DETAILED ACTION
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 the Claims
Claims 1-20 are pending and examined herein.
No claims are canceled.
Priority
As detailed on the 19 January 2024 filing receipt, the application claims no priority earlier than the filing date of 01 November 2023, and thus all claims are being accorded this priority date as the effective filing date.
Information Disclosure Statement
Information disclosure statements (IDS) were filed on 03 March 2024 and 15 June 2026. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the references are being considered by the examiner.
Drawings
The petition for color figures was granted on 13 March 2024.
The drawings are objected to because at least figure 4, 5b, 6a-b, 17, 18b, 26b-c, 28b, 30b-d, and 31 are blurry to the point of illegibility. Amendments correcting the resolution of at least these figures is required. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (pg. 36, paragraph [145]; pg. 39, paragraph [155]; pg. 50, paragraph [196]). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The specification is also objected to because of the following informality: “may indicates” should read “may indicate” (pg. 20, paragraph [92]).
Appropriate correction is required.
Claim Rejections - 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 4-9 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. The claims recite a family consistency score, a family mean calibrated score, a family classification, and a class consistency score. It is unclear from the claims in view of the specification what “class” and “family” refer to Further, the “consistency score” and “calibration score” are not described, and so it is unclear what “consistency” and “calibration” refer to in this context and thus how to calculate the scores is unclear.
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 1-20 are rejected under 35 USC § 101 because the claimed inventions are directed to an abstract idea without significantly more. "Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 § I). Abstract ideas include mathematical concepts, and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)). The claims as a whole, considering all claim elements individually and in combination, are directed to a judicial exception at Step 2A, Prong 2, and the additional elements of the claims, considered individually and in combination, do not provide significantly more at Step 2B than the abstract idea of classifying a tumor.
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of
nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The claims are directed to a system, which falls within one of the categories of statutory subject matter. [Step 1: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
Claim 1 recites identifying tumor classes using unsupervised clustering. Unsupervised clustering is a mathematical concept and identifying a tumor class is a mental step of data evaluation. Thus, this step recites abstract ideas.
Claim 1 recites generating a classification, which is part of the data evaluation step above and thus a mental concept, which is an abstract step.
Claim 1 recites generating a confidence score, where a confidence score is a mathematical concept.
Claim 1 recites updating the classifier and reference set, which is interpreted as a mental step of adding information to a corpus of data and thus an abstract idea.
Claim 2 recites the classifier comprises subclassifiers, where the classifiers are mathematical concepts resulting in a classification, where classifying is a mental step as explained above.
Claim 3 recites classifier comprises family subclassifiers about functional regions, where the classifiers are mathematical concepts resulting in a classification, where classifying is a mental step as explained above.
Claim 4 recites generating a consistency score and family mean calibrated score, which are both mathematical concepts.
Claim 5 recites generating a family classification based on the family consistency score and family mean calibrated score, where generating a classification is a mental step of data evaluation.
Claim 6 recites a subclassifier per family, where the subclassifier is further elaboration on the abstract elements described above.
Claim 7 recites generating a class consistency score and a class mean calibrated score from the class sub-classifiers, where generating a consistency score and a mean calibrated score are mathematical concepts.
Claim 8 recites generating a class and/or sub-class classification based on the class consistency score and the class mean calibrated score, where generating a classification is an abstract step of data evaluation.
Claim 9 recites the confidence score comprises a mean calibrated score of the family consistency score, the family mean calibrated score, the class consistency score, and/or the class mean calibrated score, which are all descriptions of mathematical concepts.
Claim 10 recites including identifying a tumor family, class, and sub-class based on clusters of characteristics identified by the classifier, where identifying based on clusters is a mental step of data evaluation.
Claim 11 recites the tumor is a renal tumor, hematolymphoid tumor, or CNS tumor, which is related to data regarding the methylation profile and data per se is abstract.
Claim 12 recites high confidence in the classification is when the confidence score is above a threshold of at least 0.9, which is related to data interpretation or evaluation and thus a step the human mind is practically equipped to perform.
Claim 13 recites a score below 0.5 or the classifier cannot generate a classification, which is also a data evaluation step.
