DETAILED ACTION
Applicant's Remarks, filed 10/23/2025, have been fully considered. The following rejections and/or objections are either reiterated or newly applied in view of instant application amendments. They constitute the complete set presently being applied to the instant application. Herein, "the previous Office action" refers to the Non-Final rejection of 07/23/2025.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of Claims
Claims 1-15 are currently pending.
Claim 16 is newly added.
Claims 1-16 are under examination herein.
Claims 1-16 are rejected.
Withdrawn Rejections/Objections
Rejections and/or objections not reiterated from previous office actions are hereby withdrawn in view of the 10/23/2025 amendments and Applicant’s remarks. Upon further consideration, newly applied rejections/portions are necessitated by the instant amendments are discussed below.
The specification objections are hereby withdrawn.
The objection to the drawings is hereby withdrawn,.
The claim objections are hereby withdrawn.
The rejection of claims 1-16 is withdrawn under 35 U.S.C. 112(b) as being indefinite in view of instant application amendments.
Priority
As previously discussed, this application is a U.S. National Phase of International Patent Application No. PCT/EP2019/082673, filed on November 27, 2019, which claims priority to European Application No. 18208717.1, filed November 27, 2018. Newly added claim 16 has support (in original claim set 05/21/2021).
Therefore, all claims 1-16 are examined for an effective filing date of 11/27/2018. In future actions, the effective filing date of one or more claims may change, due to claim amendments, or further analysis of the disclosure(s) of the priority application(s).
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 1-16 are rejected under 35 U.S.C. 101, because the claimed invention is directed to an abstract idea without significantly more.
The instant rejection reflects the framework as outlined in the MPEP at 2106.04:
Framework with which to Evaluate Subject Matter Eligibility:
(1) Are the claims directed to a process, machine, manufacture, or composition of matter;
(2A) Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
(2B) If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
With respect to step (1): The claimed invention is directed to methods (claims 1-13), a computer-readable, non-volatile storage medium claim 14, and a system claim 15) is directed to statutory subject matter. Claim 14 non-volatile storage medium is interpreted as a non-transitory computer-readable medium and therefore, falls within at least one of the four categories of patent eligible subject matter, therefore the answer is "yes".
With respect to step (2A)(1), the claims recite abstract ideas. To determine if the claims recite any concepts that equate to an abstract idea, law of nature, or natural phenomenon, MPEP at 2106.03 teaches abstract ideas include mathematical concepts (mathematical formulas or equations, mathematical relationships, and mathematical calculations), certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, evaluating, and organizing information (see MPEP 2106.04(a)(2)). In the instant application, the claims recite the following limitations that equate to an abstract idea with mental processes and mathematical concepts.
With respect to the instant claims, under the step (2A)(1) evaluation, the claims are found herein to recite abstract ideas that fall into the grouping of mental processes (in particular processes for analyzing and organizing stored LFA test data for antibody concentration determinations). The claims directing to abstract ideas are as follows:
Mental processes:
Claims 1 and 15: comparing the vectors with each other for identifying two or more continuous or discontinuous blocks of cells in the 2D matrix that have similar vectors…
Claim 5: wherein the genomic features are of a feature type selected from the group consisting of: an individual nucleotide; an insertion/deletion variation (INDEL) of one or more nucleotides; a gene- or exon presence or absence variation (PAV); a presence or absence of a simple sequence repeat marker (SSR); an identifier of a nucleotide-sub-sequence of predefined length; an identifier of a unique nucleotide-sub-sequence observed in a multiple-sequence alignment (MSA) of the genomes of the sources of genetic information; an amplified fragment length polymorphism (AFLP); a combination of two or more of the above-mentioned feature types.
Claim 6: wherein the set of sources of genetic information comprises less than 10 sources.
Claim 8: automatically annotating at least one of the identified blocks of cells with one or more genes located in a genomic region represented by the at least one identified block of cells/traits observed in the sources of genomic information/phenotypes, each phenotype being a composition of two or more traits… or enabling a user, preferably via a GUI, for manually annotating at least one of the identified blocks of cells… and optionally automatically analyzing the identified blocks of cells and their annotated genes for automatically identifying co-inherited genes and associated pathways, or displaying the identified cell blocks in association with their annotated genes via a GUI for enabling a user identifying co-inherited genes and associated pathways.
