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 .
DETAILED ACTION
Status of the Application
Claims 1-20 are currently pending in this case and have been examined and addressed below. This communication is a Non-Final Rejection in response to the Claims filed on 08/30/2024.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 01/16/2025 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 112
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.
Claims 1-20 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.
Claims 1 and 18 recite predicting, via blind phenotype prediction, efficacy of the one of the number of phenotype and, following the prediction, confirming, by at least one of observation, measurement, or self-identification, prioritizing at least one of a gene or gene variant based on druggability thereof. It is unclear how the step of confirming prioritizing at least one of a gene or gene variant based on druggability thereof would be conducted. The specification discloses confirming predictions to be true by observation, measurement, or self-identification and further prioritizing the predictive elements based on druggability ([0103]). This indicates two separate steps of confirming and prioritizing. However, the claim recites confirming prioritizing a gene based on druggability. It is unclear how this would be performed as one step. Therefore, the metes and bounds of the claim limitation are not clear and the claim is indefinite. For purposes of examination, Examiner will interpret the claim to be equivalent to predicting efficacy of the phenotype, confirming and prioritizing a gene or gene variant based on druggability by observation, measurement, or self-identification.
Claims 1 and 18 also recite treating a patient having with a therapeutic comprising the one of the number of phenotype. It is unclear what patient will be treated based on the claim language. Also, it is unclear how treatment can be a therapeutic comprising the phenotype, as the phenotype is not a type of treatment, but rather describes the traits or characteristics of an organism. Therefore, the metes and bounds of the claim limitation are not clear and the claim is indefinite. For purposes of examination, Examiner interprets this limitation to be treating any patient with a therapeutic.
As per Claims 2-17 and 19-20, the claims depend on Claims 1 and 18 and do not remedy the indefiniteness issues of Claims 1 and 18. As dependent claims inherit the deficiencies of the claims they depend on, they are also rejected.
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 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 1
Claims 1-17 and 18-20 fall within the statutory category of a process.
Step 2A, Prong One
As per Claims 1 and 18, the limitations of identifying a number of variant sites in the genomic data, determining that one of a number of phenotypes is relevant when a score of a degree of association with the ontological term is above a first threshold amount wherein number of phenotypes is determined to be relevant when the score of the degree of association in combination with the score of the strength of effect is above a second threshold amount, comparing a degree of match between a number of data pairs, each data pair comprising one datum of genomic data for the relevant phenotype from substantially each combination formed by two of the number of individuals, generating a report for each of the data pairs, and predicting, via blind phenotype prediction, efficacy of the phenotype and confirming, by at least one of observation, measurement, or self-identification, prioritizing at least one of a gene or gene variant based on druggability, under its broadest reasonable interpretation, covers performance of the limitation in the mind. The steps of identifying variant sites in the genomic data, determining a phenotype is relevant, comparing a degree of match between data pairs, and generating a report of the pairs include concepts performed in the human mind including observation, evaluation, judgement and opinion. If a claim limitation, under its broadest reasonable interpretation, covers the performance of the limitation in the mind but for the recitation of generic computer components, then it falls within the “Mental Processes” grouping of abstract ideas. Accordingly, the claims recite an abstract idea.
