DETAILED ACTION
This office action is based on the claim set filed on 01/07/2026.
Claims 1, 11, 15-18, and 20 have been amended.
Claims 1-20 are currently pending and have been examined.
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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 01/07/2026 has been entered.
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.
Claim 1-20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. Claims 1-17 are drawn to a system, Claims 18-19 are directed to a method, and Claim 20 is drawn to an art of manufacturer, and each of which is within the four statutory categories (i.e., a machine and a process). Claims 1-20 are further directed to an abstract idea on the grounds set out in detail below.
Under Step 2A, Prong 1, the steps of the claim for the invention represents an abstract idea of a series of steps that recite a process for associating genetic data with participants medical records. Collecting participants sequencing data to correlate the data with health records and display outcomes to a user is an abstract idea could have been performed by a human actor interacting with a system/interface to implement the abstract idea for steps collecting, providing, performing, and display data, which both the instant claims and the abstract idea are defined as Certain Methods of Organizing Human Activity.
Independent Claim 1 recites the steps of:
“a bioinformatics system configured to analyze raw sequence data generated by sequencing equipment for a plurality of sequencing participants to generate sequencing data for the sequencing participants; and
a genomic data system comprising:
a data repository configured to store the sequencing data in electronic format for the sequencing participants;
a network interface configured to communicate over a communication network
and
a cohort controller comprising a processor and memory, the processor configured to:
establish a secure connection with an electronic health record system of one or more health care providers over the communication network via the network interface;
receive electronic health record data for one or more of the sequencing participants from the electronic health record system via the secure connection, wherein the electronic health record data is formatted in Observational Medical Outcomes Partnership (OMOP) format or the processor is configured to transform the electronic health record data to OMOP format
merge the electronic health record data in OMOP format and the sequencing data for the sequencing participants by generating anonymized merge records for one or more of the sequencing participants, wherein an anonymized merge record of a sequencing participant includes the sequencing data for the sequencing participant digitally linked to the electronic health record data for the sequencing participant;
store anonymized merge records in the data repository;
provide a cohort graphical user interface to receive cohort criteria as input from a requestor via the communication network to define a cohort from a population of the sequencing participants, wherein the cohort criteria comprise one or more health conditions;
parse, automatically in response to the input from the requestor, the anonymized merge records in the data repository for the population of the sequencing participants based on the cohort criteria to identify the cohort of the sequencing participants from the population having anonymized merge records that match the cohort criteria;
provide the cohort graphical user interface to display cohort information for the cohort to the requestor via the communication network in response to receiving the cohort criteria;
wherein the processor is further configured to:
process the sequencing data for the cohort to identify a plurality of genetic variants correlated with the cohort;
calculate a magnitude of correlation for each genetic variant of the plurality of genetic variants to the cohort by comparing a first percentage of the cohort having the genetic variant with a second percentage of the population having the genetic variant; and
provide the cohort graphical user interface to display the cohort information comprising a list of the genetic variants based on the magnitude of correlation.”
Independent Claims 18 and 20 recite similar steps as in Claim 1
These limitations, as drafted, given the broadest reasonable interpretation, cover performance of the limitations by a human user/actor interaction with computing device(s) that constitute Certain Methods of Organizing Human Activity along with Mathematical concepts (e.g. calculate[ing]). For example, the limitations encompass a user the ability to collect sequencing data of a population, anonymize and merge the data to correlate the data with health records to identify a cohort based on cohort criteria, calculate degree of correlation of each variant and display the cohort information to a requesting provider, which are steps that that could have been performed by a human actor using generic computing components to implement the abstract idea. These limitations encompass activity of a single person or multiple people and a computer, interacting with other users and with computing system(s) to perform the steps of the claimed invention, e.g., correlating and providing a display, which constitutes Certain Methods of Organizing Human Activity. Accordingly, the claim limitations (in BOLD) recite an abstract idea. Any limitations not identified above as part of the process are deemed "additional elements," and will be discussed in further detail below.
