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 1-15 are examined.
Priority
This US Application 17/780,037 (05/26/2022) is a 371 of PCT/EP2020/083444 (11/26/2020) and claims priority from US Application No. 62/940,444 (11/26/2019) as reflected in the filing receipt mailed on 09/16/2022. The claims to the benefit of priority are acknowledged; and the effective filing date of claims 1-15 is 11/26/2019.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 05/26/2022 was considered by the examiner.
Claim Objections
Claim 7 is objected regarding the verb "comprises" and its lack of grammatical agreement with the plural subject.
Claim 10 is objected to because of the following informalities: each element/step of the list of elements/steps is not presented in a separate line. Each element or step of the claim should be separated by a line indentation (608.01(m) Form of Claims). Sub-steps / elements should be indented from their parent step / element. 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.
Claims 1-15 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter the invention. Claims depending from rejected claims are rejected similarly, unless otherwise noted.
Claim 1 recites "the variant" (first "determining" step), which requires but lacks antecedent, noting that previously only a plurality has been recited. This rejection might be overcome by amending to "one variant among the plurality" or another equivalent amendment. Claim 10 is rejected similarly. The same lack of clear antecedent issue recurs in each instance in the following list:
Claim 1, "the... epigenetic impact" (last "determining" step), previously "epigenetic impact status" was recited -- claims 7 and 10 are rejected similarly
Claim 2, "the step of filtering"
Claim 3, "the step of ranking"
Claims 5 and 14, "the affected gene"
Claim 8 "the functional impact information"
Claims 9 and 13 "the plurality of remaining variants"
Claim 9 and 13 "the expression of one or more genes" in which relationships are unclear regarding both "expression" and "genes" versus instances in claims 1 and 10
Claim 1 recites "a plurality of variants identified in the genomic sample" ("obtaining" step), the relationship of which is unclear versus the similar recitation in the preamble. Claim 10 is rejected similarly.
In claim 1, the relationships are unclear among the various recitations of "effect" as at "epigenetic effects..." ("obtaining" step), "an effect on splicing of a gene" (1st "determining" step), "an effect on expression of a gene" (2nd "determining" step), etc. Claims 4, 9-10 and 13 are rejected similarly.
In claim 1, the relationship is unclear between the two instances of "genes" in the recited "copy number variation for one or more genes in the genomic sample, and epigenetic effects on one or more genes in the genomic sample." Claim 10 is rejected similarly.
Claim 1 recites "impact on expression of a gene" (last "determining" step), but it is not clear what is the relationship between this new instance of "gene" and the previously recited "one or more genes in the genomic sample" ("obtaining" step). Claim 10 is rejected similarly.
Claim 1 recites "a plurality of variants and/or genes in the genomic sample," but it is unclear what are the relationships between these new instances versus those in the preamble. Claim 10 is rejected similarly.
In claim 7¸ the relationship is unclear between this new instance of "a gene" and the claim 1 instances of genes. Claim 8 is rejected similarly regarding each of its recitations of "variants" and "genes."
Claims 9 and 13 recite "for one or more of the plurality of remaining variants" which is indefinite because it is unclear what defines a variant as "remaining." In the interest of compact prosecution, a "remaining" variant is interpreted as any variant present in the list recited in claims 8 and 12, from which claims 9 and 13 depend.
Claim 10 is to a 101 machine or manufacture, i.e. a "system" in this instance, limited according to its claimed physical structure, but it is not clear what is the structure associated with the recited "(i) determine..." and similar steps. The recited "system" and "processor" are not interpreted as requiring structure clearly linking the recited "system" to the recited "configured to" in a structural sense appropriate to a claim to a machine or manufacture. This rejection might be overcome by, for example, reciting a data storage device, comprised by the "system" or "processor" and instructions stored therein, the instructions "configured" as recited; as supported at [0105].
Claim 11 repeats the same issue from claim 10 above in its recitation of "the processor is further configured to filter..."
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 1-15 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)).
101 background
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)?
Analysis of instant claims
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The instant claims are directed to a method (claims 1-9), and a system (claims 10-15), each of which falls within one of the categories of statutory subject matter. [Step 1: claims 1-15 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))?
