DETAILED ACTION
Applicant’s response filed 03/17/2025 has been fully considered. The following rejections and/or objections are either reiterated or newly applied. It is noted that the art unit of record has changed.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 04/18/2025 has been entered.
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 .
Claim Status
Claims 10, 13, 17-18 and 20-21 are cancelled by Applicant.
Claim 26 is newly added.
Claims 1-9, 11-12, 14-16, 19 and 22-26 are currently pending and are herein under examination.
Claims 1-9, 11-12, 14-16, 19 and 22-26 are rejected.
Claims 1, 22 and 24-26 are objected.
Priority
The instant application claims domestic benefit to international application PCT/IL2019/050474 filed 04/29/2019, which claims domestic benefit to U.S. Provisional Application No. 62/664,202 filed 04/29/2018. The claims to domestic benefit for claims 11-9, 11-12, 14-16, 19 and 22-26 are acknowledged. As such, the effective filing date for claims 1-9, 11-12, 14-16, 19 and 22-26 is 04/29/2018.
Drawings
The objections to the drawings are withdrawn in view of Applicant’s amendments to the drawings filed 03/17/2025.
The drawings filed 03/17/2025 are accepted.
Claim Objections
The objections to claims 1, 13, 16 and 22 are withdrawn in view of Applicant’s claim amendments.
Claims 1, 22 and 24-26 are objected to because of the following informality:
Claim 1, line 15, contains “; and” which should be “;” because step e) contains “; and”.
Claim 1 does not have a period at the end of the last line.
Claim 22, line 17, contains “; and” which should be “;” because step e) contains “; and”.
Claim 22 does not contain a period at the end of the last line.
Claim 24, line 1, recites the phrase “claim 1 wherein” which should recite “claim 1, wherein”.
Claim 25, line 1, recites the phrase “claim 22 wherein” which should recite “claim 22, wherein”.
Claim 26, line 1, recites the word “target/s” which should be changed to “target(s)”.
Claim 26, line 14, contains “; and” which should be changed to “;” because step e) contains “; and”.
Appropriate correction is required.
Withdrawn Rejections
35 USC 112(a)
The rejection of claims 1-9, 11-16, 19 and 23-24 under 35 USC 112(a) is withdrawn in view of Applicant’s claim amendments. Specifically, claims 1 and 22 now recite drugs that target specific proteins listed in the tables of the claims, rather than any drug that can target anything.
35 USC 112(b)
The rejection of claims 1-9, 11-16, 19 and 22-25 under 35 USC 112(b) is withdrawn in view of Applicant’s claim amendments.
35 USC 103
The rejection of claims 1-9, 11-12, 14-16, 19 and 22 and 24-25 under 35 U.S.C. 103 as being unpatentable over Kravchenko-Balasha et al., Välikangas et al., Ramaswamy et al. and Worst et al. is withdrawn in view of Applicant’s claim amendments. Specifically, the limitations of claim 13, which was found to be free from the prior art, have been integrated into claims 1 and 22.
Claim Rejections - 35 USC § 112
35 USC 112(b)
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.
Claims 1-9, 11-12, 14-16, 19 and 22-26 are 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.
This rejection is newly recited.
Claim 1 recites a table with 17 unbalanced processes that renders the claim indefinite. It is unclear whether an unbalanced process comprises only the set of proteins listed in the table or if the unbalanced process comprises not only the listed proteins but also additional unlisted proteins, e.g., if the listed proteins are part of a larger protein network. The latter interpretation comes from the second column being titled “Proteins that participate in the unbalanced process”, which seems to indicate that the unbalanced process may contain other proteins wherein the listed proteins may be what cause the process to be unbalanced. To overcome this rejection, it is suggested to clarify the metes and bounds of what composes an unbalanced process. Furthermore, claims 2-9, 11-12, 14-16, 19 and 23-24 are also rejected because they include the limitations of claim 1, which is rejected, and because they do not resolve the issue of indefiniteness.
Claim 1, lines 8-9, recites the phrase “c) determining within said second composite cancer-expression data set at least one unbalanced process”, which renders the claim indefinite. It is unclear if determining an unbalanced process means detecting presence of all proteins in the set of proteins listed in the table for an unbalanced process, or if it means detecting an abnormality (e.g., up or down regulation) in at least one of the listed proteins for an unbalanced process. To overcome this rejection, it is suggested to amend the claim language, for example, by clarifying whether an unbalanced process is defined by detecting the presence of all the listed proteins, if an unbalanced process is defined by not only detecting all the listed proteins but also determining that there is an abnormality (e.g., up or down regulation) in at least one of the proteins in the list, or if there is some other interpretation that is yet to be defined. Furthermore, claims 2-9, 11-12, 14-16, 19 and 23-24 are also rejected because they include the limitations of claim 1, which is rejected, and because they do not resolve the issue of indefiniteness.
