DETAILED ACTION
The Applicant’s filing, received 07 March 2023, has been fully considered. The following rejections and/or objections constitute the complete set presently being applied to the instant application.
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
The preliminary amendment received 13 May 2023 has been entered. The specification title has been amended.
Original claims 1-20 filed 5/13/20023 are pending.
Claims 1-20 are rejected.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
This application is a 371 of PCT/KR2022/018119, filed 16 November 2022,
which claims benefit of foreign application REPUBLIC OF KOREA 10-2021-0160791, filed 19 November 2021.
Information Disclosure Statement
The information disclosure statement (IDS) received 07 March 2023 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement (e.g., see paras. [06] & [0107]). 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Specification
The preliminary amendment to the specification received 13 May 2023 has been entered.
The abstract of the disclosure is objected to because:
The abstract contains 194 words, which exceeds the limit of 150 words. The abstract should be in narrative form and generally limited to a single paragraph preferably within the range of 50 to 150 words in length. The abstract should not exceed 15 lines of text. Abstracts exceeding 15 lines of text or 150 words should be checked to see that they are as concise as the disclosure permits.
A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Drawings
The drawings received 13 May 2023 have been accepted.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier. Such claim limitations are:
a population representative individual selection unit for measuring…, in claim 1;
a genetic population composition determination unit for generating…, in claims 1 and 7;
a genome data collection unit for collecting…, in claim 2;
a homogenous population classification unit for measuring…, in claims 2 and 3;
a population representative individual genome generation unit for measuring…, in claims 2, 3, 4, 5 and 6;
a hybrid data generation unit for generating…, in claims 7 and 8; and
a test target individual breed determination unit for measuring…, in claims 7, 9 and 10.
Because these claim limitations are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, they are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
The specification does not disclose a corresponding structure for the non-structural generic placeholder:
a population representative individual selection unit for measuring…, in claim 1;
a genetic population composition determination unit for generating…, in claims 1 and 7;
a genome data collection unit for collecting…, in claim 2;
a homogenous population classification unit for measuring…, in claims 2 and 3;
a population representative individual genome generation unit for measuring…, in claims 2, 3, 4, 5 and 6;
a hybrid data generation unit for generating…, in claims 7 and 8; and
a test target individual breed determination unit for measuring…, in claims 7, 9 and 10.
For each of the above, given the lack of guidance in the specification and the absence of a definition for the limitation of a ‘unit,’ the term “unit” appears to be directed to either computer hardware, e.g., a computer processor, that is used for processing the steps, i.e., the instructions of the claims, or alternatively, directed to the instructions themselves, i.e., the term ‘unit’ refers to a set of instructions.
If applicant does not intend to have these limitations interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitations to avoid them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitations recite(s) sufficient structure to perform the claimed function so as to avoid them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-10 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 1 recites the limitation “a population representative individual selection unit for measuring…,” however the disclosure does not clearly link any structure for the “population representative individual selection unit” as required by MPEP 2181. For example, the specification describes a function of the “population representative individual selection unit” (e.g., at para. [046]) but does not link any structure to the function.
Claims 1 and 7 recite the limitation “a genetic population composition determination unit for generating…,” however the disclosure does not clearly link any structure for the “genetic population composition determination unit” as required by MPEP 2181. For example, the specification describes a function of the “genetic population composition determination unit” (e.g., at para. [054]) but does not link any structure to the function.
Claim 2 recites the limitation “a genome data collection unit for collecting…,” however the disclosure does not clearly link any structure for the “genome data collection unit” as required by MPEP 2181. For example, the specification describes a function of the “genome data collection unit” (e.g., at para. [048]) but does not link any structure to the function.
Claims 2 and 3 recite the limitation “a homogenous population classification unit for measuring…,” however the disclosure does not clearly link any structure for the “homogenous population classification unit” as required by MPEP 2181. For example, the specification describes a function of the “homogenous population classification unit” (e.g., at para. [049]) but does not link any structure to the function.
Claims 2, 3, 4, 5 and 6 recite the limitation “a population representative individual genome generation unit for measuring…,” however the disclosure does not clearly link any structure for the “population representative individual genome generation unit” as required by MPEP 2181. For example, the specification describes a function of the “population representative individual genome generation unit” (e.g., at para. [050]) but does not link any structure to the function.
