DETAILED ACTION
Comments
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . 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.
Claims 1-20 are pending and examined in the instant Office action.
Information Disclosure Statement
The IDS filed on 2/13/2025 has been considered.
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.
Claim(s) 1-20 is/are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea/law of nature/natural phenomenon without significantly more. Claims 1-20 are drawn to methods.
In accordance with MPEP § 2106, claims found to recite statutory subject matter (Step 1 : YES) are then analyzed to determine if the claims recite any concepts that equate to an abstract idea, law of nature or natural phenomenon (Step 2A, Prong 1). In the instant application, the claims recite the following limitations that equate to an abstract idea:
Claims 1 and 20 recite the mental steps of determining gene expression levels of a set of genes in a patient.
Claims 1 and 20 recite the mental steps of determining mutation statuses of a different set of genes in a patient sample.
Claims 1 and 20 recite the mental steps of determining a treatment-response score as a result of performing linear regression on a combination of the gene expression levels and gene mutation statuses.
Claims 4 and 12 recite the mental step of constraining the disease analyzed to be cancer.
Claim 5 recites the mental step of constraining a mutation status to be a presence or absence of a mutation.
Claims 6 and 20 recite the mental steps of using linear regression as a form of machine learning with details and constraints on intercepts and coefficients.
Claims 7-8 recite the mental steps of requiring sets of genes to have non-zero training gene-expression coefficients.
Claim 9 recites the mental step of requiring the linear regression model to be a penalized linear regression model.
Claim 10 recites the mathematical limitation of using an Elastic-Net regression model.
Claim 13 recites the mental step of constraining the drug for treatment to have first and second sets of genes with non-zero coefficients and performing linear regression on the resultant data.
Claims 14-15 recite the mental step of requiring all of the genes in each set to be all of the genes for which there are non-zero coefficients in Tables 1A to 1I.
Claim 18 recites the mental step of determining whether the treatment-response score is within a therapeutic range.
These recitations are similar to the concepts of collecting information, analyzing it and displaying certain results of the collection and analysis in Electric Power Group, LLC, v. Alstom (830 F.3d 1350, 119 USPQ2d 1739 (Fed. Cir. 2016)), organizing and manipulating information through mathematical correlations in Digitech Image Techs., LLC v Electronics for Imaging, Inc. (758 F.3d 1344, 111 U.S.P.Q.2d 1717 (Fed. Cir. 2014)) and comparing information regarding a sample or test to a control or target data in Univ. of Utah Research Found. v. Ambry Genetics Corp. (774 F.3d 755, 113 U.S.P.Q.2d 1241 (Fed. Cir. 2014)) and Association for Molecular Pathology v. USPTO (689 F.3d 1303, 103 U.S.P.Q.2d 1681 (Fed. Cir. 2012)) that the courts have identified as concepts that can be practically performed in the human mind or mathematical relationships. Therefore, these limitations fall under the “Mental process” and “Mathematical concepts” groupings of abstract ideas. Merely reciting that a mental process is being performed in a generic computer environment does not preclude the steps from being performed practically in the human mind or with pen and paper as claimed. If a claim limitation, under its broadest reasonable interpretation, covers performance of the limitation in the mind but for the recitation of generic computer components, then if falls within the “Mental processes” grouping of abstract ideas. As such, claim(s) 1-20 recite(s) an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 1 : YES).
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). This judicial exception is not integrated into a practical application because the claims do not recite an additional element that reflects an improvement to technology or applies or uses the recited judicial exception to affect a particular treatment for a condition. Rather, the instant claims recite additional elements that amount to mere instructions to implement the abstract idea in a generic computing environment or mere instructions to apply the recited judicial exception via a generic treatment.
Claim 20 does not have an active step of administering a particular treatment, and in claim 1, the administering of the treatment is optional. While claims 17-19 administer treatment to the patient, the treatment is general and not a particular treatment.
As such, these limitations equate to mere instructions to implement the abstract idea on a generic computer that the courts have stated does not render an abstract idea eligible in Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. As such, claims 1-20 is/are directed to an abstract idea/law of nature/natural phenomenon (Step 2A, Prong 2 : NO).
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims recite additional elements that equate to mere instructions to apply the recited exception in a generic way or in a generic computing environment.
The prior art of Wang et al. [BMC Medical Genetics, volume 12, supplement 1, 2019 189pages; on IDS] teaches that obtaining patient samples and performing gene expression and gene mutation assays are routine and conventional.
