Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
This office action for the 18/712233 application is in response to the communications filed April 03, 2026.
Claims 1, 8, 14, 16 and 23 were amended April 03, 2026.
Claims 1-23 are currently pending and considered below.
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 1-23 are 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.
As per claim 1,
Step 1: The claim recites subject matter within a statutory category as a process.
Step 2A is a two-prong inquiry, in which Prong 1 determines whether a claim recites a judicial exception. Prong 2 determines if the additional limitations of the claim integrates the recited judicial exception into a practical application. If the additional elements of the claim fail to integrate the judicial exception into a practical application, claim is directed to the recited judicial exception, see MPEP 2106.04(II)(A).
Step 2A Prong 1: The claim contains subject matter that recites an abstract idea, with the steps of a method for assessing eligibility of a patient to a clinical trial of a therapy comprising one or more drugs, the method comprising: (a) providing at least one drug target for the one or more drugs, and providing a personalized molecular profile for the patient, wherein the personalized molecular profile is generated from analysis of a biological sample obtained from the patient and contains one or more clinically relevant biomarkers; (b) generating a matching score for the patient based on the personalized molecular profile and the patient's predicted response to the therapy, and setting a threshold score, wherein the generating step comprises determining impact of the therapy on the personalized molecular profile of the patient based on the number and types of biomarkers and interactions between biomarkers and the one or more drugs of the therapy; (c) providing a recommendation for clinical trial eligibility of the patient when the matching score for the patient passes requirements of the threshold score. These steps, as drafted, under the broadest reasonable interpretation recite:
certain methods of organizing human activity (e.g., fundamental economic principles or practices including: hedging; insurance; mitigating risk; etc., commercial or legal interactions including: agreements in the form of contracts; legal obligations; advertising, marketing or sales activities or behaviors; business relations; etc., managing personal behavior or relationships or interactions between people including: social activities; teaching; following rules or instructions; etc.) but for recitation of generic computer components. That is, other than reciting steps as performed by the generic computer components, nothing in the claim element precludes the step from being directed to certain methods of organizing human activity. The identified abstract idea, law of nature, or natural phenomenon identified above, in the context of this claim, encompasses a certain method of organizing human activity, namely managing personal behavior or relationships or interactions between people. This is because each of the limitations of the abstract idea recites a list of rules or instructions that a human person can follow in the course of their personal behavior. If a claim limitation, under its broadest reasonable interpretation, covers at least the recited methods of organizing human activity above, but for the recitation of generic computer components, then it falls within the “Certain Methods of Organizing Human Activity” grouping of abstract ideas. Accordingly, the claim recites an abstract idea. See MPEP 2106.04(a).
Step 2A Prong 2: The claim does not recite additional elements that integrate the judicial exception into a practical application. The entire claim is abstract. Accordingly, there are no additional elements in the claim to the abstract idea.
Accordingly, this claim is directed to an abstract idea.
Step 2B: The claim does not recite additional elements that amount to significantly more than the judicial exception. The entire claim is abstract. Accordingly, there are no additional elements in the claim to the abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 2,
Claim 2 depends from claim 1 and inherits all the limitations of the claim from which it depends. Claim 2 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein eligibilities of a plurality of patients are assessed, and the matching score is generated for each patient of the plurality of patients.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 3,
Claim 3 depends from claim 2 and inherits all the limitations of the claim from which it depends. Claim 3 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein the threshold score is set after the matching score for each patient of the plurality of patients is generated.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 4,
Claim 4 depends from claim 3 and inherits all the limitations of the claim from which it depends. Claim 4 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein the threshold score is set at a specific percentile of a range of matching scores generated for each patient of the plurality of patients.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 5,
Claim 5 depends from claim 2 and inherits all the limitations of the claim from which it depends. Claim 5 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein the threshold score is set before the matching score for each patient of the plurality of patients is generated.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 6,
Claim 6 depends from claim 1 and inherits all the limitations of the claim from which it depends. Claim 6 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein the threshold score is set based on previously analyzed clinical trial data sets.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 7,
Claim 7 depends from claim 1 and inherits all the limitations of the claim from which it depends. Claim 7 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein the threshold score is set based on a newly obtained patient data from the clinical trial.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 8,