Claims 7 and 8 recite the limitation “a hybrid data generation unit for generating…,” however the disclosure does not clearly link any structure for the “hybrid data generation unit” as required by MPEP 2181. For example, the specification describes a function of the “hybrid data generation unit” (e.g., at paras. [056]-[058]) but does not link any structure to the function.
Claims 7, 9 and 10 recite the limitation “a test target individual breed determination unit for measuring…,” however the disclosure does not clearly link any structure for the “test target individual breed determination unit” as required by MPEP 2181. For example, the specification describes a function of the “test target individual breed determination unit” (e.g., at para. [062]) but does not link any structure to the function.
Claims 2-10 are rejected for depending from claim 1 and failing to remedy the failure of claim 1 to comply with the written description requirement.
Claims 3-6 are rejected for depending from claim 2 and failing to remedy the failure of claim 2 to comply with the written description requirement.
Claims 8-10 are rejected for depending from claim 7 and failing to remedy the failure of claim 7 to comply with the written description requirement.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-20 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claims 1-10, the claim limitations “a population representative individual selection unit” (claim 1), “a genetic population composition determination unit” (claims 1 and 7), “a genome data collection unit” (claim 2), “a homogenous population classification unit” (claims 2 and 3), “a population representative individual genome generation unit” (claims 2, 3, 4, 5 and 6), “a hybrid data generation unit” (claims 7 and 8), and “a test target individual breed determination unit” (claims 7, 9 and 10) invoke 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function.
For example, the specification recites and provides literal support for a function of “a population representative individual selection unit” (para. [046]), “a genetic population composition determination unit” (para. [054]), “a genome data collection unit” (para. [048]), “a homogenous population classification unit” (para. [049]), “a population representative individual genome generation unit” (para. [050]), “a hybrid data generation unit” (paras. [056]-[058]), and “a test target individual breed determination unit” (para. [062]), however, the specification does not link any structures to the functions. Therefore, the claims are indefinite and are rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. As discussed in the MPEP at 2181(II)(A), consideration of the understanding of one skilled in the art in no way relieves the patentee of adequately disclosing sufficient structure in the specification, and it is not enough for the patentee simply to state or later argue that persons of ordinary skill in the art would know what structures to use to accomplish the claimed functions. The inquiry is whether one of skill in the art would understand the specification itself to disclose a structure, not simply whether that person would be capable of implementing that structure.
For purposes of examination and clarity of the record, the limitation “unit” with respect to the foregoing limitations has been interpreted in one embodiment to mean “a computer processor” and interpreted in an alternative embodiment to mean “instructions” (e.g., to measure and determine) executed by a computer processor.
To address the issues above, Applicant may:
(a) Amend the claim so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
If applicant is of the opinion that the support of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181.
In addition to the analysis above, claims 2-10 are indefinite for depending from claim 1 and failing to remedy the indefiniteness of claim 1, as noted above.
Claims 3-6 are indefinite for depending from claim 2 and failing to remedy the indefiniteness of claim 2, as noted above.
Claims 8-10 are indefinite for depending from claim 7 and failing to remedy the indefiniteness of claim 7, as noted above.
Additional issues under 35 U.S.C. 112(b)
Claims 8 and 18 are indefinite for reciting “wherein the Equation represents…” because the claims do not provide any equations, e.g., the table column titled “Equation” provides various expressions but does not provide any equations, and therefore it is not clear as to whether the provided table is missing the equation or if the term “Equation” is supposed to be “expression.”
Claims 1 and 11 recite the limitation "the frequency of occurrence" in line three of each claim. There is insufficient antecedent basis for this limitation in the claim.
Claims 2-10 and 12-20 are indefinite for depending from either of claims 1 or 11 and for failing to remedy the indefiniteness of the claim from which they depend.
Claims 1 and 11 recite the limitation "the respective generation" in line eight of each claim. There is insufficient antecedent basis for this limitation in the claim.
Claims 2-10 and 12-20 are indefinite for depending from either of claims 1 or 11 and for failing to remedy the indefiniteness of the claim from which they depend.
