DETAILED ACTION
This office action is based on the claim set filed on 05/19/2026.
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 .
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 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 ELIGIBILITY DECLARATION (SMED)
SUBMITTED UNDER 37 CFR § 1.132
The SMED under 37 CFR 1.132 filed 05/19/2026 by Lisa McEwen (“Dr. McEwen”) is/are insufficient to overcome the 101 rejections of claims 1-20 as set forth in the last Office action Applicant submitted a SMED traversing rejections.
As for Dr. McEwen SMED, the Affiant declared as an expert in clinical genetics data as stated on page 1, “I have worked in the field of clinical genetics data for over 10 years. Additionally, I am an Adjunct Assistant Professor in the Health Information Science Department at the University of Victoria where I have created and taught curriculum at the graduate-school level. I have also been an author on over 35 peer reviewed publications in this field”. First, this is not persuasive because Dr. McEwen credentials describe no basis understanding of the intricacies of computer science or engineering and is not qualified to opine on these matters as one of ordinary skill in the art. Second, Dr. McEwen fails to consider the broadest reasonable interpretation of the claims as written and improperly reads limitations from the specification into the claims. MPEP 716 states that it is the responsibility of the examiner "to personally review and decide whether affidavits or declarations submitted under 37 CFR 1.132 for the purpose of traversing grounds of rejection are responsive to the rejection and present sufficient facts to overcome the rejection." In reviewing the affidavit, the Examiner has not identified fact in the affidavit that would change the factual determinations underlying the eligibility analysis in the previous action.
In addition, the SMED, p. 1-2, of Dr. McEwen, is focused on asserting that the claimed subject matter and the claims do not citing a judicial exception and do not fall into an abstract idea arguing, for example, that ““I am not familiar with anyone in my field using such processes for the recited economic practices”, “I am not familiar with anyone in my field using such processes for the recited commercial or legal purposes”, “I am not familiar with anyone in my field using such processes as a process of managing people”, “Even the mind of a skilled peer would find it impracticable to perform as a mental process”, “the manipulation and application of these complex data sets in order to select a cohort cannot be suitably performed with pen and paper, or similar processes”...”, however this not entirely commensurate in scope to the actual claim language and don’t actually point to the specification indicating such allegation without providing any evidence supporting such assertion. Examiner asserts that humans can manually analyze data performed the correlation that is defining the argued abstract steps.
Furthermore, while the Affiant expressed his expertise in the field of clinical genetics data, the Affiant continues on SMED page 2, section 10 stating “A system of the pending application assembles a cohort of sequencing participants based on input from a requestor ... Thus, the requestor can determine, from the output of the cohort GUI, how closely linked certain genetic variants are to certain health conditions or the like”, however the Affiant fails to describe other than a judicial exception steps and a generic computing system to implement the identified abstract steps such as 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 that iteratively takes input data and analyzes said data to determine an output to performing generic computer functions as such merely uses a computer as a tool to perform an abstract idea.
Thus, the affidavits under 37 CFR 1.132 filed 05/19/2026 are insufficient to overcome the 101 rejections of claims 1-20 as set forth in the last Office action.
Response to Amendment
Applicant's arguments filed 05/19/2026 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 10-20.
On page 11-12 of the remarks, the Applicant argues “the Applicant argues that certain limitations of claim I have been improperly identified as falling within at least one of the groupings of abstract ideas... No evidence of record has been supplied for this position by the Office at this time to support that argument. Even if the Office can correctly argue that the "calculate" limitation is a mathematical concept under MPEP § 2106.04(a), the Applicant submits that the remaining limitations are not certain methods of organizing human activity as alleged by the Office. The attached SMED, the only evidence of record relating to § 101, fully supports the Applicant's position with testimony from an inventor with extensive expertise on the claimed subject matter...”, 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 and such steps have been interpreted, under BRI, as a process for organizing treatment steps to support decision making in linking genetic variant to health condition as such have been identified as steps that can be performed by a human user organizing data that falls in the course of human behavior which defines the identified abstract idea. In addition, as per the above rejection and the response to argument made in the prior OA rejections, it provided clear evidence explaining the position of the office why such step would fall in the bucket of certain methods of organizing human activity abstraction such that the claimed invention is directed to extracting data into intangible and using statistical methods to look for correlations.
As for argument that the attached SMED is the only evidence of record relating to § 101, fully supports the Applicant's position with testimony from an inventor with extensive expertise on the claimed subject matter, Examiner disagrees to such argument for the reason that this testament failed to consider the broadest reasonable interpretation of the claims and the Affiant failed to provide evidence to support such allegation and the Affiant approach described in SMED p. 1-3 does not describe how the steps would are not citing a judicial exception. As a preliminary measure, Affiant, Lisa McEwen, has not established proper qualifications to opine on the state of the art as it relates to computer systems for data management or how the claimed technology could produce improved technology in the field. Affiant is a graduate of University of British Columbia, possessing a degree in degree in Medical Genetics and holding a degree in Microbiology and Biochemistry form University of Victoria. Affiant has 10 years of experience in the field of clinical genetic data. These credentials describe no basis understanding of the intricacies of computer science or engineering. Simply put, the Examiner has no reason to accept Affiant's statements as a matter of fact. Affiant is not qualified to opine on these matters as one of ordinary skill in the art. However, the Examiner will consider the particular issues both the Applicant and the Affiant.