Claim 8 depends from claim 1 and inherits all the limitations of the claim from which it depends. Claim 8 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein the providing at least one drug target for the one or more drugs comprises providing an IC50 value of the one or more drugs for the at least one drug target.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 9,
Claim 9 depends from claim 1 and inherits all the limitations of the claim from which it depends. Claim 9 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein the patient is a cancer patient.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 10,
Claim 10 depends from claim 1 and inherits all the limitations of the claim from which it depends. Claim 10 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein the biological sample comprises a tissue, blood, plasma or serum sample.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 11,
Claim 11 depends from claim 1 and inherits all the limitations of the claim from which it depends. Claim 11 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein the analysis of the biological sample comprises performing a next-generation sequencing of nucleic acid molecules extracted from the biological sample.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 12,
Claim 12 depends from claim 11 and inherits all the limitations of the claim from which it depends. Claim 12 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein the analysis of the biological sample further comprises extracting a cell-free DNA from the biological sample.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 13,
Claim 13 depends from claim 1 and inherits all the limitations of the claim from which it depends. Claim 13 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein the clinical trial is a prospective clinical trial.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 14,
Claim 14 depends from claim 1 and inherits all the limitations of the claim from which it depends. Claim 14 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein generating the matching score further comprising determining impact of the one or more drugs on each of the one or more clinically relevant biomarkers.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 15,
Claim 15 depends from claim 1 and inherits all the limitations of the claim from which it depends. Claim 15 merely further defines the abstract idea and/or introduces additional elements that are insufficient to provide a practical application or something significantly more:
“wherein the one or more clinically relevant biomarkers is/are targeted by the one or more drugs of the therapy.” further describes the abstract idea. This claim limitation is still directed to “Certain Methods of Organizing Human Activity” and therefore continues to recite an abstract idea.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 16,
Claim 16 is substantially similar to claim 1. Accordingly, claim 16 is rejected for the same reasons as claim 1.
“A system for assessing eligibility of a patient to a clinical trial of a therapy comprising one or more drugs, the system comprising: a server; a computing device in communication with the server over a network, the computing device including a processor and a memory, the memory bearing computer executable code configured to perform the steps of:” introduces additional elements that is insufficient to provide a practical application or significantly more:
Step 2A Prong 2: In particular, the additional elements do not integrate the abstract idea into a practical application, other than the abstract idea per se, because the additional elements amount to no more than limitations which:
amount to mere instructions to apply an exception, see MPEP 2106.05(f), such as:
“A system for assessing eligibility of a patient to a clinical trial of a therapy comprising one or more drugs, the system comprising: a server; a computing device in communication with the server over a network, the computing device including a processor and a memory, the memory bearing computer executable code configured to perform the steps of:” which corresponds to merely using a computer as a tool to perform an abstract idea. Paragraph [00149] of the as-filed specification describes that “systems and methods disclosed herein may be implemented via one or more components, systems, servers, appliances, other subcomponents, or distributed between such elements. When implemented as a system, such systems may comprise an/or involve, inter alia, components such as software modules, general-purpose CPU, RAM, etc., found in general-purpose computers”. Implementing an abstract idea on a generic computer, does not integrate the abstract idea into a practical application in Step 2A Prong Two or add significantly more in Step 2B, similar to how the recitation of the computer in the claim in Alice amounted to mere instructions to apply the abstract idea of intermediated settlement on a generic computer.
Accordingly, this claim is directed to an abstract idea.
Step 2B: The claim does not recite additional elements that amount to significantly more than the judicial exception. As discussed above with respect to discussion of integration of the abstract idea into a practical application, the additional elements amount to no more than mere instructions to apply an exception, add insignificant extra-solution activity to the abstract idea, and/or generally link the abstract idea to a particular technological environment or field of use.
Looking at the limitations of the claim as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely recite an abstract idea and/or provide conventional computer implementation which does not impose a meaningful limit to integrate the abstract idea into a practical application and/or amount to no more than limitations which amount to elements that have been recognized as well-understood, routine, and conventional activity in particular fields.
As per claim 17,
Claim 17 is substantially similar to claim 2. Accordingly, claim 17 is rejected for the same reasons as claim 2.
As per claim 18,
Claim 18 is substantially similar to claim 3. Accordingly, claim 18 is rejected for the same reasons as claim 3.
As per claim 19,
Claim 19 is substantially similar to claim 4. Accordingly, claim 19 is rejected for the same reasons as claim 4.