Claims 1 and 11 recite the limitation "the test target individual" in lines nine and ten of each claim. There is insufficient antecedent basis for this limitation in the claim.
Claims 2-10 and 12-20 are indefinite for depending from either of claims 1 or 11 and for failing to remedy the indefiniteness of the claim from which they depend.
Claims 2 and 12 recite the limitation "the respective populations" in line two of each claim. There is insufficient antecedent basis for this limitation in the claim, because claims 1 and 11 recite “respective homogenous populations.”
Claims 3-6 are indefinite for depending from claim 2 and for failing to remedy the indefiniteness of claim 2; and claims 13-16 are indefinite for depending from claim 12 and for failing to remedy the indefiniteness of claim 12.
Claims 2 and 12 recite the limitation "the same genetic locus" in line six of each claim. There is insufficient antecedent basis for this limitation in the claim.
Claims 3-6 are indefinite for depending from claim 2 and for failing to remedy the indefiniteness of claim 2; and claims 13-16 are indefinite for depending from claim 12 and for failing to remedy the indefiniteness of claim 12.
Claims 4 and 14 recite the limitation "the highest frequency of occurrence" in line two of each claim. There is insufficient antecedent basis for this limitation in the claim, because claims 2 and 12 recite “the measured frequency of occurrence.”
Claims 4 and 14 recite the limitation "the genotype" in lines three and four of each claim. There is insufficient antecedent basis for this limitation in the claim, because claims 2 and 12 recite “a preselected genotype” and therefore it is not clear as to whether claims 4 and 14 are referencing a preselected genotype of some other genotype.
Claims 5 and 15 recite the limitation "the individual" in lines one and two of each claim. There is insufficient antecedent basis for this limitation in the claim, because claims 2 and 12 recite “individuals in the homogenous population” and “population representative individuals for the respective homogenous populations” and therefore it is not clear as to which individual claims 5 and 15 are referencing.
Claims 6 and 16 recite the limitation "the genetic similarity between the population representative individuals" in lines one and two of each claim. There is insufficient antecedent basis for this limitation in the claim, because claims 2 and 12 recite “measuring genetic similarity between populations.”
Claims 6 and 16 recite the limitation "the same generation" in line two of each claim. There is insufficient antecedent basis for this limitation in the claim, because claims 1 and 11 recite “the respective generation.”
Claims 7 and 17 recite the limitation " the respective generations" (i.e., plural) in lines two and three of each claim. There is insufficient antecedent basis for this limitation in the claim, because claims 1 and 11 recite “the respective generation” (i.e., singular).
Claims 10 and 20 recite the limitation "the order of high genetic similarity" in line two of each claim. There is insufficient antecedent basis for this limitation in the claim, and claims 10 and 20 are further indefinite because the limitation “of high” is a relative term which is not defined by the claim and the specification does not provide a standard for ascertaining the requisite degree, and therefore it is not clear as to what the metes and bounds are for the term “of high” with regard to “genetic similarity.”
Claims 10 and 20 recite the limitation "the next generation" in line six of each claim. There is insufficient antecedent basis for this limitation in the claim, because claims 7 and 17 recite “the respective generations.”
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 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claims recite: (a) mathematical concepts, (e.g., mathematical relationships, formulas or equations, mathematical calculations); and (b) mental processes, i.e., concepts performed in the human mind, (e.g., observation, evaluation, judgement, opinion).
Claim Interpretations
Claims 1-10 recite the limitation “unit.” As noted above, given the lack of guidance in the specification and the absence of a definition for the limitation of a ‘unit,’ for the purpose of the evaluation of claims 1-10 with respect to eligibility under 35 U.S.C. 101, the limitation “unit” is interpreted to recite an embodiment that means “a computer processor” and an alternative embodiment that means “instructions” executed by a computer processor.
Subject matter eligibility evaluation in accordance with MPEP 2106.
Eligibility Step 1: Step 1 of the eligibility analysis asks: Is the claim to a process, machine, manufacture or composition of matter?
Claims 11-20 recite a method (i.e., a process).
Therefore, these claims are encompassed by the categories of statutory subject matter, and thus satisfy the subject matter eligibility requirements under step 1.
