Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Applicants Amendment
Applicants’ amendment filed 4/10/2026 has been received and entered. Claims 2, 3, 11, 16, 18, 19 have been amended, and claim 1 has been cancelled.
Claims 2-19 are pending.
Election/Restriction
Applicant's election with traverse of Group I in the reply filed on 8/1/2025 was acknowledged. In review and initial search and considerations, it was agreed that it would not be an undue burden in view of the overlapping requirements of the claims. Accordingly, the restriction requirement was withdrawn.
Claims 2-19 are pending and currently under examination as they are drawn to a method of developing a patient specific treatment recommendation, a computer readable medium with instructions, and an electronic device with a plurality of nodes representing disease.
Priority
This application filed 9/23/2019 is a continuation 14/463073 filed 8/19/20214 (now abandoned), which is a CIP of 14/146743 filed 1/3/2014 (now abandoned) which claims benefit to US provisional applications 61/749288 filed 1/5/2013 and 61/749291 filed 1/5/2013; and
is related to 14/463068 filed 8/18/2014 now US Patent 11,158425;
is related to 16/579508 filed 9/23/2019 now US Patent 12,334192;
is related to 16/579496 filed 9/23/2019 now US Patent 11,450438, 17/88412 filed 8/10/2022 now US Patent 12,087453 and 18/805333 filed 8/14/2024 (Notice of allowance mailed 10/7/2025).
Applicants do not comment on the summary of priority.
Information Disclosure Statement
The information disclosure statement (IDS) submitted 4/10/2026 in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
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.
Examiner Comment:
Applicants do not appear to provide a response to the 112f analysis provided in the previous action.
Analysis of the claims
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.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
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.
Such claim limitation is provided in claim 19 as it is directed to a ‘device’ with particular functions which it is required to perform. It is acknowledged that the device comprises one or more processors and a memory where one or more programs are stored with instructions. In review of the specification, the generic support of a device with a processor and memory are supported, however there is no specific guidance to any specific memory or processor, and overall appears to support that the instructions for receiving and analyzing data are performed on a general purpose computer. There is some indication that the source of data might be received from sources outside a single computer, and in review there does not seem to be any unique system or set-up required to implement the receiving of data, nor is there any specific guidance for the possible unique types of data and data form that could be received and how this would be processed in any unique way when the instructions for analysis are performed. Overall, it is found that the structure of the device claimed and the possible breadth to a disperse data source appear to be directed to a general purpose computer and known systems which would allow for any type of data to be transferred over the internet.
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
Response to Applicants arguments
Applicants note a terminal disclaimer has been filed for 11,584425 (see TD submitted 4/10/2026; approved entered 4/10/2026).
In response, the rejection is withdrawn in view of the terminal disclaimer.
Claims 2-19 rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of U.S. Patent No. 11,158425 (application 14/463068 filed 8/18/2014) is withdrawn.
Claims 2-19 rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of copending Application No. 18/805333 filed 8/14/2024 (now US Patent 12548682) is withdrawn.
Upon consideration of applicant’s arguments and amendments to the claims, it is agreed that although the present analysis methods rely on data for treatment of other patients with similar genetic profiles which ‘333 provides to the data source, the device of ‘333 provides for announcing such information to patients for possible treatment choices, and additional limitations required make it such that the claims at issue are not identical and drawn to a distinct device and display with data handling that is different.
For 12,334192 (16/579508 filed 9/23/2019), US Patent 12,087453 (17/88412 filed 8/10/2022) and 11,450438 (16/579496 filed 9/23/2019), Applicants note limitations not specifically in the instant claims and argue the claims are patentably distinct.
In response, the differences in specific limitations are noted, however in light of the guidance of the specification it appears that the instant method of delivering encompasses and used the method steps of providing the recommendations for treatment and ‘tracking’ where analysis and possible diagnosis/progression involves recommendations for treatment as well. The instant claims comprise any disease or condition, and providing a model that would be informative for patient specific treatment, which using the same information about genetic profiles and ontologies that are correlated to the genetic information. Practicing the instant claims are effectively required and would infringe both the claims of 12,334192 (16/579508 filed 9/23/2019), US Patent 12,087453 (17/88412 filed 8/10/2022) and 11,450438 (16/579496 filed 9/23/2019).