Claim 14 recites evaluating the methylation profile, a sample of the tumor, orthogonal DNA and/or RNA data, and/or patient demographics to generate the new class or subclass, where data evaluation is a mental step and generating a new class or subclass is a data organization step, which is also a mental process.
Claim 15 recites updating the reference set with the new class or sub-class and re-train the classifier with the updated reference set, where updating the reference with the class is adding data to the reference corpus and thus a mental step of data organization, and retraining the classifier is a mathematical step.
Claim 16 recites the unsupervised clustering uses uniform manifold approximation and projection (UMAP) dimensionality reduction and/or additional dimensionality reduction methodologies, where UMAP dimensionality reduction is a description of a mathematical algorithm.
Claim 17 recites to train the classifier prior to providing the methylation profile, where training a classifier is considered to be a mathematical process.
Claim 18 recites diagnosing the tumor using the generated classification, where diagnosis is an abstract step of data evaluation performable by the human mind.
Claim 19 recites forming a treatment plan specific to the diagnosis of the tumor, where forming a plan is a step practically performed by the human mind.
Claim 20 recites to compare the classification to a histological and/or molecular evaluation of the tumor and adjust the classification based on the comparison, where data comparison and adjusting the classification are steps practically performed by the human mind.
Thus, the claims recite abstract ideas and thus must be examined further to determine whether elements in addition to the abstract ideas integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). [Step 2A Prong One: Yes]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Because the claims recite judicial exceptions, direction under Step 2A Prong Two provides that the claims must be examined further to determine whether they recite elements in addition to the abstract ideas which integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d)(III)).
Elements in addition to the abstract ideas recited in the claims include a system comprising a processor in communication with a memory (claim 1), receiving a methylation profile of a tumor and providing the profile to a classifier (claim 1), and generating an alert (claim 13).
The claims comprising computer components do not describe any specific computational steps by which the computer performs or carries out the abstract idea, nor do they provide any details of how specific structures of the computer are used to implement these functions. The claims state nothing more than that a generic computer performs the functions that constitute the abstract idea. Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; and MPEP 2106.05(f)).
Receiving and providing data to a computer system is a data gathering step and as such is insignificant extra solution activity (MPEP 2106.05(g)) and instructions to apply an exception using a computer (MPEP 2106.05(f)). The generating an alert is interpreted as an outputting step, and thus also insignificant extra solution activity (MPEP 2106.05(g)).
Thus, the claims recite elements in addition to the abstract ideas which do not integrate the abstract ideas into a practical application, and must be examined further to determine whether elements in addition to the abstract ideas provide significantly more (MPEP 2106.05). [Step 2A Prong Two: Yes]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
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 of 101 analysis determines whether the claims contain additional elements that amount to an inventive concept, and an inventive concept cannot be furnished by an abstract idea itself (MPEP 2106.05).
Elements in addition to the abstract ideas recited in the claims include a system comprising a processor in communication with a memory (claim 1), receiving a methylation profile of a tumor and providing the profile to a classifier (claim 1), and generating an alert (claim 13).
The claims recite a computer, interpreted as instructions to apply the abstract idea using a computer, where the computer does not impose meaningful limitations on the judicial exceptions, which can be performed without the use of a computer (MPEP 2106.04(d) § I; and MPEP 2106.05(f)). Storing data on a computer is a conventional computer function (Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015); OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93; MPEP 2106.05(d)).
The courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a merely generic manner or as insignificant extra-solution activity (see Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information), buySAFE, Inc. v. Google, Inc., 765 F.3d 1350, 1355, 112 USPQ2d 1093, 1096 (Fed. Cir. 2014) (computer receives and sends information over a network), Versata Dev. Group, Inc. v. SAP Am., Inc., 793 F.3d 1306, 1334, 115 USPQ2d 1681, 1701 (Fed. Cir. 2015), and OIP Techs., 788 F.3d at 1363, 115 USPQ2d at 1092-93 (storing and retrieving information in memory), as discussed in MPEP 2106.05(d)(II)(i)).