Background
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)).
Analysis of instant claims
Mental processes, defined as concepts or steps practically performed in the human mind such as steps of observations, evaluations, judgments, analysis, opinions or organizing information include:
• "determining a splice status for the variant, the splice status comprising an indication of whether a variant has an effect on splicing of a gene" (claims 1 and 10);
• "determining a variant-based expression regulation status, the variant- based expression regulation status comprising an indication of whether the variant has an effect on expression of a gene" (claims 1 and 10);
• "determining a gene-based expression regulation status, the gene- based expression regulation status comprising an indication of whether the variant has a functional impact on a target gene in a pathway" (claims 1 and 10);
• "determining a gene-based copy number variant (CNV) and epigenetic impact status, the gene-based CNV and epigenetic impact status comprising an indication of whether the CNV and/or epigenetic impact has an impact on expression of a gene" (claims 1 and 10); and
• "adjusting, based on the gene-based CNV and epigenetic impact status, the variant-based expression regulation status and/or the gene-based expression regulation status" (claims 1 and 10).
Under the BRI, the recited limitations are mental processes because a human mind is sufficiently capable of evaluate a dataset and determine an indication of an effect on a certain function; and subsequently adjust the status found depending on the dataset
Dependent claims 4-7and 14-15 recite further details about the "indication of an impact" performed by the variants; not reciting any additional non-abstract elements; all reciting further aspects of the information being analyzed, the manner in which that analysis is performed. Hence, the claims explicitly recite numerous elements that, individually and in combination, constitute abstract ideas. The instant claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d)). [Step 2A Prong One: claims 1, 4-7, 10 and 14-15 – Yes; claims 2-3, 8-9 and 11-13 – No. ]
Additionally, the instant claims recite a natural correlation by correlating the measurement of an amount of a gene/variant naturally found in the body with the functional impact/effect of said gene/variant. (see MPEP 2106.04(b).I).
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))?
Background
MPEP 2106.04(d).I lists the following example considerations for evaluating whether a judicial exception is integrated into a practical application:
An improvement in the functioning of a computer or an improvement to other technology or another technical field, as discussed in MPEP §§ 2106.04(d)(1) and 2106.05(a);
Applying or using a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition, as discussed in MPEP § 2106.04(d)(2);
Implementing a judicial exception with, or using a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim, as discussed in MPEP § 2106.05(b);
Effecting a transformation or reduction of a particular article to a different state or thing, as discussed in MPEP § 2106.05(c); and
Applying or using the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than a drafting effort designed to monopolize the exception, as discussed in MPEP § 2106.05(e).
Analysis of instant claims
Instant claims 1-3, 8-10 and 12-13 recite additional elements that are not abstract ideas:
"obtaining genomic sample information" (claims 1 and 10);
"reporting at least the adjusted variant-based expression regulation status and/or the adjusted gene-based expression regulation status" (claims 1 and 10).
Claims 10-15 relate to computers or further aspects of the information being analyzed by computers, and 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.
Dependent claims 2-3 recite further details about obtaining the genomic sample information; dependent claims 8-9, 12-13 recites further details about the "reporting" step.
The recited "obtaining genomic sample information" and the related claims 2-3 read on data gathering activities or the type of data being gathered; not amounting to a practical application. The type of data or how the data is organized does not change that it is mere data gathering or conventional computer receiving means. Said "obtaining genomic sample information" is utilized to gather data to be used by the judicial exceptions (i.e. determinations listed as mental steps above).
The recited reporting step reads on "outputting" data of whether a functional impact exists, reading on receiving or transmitting data over a network, e.g., using the Internet to gather data; which constitutes just necessary data gathering and outputting and therefore correspond to insignificant extra-solution activity. The instant claims state nothing more than that a generic computer performs the functions that constitute the abstract idea (MPEP 2106.05(f)).
Hence, these are mere instructions to apply the abstract idea using a computer and insignificant extra-solution activity and therefore the claims do not integrate that abstract idea into a practical application (see MPEP 2106.04(d) § I; 2106.05(f); and 2106.05(g)). None of the dependent claims recite any additional non-abstract elements; they are all directed to further aspects of the information being analyzed, the manner in which that analysis is performed, or the mathematical operations performed on the information.