Claims 22 and 26 contain both issues of indefiniteness as described above regarding claim 1. Therefore, both claims 22 and 26 are rejected under 35 USC 112(b) for indefiniteness. The same suggestions above regarding claim 1 are also suggested for claims 22 and 26 to overcome the rejection. Furthermore, claim 25 is also rejected because it includes the limitations of claim 22, which is rejected, and because it does not resolve the issue of indefiniteness.
Claim 1, lines 8-9, and claim 22, lines 10-11, recite the phrase “c) determining/determine within said second composite cancer-expression data set a least one unbalanced process in said expression data of said subject”, which renders the claim indefinite. Claims 1 and 22 also recite a table with 17 unbalanced processes which makes it unclear whether the “at least one unbalanced process” should be selected from at least one of the listed 17 unbalanced processes in the table, or if the table represents a set of possible unbalanced processes that may be selected. To overcome this rejection, it is suggested to amend step c) such that is recites the following phrase that is found in newly added claim 26: “wherein said at least one unbalanced process is selected from the group of unbalanced processes in the following table”. Furthermore, claims 2-9, 11-12, 14-16, 19 and 23-25 are also rejected because they include the limitations of claim 1 and 22, which are rejected, and because they do not resolve the issue of indefiniteness.
Claim 19 recites the phrase “repeating the method after a period of treatment with said at least one drug to determine at least one new druggable target”, which renders the claim indefinite. Claim 19 requires repeating the method of claim 1, which includes step f) of administering to a subject the drug that targets a druggable target. However, claim 19 intends to stop at step e) in the method of claim, i.e., selecting a drug that targets at least one druggable target. Therefore, it is unclear whether claim 19 intends to require performance of steps a)-e) or steps a)-f) in claim 1. To overcome this rejection, it is suggested to clarify what steps of claim 1 should be repeated in claim 19.
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 1-9, 11-12, 14-15, 19 and 22-26 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Any newly recited portions herein have been necessitated by claim amendment.
Step 2A, Prong 1:
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 phenomena (Step 2A, Prong 1). In the instant application, claims 1-9, 11-12, 14-15, 19 and 23-24 recite a method, claims 22 and 25 recite a computer readable medium, and claim 26 recites a method. The instant claims recite the following limitations that equate to one or more categories of judicial exception:
Claims 1, 22 and 26 recite “b. adding/add said subject's expression data to a first composite cancer-expression data set to produce a second composite cancer-expression data set; wherein said first composite cancer-expression data set comprises data from a plurality of cancer types; c. determining/determine within said second composite cancer-expression data set at least one unbalanced process in said expression data of said subject, wherein said determining comprises performing thermodynamic-based analysis; d. constructing/construct a patient-specific barcode that indicates the unbalanced process that influences said cancer of said subject;
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Claims 1 and 26 recite “e. selecting, based on said barcode, at least one drug that targets at least one druggable target within said at least one unbalanced process in said subject’s expression data, wherein said at least one druggable target is at least one protein selected from the group of proteins in the following table; thereby identifying at least one druggable target in a subject suffering from cancer;”
Claim 5 recites “further comprising normalizing said subject's expression data with a composite healthy-expression data set or with a composite healthy and cancer-expression data set.”
Claim 6 recites “wherein determining at least one unbalanced process comprises determining over and under expressed genes and/or proteins as compared to their expression in a balanced process.”
Claim 7 recites “wherein determining at least one unbalanced process comprises assembling expressed genes and/or proteins within said second data set into networks.”
Claim 8 recites “wherein said assembling is performed using functional interactions according to a STRING database.”
Claim 9 recites “wherein said thermodynamic-based analysis comprises surprisal analysis.”
Claim 11 recites “wherein said plurality of cancer types are selected from lymphoma, bladder cancer, gastric cancer, colorectal cancer, kidney cancer, ovarian cancer, endometrial cancer, lung cancer, head and neck cancer, brain cancer and breast cancer.”
Claim 12 recites “wherein said first composite cancer- expression data set comprises data from at least 10 samples.”
