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 1-4, 6, 8, 10-12, 14, 16, 20-23, 25, 33, and 41-43 are pending and examined in the instant Office action.
Information Disclosure Statement
The IDS of 10/15/2023 has been considered.
Claim Rejections - 35 USC § 112(b) - Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 12 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
The term “significantly unbalanced processes” in claim 12 is a relative term which renders the claim indefinite. The term “significantly unbalanced” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear as to what makes a process “significantly unbalanced” as opposed to just being “unbalanced.” For the purpose of examination, it is interpreted that any process that is unbalanced is also “significantly unbalanced.”
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) 1-4, 6, 8, 10-12, 16, 20-23, 25, 33, 41, and 43 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 1-4, 6, 8, 10-12, 16, 20-23, 25, 33, and 41 are drawn to methods, and claim 43 is drawn to a computer program product on non-transitory computer-readable storage media.
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 43 recite the mental step of receiving single-cell proteomic analysis data, wherein the data comprises a plurality of genes and/or proteins that deviate from steady state.
Claims 1 and 43 recite the mental step of calculating for the population of cells at least one unbalanced process active in at least one cell of the population of cells.
Claims 1 and 43 recite the mental step and/or mathematical limitation of performing a determining thermodynamic-based analysis.
Claims 1 and 43 recite the mental step of assembling the genes and/or proteins deviating from a steady state into at least one unbalanced network/signaling pathway.
Claims 1 and 43 recite the mental step of generating for a plurality of cells a cell-specific signature comprising at least one unbalanced process.
Claims 1 and 43 recite the mental step of assigning all cells with the same CSS to a cellular subpopulation.
Claims 1 and 43 recite the mental step of selecting a therapy that targets the at least one unbalanced process in the CSS.
Claim 2 recites the mental step of constraining the analysis to a single timepoint.
Claim 6 recites the mental step of constraining the analysis to include oncogenic proteins.
Claim 8 recites the mental steps of constraining the cancer to be a tumor and selecting a therapy that is subject-specific.
Claim 10 recites the mental step of constraining the thermodynamic-based analysis to be single-cell surprisal analysis.
Claim 11 recites the mental step of calculating all of the unbalanced processes active in the population of cells using a thermodynamics-based approach.
Claim 12 recites the mental step of the CSS comprising unbalanced processes.
Claim 16 recites the mental step of selecting a second therapy for the subject.
Claim 20 recites the mental step of selecting a second therapy to be applied to a cell subpopulation that increased in abundance following the first therapy.
Claim 21 recites the mental step of using CSSs to classify cells into subpopulations.
Claim 22 recites the mathematical and/or mental step of conducting percentage calculations on the subpopulations.
Claim 23 recites the mental step of selecting a therapy that targets a CSS of a plurality of subpopulations that increase in abundance following the first therapy.
Claim 25 recites the mental step of constraining the therapy to be a cancer therapy.
Claim 33 recites the mental step of assigning barcodes that indicate active unbalanced processes in each of the CSS of the cancer.
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) 1-4, 6, 8, 10-12, 16, 20-23, 25, 33, 41, and 43 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.
While the claims recite selecting cancer therapies, the claims lack the limitation of treating the subject with the specific therapy. Claim 14 is NOT rejected under this statute because claim 14 is the only claim that recites that active limitation of treating the subject with the selected therapy.
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 1-4, 6, 8, 10-12, 16, 20-23, 25, 33, 41, and 43 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 document of Wilson et al. [US PGPUB 2008/0194710 A1] teaches that digesting cells and performing FACS analysis on cells is routine and conventional in the prior art.
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 1-4, 6, 8, 10-12, 16, 20-23, 25, 33, 41, and 43 is/are not patent eligible.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
35 U.S.C. 103 Rejection #1:
Claim(s) 42 is/are rejected under 35 U.S.C. 103 as being unpatentable over Kim et al. [US PGPUB 2016/0169898 A1].
Claim 42 is drawn to a kit comprising anti-Her2 therapy and an anti-cMET therapy with a label. The intended use for the kit to be used in combination with radiotherapy does not differentiate the kit of claim 42 from other kits comprising anti-Her2 therapy and an anti-cMET therapy with a label. The intended use for the kit to be used for treating triple negative breast cancer does not differentiate the kit of claim 42 from other kits comprising anti-Her2 therapy and an anti-cMet therapy with a label.