[Step 1: YES]
Claims 1-10 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claim does not fall within at least one of the four categories of patent-eligible subject matter because:
claims 1-10 are directed to an embodiment that is software per se, because the specification does not define the limitation “unit” and one embodiment of the limitation ‘unit’ is interpreted to mean “instructions” executed by a computer processor.
This rejection at Step 1 may be overcome by amending the claimed subject matter to not recite an embodiment that is software per se, e.g., by amending the claim such that the instructions are tied to a physical structure like a computer, memory chip, or specific hardware process, or alternatively, e.g., by deleting the term “unit”. However, overcoming this rejection at Step 1 would not overcome a rejection at Step 2A or Step 2B for the reasons noted below.
[Step 1: NO]
However, in the interest of compact prosecution, claims 1-10 are examined herein with respect to whether the claim is directed to an abstract idea without significantly more.
Eligibility Step 2A: First it is determined in Prong One whether a claim recites a judicial exception, and if so, then it is determined in Prong Two whether the recited judicial exception is integrated into a practical application of that exception.
Eligibility Step 2A Prong One: In determining whether a claim is directed to a judicial exception, examination is performed that analyzes whether the claim recites a judicial exception, i.e., whether a law of nature, natural phenomenon, or abstract idea is set forth or described in the claim.
Independent claim 1 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
measuring the frequency of occurrence of preselected genotypes for individuals in homogenous populations (i.e., mental processes, e.g., counting; and mathematical concepts, e.g., counting, division, summing, proportions), and
selecting population representative individuals for the respective homogenous populations according to the measured frequency of occurrence (i.e., mental processes, e.g., decision-making; and mathematical concepts, e.g., a frequency of occurrence); and
generating hybrid data of the population representative individuals for the respective generation through repetitive hybridization between the population representative individuals (i.e., mental processes, e.g., iterating an analytical procedure), and
determining the genetic population composition of the test target individual according to the genetic similarity between the hybrid data and the test target individual (i.e., mental processes, e.g., evaluating similarity using a similarity algorithm; and mathematical concepts, e.g., calculating genotype frequencies, quantifying how closely genetic features match).
Independent claim 11 recites the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas:
a population representative individual selecting step for measuring the frequency of occurrence of preselected genotypes for individuals in homogenous populations (i.e., mental processes; and mathematical concepts) and
selecting population representative individuals for the respective homogenous populations according to the measured frequency of occurrence (i.e., mental processes; and mathematical concepts); and
a genetic population composition determining step for generating hybrid data of the population representative individuals for the respective generation through repetitive hybridization between the population representative individuals (i.e., mental processes) and
determining the genetic population composition of the test target individual according to the genetic similarity between the hybrid data and the test target individual (i.e., mental processes; and mathematical concepts).
Dependent claims 2-10 and 12-20 further recite the following steps which fall within the mental processes and/or mathematical concepts groupings of abstract ideas, as noted below.
Dependent claim 2 further recites:
measuring genetic similarity between populations using the genetic data and classifying into homogenous populations according to the measurement result (i.e., mental processes; and mathematical concepts); and
measuring the frequency of occurrence of a preselected genotype at the same genetic locus among individuals in the homogenous population and selecting population representative individuals for the respective homogenous populations according to the measured frequency of occurrence to generate a genome for the selected population representative individuals (i.e., mental processes; and mathematical concepts).
Dependent claim 3 further recites:
removes individuals that do not cluster into homogenous populations (i.e., mental processes).
Dependent claim 4 further recites:
selects an individual with the highest frequency of occurrence as the population representative individual (i.e., mental processes; and mathematical concepts),
wherein the population representative individual is randomly selected from two or more individuals having the genotype with the same frequency of occurrence.
Dependent claim 5 further recites:
removes the individual when the frequency of occurrence is less than or equal to a predetermined cutoff frequency (i.e., mental processes; and mathematical concepts).
Dependent claim 6 further recites:
measures the genetic similarity between the population representative individuals within the same generation and selects the population representative individual as one common population representative individual when the measured similarity is higher than a predetermined cutoff similarity (i.e., mental processes; and mathematical concepts).