Claim 14 recites “wherein said at least one protein is over or under expressed in said subject's expression data.”
Claim 15 recites “wherein said at least one gene or protein is a known cancer regulatory protein.”
Claim 19 recites “further comprising repeating the method after a period of treatment with said at least one drug to determine at least one new druggable target.”
Claim 23 recites “wherein said determining comprises identifying 1 to 4 unbalanced processes.”
Claims 24 and 25 recite “wherein constructing said patient-specific barcode comprises mapping identified tumor-specific barcodes associated with a plurality of patients into at least a 17-dimensional data space.”
Regarding the above cited limitations in claims 1, 5-7, 19 and 22-26 of selecting, identifying, adding, performing a thermodynamic-based analysis, constructing a patient-specific barcode, normalizing expression data, assembling genes/proteins into a network, repeating the method, and mapping barcodes into a 17-dimensional space. These limitations equate to a mental process because they 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)), which the courts have identified as concepts that can be practically performed in the human mind or by using pen and paper. Specifically, a human is equipped to select, determine, analyze, add, organize/manipulate data, and repeat steps of a method as well as perform the operations of an unspecified normalization process and thermodynamic-based analysis. Therefore, these limitations recite a mental process.
Regarding the above cited limitations in claims 8-9, 11-12 and 14-15, these limitations are included in the judicial exception recited in claim 1 because they limit the assembling, thermodynamic-based analysis, plurality of cancer types, first composite cancer-expression data set, and at least one protein but do not change the fact that these components are still a part of the judicial exception.
As such, claims 1-9, 11-12, 14-15, 19 and 22-26 recite an abstract idea (Step 2A, Prong 1: Yes).
Step 2A, Prong 2:
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). The judicial exception is not integrated into a practical application because the claims do not recite additional elements that reflect an improvement to technology (MPEP § 2106.04(d)(1)), nor provide some other meaningful limitation. Rather, the claims merely include instructions to apply the recited exception in a generic way or in a generic computing environment (MPEP § 2106.05(f)) and included insignificant extra-solution activity (MPEP § 2106.05(g)). The claims recite the following additional elements:
Claims 1, 22 and 26 recite “a. receiving/receive expression data from said subject; f. administering to said subject the at least one of said drug that targets said at least one druggable target, thereby providing a patient-specific cancer treatment.”
Claim 22 recites “A computer program product for identifying a druggable target for treating a subject suffering from cancer, comprising a non-transitory computer-readable storage medium having program code embodied thereon, the program code executable by at least one hardware processor to … e. provide, based on said patient-specified barcode, an output of at least one druggable target from said at least one unbalanced process within said subject's expression data for which a drug that targets said druggable target is known, wherein said at least one druggable target is at least one protein selected from the group of proteins in the following table”
Claim 2 recites “wherein said expression data is protein expression data or mRNA expression data.”
Claim 3 recites “wherein said receiving expression data comprising receiving a biological sample from said subject and performing high-throughput sequencing on said subject.”
Claim 4 recites “wherein said biological sample is a blood sample or a tumor biopsy.”
Regarding the above cited limitation in claim 22 of the non-transitory computer readable medium, there are no limitations that it requires anything other than a generic computing system. Therefore, this limitation equates to mere instructions to implement an abstract idea on a generic computer, which the courts have established does not render an abstract idea eligible in Alice Corp. 573 U.S. at 223, 110 USPQ2d at 1983.
Regarding the above cited limitation in claims 1-4, 22 and 26 of receiving and providing, these limitations equate to insignificant, extra-solution activity of mere data gathering and outputting.
Regarding the above cited limitation in claims 1, 22 and 26 of administering, these limitations are not a particular treatment and therefore equate to mere instructions to apply the judicial exception in a generic way (see MPEP § 2106.04(d)(2)(a)). Although these limitations require administration of a drug to target at least one druggable target in an unbalanced process of cancer, the drug is not particular because it encompasses all applications of the judicial exception (MPEP 2106.04(d)(2). In other words, the word drug is so generically recited that it could be any type of drug. The drug could even be a drug that targets an unbalanced process but does not effectively restore balance to the process. Therefore, the administered drug is not considered a particular treatment.
As such, claims 1-9, 11-15, 19 and 22-25 are directed to an abstract idea (Step 2A, Prong 2: No).