Claim 9: identifying…a predefined minimum number of genetic markers being selectively indicative of the presence of said haplotype… being independent of the length of the genomic sequence covered by the haplotype; selectively using the identified markers for performing an association study… determining the co- occurrence of the identified genetic markers in the genomes/genes, traits or phenotypes…
Claim 10: (identifying one or more genetic markers) performing… obtaining haplotypes annotated… whereby the set of sources of genetic information is a population of organisms… determining… candidate genetic markers in the genomic region represented by said haplotype; analyzing correlated occurrences of the annotated haplotypes and the determined candidate genetic markers for identifying one or more candidate genetic markers observed to be associated with one or more genes, traits or phenotypes; and using the determined candidate genetic markers as the identified genetic markers
Claim 11: (identifying a germplasm whose genome is associated with a desired first gene, trait or phenotype)performing… identifying one or more first genetic markers associated with the first desired gene, trait or phenotype in the genomes of organisms of a particular species, whereby the sources of genetic information are organisms of this species;
Claim 12: (identifying second ones of the provided germplasms having a genome associated with a desired second …) performing… identifying one or more second genetic markers associated with the second desired gene, trait or phenotype in the genomes of individuals of the particular species, whereby the sources of genetic information are organisms of this species; identifying one or more second ones of the germplasms whose genome comprises the identified second genetic markers.
Claim 13: phenotyping the genetically diverse population of training organisms to generate a phenotype training data set… of the training organisms; identifying consecutive or non-consecutive cell blocks representing training haplotypes… of the training organisms, by performing…. using the genetically diverse population of training organisms as the set of sources of genetic information; obtaining an association training data set by associating the phenotype training data set with the training haplotypes…indicative of associations of some of the training haplotypes and some of the phenotypes or traits; identifying consecutive or non-consecutive cell blocks representing breeding haplotypes of a genetically diverse population of breeding organisms… using the genetically diverse population of breeding organisms as the set of sources of genetic information; applying the association training data set on the identified breeding haplotypes for selecting breeding pairs likely to generate progeny with one or more desired genes, traits or phenotypes…… to generate progeny with one or more desired genes, traits or phenotypes.
Mathematical concepts:
Claims 1 and 15: (identifying haplotypes in a set of sources of genetic information,…being a population of organisms/set of tissues) providing a 2D matrix comprising a first and a second dimension and a plurality of 2D matrix cells, the first dimension representing a sequence of genomic positions, the second dimension representing an ordered list of the sources of genetic information, each of the plurality of cells having assigned via its respective location in the 2D matrix one of the genomic positions and one of the sources of genetic information, each of the plurality of cells comprising a genomic feature that was observed in the cell's assigned source of genetic information at the cell's assigned genomic position… computing, for each of the cells, a vector, the vector comprising multiple elements respectively representing one source in the set of sources of genetic information, each of the elements of the vector comprising an identity indicator, the identity indicator being a data value indicative of whether the genomic feature comprised in the cell is identical to a genomic feature observed in the source of genetic information represented by said vector element at the genomic position assigned to the cell…
Claim 2: computing the Euclidian distance between any two of the computed vectors and determining all cells whose vectors have an Euclidian distance below a predefined distance threshold value to be a member of a continuous or discontinuous block of cells having similar vectors.
Claim 3: identifying two or more continuous or discontinuous blocks of cells in the 2D matrix that have identical vectors and selectively using these identified blocks of cells as the block of cells having similar vectors.
Claim 7: generating a plot comprising a graphical representation of the 2D matrix, wherein matrix cells comprised in the same identified continuous or discontinuous block of cells have the same color or the same hatching, wherein different ones of the identified cell blocks have different colors or have different hatchings
Hence, the claims explicitly recite elements that, individually and in combination, constitute abstract ideas.
With respect to step (2A), under the broadest reasonable interpretation (BRI), the instant claims recite mental steps for assessment of antibody concentration.
Instant claims recite mental processes as to these methodology steps of annotating…identifying… using the identified markers/genetically diverse population… determining… analyzing…phenotyping… applying… selecting…). Under the BRI, one with ordinary skill in the art could be performed said steps simply by mentally analyzing test results (from genetic studies on sourced samples-tissues/organisms) and correlating genetic results with known traits of organisms, and finally, select breeding pairs for target traits in progeny. The courts do not distinguish between mental processes that are performed entirely in the human mind and mental processes that require a human to use a physical aid (e.g., pen and paper or a slide rule) to perform the claim limitation (see, e.g., Benson, 409 U.S. at 67, 65, 175 USPQ at 674-75, 674 (noting that the claimed "conversion of [binary-coded decimal] numerals to pure binary numerals can be done mentally," i.e., "as a person would do it by head and hand."); Synopsys, Inc. v. Mentor Graphics Corp., 839 F.3d 1138, 1139, 120 USPQ2d 1473, 1474 (Fed. Cir. 2016) (holding that claims to a mental process of "translating a functional description of a logic circuit into a hardware component description of the logic circuit" are directed to an abstract idea, because the claims "read on an individual performing the claimed steps mentally or with pencil and paper"))(see MPEP § 2106.04(a)(2), subsection III)..
