DETAILED ACTION
Notice of 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 .
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 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.
Withdrawal of Objections and Rejections
Applicant's response, filed 08/10/2026, has been fully considered.
The following rejections and/or objections are either maintained or newly applied for claims 1-20. They constitute the complete set applied to the instant application. Herein, "the previous Office action" refers to the Final Rejection of 06/02/2026.
Status of the Claims
Claims 1-20 are pending.
Claims 1, 7 and 18 are objected to.
Claims 1-20 are rejected.
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 1-20 is 11/26/2019.
Claim objections
Claims 1, 7 and 18 are objected to because of the following informalities. Appropriate correction is required.
Claim 1 recites “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” (7th claim element) which appears to be duplicated in the 8th claim element and should be removed. The duplicated recitation is not properly annotated, therefore, it is being interpreted as an error and not as a new recitation.
In claims 7 and 18, the recited “copy number variant (CNV)” in lines 1 and 3 should read “CNV” because the abbreviation has already been introduced previously in the parent claim.
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 USC § 101 because the claimed inventions are directed to one or more Judicial Exceptions (JEs) without significantly more. Regarding JEs, "Claims directed to nothing more than abstract ideas..., 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)). Any newly recited portions are necessitated by claim amendment.
101 background
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below. MPEP 2106 and the following USPTO website provide further explanation and case law citations: uspto.gov/patent/laws-and-regulations/examination-policy/examination-guidance-and-training-materials.
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 19-20) and a system (claims 10-18); each of which falls within one of the categories of statutory subject matter.
[Step 1: claims 1-20: 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
With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims found to recite abstract ideas that can fall into the grouping of mathematical concepts (in particular mathematical relationships and formulas) and mental processes (in particular procedures for observing, analyzing and organizing information) as well as a law of nature or a natural phenomenon. The identified grouping(s) for this instant claims are as follows:
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:
• "identifying, from the obtained the genomic sample information, variants of the plurality of genes in the genomic sample, gene expression information obtained from the genomic sample, copy number variation for one or more of the plurality of genes in the genomic sample, and epigenetic effects on the plurality of genes in the genomic sample" (independent claims 1, 10 and 19);
• "determining a splice status for the one or more of the plurality of variant, the splice status comprising an indication of whether a variant has an effect on splicing of a gene" (independent claims 1, 10 and 19);
• "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" (independent claims 1, 10 and 19);
• "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" (independent claims 1, 10 and 19);
• "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 one or more of the plurality of genes in the genomic sample" (independent claims 1, 10 and 19);
• "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; comprising computing an adjusted variant-based expression regulation status and/or an adjusted gene-based expression regulation status" (independent claims 1, 10 and 19);
• "associating, in a database, the adjusted variant-based expression regulation status and/or the adjusted gene-based expression regulation status with one or more of a response to therapy, a diagnosis, or a prognosis of a patient to generate one or more associations" (independent claim 19);
• "executing a matching algorithm that identifies one or more matches between a patient genomic profile of a patient and the stored one or more associations, wherein identifying the one or more match comprises generating a response of the patient to therapy, a diagnosis, or a prognosis" (independent claim 19);
• "filtering/filter 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" (claims 2 and 11); and
• "ranking/rank at least some of the plurality of variants or genes" (claims 3 and 16).
Under the BRI, the recited limitations are mental processes because a human mind is sufficiently capable of identify information from data available; evaluate/filter/rank a dataset and determine an indication of an effect on a certain function based on data; subsequently adjust the status found depending on the dataset; associate a status with a therapy; execute a match between a patient genomic profile and the associations made; and report the evaluations via a database or a table using pen and paper.
Dependent claims 4-9, 12-15, 17-18 and 20 recite further steps that limit the judicial exceptions in independent claims 1, 10 and 19 and, as such, also are directed to those abstract ideas. For example, dependent claims 4-7, 9, and 13-15, 17-18 recite further details about the "indication of an impact" performed by the variants; dependent claims 8 and 20 recite further details about the reporting step; and dependent claim 12 recites further details about the adjusting step.
Furthermore, 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 One: claims 1-20: 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))?
