DETAILED ACTION
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 Status
Claims 1-28 are pending and examined herein.
Claims 1-28 are rejected.
Priority
Claims 1-28 are granted the claim to the benefit of priority to U.S. Provisional application 63/389748 filed 15 July 2022. Thus, the effective filling date of claims 1-28 is 15 July 2022.
Information Disclosure Statement
The information disclosure statement (IDS) was received on 18 August 2023. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement has been considered by the examiner.
Drawings
The drawings received on 15 May 2023 are objected to for the reasons provided below.
The drawings are objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: “400” (in Fig. 4A), “403” (in Fig. 4A), “500” (in Fig. 5), “600” (in Fig. 6), and “700” (in Fig. 7). Corrected drawing sheets in compliance with 37 CFR 1.121(d), or amendment to the specification to add the reference character(s) in the description in compliance with 37 CFR 1.121(b) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code on pages 16-17. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Objections
Claims 1 and 15 are objected to because of the following informalities:
Claims 1 and 15 recite “identifying the number of contributors in the DNA mixture” in lines 3 of the claims but should read “identifying a number of contributors in the DNA mixture”.
Appropriate correction is required.
Claim Interpretation
Claims 1 and 15 recites “an input DNA mixture”. The BRI of the input DNA mixture encompasses data/information about the DNA mixture (see instant disclosure page 5 lines 9-13).
Claims 10 and 24 recite “wherein the supervised learning model includes at least one output from a group comprising: a probability for each possible genotype…, a predicted genotype with the highest probability score… predicted DNA profiles and corresponding prediction probabilities for…”. The BRI of the supervised learning model that includes at least one output from this group is interpreted as the supervised learning model generates at least one prediction from this group.
112/f
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 processing component configured to process an input DNA mixture” in claim 1.
“a component configured to identify the number of contributors in the DNA mixture and select mixtures comprising two DNA contributors” in claim 1.
“a component configured to identify a sex of the two DNA contributors” in claim 1.
“a component configured to identify a concentration of the two DNA contributors” in claim 1.
“a component adapted to determine an individual DNA profile for the two DNA contributors” in claim 1.
“the processing component is configured to deconvolve input DNA mixture comprising at least two DNA contributors into at least two distinct DNA profiles” in claim 11.
“the processing component is configured to determine the at least two distinct DNA profiles without performing a comparison with one or more DNA reference profiles” in claim 12.
The instant disclosure provides “any component or collection of components that perform the functions described above can be generically considered as one or more controllers that control the above-discussed functions. The one or more controllers can be implemented in numerous ways, such as with dedicated hardware or with one or more processors programmed using microcode or software to perform the functions recited above” (instant disclosure page 17 lines 10-14). The components recited in claims 1, 11, and 12 are interpreted as being computer processors which implement software to perform the recited functions.
There is not a clear link to the structure (i.e., an associated algorithm) for the processing component configured to process an input DNA mixture (in claim 1), the component configured to identify a concentration of the two DNA contributors (in claim 1), the component adapted to determine an individual DNA profile for the two DNA contributors (in claim 1), the processing component configured to deconvolve input DNA mixture comprising at least two DNA contributors into at least two distinct DNA profiles (in claim 11), and the processing component configured to determine the at least two distinct DNA profiles without performing a comparison with one or more DNA reference profiles (in claim 12).
The structure (i.e., an associated algorithm) for the component configured to identify the number of contributors in the DNA mixture and select mixtures comprising two DNA contributors is provided in the instant disclosure page 9 line 20 – page 10 line 20. The BRI of the associated algorithm to identify the number of contributors in the DNA mixture and select mixtures comprising two DNA contributors is interpreted as encompasses algorithms which utilizes a count of the number of loci with a minor allele in the mixture to make a determination of contributors.
The structure (i.e., associated algorithm) for the component configured to identify a sex of the two DNA contributors is provided in the instant disclosure page 10 line 23 – page 11 line 20. The BRI of the associated algorithm to identify a sex of the two DNA contributors is interpreted as encompassing algorithms which utilize counts of y-sex markers to determine the presence/absence of male in the mixture.