As per claim 20,
Claim 20 is substantially similar to claim 15. Accordingly, claim 20 is rejected for the same reasons as claim 15.
As per claim 21,
Claim 21 is substantially similar to claim 9. Accordingly, claim 21 is rejected for the same reasons as claim 9.
As per claim 22,
Claim 22 is substantially similar to claim 10. Accordingly, claim 22 is rejected for the same reasons as claim 10.
As per claim 23,
Claim 23 is substantially similar to claim 14. Accordingly, claim 23 is rejected for the same reasons as claim 14.
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 1-7 and 9-23 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Abraham et al. (US 2023/0416829; herein referred to as Abraham).
As per claim 1,
Abraham discloses a method for assessing eligibility of a patient to a clinical trial of a therapy comprising one or more drugs, the method comprising: (a) providing at least one drug target for the one or more drugs, and providing a personalized molecular profile for the patient, wherein the personalized molecular profile is generated from analysis of a biological sample obtained from the patient and contains one or more clinically relevant biomarkers:
(Paragraphs [0007] and [0088] of Abraham. The teaching describes comprehensive molecular profiling provides a wealth of data concerning the molecular status of patient samples. Such data can be compared to patient response to treatments to identify biomarker signatures that predict response or non-response to such treatments. This approach has been applied to identify biomarker signatures that correlate with benefit or lack of benefit of immunotherapies, e.g., checkpoint inhibitor therapies and/or chemotherapy. Traditionally, differential response to a particular therapeutic strategy has only been determined after the treatment was given, i.e., a posteriori. The “standard” approach to disease treatment relies on what is generally true about a given cancer diagnosis and treatment response has been vetted by randomized phase III clinical trials and forms the “standard of care” in medical practice. The results of these trials have been codified in consensus statements by guidelines organizations such as the National Comprehensive Cancer Network and The American Society of Clinical Oncology. The NCCN Compendium™ contains authoritative, scientifically derived information designed to support decision-making about the appropriate use of drugs and biologics in patients with cancer. The NCCN Compendium™ is recognized by the Centers for Medicare and Medicaid Services (CMS) and United Healthcare as an authoritative reference for oncology coverage policy. On-compendium treatments are those recommended by such guides. The biostatistical methods used to validate the results of clinical trials rely on minimizing differences between patients, and are based on declaring the likelihood of error that one approach is better than another for a patient group defined only by light microscopy and stage, not by individual differences in tumors. The molecular profiling methods described herein exploit such individual differences. The methods can provide candidate treatments that can be then selected by a physician for treating a patient.)
Abraham further discloses (b) generating a matching score for the patient based on the personalized molecular profile and the patient's predicted response to the therapy, and setting a threshold score, wherein the generating step comprises determining impact of the therapy on the personalized molecular profile of the patient based on the number and types of biomarkers and interactions between biomarkers and the one or more drugs of the therapy; and (c) providing a recommendation for clinical trial eligibility of the patient when the matching score for the patient passes requirements of the threshold score:
(Paragraphs [0039], [0041], [0058], [0124] and [0232] of Abraham. The teaching describes method of selecting a treatment for a subject who has a cancer, the method comprising: (a) obtaining a biological sample comprising cells and/or cell free material derived from the cancer in the subject; (b) performing an assay to assess a copy number of chromosome 9 or a portion thereof in the biological sample. In some embodiments, the method described herein further comprises preparing a molecular profile for the subject based on the copy number of chromosome 9 or the portion thereof. Therapy related tests can be used to predict and assess drug response in individual subjects, thereby providing personalized medical recommendations. Predicting a likelihood of response can be determining whether a subject is a likely responder or a likely non-responder to a candidate therapeutic agent, e.g., before the subject has been exposed or otherwise treated with the treatment. The methods and systems as described herein comprise expression profiling, which includes assessing differential expression of one or more target genes disclosed herein. Differential expression can include overexpression and/or underexpression of a biological product, e.g., a gene, mRNA or protein, compared to a control (or a reference). The control can be derived from the same patient, e.g., a normal adjacent portion of the same organ as the diseased cells, the control can be derived from healthy tissues from other patients, or previously determined thresholds that are indicative of a disease responding or not-responding to a particular drug target. The description of the molecular profile of the genes as determined for the subject may include such information as the laboratory technique used to assess each biomarker (e.g., NGS, WGS, WES, WTS, RT-PCR, FISH/CISH, PCR, FA/RFLP, CGH, aCGH, etc) as well as the result and criteria used to score each technique.)