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, 10 and 19 recite additional elements that are not abstract ideas:
• "obtaining genomic sample information comprising genomic sequencing for a complete human genome or complete human exome and comprising information for a plurality of genes" (independent claims 1 and 19)
• "genomic sample information comprising genomic sequencing for a complete human genome or complete human exome and comprising information for a plurality of genes, the genomic sample information comprising the plurality of variants identified in the genomic sample, gene expression information obtained from the genomic sample, copy number variation for the plurality of genes in the genomic sample, and epigenetic effects on one or more of the plurality of genes in the genomic sample" (independent claim 10);
• "a user interface" (independent claim 10);
• "reporting at least the adjusted variant-based expression regulation status and/or the adjusted gene-based expression regulation status for each of the plurality of variants and/or the plurality of genes in the genomic sample" (independent claims 1 and 10); and
• "reporting, via a clinical report generated relevant to the patient, the identified one or more identified matches, including the generated response of the patient to therapy, a diagnosis, or a prognosis" (independent claim 19).
Considerations under Step 2A, Prong Two
The recited limitations in claims 1, 10 and 19 are interpreted as requiring the use of a computer. Hence, the claims explicitly recite steps executed by computers and therefore can be described as computer functions or instructions to implement on a generic computer.
Further steps directed to additional non-abstract elements of a computing device/computer do not describe any specific computational steps by which the "computer parts" perform or carry out the judicial exceptions, 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 a generic computer which performs the functions that constitute the judicial exceptions.
Limitations of claims 1-20 are considered to perform the claimed abstract idea with a computer, which is not sufficient to integrate an abstract idea into a practical application (see MPEP 2106.05(f)); since steps that can be performed mentally and merely performing the mental process in a computer environment do not negate the fact that something that can be carried out in the human mind. See MPEP 2106.04(a)(2).III.C.
The recited "obtaining genomic sample information" and the related claims 2-3 read on receiving and 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). Said "genomic sample information for a plurality of genes" is interpreted as data gathered that has been stored.
Claims directed to "reporting" information are interpreted as data outputting and as such insignificant extra-solution activity.
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)).
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.
[Step 2A Prong Two: claims 1-20: No]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
According to analysis so far, the additional elements described above do not provide significantly more than the judicial exception. A determination of whether additional elements provide significantly more also rests on whether the additional elements or a combination of elements represents other than what is well-understood, routine, and conventional. Conventionality is a question of fact and may be evidenced as: a citation to an express statement in the specification or to a statement made by an applicant during examination that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
Claims 1, 10 and 19 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)).
Further, the courts have found that receiving and outputting data are well-understood, routine, and conventional functions of a computer when claimed in a 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), Versa ta 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, as discussed in MPEP 2106.05(d)(Il)(i)).
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).
The instant claims 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)).
[Step 2B: claims 1-20: No]
Conclusion: Instant claims are directed to non-statutory subject matter
For the reasons above, 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 not clearly anything significantly more.
Response to applicant's remarks in regard to Claim Rejection 35 U.S.C. ~ 101
The Remarks of 08/10/2026 have been fully considered but are not persuasive for the reasons below:
Applicant asserts starting in pg. 10 para. 5
The Patent Office is aware that this is not a sufficient analysis under the Step 2A, Prong One evaluation. Not only do the claims not "recite abstract ideas that fall into the grouping of mathematical concepts (in particular mathematical relationships and formulas)," there is no specific identification of any such recitation in the claims. Accordingly, the Patent Office has failed under the Alice analysis and the MPEP to properly assert - much less evidence - that the claims "recite abstract ideas that fall into the grouping of mathematical concepts (in particular mathematical relationships and formulas).”