Step 2A, Prong Two
The judicial exception is not integrated into a practical application because the additional elements and combination of additional elements do not impose meaningful limits on the judicial exception. In particular, the claims recite the additional element – a processor for executing the elements of the abstract idea. The processor in these steps is recited at a high-level of generality, such that it amounts to no more than mere instructions to apply the exception using a generic computer component. Accordingly, this additional element does not integrate the abstract idea into a practical application because it does not impose any meaningful limits on practicing the abstract idea. The claim also recites the additional elements of accessing genomic data of a number of individual organisms, retrieving from a first data repository a strength-of-effect associated with the variant site, retrieving from a second data repository a degree of association with an ontological term associated with the variant site, and accessing additional genomic data of the subject when the degree of match exceeds a third threshold amount which amounts to insignificant extra-solution activity, as in MPEP 2106.05(g), because the steps of accessing genomic data, retrieving a strength-of-effect and retrieving a degree of association are mere data gathering in conjunction with the abstract idea where the limitation amounts to necessary data gathering and outputting, (i.e., all uses of the recited judicial exception require such data gathering or data output). See Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; OIP Techs., Inc. v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1092-93 (Fed. Cir. 2015) (presenting offers and gathering statistics amounted to mere data gathering). The claims include treating a patient having with a therapeutic comprising the one of the number of phenotype and Claim 18 includes administering a first or second treatment which amounts to mere instructions to apply the exception. As per MPEP 2106.04(d), when determining whether a claim applies or uses a judicial exception to effect a particular treatment or prophylaxis, the particularity or generality of the treatment is relevant. For example, claiming administration of a suitable medication is not particular, and instead is merely instructions to “apply” the exception in a generic way. Therefore, it does not integrate the abstract idea into a practical application. Similarly, the limitations of treating a patient with a therapeutic comprising the number of phenotype and administering a first or second treatment is not particular and thus amounts to mere instructions to apply the exception. Because the additional elements do not impose meaningful limitations on the judicial exception, the claim is directed to an abstract idea.
Step 2B
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the additional elements when considered both individually and as an ordered combination do not amount to significantly more than the abstract idea. As discussed above with the respect to integration of the abstract idea into a practical application, the additional element of a processor to perform the method of the invention amounts to no more than mere instructions to apply the exception using a generic computing component. The processor is recited at a high level of generality and is described in the specification as a microprocessor, processing core, distributed processor, or other computing device operable to carry out computations, etc. (Specification, [0014]), which do not add meaningful limitations to the abstract idea beyond mere instructions to apply an exception. Mere instructions to apply an exception using a generic computer component cannot provide an inventive concept. The claims also include the additional elements of accessing genomic data of a number of individual organisms, retrieving from a first data repository a strength-of-effect associated with the variant site, retrieving from a second data repository a degree of association with an ontological term associated with the variant site, and accessing additional genomic data of the subject when the degree of match exceeds a third threshold amount which are elements that are well-understood, routine and conventional computer functions in the field of data management because they are claimed at a high level of generality and include receiving or transmitting data as well as storing and retrieving information from memory, which have been found to be well-understood, routine and conventional computer functions by the Court (MPEP 2106.05(d)(II)(i) Receiving or transmitting data over a network, e.g., using the Internet to gather data, Symantec, 838 F.3d at 1321, 120 USPQ2d at 1362 (utilizing an intermediary computer to forward information); TLI Communications LLC v. AV Auto. LLC, 823 F.3d 607, 610, 118 USPQ2d 1744, 1745 (Fed. Cir. 2016) (using a telephone for image transmission); OIP Techs., Inc., v. Amazon.com, Inc., 788 F.3d 1359, 1363, 115 USPQ2d 1090, 1093 (Fed. Cir. 2015) (sending messages over a network); 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); but see DDR Holdings, LLC v. Hotels.com, L.P., 773 F.3d 1245, 1258, 113 USPQ2d 1097, 1106 (Fed. Cir. 2014) ("Unlike the claims in Ultramercial, the claims at issue here specify how interactions with the Internet are manipulated to yield a desired result‐‐a result that overrides the routine and conventional sequence of events ordinarily triggered by the click of a hyperlink." (emphasis added) and (iv) Storing and retrieving information in memory, 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). The claims include treating a patient with a therapeutic comprising the one of the number of phenotype and Claim 18 includes administering a first or second treatment which are similar to limitations which have been found by the courts to be well understood, routine and conventional. As per MPEP 2106.05(d), Immunizing a patient against a disease is a treatment which is well-understood, routine and conventional. Therefore, treating a patient with a therapeutic and a treatment including a first or second treatment being administered is a well-understood, routine and conventional activity. Looking at the limitations as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of the computer or improves another technology. The claims do not amount to significantly more than the underlying abstract idea.