Claims 2-19 stand rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of U.S. Patent No. 12,334192 (16/579508 filed 9/23/2019). Although the claims at issue are not identical, they are not patentably distinct from each other because the present claims directed to a device and method of delivering treatment recommendations provides for the same overlapping steps of receiving patient data and comparing it to know alterations for diseases and possible treatments. The present claims set forth the data is organized in nodes, while ‘192 provides a more generic structure of the data in ontologies and a tuple structure, however both are generically organizing the same corpus of data where nodes and indices can be represented as a tuple structure which is analyzed relative to the patient data and any known data that might be present in a database. The allowed method claim from ‘192 is presented for comparison to the instantly pending claims and for clarity of the record.
From ‘192: A method of identifying patient-specific treatment based on genomic information, comprising:
receiving, by one or more processors a plurality of genomic alterations;
generating a plurality of genomic alteration groups by grouping the plurality of genomic alterations based on functional similarities of the plurality of genomic alterations;
receiving, by the one or more processors, a plurality of disease subtype;
generating a plurality of disease ontology groups by grouping the plurality of disease subtypes based on functional similarities of the plurality of disease subtypes- wherein the plurality of disease ontology groups comprises at least one disease ontology group corresponding to a body part and a tumor type, and
wherein the at least one disease ontology group comprises at least one disease subtype corresponding to the body part and the tumor type;
receiving, by the one or more processors, data representing a genomic alteration and a disease phenotype associated with a patient; generating, based on the data representing the genomic alteration and the disease phenotype associated with the patient, a tuple data structure comprising two elements connected by a relation:
adding the tuple data structure to a data model comprising a plurality of tuples, wherein the data model comprises a learning model configured to be improved over time;
determining if there is another patient having the same genomic alteration and the same disease phenotype associated with the patient if there is no patient having the genomic alteration and the same disease phenotype associated with the patient:
automatically identifying from the generated plurality of genomic alteration groups, by the one or more processors, a pre-defined genomic alteration group comprising the genomic alteration;
automatically identifying from the generated plurality of disease ontology groups, by the one or more processors, a pre-defined disease ontology group comprising the disease phenotype;
automatically identifying, by the one or more processors, a plurality of similar patients based on the pre-defined genomic alteration group and the pre-defined disease ontology group;
displaying, on a display, a selectable data structure corresponding to the genomic alteration, wherein the data structure comprises information related to one or more physicians that provided treatment to the plurality of similar patients;
receiving a user selection of the data structure; and
responsive to receiving the user selection, providing a user control for sending a request to one of the one or more physicians, and
identifying a patient-specific treatment for the patient based on the plurality of similar patients.
Claims 2-19 stand rejected on the ground of nonstatutory double patenting as being unpatentable over the claims of U US Patent 11,450438 (16/579496 filed 9/23/2019). Although the claims at issue are not identical, they are not patentably distinct from each other because the present method rely on data for treatment of other patients with similar genetic profiles which ‘438 provides to the data source, and the method of ‘438 provides for announcing such information to patients for possible treatment choices. The allowed method claim from ‘438 is provided for comparison to the pending claims.
From ‘438: A method for tracking cancer treatment and outcome information, comprising:
generating a model configured to analyze treatment data and outcome data, wherein generating the model includes:
indexing outcome data based on one or more genomic-based indices, and
specifying a data structure that includes the one or more genomic-based indices;
receiving, by one or more processors, a user input indicative of an update to treatment or outcome of a patient via a first user interface having one or more user interface controls categorizing treatment information and outcome information into a plurality of selectable categories to minimize time required by a physician to input data;
processing the user input according to the model dynamically identifying, by the one or more processors, a set of patients similar to the patient based on the user input model; responsive to receiving the user input, configuring a second user interface based at least partially on the model by automatically displaying at a display: generating a personalized patient specific timeline indicating one or more treatments and one or more outcomes associated with the patient according to the model correlated with outcome data in a database, and generating a user interface control for viewing the set of patients similar to the patient patients; and responsive to receiving a selection of the user interface control, configuring a third user interface , the third user interface including:
automatically displaying at the display: a treatment data structure associated with treatment data of the set of patients similar to the patient to provide actionable or advisory information for treatment decision making patients, and a genomic filter configured to filter the set of patients similar to the patient based on selected genomic information associated with each patient of the set of patients similar to the patients
wherein the third user interface is configured to allow the physician to locate treatment information and outcome information for patients with same or similar genomic alterations occurring in one or more tumor types to inform decision-making for off-label uses of a particular treatment.