It is respectfully submitted that this is not persuasive because the argued paragraph is being misinterpreted. The argument by the Applicant is an introductory paragraph that merely states the general groupings evaluated under Step 2A Prong One and it was misinterpreted. Both previous office action and this instant office actions have not identified any recitations (neither have listed any in the previous office or in this instant office action) that fall under mathematical concepts. For further clarification, the argued paragraph now reads
“With respect to the instant claims, under the Step 2A, Prong One evaluation, the claims found to recite abstract ideas that can fall into the grouping of mathematical concepts (in particular mathematical relationships and formulas) and mental processes (in particular procedures for observing, analyzing and organizing information) as well as a law of nature or a natural phenomenon. The identified grouping(s) for this instant claims are as follows:”
Applicant asserts starting in pg. 11 para. 2
Regarding the Natural Correlation category, the only assertion or analysis set forth by the Patent Office in the entirety of the Office Action is that "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)." However, the claims are not directed to the asserted natural correlation (i.e., the measurement of an amount of a gene/variant naturally found in the body with the functional impact/effect of said gene/variant). Merely reciting a natural correlation in a claim is not sufficient to assert or evidence that the claim as a whole is directed to the natural correlation, or that the claim fails to recite more than just the natural correlation. From MPEP 2106.04(b)(I): … Notably, the claims are very quickly distinguishable from the above. The claims do not simply recite gene expression with gene function; they recite a method or system for characterizing a functional impact of a plurality of variants identified from a genomic sample via a multi-step process. Although not analyzed herein example by example, the claims similarly are distinguishable from every example of a claim rejected by the courts as being directed to a natural law or correlation. As set forth by the MPEP.
It is respectfully submitted that this is not persuasive because MPEP 2106.04(b) states that the law of nature and natural phenomenon exceptions reflect the Supreme Court's view that the basic tools of scientific and technological work are not patentable, because the "manifestations of laws of nature" are "part of the storehouse of knowledge," "free to all men and reserved exclusively to none." Here, the instant claims indeed 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; similar to - iv: a correlation that is the consequence of how a certain compound is metabolized by the body, Mayo Collaborative Servs. v. Prometheus Labs., 566 U.S. 66, 75-77, 101 USPQ2d 1961, 1967-68 (2012); and xi. the natural relationship between a patient’s CYP2D6 metabolizer genotype and the risk that the patient will suffer QTc prolongation after administration of a medication called iloperidone, Vanda Pharmaceuticals Inc. v. West-Ward Pharmaceuticals, 887 F.3d 1117, 1135-36, 126 USPQ2d 1266, 1281 (Fed. Cir. 2018) See MPEP 2106.04(b). Hence, the claims are not distinguishable from examples of claims rejected by the courts as being directed to a natural law or correlation.
Applicant asserts starting in pg. 12 para. 4
Claims as a Whole …the claims are directed to a specific workflow and improvement in characterizing a functional impact of a plurality of variants identified from a genomic sample … Mental Process … The rejection's Step 2A, Prong One characterization as "mental processes" is inapposite. The claims require obtaining and processing genomic sample information … Further, the claims as amended herein are not reasonably characterized as reciting a mental process under Step 2A, Prong One. The rejection states that the claimed determinations and adjustment can be performed in the human mind or using pen and paper. That characterization is not commensurate with the claim language. The claims are directed to a method performed "using a variant analysis system" on genomic sample information that includes genomic sequencing data comprising a complete human genome, together with gene expression information, copy number variation information, and epigenetic effects. … Accordingly, the amended claim is not directed to an observation, evaluation, judgment, or opinion that is practically performable in the human mind. Accordingly, Applicant respectfully asserts that that the claims are directed
It is respectfully submitted that this is not persuasive because under the BRI, the claims still include limitations which encompass purely mental actions as set forth in the above rejections. In MPEP 2106.04(a)(2), section III(A), examples that cannot practically be performed in the mind are provided, and include a method for calculating an absolute position of a GPS receiver and an absolute time of reception of satellite signals, detecting suspicious activity by using network monitors and analyzing network packets, specific data encryption method for computer communication involving a several-step manipulation of data, a method for rendering a halftone image of a digital image where the method required the manipulation of computer data structures and the output of a modified computer data structure. In contrast, the MPEP notes that the limitations that can practically be performed in the human mind, including for example, observations, evaluations, judgments, and opinions. The MPEP therefore makes clear that limitations which cannot practically be performed in the mind are those in which the human mind is not equipped to perform the claim limitations. The term practical is not meant to indicate that as a matter of practicality, one would perform a method preferentially on a computer rather than mentally. The MPEP makes clear that “practical” indicates that a human mind is not capable of performing the recited action. In this case, the argued determinations and adjustments can be performed in a human mind, despite the recited computer aid. The use of a physical aid, such as a computer, does not negate the mental nature of said limitations at Step 2A, Prong 1 (see MPEP 2106.05(f)).
The fact that the Office action stated that “determinations and adjustment can be performed in the human mind or using pen and paper” originates from the claim evaluation at Step 2A P1 in order to identify mental processes and does commensurate with the recited claim language because the claims recite all the identified mental processes.