In Step 2A, Prong One above, claim steps and/or elements were identified as part of one or more judicial exceptions (JEs).
In this Step 2A, Prong Two immediately above claim steps and/or elements were identified as part of one or more additional elements. Additional elements are further discussed in Step 2B below.
Here in Step 2A, Prong Two, no additional step or element clearly demonstrates integration of the JE(s) into a practical application.
At this point in examination it is not yet the case that any of the Step 2A, Prong Two considerations enumerated above clearly demonstrates integration of the identified JE(s) into a practical application. Referring to the considerations above, none of 1. an improvement, 2. treatment, 3. a particular machine or 4. a transformation is clear in the record.
For example, regarding the first consideration at MPEP 2106.04(d)(1), the record, including for example the specification, does not yet clearly disclose an explanation of improvement over the previous state of the technology field. The claims do not yet clearly result in such an improvement. [Step 2A Prong Two: claims 1-15 - No]
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 the 35 USC § 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).
Claims 10-15 recite a computer or computer functions, 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)).
Claims directed to "reporting" data read on electronically outputting data on a computer which is a conventional computer function (Alice Corp. Pty. Ltd. v. CLS Bank Int'l, 573 U.S. 208, 225, 110 USPQ2d 1984 (2014) MPEP 2106.05(d)).
As explained above, the steps of "obtaining a genomic sample" and "reporting" data constitute insignificant extra solution activity, and when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(g)). Hence, these elements, when considered individually, are insufficient to constitute inventive concepts that would render the claims significantly more than an abstract idea (see MPEP 2106.05(d)).
It is known in the art that the use of replica exchange molecular dynamics to investigate proteins is well-understood, routine and conventional (Kagohara et. al. " Epigenetic regulation of gene expression in cancer: techniques, resources and analysis" Briefings in functional genomics 17(1):49-63 (2018) – "reporting" step in pg. 55 col. 2 para. 4 – "obtaining a genomic sample" in pg. 54 Fig. 3).
When the claims are considered as a whole, they do not integrate the abstract idea into a practical application; they do not confine the use of the abstract idea to a particular technology; they do not solve a problem rooted in or arising from the use of a particular technology; they do not improve a technology by allowing the technology to perform a function that it previously was not capable of performing; and they do not provide any limitations beyond generally linking the use of the abstract idea to a broad technological environment. See MPEP 2106.05(a) and 2106.05(h). [Step 2B: claims 1-15 - No]
Conclusion: Instant claims are directed to non-statutory subject matter
For these reasons, the claims in this instant application, 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 instant claims 1-15 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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 pre-AIA 35 U.S.C. 103(a) 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 1-15 are rejected under 35 U.S.C. 103(a) as being unpatentable over Kagohara " Epigenetic regulation of gene expression in cancer: techniques, resources and analysis" Briefings in functional genomics 17(1):49-63 (2018) in view of Li "RNA splicing is a primary link between genetic variation and disease." Science 352.6285:600-604 (2016) in view of Geistlinger "Widespread modulation of gene expression by copy number variation in skeletal muscle." Scientific reports 8(1):1399 (2018); as cited on the attached Form PTO-892.
Claim 1 recites "a method for characterizing a functional impact of a plurality of variants identified from a genomic sample, using a variant analysis system"; and claim 10 recites "a system for characterizing a functional impact of a plurality of variants identified from a genomic sample" which Kagohara teaches as the functional impact of methylation alterations (i.e. variants) being assessed bioinformatically (i.e. variants analysis system) in targeted experiments on model organisms and across sample population (pg. 58 col. 2 para. 2); wherein high-throughput measurement technologies enable unprecedented, quantitative measurements of the epigenetic state in cancers (i.e. from genomic samples) (pg. 58 col. 2 para. 2).