Instant claims recite mathematical concepts, including mathematical relationships and calculations, that cause the claims to be directed to the judicial exceptions include providing a 2D matrix comprising a first and a second dimension computing, for each of the cells, a vector….computing the Euclidian distance… generating a plot comprising a graphical representation. Case law, establishing the mathematical concept JE and to which the instant claims are analogized, is presented in MPEP 2106.04(a)(2).I, including examples of analogous mathematical concept JEs.
Because the claims do recite judicial exceptions, direction under step (2A)(2) provides that the claims must be examined further to determine whether they integrate the abstract ideas into a practical application (MPEP 2106.04(d). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exception, the claim is said to fail to integrate into a practical application (MPEP 2106.04(d).III).
With respect to the instant recitations, the claims recite the following additional elements considered for practical application:
Claim 1, 14, and 15: a computer-readable, non-volatile storage medium, processor parallel by at least two different processing units
Claim 7: displaying the plot on a graphical user interface of a display device.
Claims 1 and 15: outputting the identified blocks of cells, each identified block of cells representing a haplotype observed in the sources of genetic information.
Claim 13: growing a genetically diverse population of training organisms
Said steps that are “in addition” to the recited judicial exception in the instant claims represent those of mere data handling (data outputting, e.g. outputting, datasets; data types, e.g. an individual nucleotide; an insertion/deletion variation (INDEL) of one or more nucleotides; a gene- or exon presence or absence variation (PAV)…10 sources, population of organisms), “apply it” instructions or field of use limitations for genotypic/phenotypic information (phenotyping the genetically diverse population of training organisms to generate a phenotype training data set… applying the association training data set on the identified breeding haplotypes for selecting breeding pairs; test result annotation; data output formatted as a graph/plot/2D matrix), or intended use limitations (to generate progeny…), in addition to implementing the recited judicial exception in a generic computer environment. These steps are insignificant extra-solution activity and are insufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g).
Further steps herein directed to additional non-abstract elements of computer-implemented/system, computer-readable, non-volatile storage medium, processor, at least two different processing units …[FIG 2; 204 and 206] do not describe any specific computational steps by which the “computer parts” perform or carry out the abstract idea, nor do they provide any details of how specific structures of the computer, such as the computer-readable recording media, are used to implement these functions. The claims state nothing more than a generic computer which performs the functions that constitute the abstract idea. Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not integrate that abstract idea into a practical application. The courts have weighed in and consistently maintained that when, for example, a memory, display, processor, machine, etc… are recited so generically (i.e., no details are provided) that they represent no more than mere instructions to apply the judicial exception on a computer, and these limitations may be viewed as nothing more than generally linking the use of the judicial exception to the technological environment of a computer (see MPEP 2106.05(f)).
As such, the claims are lastly evaluated using the step (2B) analysis, wherein it is determined that because the claims recite abstract ideas which do not integrate the abstract ideas into a practical application, the claims also lack a specific inventive concept. The judicial exception alone cannot provide the inventive concept or the practical application and that the identification of whether the additional elements amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements of data gathering, instructions, and field of use limitations described above do not rise to the level of significantly more than the judicial exception. As directed in the Berkheimer memorandum of 19 April 2018 and set forth in the MPEP, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution 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).
With respect to the instant recitations, the claims recite the following additional elements considered for inventive concepts:
Claim 1, 14, and 15: a computer-readable, non-volatile storage medium, processor parallel by at least two different processing units
Claim 7: displaying the plot on a graphical user interface of a display device.
Claims 1 and 15: outputting the identified blocks of cells, each identified block of cells representing a haplotype observed in the sources of genetic information.
Claim 13: growing a genetically diverse population of training organisms
These additional elements do not contribute significantly more to well-known and conventional genotype and phenotype analysis of germplasm to benefit agricultural and breeding purposes, which are routinely determined and implemented by an one with ordinary skill in the art of as of the effective filing date.