The Applicant is reminded that at Step 2A, Prong 1, the claims are examined limitation by limitation to identify whether the claimed concept aligns with at least one judicial exception (see MPEP 2106.04(I)). The fact that some claims recite limitations not considered to align with a judicial exception does not negate that the claims also recites other limitations which do align. Not all limitations have been identified as mental processes but the ones that have been identified are indeed mental processes, under BRI. With that in mind, the argued “genomic sample information that includes genomic sequencing data comprising a complete human genome, together with gene expression information, copy number variation information, and epigenetic effects” have not been identified as a mental process.
Applicant asserts starting in pg. 14 para. 3
Here, the claims integrate any alleged exception into a practical application in a technical field (i.e., computational genomics) by correcting expression-regulation inferences to account for CNV and epigenetic confounders. The specification explains the technical need to consider the combined impact of CNV and epigenetic factors in clinical applications (i][008 l]) and that the framework enables identifying causal variants/genes by systematically combining multi-layer evidence (i][00116]-[00118]). This is a technology-rooted improvement in how multi-omic functional impact is computed and reported, akin to rule-based, computer-implemented improvements found eligible in Enfish and McRO. The amended claim also integrates any alleged exception into a practical application under Step 2A, Prong Two. The claim does not merely gather data and display a result. Rather, the claim requires a variant analysis system to operate on complete-human-genome sequencing data and associated multi-omic information to characterize functional impacts of genomic variants, including by determining splice, variant-based expression regulation, gene-based expression regulation, and CNV/epigenetic impact statuses, and then adjusting the expression-regulation status based on the CNV/epigenetic impact status. This ordered workflow applies the alleged analytical concepts in a concrete computational genomics context to produce adjusted functional impact characterizations for variants and/or genes in the genomic sample. The complete-human genome limitation ties the claimed workflow to the type and scale of genomic sequencing data for which the described computer implemented analysis is needed, rather than to a result that can be obtained mentally
It is respectfully submitted that this is not persuasive because the argued “correcting expression-regulation inferences to account for CNV and epigenetic confounders” is not commensurate with the claim language since there is no correcting step recited. However, the recited “adjusting” step has been identified as a mental process because the human mind is capable of judgments, observations and evaluations that would lead to adjustments with pen and paper. The argued “variant analysis system to operate on complete-human-genome sequencing data” describes language in the claims that has been identified as an additional element (i.e. the obtaining step) and not as a mental process. Despite the identification of additional elements in the claims, there is no additional element that integrates the judicial exceptions into a practical application. See claim rejections above.
Regarding the argued improvement, said improvement is being provided by the judicial exceptions. The analysis at Step 2A, Prong 2, considers the claims as a whole, i.e., the additional elements in combination with the judicial exceptions (see MPEP 2106.05(a)), although the integration or improvement provided in the claim must flow from the additional elements and not the judicial exceptions to be considered persuasive.
The argued “ordered workflow” applying concepts “in a concrete computational genomics context to produce adjusted functional impact characterizations” can be described as computer functions or instructions to implement on a generic computer. MPEP at 2106.05(f) states that claims which merely include instructions to implement an abstract idea on a computer, or merely use a computer as a tool to perform an abstract idea (i.e. computer implemented analysis), effectively add words that "apply" the judicial exception in a computer. The judicial exceptions in the claims are considered to perform the claimed abstract idea with a computer, which is not sufficient to integrate an abstract idea into a practical application (see MPEP 2106.05(f)); since steps that can be performed mentally and merely performing the mental process in a computer environment do not negate the fact that something that can be carried out in the human mind. See MPEP 2106.04(a)(2).III.C.