Dependent claim 7 further recites:
generating hybrid data of the population representative individuals for the respective generations through repetitive hybridization between the population representative individuals (i.e., mental processes); and
measuring the genetic similarity between the hybrid data and the test target individual and determining the breed of the test target individual according to the measurement result (i.e., mental processes; and mathematical concepts).
Dependent claim 8 further recites:
determines a combination according to the formula (Equation, #Representator) at the time of repeated hybridization between the first, second, third and higher generation population representative individuals, using the mathematical expressions provided in the Table in the claim (i.e., mental processes; and mathematical concepts).
Dependent claim 9 further recites:
presumes that the genetic population composition of the population representative individual corresponding to the hybrid data having the highest genetic similarity with the test target individual among the hybrid data is the genetic population composition of the test target individual (i.e., mental processes; and mathematical concepts).
Dependent claim 10 further recites:
sorts the population representative individuals in the order of high genetic similarity with the test target individual (i.e., mental processes; and mathematical concepts),
converts the genetic similarity of the respective sorted population representative individuals into a percentage (i.e., mental processes; and mathematical concepts), and
divides the converted percentage value by the proportion of the respective population representatives in the total population representatives to estimate the divided value as an approximation of a positive integer (i.e., mental processes; and mathematical concepts),
thereby identifying the genetic population composition of the test target individual of the next generation, not a specific generation (i.e., mental processes).
Dependent claim 12 further recites:
a homogenous population classifying step for measuring genetic similarity between populations using the genetic data (i.e., mental processes; and mathematical concepts) and
classifying into homogenous populations according to the measurement result (i.e., mental processes); and
a population representative individual genome generating step for measuring the frequency of occurrence of a preselected genotype at the same genetic locus among individuals in the homogenous population (i.e., mental processes; and mathematical concepts) and
selecting population representative individuals for the respective homogenous populations according to the measured frequency of occurrence to generate a genome for the selected population representative individuals (i.e., mental processes; and mathematical concepts).
Dependent claim 13 further recites:
the homogenous population classifying step removes the individual that does not cluster into homogenous populations (i.e., mental processes).
Dependent claim 14 further recites:
the population representative individual genome generating step selects an individual with the highest frequency of occurrence as the population representative individual (i.e., mental processes; and mathematical concepts),
wherein the population representative individual is randomly selected from two or more individuals having the genotype with the same frequency of occurrence.
Dependent claim 15 further recites:
the population representative individual genome generating step removes the individual when the frequency of occurrence is less than or equal to a predetermined cutoff frequency (i.e., mental processes; and mathematical concepts).
Dependent claim 16 further recites:
the population representative individual genome generating step measures the genetic similarity between the population representative individuals within the same generation (i.e., mental processes; and mathematical concepts) and
selects the population representative individual as one common population representative individual when the measured similarity is higher than a predetermined cutoff similarity (i.e., mental processes; and mathematical concepts).
Dependent claim 17 further recites:
the genetic population composition determining step comprises:
a hybrid data generating step for generating hybrid data of the population representative individuals for the respective generations through repetitive hybridization between the population representative individuals (i.e., mental processes); and
a test target individual breed determining step for measuring the genetic similarity between the hybrid data and the test target individual (i.e., mental processes; and mathematical concepts) and
determining the breed of the test target individual according to the measurement result (i.e., mental processes; and mathematical concepts).
Dependent claim 18 further recites:
the hybrid data generating step determines a combination according to the formula (Equation, #Representator) at the time of repeated hybridization between the first, second, third and higher generation population representative individuals, using the mathematical expressions provided in the Table in the claim (i.e., mental processes; and mathematical concepts).
Dependent claim 19 further recites:
the test target individual breed determining step presumes that the genetic population composition of the population representative individual corresponding to the hybrid data having the highest genetic similarity with the test target individual among the hybrid data is the genetic population composition of the test target individual (i.e., mental processes; and mathematical concepts).
Dependent claim 20 further recites:
the test target individual breed determining step sorts the population representative individuals in the order of high genetic similarity with the test target individual (i.e., mental processes; and mathematical concepts),
converts the genetic similarity of the respective sorted population representative individuals into a percentage (i.e., mental processes; and mathematical concepts), and
divides the converted percentage value by the proportion of the respective population representatives in the total population representatives to estimate the divided value as an approximation of a positive integer (i.e., mental processes; and mathematical concepts),
thereby identifying the genetic population composition of the test target individual of the next generation, not a specific generation (i.e., mental processes).