As per claim 2,
Abraham discloses the limitations of claim 1.
Abraham further discloses wherein eligibilities of a plurality of patients are assessed, and the matching score is generated for each patient of the plurality of patients:
(Paragraphs [0039], [0041], [0058], [0087], [0124] and [0232] of Abraham. The teaching describes method of selecting a treatment for a subject who has a cancer, the method comprising: (a) obtaining a biological sample comprising cells and/or cell free material derived from the cancer in the subject; (b) performing an assay to assess a copy number of chromosome 9 or a portion thereof in the biological sample. In some embodiments, the method described herein further comprises preparing a molecular profile for the subject based on the copy number of chromosome 9 or the portion thereof. Therapy related tests can be used to predict and assess drug response in individual subjects, thereby providing personalized medical recommendations. Predicting a likelihood of response can be determining whether a subject is a likely responder or a likely non-responder to a candidate therapeutic agent, e.g., before the subject has been exposed or otherwise treated with the treatment. The methods and systems as described herein comprise expression profiling, which includes assessing differential expression of one or more target genes disclosed herein. Differential expression can include overexpression and/or underexpression of a biological product, e.g., a gene, mRNA or protein, compared to a control (or a reference). The control can be derived from the same patient, e.g., a normal adjacent portion of the same organ as the diseased cells, the control can be derived from healthy tissues from other patients, or previously determined thresholds that are indicative of a disease responding or not-responding to a particular drug target. The description of the molecular profile of the genes as determined for the subject may include such information as the laboratory technique used to assess each biomarker (e.g., NGS, WGS, WES, WTS, RT-PCR, FISH/CISH, PCR, FA/RFLP, CGH, aCGH, etc) as well as the result and criteria used to score each technique. The systems and methods provided herein may be used to classify patients as more or less likely to benefit or respond to various treatments.)
As per claim 3,
Abraham discloses the limitations of claim 2.
Abraham further discloses wherein the threshold score is set after the matching score for each patient of the plurality of patients is generated:
(Paragraph [0124] of Abraham. The teaching describes that the control can also be a control found in the same sample, e.g. a housekeeping gene or a product thereof (e.g., mRNA or protein). For example, a control nucleic acid can be one which is known not to differ depending on the cancerous or non-cancerous state of the cell. The expression level of a control nucleic acid can be used to normalize signal levels in the test and reference populations. This means that when the test sample of unknown difference between normal and cancerous cells is tested before the control, the control threshold is determined after the matching score is generated for the test sample.)
As per claim 4,
Abraham discloses the limitations of claim 3.
Abraham further discloses wherein the threshold score is set at a specific percentile of a range of matching scores generated for each patient of the plurality of patients:
(Paragraphs [0110] of Abraham. The teaching describes that for the purpose of 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). The percentage identity can be determined by the algorithm of Karlin and Altschul, Proc. Natl. Acad. Sci. USA, 90:5873-5877 (1993), which is incorporated into various BLAST programs. The percentage identity can be determined by the “BLAST 2 Sequences” tool, which is available at the National Center for Biotechnology Information (NCBI) website. See Tatusova and Madden, FEMS Microbiol. Lett., 174(2):247-250 (1999).)
As per claim 5,
Abraham discloses the limitations of claim 2.
Abraham further discloses wherein the threshold score is set before the matching score for each patient of the plurality of patients is generated:
(Paragraphs [0039], [0041], [0058], [0124] and [0232] of Abraham. The teaching describes method of selecting a treatment for a subject who has a cancer, the method comprising: (a) obtaining a biological sample comprising cells and/or cell free material derived from the cancer in the subject; (b) performing an assay to assess a copy number of chromosome 9 or a portion thereof in the biological sample. In some embodiments, the method described herein further comprises preparing a molecular profile for the subject based on the copy number of chromosome 9 or the portion thereof. Therapy related tests can be used to predict and assess drug response in individual subjects, thereby providing personalized medical recommendations. Predicting a likelihood of response can be determining whether a subject is a likely responder or a likely non-responder to a candidate therapeutic agent, e.g., before the subject has been exposed or otherwise treated with the treatment. The methods and systems as described herein comprise expression profiling, which includes assessing differential expression of one or more target genes disclosed herein. Differential expression can include overexpression and/or underexpression of a biological product, e.g., a gene, mRNA or protein, compared to a control (or a reference). The control can be derived from the same patient, e.g., a normal adjacent portion of the same organ as the diseased cells, the control can be derived from healthy tissues from other patients, or previously determined thresholds that are indicative of a disease responding or not-responding to a particular drug target. The description of the molecular profile of the genes as determined for the subject may include such information as the laboratory technique used to assess each biomarker (e.g., NGS, WGS, WES, WTS, RT-PCR, FISH/CISH, PCR, FA/RFLP, CGH, aCGH, etc) as well as the result and criteria used to score each technique.)