Rausch T et al. (2008: A parallel genetic algorithm to discover patterns in genetic markers that indicate predisposition to multifactorial disease, Computers in Biology and Medicine 38(7):826-836; PTO 892 cited) teaches parallelizing genomic matrix math based on genetic algorithms with multiple processors [Rausch 4.0-4.1].
Berno A et al. (2004: US20040023275A1), discloses a method for identifying and relating genomic variations/SNP positions as genetic bases of disease-related phenotypes with variant haplotype blocks within tables and pattern data sets,
Zhang LM et al. (2018: "Sweet sorghum originated through selection of Dry, a plant-specific NAC transcription factor gene." The Plant Cell 30.10: 2286-2307) teaches transcription factor gene, at the sweet sorghum Dry locus (source/position) is derived from ancestral haplotypes with the dry, pitch stem phenotypes based on PCA/eigenvector analysis.
Yakhini Z et al. (2018: U.S. Patent No. 9,898,578. Visualizing expression data on chromosomal graphic schemes) teaches visualization of gene expression data by constructing a matrix with gene expression at defined locations in each row and different experiments in each column. Vectors are constructed describe gene expression and visualized in the various experiments.
Data (e.g. test results and parameters from generic computer of a test device) remain merely analyzed and manipulated as input/output in the judicial exception. With respect to the instant claims, the steps and additional elements do not comprise an inventive concept when considered individually or as an ordered combination that transforms the claimed judicial exception into a patent-eligible application of the judicial exception.
Therefore, the claims do not amount to significantly more than the judicial exception itself (Step 2B: No). As such, claims 1-16 are not patent eligible.
Response to 101 Remarks
The Applicant's remarks [p11-16], filed 10/23/2025, have been fully considered regarding the prior Office Action. Any newly applied rejection/portion is necessitated by instant application amendment. Applicant asserts:
Here, the claims cannot practically be performed in the human mind because they require "computing in parallel using at least two processing units... impossible without the aid of a computer.
However, it is respectfully submitted that Applicant’s assertion is not persuasive.
First, the simplest embodiment of the claims directed to sorting genetic data is not too complex, to be performed in the human mind with the aid of a pencil and paper, and even if more data of a preferred embodiment is provided (a “plurality of 2D matrix cells” is claimed), the human mind can still slowly perform the task of matching (according to a barcode identifier) and organizing target data into colors and shaped bins. The MPEP 2106.05(a) teaches applying the judicial exception with computers or devices to perform or automate an existing process, and constitute insignificant extra-solution activity, as recited: “Mere automation of manual processes, such as using a generic computer to process an application for financing a purchase, Credit Acceptance Corp. v. Westlake Services, 859 F.3d 1044, 1055, 123 USPQ2d 1100, 1108-09 (Fed. Cir. 2017) or speeding up a loan-application process by enabling borrowers to avoid physically going to or calling each lender and filling out a loan application, LendingTree, LLC v. Zillow, Inc., 656 Fed. App'x 991, 996-97 (Fed. Cir. 2016) (non-precedential).”
claims integrate the alleged abstract idea by using a computing system that includes various components in a "meaningful way … enables "the vectors [to be] computed in parallel by at least two different processing units." Published Specification at [0027]. This is a substantial improvement over prior methods because it allows for "a tremendous reduction of data size and complexity in particular in the context of using subvector identifiers as genomic features . . . [and] may be executed even on devices with limited data processing capacities such as smartphones or netbooks.
However, it is respectfully submitted that Applicant’s assertion is not persuasive as the use of multiple processing units for parallel computing of genomic matrix data as “substantial improvement over prior methods” for reduction of data size and complexity was already performed for such purposes according to Rausch’s 2008 teachings [Rausch 3.0 and 4.0-4.1].
This is analogous to the sample claims presented above because the present system similarly provides for generating a graphical user interface that can be modified by user input and updated. Therefore, Applicant submits that Claim 15 is at least as much of a practical application as the sample claim cited in Example 37 above.
