combination, to determine if the abstract idea is integrated into a practical application [see MPEP § 2106.04(d)]. If the claim contains no additional elements beyond the judicial exception, the claim fails to integrate the judicial exception into a practical application [see MPEP § 2106.04(d)(III)].
The claims recite the following additional elements in the form of data-gathering steps:
Claim 1: extracting and sequencing (i.e., acquiring data); and reporting a treatment (i.e., outputting data);
Claim 3: repeating the steps of claim 1 of extracting and sequencing (i.e., acquiring data);
Claim 5: the tissue is an animal tissue (i.e., further describing the acquired data).
Data gathering steps, such as extracting and sequencing data and descriptions of data, are not considered abstract ideas, but perform functions of inputting, collecting/acquiring, and outputting the data needed to carry out the abstract idea. These steps are considered insignificant extra-solution activity, and are not sufficient to integrate an abstract idea into a practical application as they do not impose any meaningful limitation on the abstract idea or how it is performed. To integrate a judicial exception into a practical application, the additional limitations must not be mere instructions to apply the judicial exception [see MPEP § 2106.04(d) and MPEP § 2106.05(g)].
The claims recite the following additional elements in the form of non-abstract elements:
Claim 1: treating the test portion of the tissue using the treatment;
Claim 8: a database;
Claim 9: a neural network;
Claim 10: a machine learning system;
Claims 11: a distribution of one or more of the database, identification system, and artificial intelligence system and a communications network.
The additional element of treating the test portion of the tissue using the treatment (administration step) of claim 1 is not particular, and is instead merely instructions to "apply" the exception in a generic way. Thus, the administration step does not integrate the abstract idea into a practical application [see MPEP § 2106.04(d)(2)(a)]. The treatment or prophylaxis limitation must be "particular," i.e., specifically identified so that it does not encompass all applications of the judicial exception(s). For example, consider a claim that recites mentally analyzing information to identify if a patient has a genotype associated with poor metabolism of beta blocker medications. This falls within the mental process grouping of abstract ideas enumerated in MPEP § 2106.04(a). The claim also recites "administering a lower than normal dosage of a beta blocker medication to a patient identified as having the poor metabolizer genotype." This administration step is particular, and it integrates the mental analysis step into a practical application. Conversely, consider a claim that recites the same abstract idea and "administering a suitable medication to a patient." This administration step is not particular, and is instead merely instructions to "apply" the exception in a generic way. Thus, the administration step does not integrate the mental analysis step into a practical application. [MPEP § 2106.04(d)(2)(a)].
The additional elements of a database; a neural network; a machine learning system; a distribution of one or more of the database, identification system, and artificial intelligence system and a communications network are not an improvement to computer functionality itself, or an improvement to any other technology or technical field and do not integrate the abstract idea or law of nature into a practical application [see MPEP § 2106.04(d)(1) and MPEP § 2106.05(f)]. Claims 8-11 do not describe any specific computational steps by which a database; a neural network; a machine learning system; and/or a distribution of one or more of the database, identification system, and artificial intelligence system and a communications network; perform or carry out the abstract ideas, nor do they provide details of how the specific structures of the computer components are used to implement these functions. The claims appear to require nothing more than generic computer parts and the internet to perform the functions that constitute the judicial exception. Therefore, these are mere instructions to apply the judicial exceptions using computer systems.
Thus, when all limitations in claims 1-3 and 5-11 have been considered as a whole, the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 1-3 and 5-11 are directed to an abstract idea (MPEP 2106.04(d)). (Step 2A, Prong Two: Yes).
Step 2B analysis:
Because the additional claim elements do not integrate the abstract idea or law of nature into a practical application, the claims are further examined under Step 2B, which evaluates whether the additional elements, individually and in combination, amount to significantly more than the judicial exception itself by providing an inventive concept. An inventive concept is furnished by an element or combination of elements that is recited in the claim in addition to the judicial exception, and is sufficient to ensure that the claim, as a whole, amounts to significantly more than the judicial exception itself (see MPEP § 2106.05).
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exceptions because the claims recite additional elements that are generic, conventional, or nonspecific.