Claim 1 recites "obtaining genomic sample information, the genomic sample information comprising at least a plurality of variants identified in the genomic sample, gene expression information obtained from the genomic sample, copy number variation for one or more genes in the genomic sample, and epigenetic effects on one or more genes in the genomic sample"; and claim 10 recites "genomic sample information, the genomic sample information comprising at least a plurality of variants identified in the genomic sample, gene expression information obtained from the genomic sample, copy number variation for one or more genes in the genomic sample, and epigenetic effects on one or more genes in the genomic sample" which Kagohara teaches as DNA methylation of 1001 cancers being measured along with therapeutic sensitivity, copy number, somatic mutations and gene expression (pg. 55 col. 1 para. 3); wherein bioinformatics methods can aggregate over epigenetic modifications with similar effects on gene expression (i.e. epigenetic effects on one or more genes in the genomic sample) (pg. 57 col. 2 para. 3).
Claim 3 recites " the step of ranking at least some of the plurality of variants or genes" which Kagohara teaches as the frequency of mutations in histone modifying genes varying by tumor type, occurring with highest frequency in brain tumors and leukemias (30% of the cases (pg. 51 col. 2 para. 2).
Claim 10 recites " a user interface configured to report" which Kagohara teaches as genome browsers used as tools to visualize and integrate epigenetics data from publicly available repositories; with an unique interface, set of features and capacity for data integration from external data sources (pg. 55 col. 2 para. 4).
Ascertainment of the Difference Between Scope the Prior Art and the Claims
(MPEP §2141.02)
Regarding claims 1 and 10, Kagohara does not teach " determining/determine a splice status for the variant, the splice status comprising an indication of whether a variant has an effect on splicing of a gene." However, Li teaches as a detailed accounting of the effects of genetic variants on gene regulation (pg. 600 col. 2 para. 2); teaching a new method to detect splicing variation (pg. 603 col. 2 para. 2); wherein splicing was most strongly affected by variants near splice sites (i.e. determination of whether a variant has an effect on splicing of a gene) (pg. 603 col. 3 para. 2).
Regarding claims 1 and 10, Kagohara does not teach " determining/determine a variant-based expression regulation status, the variant- based expression regulation status comprising an indication of whether the variant has an effect on expression of a gene." However, Li teaches as genetic variants located in active promoters, strong enhancers, and weak promoters were most likely to affect gene expression (i.e. determination of whether the variant has an effect on expression of a gene) (pg. 603 col. 3 para. 2).
Regarding claims 1 and 10, Kagohara does not teach " determining/determine a gene-based expression regulation status, the gene- based expression regulation status comprising an indication of whether the variant has a functional impact on a target gene in a pathway." However, Li teaches as the identification of three main pathways that mediate the impact of genetic variation on gene regulation with phenotypic and pathogenic consequences (i.e. variant having a functional impact on a target gene in a pathway) (pg. 604 col. 1 para. 5 and Fig. 4D in pg. 603).
Regarding claims 1 and 10, Kagohara does not teach "determining/determine a gene-based copy number variant (CNV) and epigenetic impact status, the gene-based CNV and epigenetic impact status comprising an indication of whether the CNV and/or epigenetic impact has an impact on expression of a gene." However, Geistlinger teaches as an integrative study on copy number variation (CNV) and genome wide gene expression where CNV is frequently observed deviation from the diploid state due to duplication or deletion of genomic regions and where expression changes coincided with CNVs in the respective genes (pg. 1 para. 1).
Regarding claims 1 and 10, Kagohara does not teach "determining/determine a gene-based copy number variant (CNV) and epigenetic impact status, the gene-based CNV and epigenetic impact status comprising an indication of whether the CNV and/or epigenetic impact has an impact on expression of a gene." However, Geistlinger teaches as an integrative study on copy number variation (CNV) and genome wide gene expression where CNV is frequently observed deviation from the diploid state due to duplication or deletion of genomic regions and where expression changes coincided with CNVs in the respective genes (pg. 1 para. 1)
Regarding claims 1 and 10, Kagohara does not teach "adjusting/adjust, based on the gene-based CNV and epigenetic impact status, the variant-based expression regulation status and/or the gene-based expression regulation status." However, Geistlinger teaches as a variety of long-range CNV effects that modulated gene expression in an orchestrated and intertwined fashion; with CNVs being able to fine-tune core regulators (i.e. CNV based adjustment of gene expression) located in their vicinity, propagating these effects to genome-wide gene expression (i.e. epigenetic impact) (pg. 8 para. 6).