Under Step 2A, Prong 2, this judicial exception is not integrated into a practical application because the remaining elements amount to no more than general purpose computer components programmed to perform the abstract ideas, linking the abstract idea to a particular technological environment. In particular, the claims recite the additional elements such as “processor, memory/data repository, non-transitory computer readable medium, communication network, graphical user interface, controller, electronic record, sequencing equipment, bioinformatics system, network interface” that iteratively takes input data and analyzes said data to determine an output to performing generic computer functions for determining a metabolic dysfunction such that it amounts no more than adding the words "apply it" (or an equivalent) with the judicial exception, or mere instructions to implement an abstract idea on a computer, or merely uses a computer as a tool to perform an abstract idea, (e.g. “store[ing]...”, “display[ing]…”), see MPEP 2106.05(f), generally linking the use of the judicial exception to a particular technological environment or field of use, see MPEP 2106.05(h), and adding insignificant extra-solution activity to the judicial exception, (e.g. “receive[ing]… via communication network”, “establish a secure connection...”) which is/are analyzed as a nominal or tangential addition to the abstract idea and does not affect the generation of the data object and as such amounts to insignificant post/extra-solution activity to apply the exception using generic computer component such as causing the computer system to perform the instructions and mere data gathering process that does not add a meaningful limitation to the above abstract idea, see MPEP 2106.05(d)-(g). As set forth in the 2019 Eligibility Guidance, 84 Fed. Reg. at 55 "merely include[ing] instructions to implement an abstract idea on a computer" is an example of when an abstract idea has not been integrated into a practical application. Accordingly, looking at the claim as a whole, individually and in combination, these additional elements do not integrate the abstract idea into a practical application because they do not impose any meaningful limits on practicing the abstract idea. The claim is directed to an abstract idea.
Under step 2B, the claims do not include additional elements that are sufficient to amount to "significantly more" than the judicial exception because as mentioned above, the additional elements amount to no more than generic computing components, recited at a high level of generality, do not present improvements to another technology or technical field, nor do they affect an improvement to the functioning of the computer itself, that amount to no more than mere instruction to perform the abstract idea such that it amounts no more than adding the words "apply it" (or an equivalent) to apply the exception using generic computer component, see MPEP 2106.05(f), adding insignificant, extra solution activity that has been found to not amount to significantly more than an abstract idea and mere data gathering that does not add a meaningful limitation to the above abstract idea, see MPEP 2106.05(d)-(g), and Symantec and OIP Techs. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely provide conventional computer implementation and mere instructions to apply an exception using a generic computer component cannot provide an inventive concept, See Alice, 573 U.S. at 223 ("mere recitation of a generic computer cannot transform a patent-ineligible abstract idea into a patent-eligible invention."). The claims are not patent eligible.
Dependent Claims 2-17 and 19 include all of the limitations of claim(s) 1 and 18, and therefore likewise incorporate the above-described abstract idea. While the depending claims add additional limitations, such as
As for claims 2-3, 5-15, and 19, the claim(s) recite limitations that are under the broadest reasonable interpretation, further define the abstract idea noted in the independent claim(s) that covers performance by a human interaction but for, the recitation of the generic computer components which are similarly rejected because, neither of the claims, further, defined the abstract idea and do not further limit the claim to a practical application or provide an inventive concept such that the claims are subject matter eligible. The claims recite additional elements “communication network/secure connection, repository, electronic record, graphical user interface, sequencing equipment” that implement the identified abstract idea, recited in the claim(s) at a high level as a tool to apply the exceptions, i.e., “store[ing]...”, “display[ing]...”, that amount to no more than the words "apply it" with a computer and no more than mere instructions to apply the exception using generic computer components, and mere data gathering process that does not add a meaningful limitation to the above abstract idea, see MPEP 2106.04(d). Mere instructions to apply an exception using a generic computer component cannot provide an inventive concept ("significantly more").
As for claims 16, the claim(s) recite limitations that are under the broadest reasonable interpretation, further define the abstract idea noted in the independent claim(s) that covers performance by a human interaction along with mathematical calculations that constitute Mathematical Concepts but for, the recitation of the generic computer components which are similarly rejected because, neither of the claims, further, defined the abstract idea and do not further limit the claim to a practical application or provide an inventive concept such that the claims are subject matter eligible. The claims recite additional elements “graphical user interface” that implement the identified abstract idea, recited in the claim(s) at a high level as a tool to apply the exceptions, i.e., “ “display[ing]...”, that amount to no more than the words "apply it" with a computer and no more than mere instructions to apply the exception using generic computer components, and mere data gathering process that does not add a meaningful limitation to the above abstract idea, see MPEP 2106.04(d). Mere instructions to apply an exception using a generic computer component cannot provide an inventive concept ("significantly more").