Claims 2-19 are rejected on the ground of nonstatutory double patenting as being unpatentable over the claims US Patent 12,087453 (17/88412 filed 8/10/2022). Although the claims at issue are not identical, they are not patentably distinct from each other because the present method rely on data for treatment of other patients with similar genetic profiles which ‘453 provides to the data source, and the method of ‘453 provides for announcing such information to patients for possible treatment choices. The allowed method claim from ‘453 is provided for comparison to the pending claims.
From ‘453: A method for tracking cancer treatment and outcome information comprising:
generating a model configured to analyze treatment data and outcome data, wherein generating the model includes:
indexing outcome data based on one or more genomic-based indices, and specifying a data structure that includes the one or more genomic-based indices; receiving, by one or more processors, a user input indicative of an update to treatment or outcome of a patient via a first user interface having one or more user interface controls categorizing treatment information and outcome information into a plurality of selectable categories to minimize time required by a physician to input data; processing the user input according to the model; dynamically identifying, by the one or more processors, a set of patients similar to the patient based on the model; receiving an instruction for viewing similar patients; and
responsive to receiving the instruction for viewing similar patients, configuring a second user interface based at least partially on the model by generating a treatment data structure associated with the set of patients similar to the patient to provide actionable information or advisory information for treatment decision making, wherein the set of patients similar to the patient is dynamically identified based on the model and a genomic filter configured to filter the set of patients similar to the patient based on selected genomic information associated with each patient,
wherein the second user interface is configured to allow the physician to locate the treatment information and the outcome information for the set of patients similar to the patient dynamically identified based on the model patients with same or similar genomic alterations occurring in one or more tumor types to inform decision-making for off-label uses of a particular treatment.
As noted previously, a timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
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 2-19 stand rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Claim analysis
Claim 2 has been amended and still is generally directed to a method and claim 19 has been amended consistently for the device which implements instructions that provides patient specific treatment recommendations based on genetic information. More specifically, the independent claims require a second receiving step of receiving information about prior patients that comprises pathology and genetic information, and using the information to generate a graph model based on the information using the same steps previously provided, and an additional step of ‘recomputing’ a topology of the graph model to provide genomic alterations with the same actionable item from the data, and applying the correlation within the data to patient care recommendations. The method steps provide for receiving patient genetic data and analyzing it using a graph model information of correlated genetic data, disease information and treatments stored at nodes and which are coupled by indices.
Generally, in light of the specification the basis of the invention is found at page 25 which teaches ‘To exploit the granular data elements necessary for a precision medicine representation model, consider a case in oncology where a physician is looking for information on whether a set of biomarkers for a given patient will affect treatment decisions, i.e. whether these biomarkers, combined with the patient's specific pathology, provide information on the patient's susceptibility or resistance to a particular set of therapies or whether the patient is eligible to enroll a clinical trial. For the purposes of the model, actionability may be defined as the potential to reach one or more leaf nodes as the results of walking a decision graph. Leaf nodes, in one implementation, may either be therapies or clinical trials (e.g., actionable items). In another example implementation, tree branch decisions are based on context items (e.g., disease or gene alteration). Actionability items (e.g., therapies, clinical trials) are therefore, in one example implementation, a function of context items (disease and gene state):
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With respect to the data structure encompassed by the claims for a graph model, on page 12 a ‘leaf node’ is defined as a terminal node in a decision tree, and is consistent with the data being stored in a graph based structure. Dependent claims provide for how the assessment of the patient data is evaluated within the data structure generically for claims 3-6, and limitations implying computer use for terms like ‘tuple’ in the assessment of a ‘trust score’. In review of the teaching of the specification, no new or unique data structure is provided, nor is there any specific teaching for the data itself and clearly relies on the corpus of what is already known in the art for the association of genetic data and any correlation to a disease state, and any ability to provide for ‘scoring’ based on the strength of the association of the genetic marker and the disease, as well as any general or specific treatments which may be known or used.