Regarding claims 1 and 10, Kagohara does not teach "reporting/report at least the adjusted variant-based expression regulation status and/or the adjusted gene-based expression regulation status for each of a plurality of variants and/or genes in the genomic sample." However, Geistlinger teaches as samples carrying either 0n for R727 gene or 3n for R2440 gene individually displayed increased expression of associated genes (adjusted expression based on CNV), showing a strong synergistic effect for samples carrying both expression-increasing alleles (pg. 5 para. 4); which was reported as boxplots (pg. 7 Fig. 5a/b).
Regarding claims 2 and 11, Kagohara does not teach "the step of filtering at least some of the plurality of variants or genes based at least on the adjusted variant-based expression regulation status and/or the adjusted gene-based expression regulation status associated with each respective variant and/or gene." However, Geistlinger teaches as the analysis of expression effects including filtering genes for sufficient expression and samples with overlapping CNV calls (pg. 2 para. 4).
Regarding claim 4, Kagohara does not teach " wherein the splice status further comprises an indication of a strength of splicing evidence for the effect on splicing of the gene." However, Li teaches as splicing being most strongly affected by variants near splice sites and by synonymous and missense variants (i.e. indication of a strength of splicing evidence for the effect on splicing of the gene) (pg. 603 col. 3 para. 2).
Regarding claims 5 and 14, Kagohara does not teach "wherein the variant-based expression regulation status further comprises an indication of whether the affected gene is local or remote." However, Geistlinger teaches as CNV-expression analysis showing local effects, where expression changes coincide with CNVs in the respective genes and distal effects, where CNVs supposedly affect trans-acting regulators (pg. 3 para. 4).
Regarding claims 6 and 15, Kagohara does not teach "wherein the gene-based expression regulation status further comprises an indication of whether the target gene is upregulated or downregulated." However, Geistlinger teaches as the distal expression effects of copy number variation with indication of how many genes showed either an increase (orange) or decrease (green) in expression with gain in copy number in the corresponding region (pg. 4 Fig. 3).
Regarding claim 7, Kagohara does not teach "wherein the gene-based copy number variant (CNV) and epigenetic impact status further comprises an indication of whether the copy number variant (CNV) and/or epigenetic impact results in upregulation or downregulation of a gene." Geistlinger teaches as the distal expression effects of copy number variation with indication of genes showing a high degree of variation in copy number for substantial subsets of the population with a significant decrease in expression upon loss of copies (pg. 2 para. 6).
Regarding claims 8 and 12, Kagohara does not teach "wherein reporting comprises a table or other data structure comprising a list of variants and/or genes and the functional impact information associated with each variant and/or gene."
Regarding claims 9 and 13, Kagohara does not teach wherein the functional impact information comprises, for one or more of the plurality of remaining variants, an indication of an effect of the variant on the expression of one or more genes." However, Geistlinger teaches as table for the functional characterization of distal CNV regions with phenotype for significant expression changes associated with the corresponding CNV region (pg. 5 Table 1).
Finding of Prima Facie Obviousness Rationale and Motivation
(MPEP §2142-2143)
Regarding claims 1-15, one of ordinary skill in the art would be motivated to apply the teachings by Li and Geistlinger to the method by Kagohara because Li teaches a comprehensive view of the mechanisms linking genetic variation to variation in human gene regulation (pg. 1 para. 1 Li) and Geistlinger teaches the detection of multi-level associations at the interface of copy number variation, gene expression and phenotype (i.e. functional impact) (pg. 6 Fig. 4 Geistlinger). One of ordinary skill in the art would be able to motivated to combine the teachings in these references with a reasonable expectation of success since the described teachings pertain to methods for associating genetic variation to gene regulation and functional impact.
Conclusion
No claims are allowed.
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/F.F.L./Examiner, Art Unit 1685
/G. STEVEN VANNI/Primary patents examiner, Art Unit 1686