As for claims 17, the claim(s) recite limitations that are under the broadest reasonable interpretation, further define the abstract idea noted in the independent claim(s) that covers performance by a human interaction along with mathematical calculations that constitute Mathematical Concepts, but for, the recitation of the generic computer components which are similarly rejected because, neither of the claims, further, defined the abstract idea and do not further limit the claim to a practical application or provide an inventive concept such that the claims are subject matter eligible. Mere instructions to apply an exception using a generic computer component cannot provide an inventive concept ("significantly more").
Subject Matter Free of Prior Art
Claims 1-20 have been found by the examiner to be free of prior art. A thorough search of the prior art was conducted and the examiner could not find a single reference or combination of references with adequate rationale to combine that would teach the claimed invention. Specifically, the examiner, for example, finds that the language “calculate a magnitude of correlation for each genetic variant of the plurality of genetic variants to the cohort by comparing a first percentage of the cohort having the genetic variant with a second percentage of the population having the genetic variant” in independent claims 1, 18, and 20, to be free of prior art. In the examiner's search of prior art. The closest prior art(s) was/were found are:
US 2023/0187074 A1- “Nothaft” discloses filtering a population with a disease to generate a cohort or group comprising genetic variant(s) where the filtered group specify the percentage of the different genetic alteration in the filtered group but does not compare the percentage of the cohort to the percentage of population.
US 20230223121A1- “Colley” discloses generating from a base population of subjects first and second plurality of subjects as control cohorts and determine percentage of the disease in the cohort but does not compare the percentage of the cohort to the percentage of population.
However, the cited references fail to individually disclose, or suggest when combined, the limitations of the claim.
No prior art was found teaching individually, or suggesting in combination, all of the features of the applicants' invention, as disclosed in the claimed invention.
Response to Amendment
Applicant's arguments filed 01/07/2026 have been fully considered by the Examiner and addressed as the following:
In the remarks, Applicant argues in substance that:
Applicant's arguments with respect to the 35 U.S.C. § 101 rejection on page 13-17.
On page 13-14 of the remarks, the Applicant argues “These limitations of claim 1 are not methods of organizing human activity” Examiner respectfully disagrees. The claims are given their broadest reasonable interpretation for the purpose of determining whether they encompass a judicial exception. As described in the rejection above, the claim steps, under BRI, recite organizing and arranging a participant in sequencing data using the participant health record in combination with an obtained sequencing data which recites steps that falls under methods of organizing human activity, such as managing personal behavior and following rules and instructions for organizing and filtering health data.
Furthermore, the Applicant argues that “sequencing and analysis can involve billions of base pairs. Even if a portion of a genome is examined, the corresponding sequencing and analysis can involve millions of base pairs, which is not practical in the mind of a human”, Examiner disagrees to the Applicant argument. Although the sequencing of data is disclosed in the claim, the claim does not recite the size of the pairs in addition the sequencing is performed by a machine (sequencing equipment) performing a well-known process in the industry1 where this process has been analyzed as additional element that does not affect the abstract idea for arranging the sequencing participant data. As described in the prior rejection, the claim recites a use of bioinformatic system and sequencing equipment for generating sequencing data, however, “analyzing, filtering, and organizing data” is considered an abstract idea because it is a basic human thought and ability to process original information collected directly from a source without any manipulation, organization, or analysis. In addition, the bioinformatics system is recited at a high level of generality and as a tool to perform the function of analyze and/or process the raw sequence data, see (Applicant [0032]), through leveraging computing technology in a well understood manner such as receiving sequencing data however the data analysis is performed using a generic computer component that is programmed to apply the steps of the claimed invention for organizing and analyzing the sequencing participants data and displaying it which is no more than adding the words "apply it" using a generic components that is not configured in a manner other than a commercially available computing system that is capable of being programmed to perform the steps of the claim.
On page 15-16 of the remarks, the Applicant argues “Even assuming, arguendo, that the claims are directed to one or more judicial exceptions to patentability, the Applicant submits that claim 1, as a whole, integrates any judicial exception into a practical application under at least Step 2A Prong Two ... Identifying a cohort as in claim 1 is important in the field of population genomics, as a large number of sequencing participants may be identified that satisfy the cohort criteria ... Based on the above, the Applicant submits that claim 1 as a whole provides improvements to the technical field of population genomics,” Examiner respectfully disagrees. As discussed above and in the prior Office Action response to remarks that the claim does not describe a particular improvement of computer’s functionality or a technical field, rather using additional elements, “e.g., processor, memory/data repository, non-transitory computer readable medium, communication network, graphical user interface, controller, electronic record”, to perform the steps abstract idea such as collecting/obtaining, merging/consolidating, anonymizing/de-identifying, parsing data, and displaying through leveraging computing technology in a well understood manner however improving upon an abstract idea does not make the abstract idea any less abstract. The features listed in the claims, are not considered an improvement to another technology, or technical field, or an improvement to the functioning of the computer itself rather describes an improvement to analyzing and consolidating patient cohort data which is solving a health facility an administrative and clinical problem, e.g., reducing pharmaceuticals patient risk, using computers, for identify a cohort of individuals having both the genetic variant and the health condition. The alleged benefits that Applicants tout such as to identifying identify a cohort of individuals having both the genetic variant and the health condition, using computers, rather than any improvement to another technology or technical field, or an improvement to the functioning of the computer itself.