Applicant asserts starting in pg. 15 para. 2
For similar reasons, the amended claim recites significantly more under Step 2B. Even if some individual determinations could be characterized at a high level as evaluative, the claim as a whole requires the variant analysis system to process complete-human-genome sequencing data together with multiple heterogeneous genomic data modalities and to generate adjusted functional impact statuses from that data. This is not merely the generic use of a computer to receive and output information. The amendment makes explicit that the claimed method is performed on complete-human-genome sequencing data, and the Specification explains that the disclosed analysis involves millions of calculations that the human mind is not equipped to perform. See Spec. [00122]. Thus, the ordered combination imposes meaningful practical limits on the claim and provides more than an instruction to apply an abstract idea using a generic computer. Accordingly, Applicant respectfully asserts that that the claims are directed to patent eligible subject matter under the Alice framework. Applicant respectfully requests that the rejection of the pending claims under 35 U.S C. 101 be withdrawn
It is respectfully submitted that this is not persuasive because MPEP 2106.05(d) sets forth that, at Step 2B, it is the additional elements which are examined to determine whether they are well-understood, routine, conventional activities previously known to the industry. The analysis at Step 2A, Prong 2, considers the claims as a whole, i.e., the additional elements in combination with the judicial exceptions (see MPEP 2106.05(a)), although the integration or improvement provided in the claim must flow from the additional elements and not the judicial exceptions to be considered persuasive. However, Step 2B instructs that an inventive concept cannot be provided the by judicial exception. An “inventive concept” is furnished by an element or combination of elements that is recited in the claim in addition to (beyond) the judicial exception, and is sufficient to ensure that the claim as a whole amounts to significantly more than the judicial exception itself (Alice Corp., 573 U.S. at 27-18, 110 USPQ2d at 1981 (citing Mayo, 566 U.S. at 72-73, 101 USPQ2d at 1966)). The limitations pointed to be Applicant are considered to recite a judicial exception (i.e. mental processes) as described above and are therefore not considered at Step 2B. The use of a computer is considered for the evaluation at step 2B, however, such recitations are 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)).
Claim Rejections - 35 USC § 103
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.
Claims 1-20 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 12/18/2025 Form PTO-892. Any newly recited portions are necessitated by claim amendment.
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, comprising"; claim 10 recites "a system for characterizing a functional impact of a plurality of variants identified from a genomic sample"; and claim 19 recites "a method for generating a report characterizing, within a patient context, a functional impact of a plurality of variants identified from a genomic sample, comprising."
The prior art to Kagohara discloses methods and systems 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).
The steps performed by the methods of claims 1 and 19 comprise:
obtaining genomic sample information comprising genomic sequencing for a complete human genome or complete human exome and comprising information for a plurality of genes
• Kagohara teaches as DNA methylation of 1001 cancers being measured (i.e. obtained genomic sample) (pg. 55 col. 1 para. 3); wherein genome-wide characterization (i.e. complete human genome) of epigenetic aberrations is crucial for the development of new therapies for clinical use and to identify new biomarkers for existing epigenetic inhibitors (pg. 50 col. 2 para. 1).
identifying, from the obtained the genomic sample information, variants of the plurality of genes in the genomic sample, gene expression information obtained from the genomic sample, copy number variation for one or more of the plurality of genes in the genomic sample, and epigenetic effects on the plurality of genes in the genomic sample
• Kagohara teaches as DNA methylation of 1001 cancers (i.e. obtained genomic sample) being measured along with therapeutic sensitivity, copy number, somatic mutations (i.e. copy number variation for one or more of the plurality of genes in the genomic sample) and gene expression (i.e. gene expression information obtained from the genomic sample) (pg. 55 col. 1 para. 3); wherein changes in chromatin landscape co-occur with alterations of DNA methylation (i.e. identifying variants of the plurality of genes in the genomic sample) (pg. 51 col. 2 para. 1) wherein bioinformatics methods can aggregate over epigenetic modifications with similar effects on gene expression (i.e. epigenetic effects on the plurality of genes in the genomic sample) (pg. 57 col. 2 para. 3).
determining a splice status for the one or more of the plurality of variant, the splice status comprising an indication of whether a variant has an effect on splicing of a gene
• Kagohara does not teach the recitation above. 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).
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
• Kagohara does not teach the recitation above. 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).
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
• Kagohara does not teach the recitation above. 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).
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 one or more of the plurality of genes in the genomic sample
• Kagohara does not teach the recitation above. 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).
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, comprising computing an adjusted variant-based expression regulation status and/or an adjusted gene-based expression regulation status
• Kagohara does not teach the recitation above. 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. here, the “regulating” – a synonym for “adjusting” - performed by said CNVs reads on 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); wherein CNVs can be experimentally detected based on comparative genomic hybridization and can also be computationally inferred from SNP-arrays or detected from next-generation sequencing data (i.e. computing an adjusted variant-based expression regulation status and/or an adjusted gene-based expression regulation status) (pg. 1 para. 3).