The abstract ideas recited in the claims are evaluated under the broadest reasonable interpretation (BRI) of the claim limitations when read in light of and consistent with the specification. As noted in the foregoing section, the claims are determined to contain limitations that can practically be performed in the human mind with the aid of a pen and paper (e.g., selecting population representative individuals for the respective homogenous populations according to the measured frequency of occurrence), and therefore recite judicial exceptions from the mental process grouping of abstract ideas. Additionally, the recited limitations that are identified as judicial exceptions from the mathematical concepts grouping of abstract ideas (e.g., measuring the frequency of occurrence of preselected genotypes for individuals in homogenous populations) are abstract ideas irrespective of whether or not the limitations are practical to perform in the human mind.
Therefore, claims 1-20 recite an abstract idea.
[Step 2A Prong One: YES]
Eligibility Step 2A Prong Two: In determining whether a claim is directed to a judicial exception, further examination is performed that analyzes if the claim recites additional elements that when examined as a whole integrates the judicial exception(s) into a practical application (MPEP 2106.04(d)). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed 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 abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d)(III)).
The judicial exceptions identified in Eligibility Step 2A Prong One are not integrated into a practical application because of the reasons noted below.
In the instant application, the claims provide additional elements for collecting and processing ‘genomic data for the respective populations’, however once the data is collected, the subsequent steps only perform analysis and/or calculations using the data to determine the genetic population composition. Thus, the claims do not recite any limitations to which the determined genetic population composition result is practically applied.
Independent claim 11 and dependent claims 13-20 do not further recite any elements in addition to the judicial exception, and thus are part of the judicial exception.
The additional elements in independent claim 1 include:
a population representative individual selection unit (i.e., a computer processor); and
a genetic population composition determination unit (i.e., a computer processor).
The additional elements in dependent claims 2-10 and 12 include:
a genome data collection unit (i.e., a computer processor) (claim 2);
a homogenous population classification unit (i.e., a computer processor) (claims 2 and 3);
a population representative individual genome generation unit (i.e., a computer processor) (claims 2, 3, 4, 5 and 6);
a genetic population composition determination unit (i.e., a computer processor) (claim 7);
a hybrid data generation unit (i.e., a computer processor) (claims 7 and 8);
a test target individual breed determination unit (i.e., a computer processor) (claims 7, 9 and 10); and
collecting genomic data for the respective populations (i.e., gathering data) (claims 2 and 12).
The additional element of a computer processor (claims 1-10) invokes a computer and/or computer-related components merely as a tool for use in the claimed process, such that it amounts to no more than mere instructions to apply the exceptions using a generic computer (MPEP 2106.05(f)), and therefore is not an improvement to computer functionality itself, or an improvement to any other technology or technical field, and thus, does not integrate the judicial exceptions into a practical application (MPEP 2106.04(d)(1)).
The additional element of collecting genomic data for the respective populations (i.e., gathering data) (claims 2 and 12) is merely a pre-solution activity of gathering data for use in the claimed process – a nominal or tangential addition to the claims that does not meaningfully limit the claims, and therefore does not add more than insignificant extra-solution activity to the judicial exceptions (MPEP 2106.05(g)).
Thus, the additionally recited elements merely invoke a computer and/or computer related components as tools; and/or amount to insignificant extra-solution activity; and as such, when all limitations in claims 1-20 have been considered as a whole (i.e., the analysis takes into consideration all the claim limitations and how those limitations interact and impact each other when evaluating whether the exception is integrated into a practical application), the claims are deemed to not recite any additional elements that would integrate a judicial exception into a practical application, and therefore claims 1-20 are directed to an abstract idea (MPEP 2106.04(d)).
[Step 2A Prong Two: NO]
Eligibility Step 2B: Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims are probed for a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they amount to significantly more than the judicial exception (MPEP 2106.05A i-vi).
The claims do not include any additional elements that are sufficient to amount to significantly more than the judicial exception(s) because of the reasons noted below.