Response to Applicants arguments
Applicants note and provide an overview of the declaration of Dr. Douglas Mata (senior director of the Applicant of the instant application). Applicants argue that claim 2 is not directed to a mathematical concept noting the guidance of the MPEP and Example 39, and argue the graph model provides several steps and does not recite a mathematical relationship.
In response, it is noted that claim 2 does not recite a specific mathematical algorithm, however in evaluation of dependent claims, for example claims 9-10, the steps require providing a ‘trust score’ in developing the relationship of the data in the model. As such, embodiments claimed and encompassed by the independent claims were evaluated for judicial exception required of the claims. It is generally acknowledged that the claims do not provide a specific algorithm for a ‘trust value’ or means of establishing the relationships of the graph model defined in the specification, but clearly a term such as ‘value’ and steps reciting ‘’calculating’ (see claim 11 for example) requires providing an assessment which could be mathematical and therefore this assessment has been made of record. With respect to the judicial exception, it is included because the claims clearly encompass steps which generically are directed to providing a mathematical evaluation and ‘score’ which represents the correlation of a genetic alteration and a respective disease (see claim 6 for example).
Applicants argue that the claims are not directed to a mental process because the mind is not equipped to perform the claim limitations noting the recitation of ‘generating, by one or more processors’ and citing SRI Int as related to network monitoring. Referring to the declaration of Dr. Mata, an explanation of how the data could be organized in a graph model and how explicit relationships are represented and interconnected, and such operations require a ‘structured data model’ and cannot be practically performed mentally.
In response, the statements of Dr. Mata are acknowledged, however the analysis steps of the claims do not require any specific data source or amount of data, and arguments that the data is so large it cannot practically be evaluated appear inconsistent with the breadth of the claims. Further, the embodiments that a processor is used to perform the analysis has been evaluated in the basis of the rejection and found to be a general purpose computer used to perform the analysis. In review of the fact pattern of SRI Int, the fact pattern appears to apply to how a computer operates, whereas here the steps of analysis as generically set forth can be practiced mentally and are not tied to any specific computer nor is there evidence that the analysis steps affect the computer function itself. The claims do not require any specific data ‘structure’ in the recitation of a graph model, and clearly any model created would only be relevant to the data used to create it. More importantly, it is not the data that is required of the claims, but rather the evaluation of what is recited, required and encompassed by the claims and here it has been determined that they broadly provide for steps of correlating genetic data and disease states and representation in a ‘graph model’. Given the generic and broad nature of the claim requirements the representation of a correlation of genetic state and disease could be represented as a table, and the strength of the correlation, index value or use of tuples of the claims, represented as the statistical correlation for what is represented by the data. Again, there is no specific data nor specific rules of establishing any correlation which can be observed, nor is there any specific guidance for any disease as to what the ‘actionable items’ would be once anything is observed.
Applicants argue that the claims integrate any possible judicial exception into a practical application citing the 2024 and 2019 PEG guidance, and as a whole provides a particular solution to a technical problem of ‘data sparsity’ citing also the declaration of Dr. Mata.