Claim 1 only further recites:
reporting at least the adjusted variant-based expression regulation status and/or the adjusted gene-based expression regulation status for each of the plurality of variants and/or the plurality of genes in the genomic sample
• Kagohara does not teach the recitation above. 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).
Claim 19 only further recites:
associating, in a database, the adjusted variant-based expression regulation status and/or the adjusted gene-based expression regulation status with one or more of a response to therapy, a diagnosis, or a prognosis of a patient to generate one or more associations;
executing a matching algorithm that identifies one or more matches between a patient genomic profile of a patient and the stored one or more associations, wherein identifying the one or more match comprises generating a response of the patient to therapy, a diagnosis, or a prognosis; and
reporting, via a clinical report generated relevant to the patient, the identified one or more identified matches, including the generated response of the patient to therapy, a diagnosis, or a prognosis
• Kagohara teaches current resources to discover reversible epigenetic events in cancer (i.e. adjusting variant-based expression regulation status) that may be targeted therapeutically in cancer (pg. 50 col. 2 para. 2) and techniques to determine the functional impacts of chromatin regulation (i.e. adjusting gene-based expression regulation status) from time course data of cancer development, metastasis and therapeutic resistance (i.e. response to therapy, a diagnosis, or a prognosis of a patient to generate one or more associations) (pg. 57 col. 2 para. 3); wherein complete data integration to determine epigenetic regulation of gene expression can be performed for data sets containing both gene expression data and
epigenetic data to determine their functional impact in cancer (i.e. associating in a database and executing a matching algorithm that identifies one or more matches between a patient genomic profile of a patient and the stored one or more associations, wherein identifying the one or more match comprises generating a response of the patient to therapy, a diagnosis, or a prognosis) (pg. 58 Fig. 4).
• Furthermore, Kagohara teaches a Web-based tool that stores all DNA methylation data from The Cancer Genome Atlas for gene-level analysis using a database to query by gene and tumor type (i.e. report relevant to the matches) and then correlates clinical covariates and expression with measurements of DNA methylation for that gene from The Cancer Genome Atlas, which involves an analysis across all probes in the array for the query gene to distinguish the impact of epigenetic alterations (i.e. reporting, via a clinical report generated relevant to the patient, the identified one or more identified matches, including the generated response of the patient to therapy, a diagnosis, or a prognosis) (pg. 56 col.1 para. 3).
Claim 10 recites:
genomic sample information comprising genomic sequencing for a complete human genome or complete human exome and comprising information for a plurality of genes, the genomic sample information comprising the plurality of variants identified in the genomic sample, gene expression information obtained from the genomic sample, copy number variation for the plurality of genes in the genomic sample, and epigenetic effects on one or more of the plurality of genes in the genomic sample
• Kagohara teaches as DNA methylation of 1001 cancers being measured (i.e. obtained genomic sample) being measured along with therapeutic sensitivity, copy number, somatic mutations (i.e. copy number variation for one or more of the plurality of genes in the genomic sample) and gene expression (i.e. gene expression information obtained from the genomic sample) (pg. 55 col. 1 para. 3); wherein changes in chromatin landscape co-occur with alterations of DNA methylation (i.e. identifying variants of the plurality of genes in the genomic sample) (pg. 51 col. 2 para. 1) wherein bioinformatics methods can aggregate over epigenetic modifications with similar effects on gene expression (i.e. epigenetic effects on the plurality of genes in the genomic sample) (pg. 57 col. 2 para. 3); wherein genome-wide characterization (i.e. complete human genome) of epigenetic aberrations is crucial for the development of new therapies for clinical use and to identify new biomarkers for existing epigenetic inhibitors (pg. 50 col. 2 para. 1).
a processor configured to execute instructions stored on anon-transitory storage medium, the instructions directed the processor
• Kagohara teaches the functional impact of methylation alterations (i.e. variants) being assessed bioinformatically (i.e. variants analysis system - a processor configured to execute instructions stored on anon-transitory storage medium, the instructions directed the processor) in targeted experiments on model organisms and across sample population (pg. 58 col. 2 para. 2).
(i) determine a splice status for one or more of the plurality of variants, the splice status comprising an indication of whether a variant has an effect on splicing of a gene
• Kagohara does not teach the recitation above. 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).