Independent claim 11 and dependent claims 13-20 do not further recite any elements in addition to the judicial exception(s).
The additional elements recited in independent claim 1 and dependent claims 2-10 and 12 are identified above, and carried over from Step 2A Prong Two along with their conclusions for analysis at Step 2B. Any additional element or combination of elements that was considered to be insignificant extra-solution activity at Step 2A Prong Two was re-evaluated at Step 2B, because if such re-evaluation finds that the element is unconventional or otherwise more than what is well-understood, routine, conventional activity in the field, this finding may indicate that the additional element is no longer considered to be insignificant; and all additional elements and combination of elements were evaluated to determine whether any additional elements or combination of elements are other than what is well-understood, routine, conventional activity in the field, or simply append well-understood, routine, conventional activities previously known to the industry, specified at a high level of generality, to the judicial exception, per MPEP 2106.05(d).
The additional elements of a computer processor (claims 1-10) and gathering data (claims 2 and 12) are conventional computer components and/or functions (see MPEP at 2106.05(b) and 2106.05(d)(II) regarding conventionality of computer components and computer processes).
Therefore, when taken alone (i.e., individually), all additional elements in claims 1-20 do not amount to significantly more than the above-identified judicial exception(s). Even when evaluated as an ordered combination, the additional elements fail to transform the exception(s) into a patent-eligible application of that exception. Thus, claims 1-20 are deemed to not contribute an inventive concept, i.e., amount to significantly more than the judicial exception(s) (MPEP 2106.05(II)).
[Step 2B: NO]
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over Daw Elbait et al. (“A population-specific major allele reference genome from the United Arab Emirates population.” Frontiers in Genetics, 2021, vol. 12, pp. 1-15) and Dutilh et al. (“Increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly.” Bioinformatics, 2009, vol. 25, no. 21, pp. 2878-2881).
Independent claims 1 and 11 encompass a system and method for generating specific reference genetic data of mixture of population and disease population or breed or hybrid and determining genetic population composition, the method comprising: a population representative individual selecting step for measuring the frequency of occurrence of preselected genotypes for individuals in homogenous populations and selecting population representative individuals for the respective homogenous populations according to the measured frequency of occurrence; and a genetic population composition determining step for generating hybrid data of the population representative individuals for the respective generation through repetitive hybridization between the population representative individuals and determining the genetic population composition of the test target individual according to the genetic similarity between the hybrid data and the test target individual.
Dependent claims 2-10 and 12-20 further define the computational steps used for building the population-specific representative genomes, e.g., repeatedly hybridizing those representatives to create reference data for mixed-generation hybrids, and comparing the test individual against this expanding set of hybrid references to infer the most likely population composition.
Daw Elbait et al. teaches a method for constructing a population specific major allele reference genome from the United Arab Emirates (UAE) population, referred to as the United Arab Emirates Reference Genome (UAERG), and shows that the ethnic composition of the population of a country contributes to the uniqueness of each national DNA sequencing project and, ideally, individual reference genomes are required to reduce the confounding nature of ethnic bias (Abstract).
Dutilh et al. teaches a method for increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly, and shows that the complexity in a natural population may cause an enrichment culture of microbial species to contain multiple related strains, and that this diversity can confound existing strict assembly programs and lead to a fragmented assembly (Abstract).
Regarding independent claims 1 and 11, Daw Elbait et al. shows that a total of 1,028 UAE nationals were recruited as part of the 1,000 Arab genome project, with one thousand of the samples genotyped using the Illumina OmniExome genotype arrays, and of these samples, 129 samples – 125 for the UAE genome reference construction and four for testing – were selected as the most representative individuals among the sampled set of the population (page 2, col. 2, para. 4).
Regarding independent claims 1 and 11, Daw Elbait et al. does not show a genetic population composition determining step for generating hybrid data of the population representative individuals for the respective generation through repetitive hybridization between the population representative individuals and determining the genetic population composition of the test target individual according to the genetic similarity between the hybrid data and the test target individual.