The additional elements of data gathering of extracting and sequencing (i.e., acquiring data) and reporting a treatment (i.e., outputting data) (claim 1); repeating the steps of claim 1 of extracting and sequencing (i.e., acquiring data) (claim 3); describing the tissue as an animal tissue (i.e., further describing the acquired data) (claim 5) do not cause the claims to rise to the level of significantly more than the judicial exception. The additional elements of a database (claim 8); a neural network (claim 9); a machine learning system (claim 10); and a distribution of one or more of the database, identification system, and artificial intelligence system and a communications network (claim 11); are referred to in a generic and non-specific way in both the claims and the specification are conventional (see MPEP § 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
The additional element of treating the test portion of the tissue using the treatment (administration step) of claim 1 is not particular (merely instructions to "apply" the exception in a generic way [MPEP § 2106.04(d)(2)(a)]) and does not amount to more than generally linking the use of a judicial exception to a particular technological environment or field of use (i.e., generic treatment or prophylaxis). An example of a limitation that the courts have described as merely indicating a field of use or technological environment in which to apply a judicial exception include “i. A step of administering a drug providing 6-thioguanine to patients with an immune-mediated gastrointestinal disorder, because limiting drug administration to this patient population did no more than simply refer to the relevant pre-existing audience of doctors who used thiopurine drugs to treat patients suffering from autoimmune disorders, Mayo Collaborative Servs. v. Prometheus Labs. Inc., 566 U.S. 66, 78, 101 USPQ2d 1961, 1968 (2012)” [MPEP § 2106.05(h)].
All claims have also been analyzed with respect to Step 2B, and none of these claims provide a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception. Considering these elements alone and in combination, they do not provide an inventive concept, and do not amount to significantly more than the judicial exception itself. Thus, the additional elements do not provide an inventive concept that transforms the judicial exception into a patent eligible application of the exceptions, and the claims do not amount to significantly more that the judicial exception itself. (Step2B: No).
Therefore, the claims, when the limitations are considered individually and as a whole, are rejected under 35 U.S.C. § 101 as being directed to non-statutory subject matter.
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)(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 1-2 and 5-6 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Von Hoff et al. (US PGPUB No US 2010/0304989 A1).
Regarding claim 1, the biological samples of Von Hoff et al., "…obtained from diseased patients by taking a biopsy of a tumor, conducting minimally invasive surgery if no recent tumor is available, obtaining a sample of the patient's blood, or a sample of any other biological fluid including, but not limited to, cell extracts, nuclear extracts, cell lysates or biological products or substances of biological origin such as excretions, blood, sera, plasma, urine, sputum, tears, feces, saliva, membrane extracts, and the like" (pg. 170 of 182, paragraph [0255]). Von Hoff et al. teaches a biological sample that "… typically comes from an individual with a suspected or known disease or disorder, such as, but not limited to, a biopsy sample from a cancer patient” (pg. 99-100 of 182, paragraph [0051]). Von Hoff et al. further teaches a control sample as “The control can include similar cells to the sample but without the disease. The control can be derived from the same patient, e.g., a normal adjacent portion of the same organ as the diseased cells...." (pg.100 of 182, paragraph [0052]). The biological sample and control of Von Hoff et al. read on “A method of testing tissues comprising: selecting a test portion of a tissue; selecting a control portion of the tissue; extracting a test sample from the test portion; extracting a control sample from the control portion.”
Von Hoff et al. further teaches sequencing the test and control samples as “Molecular profiling of the sample can also be performed by any number of techniques that assess the amount or state of a biological factor, such as a DNA sequence, an mRNA sequence or a protein. Such techniques include… various types of sequencing (Sanger, pyrosequencing, etc), comparative genomic hybridization (CGH), NextGen sequencing, …and any other appropriate technique under development to assay the presence or quantity of a biological molecule of interest” (pg.100 of 182, paragraph [0052]) which reads on “sequencing DNA of the test sample; sequencing DNA of the control sample.”
Von Hoff et al. further teaches the comparison of the DNA sequences of the test and control samples as "…comparing two different nucleic acid or polypeptide sequences, one sequence (test sequence) may be described to be a specific percentage identical to another sequence (comparison sequence)" (pg. 103 of 182, paragraph [0079]). Von Hoff et al. further teaches comparing the DNA sequences of the test and control samples and identifying the differences as the “Percent identity of two sequences is calculated by aligning a test sequence with a comparison sequence using BLAST, determining the number of amino acids or nucleotides in the aligned test sequence that are identical to amino acids or nucleotides in the same position of the comparison sequence, and dividing the number of identical amino acids or nucleotides by the number of amino acids or nucleotides in the comparison sequence" (pg. 103 of 182, paragraph [0079]); the percentage of cancer in a sample can be determined by methods known to those of skill in the art, e.g., using pathology techniques… A sample may be required to have a certain threshold of cancer cells before it is used for molecular profiling... The threshold can be at least about 5, 10, 20, 30, 40, 50 60, 70, 80, 90 or 95% cancer cells… the diseased sample is compared to a normal sample taken from the same patient, e.g., adjacent but non-cancer tissue (pg. 27 of 182, paragraph [0203]); and “… a determination is made as to whether one or more of the targets that were tested for in… exhibit a change in expression compared to a normal reference for that particular target” (pg.170 of 182, paragraph [0256]) which read on “identifying a mutation based on a difference between the DNA sequence of the test sample and the DNA sequence of the control sample.”