In response, the guidance is acknowledged and has been fully considered in evaluating the claims. However, the correlation of genetic data and diseases is not new and given the evidence of record has been successfully performed prior to the instant application. Further, the claims do not require any specific data and what is evaluated are the limitations required of the claim, here generic steps to provide data and represent correlations in a graph model. There is no requirement of the data, nor any evidence that practicing the claims address ‘sparsity, of data if or when it exists, and appears again all relative to the data provided and not inherently flowing from the steps of the claims. The citations of the specification and teaching as a whole have been reviewed and acknowledged, but appear to be prophetic possibilities and not representative of the breadth of the claims for how the analysis is performed, and more descriptive of possible issues of specific data which do not appear to be addressed in the generic steps of analysis. It has been acknowledged that there is a representation of the data in a graph model, and for a one to one correlation of genetic data and a disease is simply a table representing the correlation, and limitations of a score or use of tuples appears to be broadly consistent with establishing the correlation and possible strength of the correlation. With respect to ‘sparse’ data sources, there is no evidence that the analysis broadly claimed would provide any improvement in the evaluation, and again appears all relative to the data, how the data could be represented in a graph model, ie. correlation of the genetic and disease data, and then how it may apply when analyzing a different data source which may or may not be represented by the graph model generated by a different data source. The figures are acknowledged and appear to support the broad interpretation of the claims and how for any given data set, for example S1-S5 inputs, could be evaluated and correlated to common treatments, again this all appears to relative to the data and not the broad generic steps of analysis or applying a graph model to represent the data, and the evaluation is effectively clustering the information based on actionable items, i.e. TT1-TT3 as represented in Figure 13 provided in the arguments. Unlike the fact part of Desjardins, the present claims have no specific means of evaluating the data or in ‘learning’ process to create a model or in the application of AI broadly. There does not appear to be any change in structure of the data or model, rather the model is simply a different representation of the data as it could be correlated based on actionable items and all relative and driven by the data itself and not the method steps of the instant claims. The claims are broad as they encompass any genetic alteration known or unknown, and a correlation with any possible disease all which is accomplished with the lack of any specific rules on how any index value, tuple or general correlation is established, and given the art of record such correlations have and can be established with the correct data sources.
As noted previously, one way to overcome a rejection for non-patent-eligible subject matter is to persuasively argue that the claimed subject matter is not directed to a judicial exception. Another way for the applicants to overcome the rejection is to persuasively argue that the claims contain elements in addition to the judicial exception that either individually or as an ordered combination are not well understood, routine, or conventional. Another way for the applicants to overcome the rejection is to persuasively argue that the claims as a whole result in an improvement to a technology. Persuasive evidence for an improvement to a technology could be a comparison of results of the claimed subject matter with results of the prior art, or arguments based on scientific reasoning that the claimed subject matter inherently results an improvement over the prior art. The applicants should show why the claims require the improvement in all embodiments.
Detailed analysis under 101
For step 1 of the 101 analysis, the claims are found to be directed to a statutory category of a method and product
For step 2A of the 101 analysis, the judicial exception of the claims are the steps of accessing patient sequence data for possible correlations that might exist in a database which provides for a correlations of known genetic markers and diseases. To accomplish the comparison of patient and database data, a step of aligning and comparing sequence to arrive at the identification of informative sequences are instructional steps. The claim requires broadly comparing genetic data, for example information that could be present in a table but provided in a graph model for analysis using a computer. The judicial exception is a set of instructions for analysis of sequence data appear to fall into the category of a Mental Processes, that is concepts performed in the human mind (including an observation, evaluation, judgment, opinion) because the association of genetic data can be performed by observation, and appears to also encompass Mathematical Concepts, that is mathematical formulas or equations to arrive at a score, though the specification does not provide any specific requirement on how this is assessed for the huge range of possible diseases and treatments.
The breadth of “receiving”, “obtaining”, and “providing” encompasses non-transformative visual assessment of an individual for given phenotype, coupled with prior knowledge of the correlation of said phenotype with the presence of particular genotype; for example, a known genetic mutation associated with a disease such as PKU. This breadth does not impose a meaningful limit on the claim scope, such that all others are not precluded from using the natural principle of associating known genetic data and disease in the potential treatment of another patient with the same genetic mutation. Although the claims recite the use of a processor and graph based models for the structure of the data, the courts have also identified limitations that did not integrate a judicial exception into a practical application; for example, merely including instructions to implement an abstract idea on a computer, or merely using a computer as a tool to perform an abstract idea, as discussed in MPEP § 2106.05(f). Computing, constructing datasets and using statistical models was well understood, conventional, and routinely performed in the art at the time the application was filed. Furthermore, the limitation of providing patient specific recommendations to individuals at a in view of identified markers or alleles does not change the steps to be performed for the analysis. See MPEP § 2106.05(g) for a discussion on adding insignificant extra-solution (both pre-solution and post-solution) activity to the judicial exception. See also MPEP § 2106.05(h) for a discussion on generally linking the use of a judicial exception to a particular technological environment or field of use. The claims appear to fall into the category of Mathematical Concepts, as it applies the use of statistics and mathematical relationships in analyzing probabilities, and also into the category of mental processes, as concepts performed in the human mind (including an observation, evaluation, judgment, opinion) because there is no apparent complexity to or amount of data that is collected and analyzed as presently claimed.