As per claim 6,
Abraham discloses the limitations of claim 1.
Abraham further discloses wherein the threshold score is set based on previously analyzed clinical trial data sets:
(Paragraphs [0039], [0041], [0058], [0124] and [0232] of Abraham. The teaching describes method of selecting a treatment for a subject who has a cancer, the method comprising: (a) obtaining a biological sample comprising cells and/or cell free material derived from the cancer in the subject; (b) performing an assay to assess a copy number of chromosome 9 or a portion thereof in the biological sample. In some embodiments, the method described herein further comprises preparing a molecular profile for the subject based on the copy number of chromosome 9 or the portion thereof. Therapy related tests can be used to predict and assess drug response in individual subjects, thereby providing personalized medical recommendations. Predicting a likelihood of response can be determining whether a subject is a likely responder or a likely non-responder to a candidate therapeutic agent, e.g., before the subject has been exposed or otherwise treated with the treatment. The methods and systems as described herein comprise expression profiling, which includes assessing differential expression of one or more target genes disclosed herein. Differential expression can include overexpression and/or underexpression of a biological product, e.g., a gene, mRNA or protein, compared to a control (or a reference). The control can be derived from the same patient, e.g., a normal adjacent portion of the same organ as the diseased cells, the control can be derived from healthy tissues from other patients, or previously determined thresholds that are indicative of a disease responding or not-responding to a particular drug target. The description of the molecular profile of the genes as determined for the subject may include such information as the laboratory technique used to assess each biomarker (e.g., NGS, WGS, WES, WTS, RT-PCR, FISH/CISH, PCR, FA/RFLP, CGH, aCGH, etc) as well as the result and criteria used to score each technique.)
As per claim 7,
Abraham discloses the limitations of claim 1.
Abraham further discloses wherein the threshold score is set based on a newly obtained patient data from the clinical trial:
(Paragraphs [0039], [0041], [0058], [0124] and [0232] of Abraham. The teaching describes method of selecting a treatment for a subject who has a cancer, the method comprising: (a) obtaining a biological sample comprising cells and/or cell free material derived from the cancer in the subject; (b) performing an assay to assess a copy number of chromosome 9 or a portion thereof in the biological sample. In some embodiments, the method described herein further comprises preparing a molecular profile for the subject based on the copy number of chromosome 9 or the portion thereof. Therapy related tests can be used to predict and assess drug response in individual subjects, thereby providing personalized medical recommendations. Predicting a likelihood of response can be determining whether a subject is a likely responder or a likely non-responder to a candidate therapeutic agent, e.g., before the subject has been exposed or otherwise treated with the treatment. The methods and systems as described herein comprise expression profiling, which includes assessing differential expression of one or more target genes disclosed herein. Differential expression can include overexpression and/or underexpression of a biological product, e.g., a gene, mRNA or protein, compared to a control (or a reference). The control can be derived from the same patient, e.g., a normal adjacent portion of the same organ as the diseased cells, the control can be derived from healthy tissues from other patients, or previously determined thresholds that are indicative of a disease responding or not-responding to a particular drug target. The description of the molecular profile of the genes as determined for the subject may include such information as the laboratory technique used to assess each biomarker (e.g., NGS, WGS, WES, WTS, RT-PCR, FISH/CISH, PCR, FA/RFLP, CGH, aCGH, etc) as well as the result and criteria used to score each technique. This means that when the test sample of unknown difference between normal and cancerous cells is tested before the control, the control threshold is determined after the matching score is generated for the test sample.)
As per claim 9,
Abraham discloses the limitations of claim 1.