Regarding independent claims 1 and 11, Dutilh et al. shows a process to decipher the consensus genome of parallel populations of a quasispecies sequenced with short-read Solexa sequencing by using a related genome as a scaffold, and then first mapping the reads to their best possible position on this reference, then asking per reference position which nucleotide is the most highly represented in the population of strains, and because the resulting assembly is already a better approximation of the sequences in the strain population than the external reference, subsequently performing steps to iterate the mapping and assembly procedure to increase the coverage, with the final consensus assembly capturing the majority vote of the genomes in the multi-strain population (page 2878, col. 2, para. 4) using a similarity search algorithm (page 2879, col. 2, paras. 3-4).
Regarding dependent claims 2 and 12, Dutilh et al. further shows collecting genomic sequence read data (page 2879, Section 2.1); forming a consensus genome describing the majority of the population using a similarity search algorithm (page 2879, Section 3.1); and the nucleotide with the highest occurrence in the community was called to align to a particular reference position (page 2879, col. 2, para. 1).
Regarding dependent claims 3 and 13, Dutilh et al. further shows employing a filter for spurious short hits, and thus selecting only those reads that were aligned to the reference over at least 20 nt (page 2879, col. 2, para. 4).
Regarding dependent claims 4 and 14, Daw Elbait et al. further shows that to avoid sampling bias, the WGS samples were carefully chosen from a cohort of 1,000 samples for which genotype array data was available, and the choice of the representative samples was guided by a systematic phylogenetic analysis that selected samples from different parts of the tree to include samples with different ethnic admixtures that better represented the current UAE population (page 12, col. 2, para. 2).
Regarding dependent claims 5 and 15, Daw Elbait et al. further shows genotyping 1,000 samples and selecting those that were the most representative individuals among the sampled set of the population (page 2, col. 2, para. 4).
Regarding dependent claims 6 and 16, Dutilh et al. further shows that after assembly, the whole procedure was iterated, with positions with zero coverage in the assembly being replaced with the nucleotide in the reference genome, and all Solexa reads being re-queried against this new reference, and then carrying out this iteration for at least 10 iterations (page 2879, col. 2, paras. 2-5).
Regarding dependent claims 7 and 17, Dutilh et al. further shows that after assembly, the whole procedure was iterated, with positions with zero coverage in the assembly being replaced with the nucleotide in the reference genome, and all Solexa reads being re-queried against this new reference, and then carrying out this iteration for at least 10 iterations (page 2879, col. 2, paras. 2-5), and further shows that coverage increases by iteration (page 2879, Section 3.2).
Regarding dependent claims 8 and 18, Dutilh et al. does not show the particular formula and/or equation for generating hybrid data at the time of repeated hybridizations between generations of the population, however Dutilh et al. does show a custom script for assembling a consensus genome where for each position on the reference genome, it assessed which of the reads covered it with an aligned region of at least 20 nt, and then the nucleotide with the highest occurrence in the community was called to align to that reference position (page 2879, Section 2.3).
Regarding dependent claims 9 and 19, Dutilh et al. further shows that the method is suited to construct the consensus genome of the most abundant lineage in the sample (page 2880, col. 2, para. 3).
Regarding dependent claims 10 and 20, Dutilh et al. does not show the particular steps for identifying the genetic population composition of the test target individual, however Dutilh et al. does shows that the method is suited to construct the consensus genome of the most abundant lineage in the sample (page 2880, col. 2, para. 3).
Therefore, 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 have modified the method shown by Daw Elbait et al. by incorporating methods for increasing the coverage of a metapopulation consensus genome by iterative read mapping and assembly, as shown by Dutilh et al. and discussed above. One of ordinary skill in the art would have been motivated to combine the methods of Daw Elbait et al. with the methods of Dutilh et al., because Dutilh et al. shows that sequencing coverage increases after each round of querying and assembling the reads to the consensus genome, and therefore more reads can be mapped as the reference is adjusted to the reads, indicating that the assembly becomes more similar to the consensus genome of the community. This modification would have had a reasonable expectation of success given that both Daw Elbait et al. and Dutilh et al. disclose methods for generating a population-specific consensus reference sequence.
Conclusion
No claims are allowed.
This Office action is a Non-Final action. A shortened statutory period for reply to this action is set to expire THREE MONTHS from the mailing date of this application.
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/STEVEN W. BAILEY/Examiner, Art Unit 1687
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