Von Hoff et al. further teaches comparing the identified sequence differences to at least one database as “…performing DNA sequencing on the sample to determine a sequencing mutation profile on at least one gene; and comparing …the sequencing mutation profile against a rules database, wherein the rules database comprises a mapping of treatments whose biological activity is known against diseased cells that: … have zero or more mutations in one or more genes included in the sequencing mutation profile; and identifying the treatment if the comparison against the rules database indicates that the treatment should have biological activity against the diseased cells; and the comparison against the rules database does not contraindicate the treatment for treating the diseased cells" (pg. 118 of 182, paragraph [0191]). Von Hoff also teaches databases with a plurality of known conditions as “Various databases used herein may include: …biological sample data, prior treatment and protocol data, patient clinical data, molecular profiling data of biological samples, data on therapeutic drug agents and/or investigative drugs, a gene library, a disease library, a drug library…” (pg. 166 of 182, paragraph [0221]). Von Hoff et al. further teaches the present invention provides methods and system for molecular profiling, using the results from molecular profiling to identify treatments for individuals (paragraph [0007]); the rules database comprises a mapping of treatments whose biological activity is known against cancer cells that: i) overexpress or underexpress one or more proteins included in the IHC expression profile; ii) overexpress or underexpress one or more genes included in the microarray expression profile; iii) have no mutations, or one or more mutations in one or more genes included in the FISH mutation profile; and/or iv) have no mutations, or one or more mutations in one or more genes included in the sequencing mutation profile; the candidate treatment is identified if: i) the comparison step indicates that the treatment should have biological activity against the cancer; and ii) the comparison step does not contraindicate the treatment for treating the cancer (paragraph [0013]); and the candidate treatment comprises administration of one or more candidate therapeutic agents (paragraph [0023]) which read on “comparing the mutation against a database comprising a plurality of known conditions each of which having a known DNA mutation associated therewith”; “identifying a condition based on a similarity between the mutation and the known DNA mutation associated with said condition”; “reporting a treatment for the condition”; and “treating the test portion of the tissue using the treatment.”
Regarding claim 2, Von Hoff et al. further teaches comparing the DNA sequences of the test and control samples and determining a percent identity as “…comparing two different nucleic acid or polypeptide sequences, one sequence (test sequence) may be described to be a specific percentage identical to another sequence (comparison sequence)” (pg. 103 of 182, paragraph [0079]). Von Hoff et al. further teaches performing an immunohistochemistry (IHC) analysis on a sample from the subject to determine an IHC expression profile on at least five proteins; performing a microarray analysis on the sample to determine a microarray expression profile on at least ten genes; performing a fluorescent in-situ hybridization (FISH) analysis on the sample to determine a FISH mutation profile on at least one gene; performing DNA sequencing on the sample to determine a sequencing mutation profile on at least one gene; and comparing the IHC expression profile, microarray expression profile, FISH mutation profile and sequencing mutation profile against a rules database, wherein the rules database comprises a mapping of treatments whose biological activity is known against diseased cells that: i) overexpress or underexpress one or more proteins included in the IHC expression profile; ii) overexpress or underexpress one or more genes included in the microarray expression profile; iii) have zero or more mutations in one or more genes included in the FISH mutation profile; and/or iv) have zero or more mutations in one or more genes included in the sequencing mutation profile; and identifying the treatment if the comparison against the rules database indicates that the treatment should have biological activity against the diseased cells; and the comparison against the rules database does not contraindicate the treatment for treating the diseased cells (pg. 23 of 182, paragraph [0191]) which reads on “determining whether the mutation is within predetermined requirements.”
Regarding claim 5, Von Hoff et al. teaches the sample can be an animal tissue as "A subject can be any animal which may benefit from the methods of the invention…" (pg. 103 of 182, paragraph [0080]) which reads on “wherein the tissue is an animal tissue.”
Regarding claim 6, Von Hoff et al. teaches the test sample comprising a characteristic that the control does not have as "The control can include similar cells to the sample but without the disease. The control can be derived from the same patient, e.g., a normal adjacent portion of the same organ as the diseased cells, or the control can be derived from healthy tissues from other patients” (pg.100 of 182, paragraph [0052]) which reads on “wherein the test portion of the tissue comprises a characteristic, and wherein the control portion of the tissue does not comprise the characteristic.”
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