(ii) 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
• Kagohara does not teach the recitation above. 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).
(iii) 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
• Kagohara does not teach the recitation above. 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).
(iv) 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 a CNV and/or an epigenetic factor impact has an impact on expression of one or more of the plurality of genes in the genomic sample
• Kagohara does not teach the recitation above. 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).
(v) 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; comprising computing an adjusted variant-based expression regulation status and/or an adjusted gene-based expression regulation status
• Kagohara does not teach the recitation above. 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. here, the “regulating” – a synonym for “adjusting” - performed by said CNVs reads on 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); wherein CNVs can be experimentally detected based on comparative genomic hybridization and can also be computationally inferred from SNP-arrays or detected from next-generation sequencing data (i.e. computing an adjusted variant-based expression regulation status and/or an adjusted gene-based expression regulation status) (pg. 1 para. 3).
a user interface configured to report at least the adjusted variant-based expression regulation status and/or the adjusted gene-based expression regulation status for each of the plurality of variants and/or the plurality of genes in the genomic sample
• 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).
Claims 2 and 11 recite:
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
• Kagohara does not teach the recitation above. 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).
Claims 3 and 16 recite:
ranking at least some of the plurality of variants or genes
• 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).
Claims 4 and 17 recites:
wherein the splice status further comprises an indication of a strength of splicing evidence for the effect on splicing of the gene
• Kagohara does not teach the recitation above. 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).
Claims 5 and 14 recite:
wherein the variant-based expression regulation status further comprises an indication of whether an affected gene is local or remote
• Kagohara does not teach the recitation above. 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).
Claims 6 and 15 recite:
wherein the gene-based expression regulation status further comprises an indication of whether the target gene is upregulated or downregulated
• Kagohara does not teach the recitation above. 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).
Claims 7 and 18 recite:
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 the epigenetic factor results in upregulation or downregulation of the one or more of the plurality of genes in the genomic sample
• Kagohara does not teach the recitation above. However, 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).
Claims 8 and 20 recite:
wherein reporting comprises a table or other data structure comprising a list of variants and/or genes and functional impact information associated with each variant and/or gene
• Kagohara does not teach the recitation above. 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).
Claims 9 and 13 recite:
wherein the functional impact information comprises, for one or more of a plurality of remaining variants, an indication of an effect of the variant on expression of one or more of the one or more genes in the genomic sample
• Kagohara does not teach the recitation above. 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).
Claim 12 recites:
wherein the adjusted variant-based expression regulation status and/or the gene-based expression regulation status comprises a table or other data structure comprising a list of variants and/or genes and functional impact information associated with each variant and/or gene
• Kagohara does not teach the recitation above. 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); where said CNV effects are listed in a table describing the functional characterization of distal CNV regions with phenotype for significant expression changes associated with the corresponding CNV region (pg. 5 Table 1).
Rationale for combining (MPEP §2142-2143)
Regarding claims 1-20, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine, in the course of routine experimentation and with a reasonable expectation of success, the methods of Kagohara in view of Li and Geistlinger because all references disclose methods for associating genetic variation to gene regulation and functional impact. The motivation would have been to:
• incorporate a comprehensive view of the mechanisms linking genetic variation to variation in human gene regulation (pg. 1 para. 1 Li) and
• incorporate 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).
Therefore it would have been obvious to one of ordinary skill in the art to substitute the associating genetic variation to gene regulation and functional impact method of Kagohara to the methods by Li and Geistlinger because such a substitution is no more than the simple substitution of one known element for another. 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.