However, it is respectfully submitted that Applicant’s assertion is not persuasive as the instant claims do not match the fact pattern of Example 37, which was performed in a particular GUI or computer memory or machine environment. Applicant asserts occurs in or Example 37 particular manipulation of graphical user interface based on the user USE of the GUI (number of times an icon was used to rearrange the icons). The instant claims utilize the math concepts (JE) to produce the representation of the haploblock plot, for which the GUI merely acts as a passive conduit of data, a generic display for projecting the output of the JE, as exemplified by the specification:
[p4] According to an embodiment, the step of providing the 2D matrix is implemented as reading the 2D matrix from a volatile or non-volatile storage medium. The storage medium can be a local storage medium or a remote storage medium that is accessible via a network, e.g. the Internet or an Intranet. The step of providing the 2D matrix can also comprise reading sequence information of each of the sources of genetic information (e.g. from a storage medium and/or from a sequencing machine)… The color-coded 2D matrix (which may or may not comprise a graphical representation of the vectors of the matrix cells) is displayed as a haploblock plot on a display that is operatively coupled to the computer system. In addition, or alternatively, the haploblock plot is printed on paper or sent via a message of any format (e.g. e-mail, SOAP messages, etc.) to another computer system. In addition, or alternatively, the identified haplotypes and/or the haploblock plot are stored on a local or remote non-volatile storage medium…
[p31] can be graphically represented as color-coded matrix cell blocks and displayed to a user via an electronic display 218, e.g. an LCD display of a standard computer system or via a touchscreen of a smartphone). Thanks to the parallelizability of the vector computation and comparison, thanks to a tremendous reduction of data size and complexity in particular in the context of sing sub- vector identifiers as genomic features (see figure 7), the software 210 may be executed even on devices with limited data processing capacities such as smartphones or netbooks.
The instant claims are analogous to the patent-ineligible limitations of arranging transactional information on a graphical user interface in a manner that assists traders in processing information more quickly (Trading Technologies v. IBG LLC).
Independent Claim 1 recites a series of steps, notably "computing in parallel using at least two processing units, for each of the cells, a vector" that allows for haplotype identification with reduced computing needs. Independent Claim 15 recites similar features. And as the Federal Circuit recently reaffirmed, "when the claim limitations involve more than performance of well- understood, routine, and conventional activities previously known to the industry
However, it is respectfully submitted that Applicant’s assertion is not persuasive as Applicant’s arguments do not comply with 37 CFR 1.111(c) because they do not clearly point out the patentable novelty which he or she thinks the claims present in view of the state of the art disclosed by the references cited, including Rausch, and/or the objections. As discussed above, Rausch teaches in 2008 creating vectors and parallelizing matrix math based with multiple processors to be state of the art, as of the application’s effective filing date [Rausch 3.0 and 4.0-4.1].
Prior Art
It is noted independent claims 1 and 15 appear free from the prior art as the prior art does not teach nor fairly suggest wherein for each cell in a 2D matrix a vector is calculated and wherein the elements of the vectors contain identity indicators with regard to genetic variations at a specified positions in the sources which are used to construct the 2D matrix of claims 1 and 15, followed by identifying continuous blocks of similar or identical vectors, thus identifying haplotype patterns. The closest prior art, Berno A et al. (2004: US20040023275A1), discloses a method for identifying and relating genomic variations/SNP positions as genetic bases of disease-related phenotypes with variant haplotype blocks of a table and pattern data sets, but not with vector analysis of 2D matrix blocks that are set forth in the claimed invention.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Zhang LM et al. (2018: "Sweet sorghum originated through selection of Dry, a plant-specific NAC transcription factor gene." The Plant Cell 30.10: 2286-2307) teaches transcription factor gene, at the sweet sorghum Dry locus (source/position) is derived from ancestral haplotypes with the dry, pitch stem phenotypes based on PCA/eigenvector analysis but not based in specialized display matrices.
Yakhini Z et al. (2018: U.S. Patent No. 9,898,578. Visualizing expression data on chromosomal graphic schemes) teaches visualization of gene expression data by constructing a matrix with gene expression at defined locations in each row and different experiments in each column. Vectors are constructed describe gene expression and visualized in the various experiments.
Conclusion
No claims are allowed.
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 nonprovisional extension fee (37 CFR 1.17(a)) 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 mailing date of this final action.
E-mail Communications Authorization
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Written authorizations submitted to the Examiner via e-mail are NOT proper. Written authorizations must be submitted via EFS-Web or Central Fax (571-103-8300). A paper copy of e-mail correspondence will be placed in the patent application when appropriate. E-mails from the USPTO are for the sole use of the intended recipient, and may contain information subject to the confidentiality requirement set forth in 35 USC § 122. See also MPEP 502.03.
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/VR/
Examiner
Art Unit 1685
/MARY K ZEMAN/ Primary Examiner, Art Unit 1686
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