Recent guidance from the office requires that the judicial exception be evaluated under a second prong to determine whether the judicial exception is practically applied. In the instant case, the claims do not have an additional element and only provide giving a ‘recommendation’ as a final step. This judicial exception requires steps recited at high level of generality and for the products are only stored on a non-transitory, and is not found to be a practical application of the judicial exception as broadly set forth.
For step 2B of the 101 analysis, each of the independent claims recites possible additional elements for the ability to ‘receive’ data, and are found to be the steps of obtaining sequence data. As such, the claims do not provide for any additional element to consider under step 2B beyond providing data for further analysis. It is noted that in explaining the Alice framework, the Court wrote that "[i]n cases involving software innovations, [the step one] inquiry often turns on whether the claims focus on the specific asserted improvement in computer capabilities or, instead, on a process that qualifies as an abstract idea for which computers are invoked merely as a tool." The Court further noted that "[s]ince Alice, we have found software inventions to be patent-eligible where they have made non-abstract improvements to existing technological processes and computer technology." Moreover, these improvements must be specific -- "[a]n improved result, without more stated in the claim, is not enough to confer eligibility to an otherwise abstract idea . . . [t]o be patent-eligible, the claims must recite a specific means or method that solves a problem in an existing technological process." As indicated in the summary of the judicial exception above and in view of the teachings of the specification, the steps are drawn to analysis of sequence data. While the instruction are stored on a medium and could be implemented on a computer, together the steps do not appear to result in significantly more than a means to compare sequences. The judicial exception of the method as claimed can be performed by hand and in light of the previous claims to a computer medium and in light of the teaching of the specification on a computer. In review of the instant specification the methods do not appear to require a special type of processor and can be performed on a general purpose computer. Based upon an analysis with respect to the claim as a whole, claims 2-19 do not recite something significantly different than a judicial exception. Claims 2-19 are directed towards a method of receiving sequence data and comparing the data to identify possible correlations to known sequences. Dependent claims set forth additional steps which are more specifically define the considerations and steps of calculating, and comparing, and do not add additional elements which result in significantly more to the claimed method for the analysis. As such, the instant claims set forth an inventive concept that are drawn only to an abstract process that only manipulates data and, therefore, are not directed to statutory subject matter. No additional steps are recited in the instantly claimed invention that would amount to significantly more than the judicial exception. Without additional limitations, a process that employs mathematical algorithms (aligning sequences) to manipulate existing information (correlations of known genetic diseases) to generate additional information (recommendation of patient treatment) is not patent eligible. Furthermore, if a claim is directed essentially to a method of calculating, using a mathematical formula, even if the solution is for a specific purpose, the claimed method is non-statutory. In other words, patenting abstract idea (designing probes to a target sequence) cannot be circumvented by attempting to limit the use to a particular technological environment or purpose and desired result.
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 2-19 rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Business Wire (1999), Caulfield (1999) (both in IDS 8/1/2025), Wang et al. (2010) and Maenhout et al. (2010) is withdrawn.
In view of the amendments, it is agreed that the cited references fail to provide for a graph model where the topology is recomputed using genomic alteration groups with actionable items reducing the complexity of the model and preserving gene states and actionable items when they exist.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
In prosecution the association of specific genes with specific conditions and treatments was known as evidenced by Caulfield teaches that gene testing is a type of test patients can receive, providing the example of BRCA1/2 testing as a known genetic lab test and the possible discussions and treatment based on the patient. Such data could also be provided to doctors and patients through various types of portals as evidenced by LabDat, Inc. which provides an internet based program that allows patients to view their clinical information, and using a Knowledge Base provides an overview of the meaning of the results which may be indicative of disease or organ function and serves to provide patient guidance for the medical utility of the test results in the record. Also, at the time graph-based similarity assessments for ontologies and genetics were known as demonstrated by Wang et al. and Maenout et al. who use graph-based data selection and analysis for genomic predictions. However, neither, Wang et al. and Maenout et al. teach that this analysis should be applied to patient records, or for the specific model creation required of the amended claims.
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/Joseph Woitach/Primary Examiner, Art Unit 1687
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