Therefore, the recited additional elements, alone or in combination, do not appear to provide an inventive concept. [Step 2B: No]
Conclusion: Claims are Directed to Non-statutory Subject Matter
For these reasons, the claims, when the limitations are considered individually and as a whole,
are directed to an abstract idea and lack an inventive concept. Hence, the claimed invention does not
constitute significantly more than the abstract idea, so the claims are rejected under 35 USC § 101 as
being directed to non-statutory subject matter.
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.
Claims 1, 12, and 16-19
Claims 1, 12, and 16-19 are rejected under 35 U.S.C. 103 as being unpatentable over Maher (US 20200372296 A1; previously cited on the 04 March 2024 PTO-892 form) in view of Filippova (US 20200294624 A1; previously cited on the 04 March 2024 PTO-892 form) and Skinner (US 20170132362 A1; newly cited).
Claim 1 recites to receive a methylation profile of the tumor.
Maher teaches a methylation pattern as a methylation status (paragraph [161]) – also called a methylation profile (paragraph [179]) – which may be derived from tumor tissue (paragraph [28]).
Claim 1 recites to provide the methylation profile to a classifier trained to identify tumor classes using unsupervised clustering.
Maher teaches using an unsupervised training model (paragraph [288]) and a clustering algorithm (paragraph [367]) such as UMAP (paragraph [365]).
Claim 1 recites to generate a classification of the tumor based on the methylation profile and
a reference set, wherein the reference set is generated from training the classifier.
Mayer teaches classification by specific cancer type (paragraph [313]), where a specific cancer type is considered to be a class, and a training set (paragraph [375]).
Claim 1 recites to generate a confidence score based on the correlation of the methylation profile to the classification from the classifier.
Maher does not teach a confidence score based on correlation between the methylation profile and the classification.
Claim 1 recites to update the classifier and reference set with the methylation profile and classification.
Maher does not teach updating the classifier and reference.
Claim 1 recites the steps are carried out on a system comprising a processor in communication with a memory, the memory including instructions executable by the processor to perform the steps.
Maher teaches the system comprises at least one processor and a memory storing at least one program for execution by the at least one processor (paragraph [11]).
Filippova teaches determining a degree of confidence (paragraph [183]).
Skinner teaches iteratively updating a classifier (paragraph [56]).
Claim 11 recites the tumor is a renal tumor, hematolymphoid tumor, or CNS tumor.
Maher teaches a second tissue type being a solid tumor including renal tissue (paragraph [26]).
Claim 12 recites there is high confidence in the classification when the confidence score is above a threshold of at least 0.9.
Filippova teaches ROC-AUC for diagnostic utility which can range from 0.5 to 1 (paragraph [104]).
Claim 16 recites the unsupervised clustering uses uniform manifold approximation and projection (UMAP) dimensionality reduction and/or additional dimensionality reduction methodologies.
Maher teaches UMAP (paragraph [41]).
Claim 17 recites including instructions executable by the processor to train the classifier prior to providing the methylation profile.
Maher teaches classifier training (abstract).
Claim 18 recites including instructions executable by the processor to diagnose the tumor using the generated classification.
Maher teaches the information is relevant to the diagnosis of cancer (paragraph [437]).
Claim 19 recites including instructions executable by the processor to form a treatment plan specific to the diagnosis of the tumor.
Maher teaches to determining a treatment regimen based on the classifier (paragraph [384]).
Combining Maher, Filippova, and Skinner
An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have motivated to combine the works of Maher and Filippova because Maher teaches classifications and Filippova teaches confidence in said classifications, where a metric such as ROC-AUC is useful because it suggests limited utility versus great diagnostic utility (Filippova: paragraph [104]), where diagnostic utility in the form of higher sensitivity and/or specificity is valuable in classification. Further combination with Skinner would be valuable because Skinner teaches learning genomic features associated with epigenetic control, including methylation patterns, and iteratively learning in use of a classifier (paragraph [56]), which is a strength of learning algorithms. Maher, Filippova, and Skinner are all directed to the shared field of endeavor of classification using methylation state and their combination is prima facie obvious.
Claims 2-3
Claims 2-3 are rejected under 35 U.S.C. 103 as being unpatentable over Maher, Filippova, and Skinner as applied to claims 1, 12, and 16-19 above and further in view of Widschwendter (US 20220205049 A1; newly cited).