Step 2B:
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). These claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because these claims recite additional elements that equate to instructions to apply the recited exception in a generic way or in a generic computing environment (MPEP § 2106.05(f)) and to well-understood, routine and conventional (WURC) limitations (MPEP § 2106.05(d)). The instant claims recite the following additional elements:
Claims 1, 22 and 26 recite “a. receiving/receive expression data from said subject; f. administering to said subject the at least one of said drug that targets said at least one druggable target, thereby providing a patient-specific cancer treatment.”
Claim 22 recites “A computer program product for identifying a druggable target for treating a subject suffering from cancer, comprising a non-transitory computer-readable storage medium having program code embodied thereon, the program code executable by at least one hardware processor to … e. provide, based on said patient-specified barcode, an output of at least one druggable target from said at least one unbalanced process within said subject's expression data for which a drug that targets said druggable target is known, wherein said at least one druggable target is at least one protein selected from the group of proteins in the following table”
Claim 2 recites “wherein said expression data is protein expression data or mRNA expression data.”
Claim 3 recites “wherein said receiving expression data comprising receiving a biological sample from said subject and performing high-throughput sequencing on said subject.”
Claim 4 recites “wherein said biological sample is a blood sample or a tumor biopsy.”
Regarding the above cited limitations in claim 22 of the non-transitory computer readable medium, this limitation equates to instructions to implement an abstract idea on a generic computing environment, which the courts have established does not provide an inventive concept in Intellectual Ventures I LLC v. Capital One Bank (USA), 792 F.3d 1363, 1367, 115 USPQ2d 1636, 1639 (Fed. Cir. 2015).
Regarding the above cited limitations in claims 1, 22 and 26 of receiving expression data and providing an output, these limitations equate to transmitting/receiving data over a network, which the courts have established as a WURC limitation of a generic computer in buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014). Similarly, the limitation in claim 2 also equates to transmitting/receiving data over a network because it attempts to limit the type of data but does not change the fact that data is being transmitted/received.
Regarding the above cited limitations in claims 1, 3-4, 22 and 26 of administering a drug, receiving a biological sample and performing high-throughput sequencing on a tumor biopsy, these limitations are WURC as disclosed by Worst et al. (“Worst”; European journal of cancer 65 (2016): 91-101; previously cited on PTO892 mailed on 01/11/2024), Harris et al. (“Harris”; JAMA oncology 2, no. 5 (2016): 608-615; previously cited on PTO892 mailed on 09/17/2024) and Chang et al. (“Chang”; Clinical cancer research 22, no. 15 (2016): 3810-3820; previously cited on PTO892 mailed on 09/17/2024). The paragraphs below disclose the WURC nature of these limitations:
Worst discloses performing RNA sequencing on cancer biopsies (abstract), wherein druggable targets were discovered from the expression data (Figure 1), and matching targeted therapies were administered to the patents (pg. 97, col. 2, last para.). Worst shows in Figure 3 a druggable target PTEN (which is listed in unbalanced process 13 and 15 in the instant claims). Worst discloses using computer software such as BWA and deFuse (ph. 95, col. 2, para. 1), indicating that the method is compatible with computers.
Harris discloses a study of tumor molecular profiling to inform therapeutic decisions in advanced pediatric solid tumors (title), wherein tumor biopsies were collected (pg. 609, col. 2, para. 1) and a targeted next-generation sequencing OncoPanel using Agilent SureSelect for target capture and Illumina HiSeq for sequencing was performed on the samples (pg. 609, col. 2, para. 2). This data was then put into a system called iCat that produces therapeutic recommendations based on the genomic data, wherein patients then received a targeted therapy based on the iCat recommendations (Figure 2; Table 4; pg. 611, col. 2, last para.). Harris shows in eTable 2 of Supplement 2 that a mutation in BRAF can be treated with Vemurafenib (which is a gene listed in unbalanced process 4, 10 and 14 of the instant claims). Harris uses the computer software PRARA to analyze RNA sequencing data (pg. 610, col. 2, para. 2), indicating that the method is compatible with a computer.
Chang discloses a multidimensional clinomics for precision therapy for children with relapsed and refractory cancer (title). Patients with non-central nervous system solid tumors underwent whole exome and whole genome sequencing wherein clinically actionable alterations were identified and matched with a targeted drug (abstract). Tumor tissue was sampled (pg. 3811, col. 1, para. 3), genome sequencing was then performed (pg. 3811, col. 1, para. 4), actionable mutations were discovered, (pg. 3811, col. 1, last para.), and then patients were administered the targeted drug therapies (pg. 3815, col. 2, para 2-3). Chang shows in Table 2 a list of genes that have mutations that can be targeted by a specific drug, one gene is BRAF (which is listed in unbalanced process 4, 10 and 14 of the instant claims). Chang also discloses that a high-performance cluster computer was used to analyze data (pg. 3819, col. 2, para. 1), indicating that the method is compatible with computers. Therefore, these limitations are WURC individually and when considered in combination with a generic computer.