Abraham further discloses wherein the patient is a cancer patient:
(Paragraphs [0039], [0041], [0058], [0124] and [0232] of Abraham. The teaching describes method of selecting a treatment for a subject who has a cancer, the method comprising: (a) obtaining a biological sample comprising cells and/or cell free material derived from the cancer in the subject; (b) performing an assay to assess a copy number of chromosome 9 or a portion thereof in the biological sample. In some embodiments, the method described herein further comprises preparing a molecular profile for the subject based on the copy number of chromosome 9 or the portion thereof. Therapy related tests can be used to predict and assess drug response in individual subjects, thereby providing personalized medical recommendations. Predicting a likelihood of response can be determining whether a subject is a likely responder or a likely non-responder to a candidate therapeutic agent, e.g., before the subject has been exposed or otherwise treated with the treatment. The methods and systems as described herein comprise expression profiling, which includes assessing differential expression of one or more target genes disclosed herein. Differential expression can include overexpression and/or underexpression of a biological product, e.g., a gene, mRNA or protein, compared to a control (or a reference). The control can be derived from the same patient, e.g., a normal adjacent portion of the same organ as the diseased cells, the control can be derived from healthy tissues from other patients, or previously determined thresholds that are indicative of a disease responding or not-responding to a particular drug target. The description of the molecular profile of the genes as determined for the subject may include such information as the laboratory technique used to assess each biomarker (e.g., NGS, WGS, WES, WTS, RT-PCR, FISH/CISH, PCR, FA/RFLP, CGH, aCGH, etc) as well as the result and criteria used to score each technique.)
As per claim 10,
Abraham discloses the limitations of claim 1.
Abraham further discloses wherein the biological sample comprises a tissue, blood, plasma or serum sample:
(Paragraph [0029] of Abraham. The teaching describes that the biological sample comprises formalin-fixed paraffin-embedded (FFPE) tissue, fixed tissue, a core needle biopsy, a fine needle aspirate, unstained slides, fresh frozen (FF) tissue, formalin samples, tissue comprised in a solution that preserves nucleic acid or protein molecules, a fresh sample, a malignant fluid, a bodily fluid, a tumor sample, a tissue sample, or any combination thereof.)
As per claim 11,
Abraham discloses the limitations of claim 1.
Abraham further discloses wherein the analysis of the biological sample comprises performing a next-generation sequencing of nucleic acid molecules extracted from the biological sample:
(Paragraph [0090] of Abraham. The teaching describes that molecular profiling can be performed by any known means for detecting a molecule in a biological sample. Molecular profiling comprises methods that include but are not limited to, nucleic acid sequencing, such as a DNA sequencing or RNA sequencing; immunohistochemistry (IHC); in situ hybridization (ISH); fluorescent in situ hybridization (FISH); chromogenic in situ hybridization (CISH); PCR amplification (e.g., qPCR or RT-PCR); various types of microarray (mRNA expression arrays, low density arrays, protein arrays, etc); various types of sequencing (Sanger, pyrosequencing, etc); comparative genomic hybridization (CGH); high throughput or next generation sequencing (NGS);)
As per claim 12,
Abraham discloses the limitations of claim 11.
Abraham further discloses wherein the analysis of the biological sample further comprises extracting a cell-free DNA from the biological sample:
(Paragraphs [0030] and [0031] of Abraham. The teaching describes the cells and/or cell free materials derived from the cancer are from a solid tumor. In some embodiments, the biological sample comprises a bodily fluid, and wherein optionally the material derived from cancer cells comprises cell free nucleic acids.)
As per claim 13,
Abraham discloses the limitations of claim 1.
Abraham further discloses wherein the clinical trial is a prospective clinical trial:
(Paragraph [0086] and [0216] of Abraham. The teaching describes molecular profiling approach provides a method for selecting a candidate treatment for an individual that could favorably change the clinical course for the individual with a condition or disease, such as cancer. The molecular profiling approach provides clinical benefit for individuals, such as identifying therapeutic regimens that provide a longer progression free survival (PFS), longer disease free survival (DFS), longer overall survival (OS) or extended lifespan.)
As per claim 14,
Abraham discloses the limitations of claim 1.