Claim 2 recites the classifier comprises a plurality of subclassifiers.
Widschwendter teaches sub-classifiers in a classification model (paragraph [489]).
Claim 3 recites a plurality of family subclassifiers for separate functional regions of the methylation profile.
Widschwendter teaches methylation in functional subregions including promoters (paragraph [163]), where the regions are CpGs, which are related to regulation (paragraph [489]).
Combining Maher, Filippova, Skinner, and Widschwendter
An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have motivated to combine the previously combined works with the teachings of Widschwendter because Widschwendter teaches subclassifications in the classifier model, where methylation in promoter regions for sub-classifiers were used to determine bins with signal (paragraph [489]). This is relevant because a functional region like a promoter being methylated affects transcription. Like the previously combined art, Widschwendter is directed to using methylation status of classify cancer status, and thus their combination is prima facie obvious.
Claim 4
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Maher, Filippova, Skinner, and Widschwendter as applied to claims 1-3, 12, and 16-19 above and further in view of Sill (Human Molecular Genetics 29: 205-213, 2020; newly cited).
Claim 4 recites instructions executable by the processor to generate a family consistency score and a family mean calibrated score from the sub-classifiers.
The consistency score and calibrated score are not explicitly explained in the claims and are given their broadest reasonable interpretation as metrics of reliability of placement based on the sub-classifiers.
Filippova teaches determining a degree of confidence (paragraph [183]) but not application to sub-classifiers.
Widschwendter teaches sub-classifiers in a classification model (paragraph [489]) and degree of confidence in a classification using the ROC AUC (paragraph [220]).
Sill teaches calibrating scores by post-processing strategies (pg. 206, col. 1, fifth paragraph).
Combining Maher, Filippova, Skinner, Widschwendter, and Sill
An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have motivated to combine the previously combined works with the teachings of Sill because Sill teaches calibration as part of a classification model using Platt scaling, which is disclosed as famous and thus known to one having ordinary skill in the art (pg. 206, col. 1, fifth paragraph). Like the previously combined art, Sill is directed to using methylation status for molecular tumor classification, and thus their combination is prima facie obvious.
Claims 10 and 20
Claims 10 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Maher, Filippova, and Skinner as applied to claims 1, 12, and 16-19 above and further in view of Brannon (Genes & Cancer 1(2): 152-163, 2010; newly cited).
Claim 10 recites including instructions executable by the processor to identify a tumor family, class, and sub-class based on clusters of characteristics identified by the classifier.
Maher teaches tumor classification but not family, class, and sub-class.
Brannon teaches classification of renal tumor, renal cell carcinoma, clear cell renal cell carcinoma (ccRCC) (abstract) and ccA and ccB (Table 2), representing tiers of identification of the tumor.
Claim 20 recites including instructions executable by the processor to compare the classification to a histological and/or molecular evaluation of the tumor and adjust the classification based on the comparison.
Brannon teaches validating the clustering using rt-PCR (Fig. 4, caption), interpreted as molecular evaluation.
Combining Maher, Filippova, Skinner, and Brannon
An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have motivated to combine the previously combined works with the teachings of Brannon because Brannon teaches clustering to determine optimal subclasses (abstract), where subclasses for renal cancer of the type ccRCC are disclosed as at least ccA and ccB (Table 2), and validation of the classification using reverse transcription PCR (pg. 153, col. 1, fourth paragraph), where validation is confirmed the subtypes which is in turn related to downstream investigation and prognosis.
Subject Matter Not Taught by the Prior Art
Claims 5-9 are pending clarification under 35 USC 112(b) as it is unclear what the claims are requiring. Claim 13 recites alerting the user that a new class has been created given a low confidence. Filippova teaches ROC-AUC values near 0.5 have lower utility (paragraph [104]) and Brannon teaches generation of an unclassified subclass (pg. 157, col. 1, last paragraph), but an alert predicated on a low confidence is not taught.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Robert J Kallal whose telephone number is (571)272-6252. The examiner can normally be reached Monday through Friday 8 AM - 4 PM EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Olivia M. Wise can be reached at (571) 272-2249. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Robert J. Kallal/Examiner, Art Unit 1685