Dependent Claims 2-17 and 19-20 add further limitations which are also directed to an abstract idea. Claims 2-5, 9, and 19-20 include limitations which further specify or limit the elements of the independent claims, and hence are nonetheless directed towards fundamentally the same abstract idea as independent Claim 1. Claims 6-7 include generating a spectral clustering report, generating an intrinsic dimensionality report as further specifying the limitation of generating a report from the independent claim. This is directed towards a mental process as per the independent claim. The generation of a spectral clustering report and intrinsic dimensionality report can also fall into the grouping of mathematical concepts as mathematical relationships and calculations can be used to carry out the spectral clustering and intrinsic dimensionality. As per MPEP 2106.04(a), a claim can recite more than one judicial exception and claims which recite a series of steps that recite mental steps which are also mathematical calculations are identified as both. Claim 8 includes determining the phenotype is above the first threshold amount which, similar to the independent claim, is directed to a mental process. Claim 10 further specifies the limitation of identifying the number of phenotypes including applying a Hidden Markov model to obtain predications of molecular entities which recites mathematical concepts. Claim 11 includes ranking entries which is a mental process because the ranking can be performed in the human mind using evaluation and judgement. Claim 12 further specifies the ranking of Claim 11 and therefore also recites a mental process. Claim 13 further limits the independent claim by including deriving a score utilizing TF-IDF which recites a mathematical concept such as mathematical relationships. Claim 14 includes comparing a distance between each pair of genomic data and deriving eigenvalues and eigenvectors from the comparison, which further limit the elements of the independent claims and therefore fall into the mental processes abstract idea grouping similar to the independent claims. The determination of eigenvalues and eigenvectors is recited at a high level of generality such that it can be accomplished in any manner which can be done in the human mind or by using mathematical relationships and therefore, can also fall into the abstract grouping of mathematical concepts. Claims 15 and 16 recite additional mathematical relationships as mathematical formulas or equations, which fall into the abstract grouping of mathematical concepts. Claim 17 includes administering a treatment to the subject based on the report. This is an additional element as it does not fall into one of the groupings of abstract ideas. The additional element of administering a treatment is recited at a high-level of generality such that it is not considered a particular treatment or prophylaxis since a particular treatment is not specified in the claim language. Therefore, this amounts to insignificant extra-solution activity, as an insignificant application similar to cutting hair after determining the hair style, as per MPEP 2106.05(g). The administration of a treatment is also found to be a well-understood, routine and conventional activity in the life science arts, as per MPEP 2106.05(d)(II), because it is claimed in a merely generic manner similar to immunizing a patient against a disease which has been found by the courts to be well-understood, routine and conventional. Because the additional elements do not impose meaningful limitations on the judicial exception and the additional elements are well-understood, routine and conventional functionalities in the art, the claims are directed to an abstract idea and are not patent eligible.
Subject Matter Free of the Prior Art
The following is an examiner’s statement of subject matter free of the prior art: The limitations in Claims 1 and 18 stating: determining a phenotype to be relevant based on the score of the degree of association being above a threshold amount in combination with the score of the strength of effect being above a second threshold amount in combination with the limitations of Claims 1 and 18 is not taught by the prior art.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Chen et al. (Chen YC, Douville C, Wang C, Niknafs N, Yeo G, Beleva-Guthrie V, Carter H, Stenson PD, Cooper DN, Li B, Mooney S, Karchin R. A probabilistic model to predict clinical phenotypic traits from genome sequencing. PLoS Comput Biol. 2014 Sep 4;10(9):e1003825.) teaches predicting a phenotype using a model based on a population dataset incorporating a genome sequence and phenotype prevalence.
Trakadis (US 2014/0310215 A1) teaches identifying a number of variant sites in genomic data, degree of association with an ontological term, determine a phenotype is relevant when a score is above a threshold, comparing a degree of match between data pairs, and ranking possible phenotypes.
Yandell et al. (US 2016/0092631 A1) teaches a data repository storing strength of effect associated with variant sites, and a score of phenotypes for degree of association with an ontological term.
Torkamani (US 2016/0048634 A1) teaches predicting risk of a disease including obtaining genetic variant data from variants of genome, determining associations between genomes and phenotypes.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Evangeline Barr whose telephone number is (571)272-0369. The examiner can normally be reached Monday to Friday 8:00 am to 4:00 pm.
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/EVANGELINE BARR/Primary Examiner, Art Unit 3682
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