On page 12-13 of the remarks, the Applicant argues “The rejection did not clearly indicate how these claim limitations describe methods of organizing human activity... the Office has failed to make a prima facie case under§ 101... However, human interaction with a computing device is not one of the concepts enumerated for methods of organizing human activity under MPEP § 2106.04(a)(2)(11) ... steps are not inherently abstract merely because a computer may be involved. Use of a computer is not one of the concepts enumerated for methods of organizing human activity under MPEP § 2106.04(a)(2)(11), and hence no prima facie case has been made establishing the claims as abstract”, Examiner respectfully disagree. The claims of the instant application, under BRI, recite steps for organizing information and manipulating information through mathematical correlations while interacting with computer following rules or instructions to perform such process which defines the identified abstract idea, “certain activity between a person and a computer may fall within the "certain methods of organizing human activity" grouping”, see MPEP 2106.04(a)(2). Moreover, Examiner asserts that a prima facie case of patent-ineligibility is made when the rejection: i. identifies and clearly articulates the judicial exception recited in the claims, ii. identifies any additional elements recited in the claims, and iii. explains why the additional elements do not amount to significantly more than the exception. Notably, documentary evidence is not required to establish that an abstract idea is recited in the claim. Numerous court cases (Alice, Bilski, Diehr, Flook, Benson) did not rely on evidence to find the claims to be directed to a judicial exception without significantly more. Because the claims have been shown to recite an abstract idea that is similar to abstract ideas previously found by the courts to be abstract, and the additional elements do not amount to significantly more than the abstract idea, a prima facie case of patent ineligibility has been established.
On page 13 of the remarks, the Applicant argues “the Office appears to be asserting that the limitations are mental processes; not methods of organizing human activity. For example, MPEP § 2106.04(a)(2)(111) discusses mental processes that "can be performed in the human mind" and "performing a mental process on a generic computer". Thus, the Office appears to be mixing rationale regarding what constitutes an abstract idea and under what enumerated grouping. If the Office wishes to maintain this rejection in light of the attached SMED, the Applicant respectfully asks the Office to clearly (1) identify the specific limitation(s) in the claim under examination that the examiner believes recites an abstract idea, and (2) which of the enumerated groupings the specific limitation(s) fall within...”, Examiner respectfully disagree to this argument. The office action (OA) has clearly identified the limitation(s) (emphasized in BOLD) that recites, under BRI, and abstract idea. The OA has clearly described why such limitation identified as certain methods of organizing human activity along with mathematical process. The OA has not asserted any limitation as mental process. Moreover, as per the above, Examiner finds the attached SMED not persuasive and insufficient to be considered for overcoming the 101 rejections.
On page 14 of the remarks, the Applicant argues that claim I are not mental processes “the reasonable interpretation of the claims in light of the Specification, even at its broadest, does not support the practice of the claimed invention as an abstract mental process... the Applicant submits that this limitation is not a mental process as automatic parsing of anonymized merge records for a population of sequencing participants cannot be practically performed by a human ... A human cannot practically parse anonymized merge records for a large population in an automated manner...”, Examiner respectfully disagree. The OA has not asserted any of the limitation of claim 1 as an abstract mental process. Although the OA rejection identified the claim steps as Organizing Human Activity and Mathematical process, Examiner also would like to emphasize that parsing, merging, and anonymizing data are functions that a human can perform manual data extraction, merging data entry and cross-referencing, and anonymize data. In addition, the specification [0002] describes “Present solutions for finding insights utilize automated algorithms to scan research datasets describing the genomes of tens or hundreds of thousands of individuals”, however neither the claim(s) nor the specification describes the size of the pairs considered by the current application.
On page 16-18 of the remarks, the Applicant argues “The Applicant first submits that these additional elements provide an improvement in the functioning of a computer... Applicant has drawn a red box around a variant graphical element 1324 of a cohort GUI 406 that displays genetic variants ... Thus, the additional elements of claim 1 provide an improved user interface... This may allow the requestor to identify, for example, high-risk individuals regarding the health condition(s). This represents an improved user interface...”, Examiner respectfully disagree. Examiner respectfully disagrees. Drawing a box around a graphical element is simply highlighting or bordering a selected element that is a feature that can be done by a human for organizing information but for a generic computer implementation and does not transform the abstract idea into a patent-eligible invention, as the computer is merely acting as a tool to execute the mental process. 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 and/or the specification, 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.
On page 18 of the remarks, the Applicant argues “The Applicant further submits that these additional elements provide an improvement to a technology or technical field ... A technical benefit is the genetic variants 1242 having the strongest correlation to the cohort are clearly displayed through the cohort explorer interface 810. Thus, the additional elements of claim 1 provide an improvement to the technical field of population genomics...”, Examiner respectfully disagree. As mentioned above, the claim(s) of the current application describes no improvement to another technology, or technical field, or an improvement to the functioning of the computer itself rather it describes analyzing patient(s) genetic data and displaying the analyzed information that may be used by a user(s) to support an administrative issue and may be improving efficiency of user to navigate the displayed information. 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).
On page 19 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... The Applicant submits that the additional elements amount to improvements to the functioning of a computer, and improvements to any other technology or technical field for similar reasons discussed above for Step 2A, Prong Two”, Examiner respectfully disagree. As mentioned above and discussed in the prior rejection, 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").
Furthermore, the Applicant argues that “The lack of a prior art rejection confirms that the limitations of claim 1 are unconventional in the art”, Examiner asserts that all of the requirements for patentability as provided in 35 U.S.C. 101, 102, 103, and 112 must be met before a claim is allowed, see MPEP 706(I).
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.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a). A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
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/ALAAELDIN M. ELSHAER/Primary Examiner, Art Unit 3687
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