Therefore, when these additional elements are considered individually and in combination, they do not comprise an invention concept that transforms the judicial exception into a patent eligible application of the judicial exception itself (Step 2B: No).
As such, claims 1-9, 11-12, 14-15, 19 and 22-26 are not patent eligible.
Response to Arguments under 35 USC 101
Applicant's arguments filed 03/17/2025 have been fully considered but they are not persuasive.
Applicant argues that claims 1 and 22 recite a particular treatment because they require administering to a subject with cancer a suitable drug that targets a protein in an unbalanced process. Applicant’s argument is not persuasive for the following reasons:
MPEP 2106.04(d)(2).a recites:
“When determining whether a claim applies or uses a recited judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, the following factors are relevant.
a. The Particularity Or Generality Of The Treatment Or Prophylaxis
The treatment or prophylaxis limitation must be "particular," i.e., specifically identified so that it does not encompass all applications of the judicial exception(s). For example, consider a claim that recites mentally analyzing information to identify if a patient has a genotype associated with poor metabolism of beta blocker medications. This falls within the mental process grouping of abstract ideas enumerated in MPEP § 2106.04(a). The claim also recites "administering a lower than normal dosage of a beta blocker medication to a patient identified as having the poor metabolizer genotype." This administration step is particular, and it integrates the mental analysis step into a practical application. Conversely, consider a claim that recites the same abstract idea and "administering a suitable medication to a patient." This administration step is not particular, and is instead merely instructions to "apply" the exception in a generic way. Thus, the administration step does not integrate the mental analysis step into a practical application.”
Using any drug that can “target” (inhibit, activate, upregulated, downregulated) a protein is not a particular treatment. Rather, claims 1 and 22 encompass all applications of the judicial exception by claiming any type of drug that “targets” a listed protein in the table. Therefore, the administration step in claims 1 and 22 equates to mere instructions to “apply” the exception in a generic way.
MPEP 2106.05(f) recites “(3) The particularity or generality of the application of the judicial exception. A claim having broad applicability across many fields of endeavor may not provide meaningful limitations that integrate a judicial exception into a practical application or amount to significantly more. For instance, a claim that generically recites an effect of the judicial exception or claims every mode of accomplishing that effect, amounts to a claim that is merely adding the words ‘apply it’ to the judicial exception.” In the instant claims, the drug, which may be any type of drug, equates to “every mode of accomplishing that effect”, wherein the effect is providing a patient-specific cancer treatment.
This evaluation is in contrast to claim 16, which was found to be patent-eligible, because it recites specific drugs, rather than claiming any type of drug.
Conclusion
No claims are allowed.
Claims 1-9, 11-12, 14-16, 19 and 22-26 are free from the prior art because the prior art does not fairly teach or suggest the limitation in claims 1, 22 and 26 of “c) determine/determining within said second composite cancer-expression data set at least one unbalanced process”, wherein the unbalanced process is selected from the table listed in claims 1, 22 and 26. The closest prior art is Kravchenko-Balasha et al. (“Balasha”; The Journal of Physical Chemistry B 120, no. 26 (2016): 5990-5997; previously cited on PTO892 mailed 01/11/2024) who discloses using thermodynamic analysis of tumors to detect unbalanced processes. However, Balasha does not disclose the specific set of proteins that compose each unbalanced process listed in the tables of claims 1, 22 and 26.
It is noted that in claims 1, 22 and 26 step c) of determining at least on unbalanced processed is being interpreted to require detecting all proteins within the set of proteins listed in the table for an unbalanced process, wherein at least one of the detected proteins has abnormal expression compared to a healthy individual (i.e., up or down regulated). If Applicant does not wish for step c) to be interpreted in this way, it is suggested to provide a written statement on record or amend step c).
Inquiries
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Noah A. Auger whose telephone number is (703)756-4518. The examiner can normally be reached M-F 7:30-4:30 EST.
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/N.A.A./Examiner, Art Unit 1687
/Karlheinz R. Skowronek/Supervisory Patent Examiner, Art Unit 1687