In addition, by relying on computing devices to perform routine tasks more quickly or more accurately is insufficient to render a claim patent eligible (See Alice, 134 S. Ct. at 2359 "use of a computer to create electronic records, track multiple transactions, and issue simultaneous instructions" is not an inventive concept). As mentioned above, the steps recited in independent claims, when viewed as a whole, recite abstract steps for analyzing, filtering, organizing and displaying health data and the recitation of computing components have been analyzed under Step 2A, Prong Two as an additional element cited as a tool for implementing claim steps that amounts to no more than mere instructions to implement “apply” the exception using a generic computer component and no more than adding the words "apply it" (or an equivalent) with the judicial exception.
On page 16-17 of the remarks, the Applicant argues “Even if the pending claims are determined to be ineligible under Step 2A Prong Two, the Applicant submits that the pending claims amount to significantly more than the judicial exception under Step 2B ... claim I provides other meaningful limitations beyond generally linking the use of any judicial exception ... Thus, claim 1 amounts to significantly more than any JE indicated by the Office” Examiner respectfully disagrees. As mentioned above, the claims under BRI recites an abstract idea for organizing health data to associate genetic data with a user health record while citing addition element described at high level and as tool(s) to perform the abstract idea as such the thrust of Applicant's invention is to improve the abstract idea through leveraging computing technology, e.g., processor, controller, electronic health records (EHR), databases, user interface, network, in a well understood manner. The fact that the judicial exception, identified in the rejection above, relies upon collecting user data, merging, parsing, analyzing the data and performing mathematical process for calculating correlation and displaying outcomes, does not impart an improvement to any existing computer, or any other technology or technical field. At best, the idented abstract steps may improve the abstract idea of solve managing clinical and administrative issue. However, improving upon an abstract idea does not make the abstract idea any less abstract. Accordingly, this process for correlating user health data records with genetic data while using computing components that have been analyzed under Step 2A P2 as additional elements amount to more than mere instruction to apply the exception using generic computer component and have been re-evaluated under the “significantly more” analysis. Mere instructions to apply an exception using a generic computer component cannot provide an inventive concept ("significantly more").
Therefore, the Examiner has addressed the Applicant argument(s) and found this argument is not found to be persuasive. Hence, Examiner remains the 101 rejections of claims which have been updated to address Applicant's amendments.
Applicant's arguments with respect to the 35 U.S.C. § 103 rejection on page 17-19.
On page 18 of the remarks, the Applicant argues “The Applicant amended some subject matter from claims 16-17 into claim 1, and submit that the combination of Nothaft and Colley fails to teach these limitations ... There is no teaching or suggestion that the fourth region 300d of Nothaft indicates "a magnitude of correlation" as in claim 1 determined by comparing "a first percentage of the cohort having the genetic variant with a second percentage of the population having the genetic variant" ... There is no comparison between a cohort and the population of patients as in claim 1.” Examiner find the Applicant argument is persuasive and the argued feature is free of prior art. Accordingly, Examiner withdraws the 103 rejections.
Prior Art Cited but not Applied
The following document(s) were found relevant to the disclosure but not applied:
US 11,620,673 “Paquette” discloses master data comprising records having first de-identified token values associated with health data and second data comprising records having second de-identified token values associated with historical media delivery data.
“Zimmermann”- “Interpreting Sequence Variation in PDAC-Predisposing Genes Using a Multi-Tier Annotation Approach Performed at the Gene, Patient, and Cohort Level”.
“Lunenburg” – “Pharmacogenetic genotype and phenotype frequencies in a large Danish population-based case-cohort sample”
The references are relevant since it discloses analyzing genetic variant and de0identifying individual data.
Conclusion
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/ALAAELDIN M. ELSHAER/Primary Examiner, Art Unit 3687
1 US20150066385A1