Abraham further discloses wherein generating the matching score further comprising determining impact of the one or more drugs on each of the one or more clinically relevant biomarkers:
(Paragraphs [0039], [0041], [0058], [0087], [0124] and [0232] of Abraham. The teaching describes method of selecting a treatment for a subject who has a cancer, the method comprising: (a) obtaining a biological sample comprising cells and/or cell free material derived from the cancer in the subject; (b) performing an assay to assess a copy number of chromosome 9 or a portion thereof in the biological sample. In some embodiments, the method described herein further comprises preparing a molecular profile for the subject based on the copy number of chromosome 9 or the portion thereof. Therapy related tests can be used to predict and assess drug response in individual subjects, thereby providing personalized medical recommendations. Predicting a likelihood of response can be determining whether a subject is a likely responder or a likely non-responder to a candidate therapeutic agent, e.g., before the subject has been exposed or otherwise treated with the treatment. The methods and systems as described herein comprise expression profiling, which includes assessing differential expression of one or more target genes disclosed herein. Differential expression can include overexpression and/or underexpression of a biological product, e.g., a gene, mRNA or protein, compared to a control (or a reference). The control can be derived from the same patient, e.g., a normal adjacent portion of the same organ as the diseased cells, the control can be derived from healthy tissues from other patients, or previously determined thresholds that are indicative of a disease responding or not-responding to a particular drug target. The description of the molecular profile of the genes as determined for the subject may include such information as the laboratory technique used to assess each biomarker (e.g., NGS, WGS, WES, WTS, RT-PCR, FISH/CISH, PCR, FA/RFLP, CGH, aCGH, etc) as well as the result and criteria used to score each technique. The systems and methods provided herein may be used to classify patients as more or less likely to benefit or respond to various treatments.)
As per claim 15,
Abraham discloses the limitations of claim 1.
Abraham further discloses wherein the one or more clinically relevant biomarkers is/are targeted by the one or more drugs of the therapy:
(Paragraphs [0039], [0041], [0058], [0087], [0124] and [0232] of Abraham. The teaching describes method of selecting a treatment for a subject who has a cancer, the method comprising: (a) obtaining a biological sample comprising cells and/or cell free material derived from the cancer in the subject; (b) performing an assay to assess a copy number of chromosome 9 or a portion thereof in the biological sample. In some embodiments, the method described herein further comprises preparing a molecular profile for the subject based on the copy number of chromosome 9 or the portion thereof. Therapy related tests can be used to predict and assess drug response in individual subjects, thereby providing personalized medical recommendations. Predicting a likelihood of response can be determining whether a subject is a likely responder or a likely non-responder to a candidate therapeutic agent, e.g., before the subject has been exposed or otherwise treated with the treatment. The methods and systems as described herein comprise expression profiling, which includes assessing differential expression of one or more target genes disclosed herein. Differential expression can include overexpression and/or underexpression of a biological product, e.g., a gene, mRNA or protein, compared to a control (or a reference). The control can be derived from the same patient, e.g., a normal adjacent portion of the same organ as the diseased cells, the control can be derived from healthy tissues from other patients, or previously determined thresholds that are indicative of a disease responding or not-responding to a particular drug target. The description of the molecular profile of the genes as determined for the subject may include such information as the laboratory technique used to assess each biomarker (e.g., NGS, WGS, WES, WTS, RT-PCR, FISH/CISH, PCR, FA/RFLP, CGH, aCGH, etc) as well as the result and criteria used to score each technique. The systems and methods provided herein may be used to classify patients as more or less likely to benefit or respond to various treatments.)
As per claim 16,
Claim 16 is substantially similar to claim 1. Accordingly, claim 16 is rejected for the same reasons as claim 1.
As per claim 17,
Claim 17 is substantially similar to claim 2. Accordingly, claim 17 is rejected for the same reasons as claim 2.
As per claim 18,
Claim 18 is substantially similar to claim 3. Accordingly, claim 18 is rejected for the same reasons as claim 3.
As per claim 19,
Claim 19 is substantially similar to claim 4. Accordingly, claim 19 is rejected for the same reasons as claim 4.
As per claim 20,
Claim 20 is substantially similar to claim 15. Accordingly, claim 20 is rejected for the same reasons as claim 15.
As per claim 21,
Claim 21 is substantially similar to claim 9. Accordingly, claim 21 is rejected for the same reasons as claim 9.
As per claim 22,
Claim 22 is substantially similar to claim 10. Accordingly, claim 22 is rejected for the same reasons as claim 10.
As per claim 23,
Claim 23 is substantially similar to claim 14. Accordingly, claim 23 is rejected for the same reasons as claim 14.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Abraham in view of Kurzrock et al. (US 2019/0233895; herein referred to as Kurzrock).
As per claim 8,
Abraham discloses the limitations of claim 1.