Response to applicant's remarks in regard to Claim Rejection 35 U.S.C. ~ 103
The Remarks of 08/10/2026 have been fully considered but are not persuasive for the reasons below:
Applicant asserts starting in pg. 18 para. 2
…However, CNVs are shown to be modulators of gene expression (such as "in an orchestrated and intertwined fashion"), does not disclose the adjustment of the claimed determined "variant-based expression regulation status and/or gene-based expression regulation status." Indeed, the claimed determined variant-based expression regulation status comprises "an indication of whether the variant has an effect on expression of a gene," and the claimed determined gene-based expression regulation status comprises "an indication of whether the variant has a functional impact on a target gene in a pathway." The gene-based copy number variant (CNV) and epigenetic impact status, which comprises "an indication of whether a CNV and/or an epigenetic factor has an impact on expression of one or more of the plurality of genes in the genomic sample," is utilized to adjust one or both of those regulation statuses (i.e., the variant based expression regulation status and/or the gene-based expression regulation status). At best, Geistlinger teaches that CNV s modulate gene expression. However, the claims do not recite simply "adjusting gene expression based on CNV status." Rather, the claims recite a complex, multi-step process in which a specific determined "variant-based expression regulation status and/or gene-based expression regulation status" -… Further, as amended, the claims further clarify that the claimed method … "computing an adjusted variant-based expression regulation status and/or an adjusted gene-based expression regulation status." Thus, the claims do not merely require recognizing that CNV s may biologically modulate gene expression
It is respectfully submitted that this is not persuasive because the argued recitation “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; comprising computing an adjusted variant-based expression regulation status and/or an adjusted gene-based expression regulation status” has been taught by the prior art. See claim rejections above.
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. here, the “regulating” – a synonym for “adjusting” - performed by said CNVs reads on 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); wherein CNVs can be experimentally detected based on comparative genomic hybridization and can also be computationally inferred from SNP-arrays or detected from next-generation sequencing data (i.e. computing an adjusted variant-based expression regulation status and/or an adjusted gene-based expression regulation status) (pg. 1 para. 3).
Furthermore, the modulation of gene expression inherently yields a functional impact adjustment because alterations in genetic expression are directly correlated to functional alterations as evidenced by Kagohara (pg. 50 col. 1 para. 3-4). Therefore a gene regulator as taught by Geistlinger would inherently cause an adjustment in functional impact.
Therefore the prima facie case of obviousness has been established. MPEP 2141.III for "RATIONALES TO SUPPORT REJECTIONS UNDER 35 U.S.C. 103"; wherein "(G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention." Furthermore, in this instant application, the amendments support existing claim rejections, in which the recited limitations are all addressed, see Claim Rejections above.
…The Examiner relies on Geistlinger for the "adjusting" limitation, citing Geistlinger' s disclosure of long-range CNV effects that modulated gene expression, fine-tuned core regulators, and propagated effects to genome-wide gene expression. Applicant respectfully submits that this disclosure does not teach or suggest the amended claim limitation. At most, Geistlinger describes a biological relationship in which CNVs are associated with modulation of gene expression. That is not the same as computing an adjusted variant-based expression regulation status or an adjusted gene-based expression regulation status in a variant analysis system. The claim language is directed to adjustment of a determined status used to characterize functional impact, not to a naturally occurring change in gene expression inside a biological sample … The amended claim language tracks this disclosed distinction by expressly requiring computing an adjusted regulation status, rather than merely observing expression modulation. The Patent Office's inherency rationale does not cure this deficiency. … The cited passages of Geistlinger do not necessarily produce the claimed computed adjusted status, and the Office Action has not identified any teaching in Kagohara or Li that supplies this missing computation
It is respectfully submitted that this is not persuasive because the argued “adjusting” recitation has been taught by the prior art. 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. here, the “regulating” – a synonym for “adjusting” - performed by said CNVs reads on 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); wherein CNVs can be experimentally detected based on comparative genomic hybridization and can also be computationally inferred from SNP-arrays or detected from next-generation sequencing data (i.e. computing an adjusted variant-based expression regulation status and/or an adjusted gene-based expression regulation status) (pg. 1 para. 3).
Similarly, the computed adjusted status is also taught by the prior art because Geistlinger teaches that CNVs being able to fine-tune core regulators where said can also be computationally inferred from SNP-arrays or detected from next-generation sequencing data. Therefore, the adjusted status argued would inherently be computed as a result of computing said CNVs. "The rationale to modify or combine the prior art does not have to be expressly stated in the prior art; the rationale may be expressly or impliedly contained in the prior art or it may be reasoned from knowledge generally available to one of ordinary skill in the art, established scientific principles, or legal precedent established by prior case law" See MPEP 2144.I Therefore the step of ( ) is well known in the art and thus accepted as a rational to combine the teachings in the prior art.
Conclusion
No claims are allowed.
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/F.F.L./Examiner, Art Unit 1685
/JANNA NICOLE SCHULTZHAUS/Examiner, Art Unit 1685
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