The document of Kim et al. studies methods for predicting and improving the survival of colorectal cancer patients [title]. Paragraphs 19-23 of Kim et al. teach both anti-Her2 therapy and anti-cMet therapy. Kim et al. does not teach that the combination of therapies has a label.
It would have been obvious to someone of ordinary skill in the art at the time of the instant application to modify the cancer therapies of Kim et al. to include a label wherein the motivation would have been that labeling the cancer therapy with the type of cancer therapy facilitates health care professionals selections of the specific cancer therapies [paragraphs 19-23 of Kim et al.].
35 U.S.C. 103 Rejection #2:
Claim(s) 1-2, 6, 8, 10-12, 14, 16, 33, and 43 is/are rejected under 35 U.S.C. 103 as being unpatentable over Borrebaeck et al. [WO 2017/050939 A2; on IDS] in view of Kravchenko-Balasha et al. [The Journal of Physical Chemistry B, 2016, pages 5990-5997].
Claim 1 is drawn to a method for selecting a therapy for a cancer. The method comprises obtaining a sample comprising a population of cells derived from the cancer and subjecting the cells to a single-cell proteomic analysis. The method comprises receiving data from the single-cell proteomic analysis. The data comprises a plurality of genes and/or proteins that deviate from a steady states. The method comprises calculating for the population of cells at least one unbalanced process active in at least one cell of the population of cells. The calculating comprises performing a deterministic thermodynamic-based analysis of the data from the single-cell proteomic analysis. The method comprises assembling the genes and/or proteins deviating from a steady state into at least one unbalanced network/signaling pathway in order to produce a list of at least one calculated unbalanced process. The method comprises generating for a plurality of cells of the population a CSS comprising at least one unbalanced process from the list. The method comprises assigning all cells with the same CSS to a cellular subpopulation. The method comprises selecting a therapy that targets the at least one unbalanced process in the CSS.
Claim 43 is drawn to similar subject matter as claim 1, except claim 43 is drawn to a computer program product on non-transitory computer-readable storage media.
Page 29 of Borrebaeck et al. teaches that the summary of the invention is to provide therapy for an individual with solid, pancreatic cancer. Claims 1 and 2 of Borrebaeck et al. teach providing a cellular pancreatic cancer and wild type samples with protein/gene expression indicating a biomarker signature specifying of the status of the cell. Claim 1 of Borrebaeck et al. teaches a subpopulation of cells with CSSs indicative of the presence of pancreatic cancer. The paragraph bridging pages 29-30 of Borrebaeck et al. teaches selecting personalized treatments for the subject with pancreatic cancer.
Borrebaeck et al. does not teach a thermodynamic-based analysis of cellular steady state and unbalanced processes.
The document of Kravchenko-Balasha et al. studies a thermodynamic-based interpretation of protein expression heterogeneity in different glioblastoma multiforme tumors in order to identify tumor-specific unbalanced processes [title]. The abstract and illustration in the abstract teaches a thermodynamic-based analysis of steady state process in the cell and unbalanced processes in the cell.
With regard to claim 2, claims 1 and 2 of Borrebaeck et al. are executed at a timepoint.
With regard to claim 6, claim 1 of Borrebaeck et al. indicated oncogenic proteins as being expressed in the cell signature.
With regard to claims 8 and 14, the paragraph bridging pages 29-30 of Borrebaeck et al. teaches selecting and administering personalized treatments for the subject with pancreatic cancer. The paragraph bridging pages 45-46 of Borrebaeck et al. suggests future personalized therapies.
With regard to claims 10-12, the abstract of Kravchenko-Balasha et al. teaches thermodynamic single-cell analysis of imbalances processes in the cell. Claim 1 of Borrebaeck et al. teaches finding cell signature of cells indicating prostate cancer.
With regard to claims 16 and 25, the paragraph bridging pages 29-30 of Borrebaeck et al. teaches selecting combination cancer therapies.
With regard to claim 33, Figure 1 of Kravchenko-Balasha et al. indicates barcode-like heat maps indicative of cancer.