Abraham does not explicitly teach wherein the providing at least one drug target for the one or more drugs comprises providing an IC50 value of the one or more drugs for the at least one drug target.
However, Kurzrock teaches providing at least one drug target for a drug comprises providing an IC50 value of the drug for the at least one drug target:
(Paragraphs [0149]-[0153] of Kurzrock. The teaching describes that a pharmacology researcher wants to study the effect of a combination of drugs in a human cancer cell-line's proliferation. He previously defined a set of five different targets (A, B, C, D and E) and a library encompassing 150 selective compounds biologically-active against these targets (10 drugs targeting the target A, 25 for B, 30 for C, 40 for D, 40 for E, and 5 drugs targeting simultaneously D and E). Based on this data, the decision-making machine will pick one drug for each of the target. In this example, the decision-making machine uses a scoring system based on the activity of each drug against its target, define by the IC50 (half maximal inhibitory concentration). A scale of activity is defined for each {drug-target} pair, with a maximum score of 5 when the activity is at the best level and 0 when the activity is weak.)
It would have been obvious to one of ordinary skill in the art before the time of filing to add to the molecular profile teachings of Abraham, the molecular profiling teachings of Kurzrock. Paragraph [0036] of Kurzrock teaches that the methods disclosed are aimed at improving the process of molecular processing. One of ordinary skill in the art would have added to the teaching of Abraham, the teaching of Kurzrock based on this incentive without yielding unexpected results.
Response to Arguments
Applicant's arguments filed April 03, 2026 have been fully considered.
Applicant’s arguments pertaining to rejections made under 35 U.S.C. 101 are not persuasive.
The Applicant argues that the limitation of “(c) providing a recommendation for clinical trial eligibility of the patient when the matching score for the patient passes requirements of the threshold score” provides “significantly more” than the alleged abstract idea.
The Examiner respectfully disagrees. The Applicant has provided no reasoning as to why this limitation provides something significantly more than the identified abstract idea. In contrast, the Examiner has provided a detailed explanation as to why this limitation specifically does not. Accordingly, this argument is not persuasive for this reason alone. However, the Examiner further points out that only an additional element to the abstract idea can provide something significantly more than an abstract idea. If an element in a claim is abstract, that same element cannot be considered as an additional element to the abstract idea. These characterizations are mutually exclusive. In the instance of claim 1, there are no additional elements to the abstract idea. The entire claim language is abstract. Accordingly, claim 1 in its current form is not possible to be patent eligible. The Applicant has the ability to challenge or argue the Examiner’s characterization, but the Applicant has failed to do this. The Applicant has merely asserted that an element is eligible with no reasoning whatsoever. This is not a proper challenge or argument against the Examiner’s prima facie case patent illegibility.
Applicant’s arguments pertaining to rejections made under 35 U.S.C. 102 are not persuasive.
The Applicant argues that Abraham does not disclose a personalized molecular profile. Abraham merely relies on the copy-number status of chromosome 9 for predicting a cancer patient’s response to immunotherapy.
The Examiner respectfully disagrees. The Applicant’s own argument here undermines the point they are trying to prove. Relying on the copy-number status of chromosome 9 for predicting a cancer patient’s response to immunotherapy is necessarily a personalization to a specific patient. The Applicant’s argument here is self-defeating. Furthermore, paragraph [0088] of Abraham explicitly underlines and articulates the personalized nature of the disclosed molecular profile: “The biostatistical methods used to validate the results of clinical trials rely on minimizing differences between patients, and are based on declaring the likelihood of error that one approach is better than another for a patient group defined only by light microscopy and stage, not by individual differences in tumors. The molecular profiling methods described herein exploit such individual differences. The methods can provide candidate treatments that can be then selected by a physician for treating a patient.” This excerpt from the cited portion of Abraham clearly articulate this personalized approach to molecular profiling as a distinct process beyond the more generalized groupings that preceded Abraham. It is manifestly apparent that Abraham discloses a personalized molecular profile. Accordingly, the Applicant’s argument is not persuasive.
Applicant’s remaining arguments are rendered moot in light of the foregoing.
Conclusion
THIS ACTION IS MADE FINAL. 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHAD A NEWTON whose telephone number is (313)446-6604. The examiner can normally be reached M-F 8:00AM-4:00PM (EST).
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, PETER H. CHOI can be reached at (469) 295-9171. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/CHAD A NEWTON/Primary Examiner, Art Unit 3681
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