As discussed above, there are no additional limitations to indicate that the claimed analysis engine requires anything other than generic computer components in order to carry out the recited abstract idea in the claims. Claims that amount to nothing more than an instruction to apply the abstract idea using a generic computer do not render an abstract idea eligible. Alice Corp., 573 U.S. at 223, 110 USPQ2d at 1983. See also 573 U.S. at 224, 110 USPQ2d at 1984. MPEP 2106.05(f) discloses that mere instructions to apply the judicial exception cannot provide an inventive concept to the claims. The additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception. Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B : No). As such, claims 1-20 is/are not patent eligible.
Claim Rejections - 35 USC § 112(a) - Written Description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Page 10 of the specification discloses that the treatment response score is a linear combination of gene expressions weighted by coefficients, mutation statuses weighted by other coefficients, and an intercept. While page 10 adequately describes the model for linear regression, the specification does not possess a derivation of this model or why linear (i.e. as opposed to non-linear) regression is used.
Claim Rejections - 35 USC § 112(a) - Enablement
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
1. The claims recite using linear regression based on gene expression and gene mutation data to predict treatment response.
2. Page 10 of the specification teaches that the treatment response score is a linear combination of gene expressions weighted by coefficients, mutation statuses weighted by other coefficients, and an intercept. While page 10 adequately teach the model for linear regression, the specification does not teach how to derive this model or why linear (i.e. as opposed to non-linear) regression is used. While pages 37-53 of the specification allege working examples of the linear regression model, the specification does not display the linear regression data to support the analysis or a reasoning of how linear regression is the most effective model.
3. The prior art of Molina-Arcas et al. [Cancer Discover., volume 3, 2013, pages 548-563; on IDS] teaches the coordination of direct input of both KRAS and IGH1 receptors to activation of PI 3-kinase in KRAS mutant lung cancer. Figure 1 of Molina-Arcas illustrates a sigmoidal (i.e. non-linear) responses to gene expression and mutation with increasing drug levels. Likewise, the document of Zhao et al. [JNCI, volume 11, 2019, pages 301-310; on IDS] studies the immune landscape of prostate cancer and nomination of PD-L2 as a potential therapeutic target [title]. Figure 1B teaches an immune content score that is interpreted to reflect similar principles as a treatment response score. However, instead of being linear relation, the immune content score also looks sigmoidal. Finally, the document of Safikhani et al. [F1000Research 2017, 46 pages, on IDS] studies inconsistencies in large pharmacogenomic studies [title]. Column 2 on page 21 of Safikhani et al. teaches the equation for fitting the treatment-response data to be in a sigmoidal, non-linear curve.
4. The claims teach using linear regression to assess treatment response to drugs based on gene expression and gene mutation data. While the specification teaches the supporting linear regression model with some alleged positive working examples, the specification does not teach how the linear model is derived, and its advantages over non-linear models. The prior art examined overwhelmingly teaches treatment response to drugs as being sigmoidal in nature and non-linear. In the absence of guidance on why a linear model is used to model treatment response data over any of the other many types of modeling techniques available, it is unpredictable as to why to choose this linear model over other models. Such unpredictability yields UNDUE EXPERIMENTATION.
In view of the above, it is the Examiner’s position that with the insufficient guidance and working examples and in view of unpredictability and the state of art, one of skill in the art could not make and/or use the invention with the claimed breadth without an undue amount of experimentation.
E-mail Communications Authorization
Per updated USPTO Internet usage policies, Applicant and/or applicant’s representative is encouraged to authorize the USPTO examiner to discuss any subject matter concerning the above application via Internet e-mail communications. See MPEP 502.03. To approve such communications, Applicant must provide written authorization for e-mail communication by submitting the following statement via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300):
Recognizing that Internet communications are not secure, I hereby authorize the USPTO to communicate with the undersigned and practitioners in accordance with 37 CFR 1.33 and 37 CFR 1.34 concerning any subject matter of this application by video conferencing, instant messaging, or electronic mail. I understand that a copy of these communications will be made of record in the application file.
Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web (using PTO/SB/439) or Central Fax (571-273-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Russell Negin, whose telephone number is (571) 272-1083. This Examiner can normally be reached from Monday through Thursday from 8 am to 3 pm and variable hours on Fridays.
If attempts to reach the Examiner by telephone are unsuccessful, the Examiner’s Supervisor, Larry Riggs, Supervisory Patent Examiner, can be reached at (571) 270-3062.
/RUSSELL S NEGIN/ Primary Examiner, Art Unit 1686 10 August 2026
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