It would have been obvious to someone of ordinary skill in the art at the time of the instant application to modify the cell signature analysis and treatment techniques of Borrebaeck et al. by use of the thermodynamic analysis of Kravchenko-Balasha et al. wherein the motivation would have been that the additional mathematical analysis facilitates the understanding of unbalanced processes in the cell [abstract of Kravchenko-Balasha et al.]. There would have been a reasonable expectation of success in combining the pancreatic cancer analysis of Borrebaeck et al. and the glioblastoma multiforme analysis of Kravchenko-Balasha et al. because both studies are analogously applicable to relating the mechanics of subcellular processed to the presence of cancer in the cell.
35 U.S.C. 103 Rejection #3:
Claim(s) 3-4 is/are rejected under 35 U.S.C. 103 as being unpatentable over Borrebaeck et al. in view of Kravchenko-Balasha et al. as applied to claims 1-2, 6, 8, 10-12, 14, 16, 33, and 43 above, in further view of Hause et al. [US PGPUB 2020/0292526 A1].
Claim 3 is further limiting wherein the sample is digested into a single-cell suspension before proteomic analysis of single cells.
Claim 4 is further limiting wherein the proteomic analysis comprises single-cell FACS analysis.
Borrebaeck et al. and Kravchenko-Balasha et al. make obvious thermodynamic analysis of cell signature data, as discussed above.
Borrebaeck et al. and Kravchenko-Balasha et al. do not teach digesting the cell sample or FACS analysis.
The document of Hause et al. studies methods for identifying cellular attributes related to outcomes associated with cell therapy [title]. Paragraphs 132-133 of Hause et al. teaches cell digestion and FACS.
It would have been obvious to someone of ordinary skill in the art at the time of the instant application to modify the cell signature analysis and treatment techniques of Borrebaeck et al. and the thermodynamic analysis of Kravchenko-Balasha et al. by use of the empirical cellular analysis techniques of Hause et al. wherein the motivation would have been that the empirical techniques of Hause et al. provided needed cellular data for the signature and thermodynamic analysis [paragraphs 132-133 of Hause et al.].
35 U.S.C. 103 Rejection #4:
Claim(s) 41 is/are rejected under 35 U.S.C. 103 as being unpatentable over Borrebaeck et al. in view of Kravchenko-Balasha et al. as applied to claims 1-2, 6, 8, 10-12, 14, 16, 33, and 43 above, in further view of Kim et al.
Claim 41 requires the method of claim 1 to contain a kit comprising anti-Her2 therapy and an anti-cMET therapy with a label. The intended use for the kit to be used in combination with radiotherapy does not differentiate the kit of claim 42 from other kits comprising anti-Her2 therapy and an anti-cMET therapy with a label.
Borrebaeck et al. and Kravchenko-Balasha et al. make obvious thermodynamic analysis of cell signature data, as discussed above.
Borrebaeck et al. and Kravchenko-Balasha et al. do not teach the recited kit.
The document of Kim et al. studies methods for predicting and improving the survival of colorectal cancer patients [title]. Paragraphs 19-23 of Kim et al. teach both anti-Her2 therapy and anti-cMet therapy. Kim et al. does not teach that the combination of therapies has a label.
It would have been obvious to someone of ordinary skill in the art at the time of the instant application to modify the cancer therapies of Kim et al. to include a label wherein the motivation would have been that labeling the cancer therapy with the type of cancer therapy facilitates health care professionals selections of the specific cancer therapies [paragraphs 19-23 of Kim et al.].
It would have been obvious to someone of ordinary skill in the art at the time of the instant application to modify the cell signature analysis and treatment techniques of Borrebaeck et al. and the thermodynamic analysis of Kravchenko-Balasha et al. by use of the kit of Kim et al. wherein the motivation would have been that the empirical treatment techniques of Kim et al. provided potential solutions to the cancer cell signatures [paragraphs 19-23 of Kim et al.].
Related Prior Art
The document of Gavasso et al. [Expert Review of Molecular Diagnostics, volume 16, 2016, pages 579-589; on IDS] teaches single-cell proteomics [title]. The document of Gavasso et al. provides a review of techniques used to analysis signaling pathways and histopathological analysis of cells [abstract].
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 September 2026
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