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/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 limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/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
112/a
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 1-14 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 “a processing component configured to process an input DNA mixture”, “a component configured to identify a concentration of the two DNA contributors, and “a component adapted to determine an individual DNA profile for the two DNA contributors”, claim 11 recites “the processing component configured to deconvolve input DNA mixture comprising at least two DNA contributors into at least two distinct DNA profiles”, and claim 12 recites “the processing component configured to determine the at least two distinct DNA profiles without performing a comparison with one or more DNA reference profiles”. The MPEP states “When a claim containing a computer-implemented 35 U.S.C. 112(f) claim limitation is found to be indefinite under 35 U.S.C. 112(b) for failure to disclose sufficient corresponding structure (e.g., the computer and the algorithm) in the specification that performs the entire claimed function, it will also lack written description under 35 U.S.C. 112(a). See MPEP § 2163.03, subsection VI” (see MPEP 2181(II)(B)). There is an insufficient disclosure for clearly linking the associated structure (i.e., algorithm) for these components. As described below in further detail, it is unclear what the associated structure (i.e., algorithms) are for these separate components due to overlapping function of the processing component and the component adapted to determine an individual DNA profile for the two DNA contributors it is unclear what structure (i.e., algorithm) is associated with which component and it is unclear what the structure (i.e., steps of an algorithm) for a component configured to identify a concentration of the two DNA contributors is. Thus, the claims lack a written description for failure to disclosure corresponding structure (i.e., an algorithm) for each of the separately recited components of the system. Dependent claims 2-10, 13, and 14 are rejected by virtue of their dependency on a rejected claim without alleviating the issue.
112/b
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 1-14, 16, 22, and 23 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.
Claim limitations “a processing component configured to process an input DNA mixture” (in claim 1), “a component configured to identify a concentration of the two DNA contributors” (in claim 1), “a component adapted to determine an individual DNA profile for the two DNA contributors” (in claim 1), “the processing component configured to deconvolve input DNA mixture comprising at least two DNA contributors into at least two distinct DNA profiles” (in claim 11), and “the processing component configured to determine the at least two distinct DNA profiles without performing a comparison with one or more DNA reference profiles” (in claim 12 invokes 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.
There is an insufficient disclosure for clearly linking the associated structure (i.e., algorithm) for “a processing component configured to process an input DNA mixture” (in claim 1), “a component adapted to determine an individual DNA profile for the two DNA contributors” (in claim 1), “the processing component configured to deconvolve input DNA mixture comprising at least two DNA contributors into at least two distinct DNA profiles” (in claim 11), and “the processing component configured to determine the at least two distinct DNA profiles without performing a comparison with one or more DNA reference profiles” (in claim 12). The instant disclosure provides processes for a deconvolution of SNP profiles in the instant disclosure page 12 line 18 – page 13 line 27). However, these processes for deconvolution are not clearly linked to a particular component which renders the metes and bounds of the claims indefinite. The system claim provides a component adapted to determine an individual DNA profile for the two DNA contributors (in claim 1) and also provides that the processing component (which is interpreted as being a separate component) is configured to deconvolve input DNA mixture comprising at least two DNA contributors into at least two distinct profiles (in claim 11) and the processing component is configured to determine the at least two distinct DNA profiles without performing a comparison with one or more DNA reference profiles (in claim 12). Thus, it is unclear what structure (i.e., algorithm) is associated with which component (e.g., do these separate components have the same structure or a different structure and if they have different structures, it is unclear which structure is associated with which component). Dependent claims 2-10, 13, and 14 are rejected by virtue of their dependency on a rejected claim without alleviating the indefiniteness. For the sake of furthering examination, “a processing component configured to process an input DNA mixture” will be interpreted as a component which receives data for processing DNA data through the subsequent components, “a component adapted to determine an individual DNA profile for the two DNA contributors” will be interpreted as encompassing any algorithm for determining an individual DNA profile for the two DNA contributors, “the processing component configured to deconvolve input DNA mixture comprising at least two DNA contributors into at least two distinct DNA profiles” will be interpreted as encompassing any algorithm for determining an individual DNA profile for the two DNA contributor, and “the processing component configured to determine the at least two distinct DNA profiles without performing a comparison with one or more DNA reference profiles” will be interpreted as encompassing an algorithm for determining an individual DNA profile for the two DNA contributor which does not rely on reference DNA profiles.
There is an insufficient disclosure for clearly linking the associated structure (i.e., algorithm) for the component configured to identify a concentration of the two DNA contributors (in claim 1). The instant disclosure provides “a small portion of the SCOPE method such as the exemplary Equation described below may be leveraged to determine the number of contributors in the DNA mixture and the Unknown Concentration Estimation (UCE) method may be leveraged to determine the contributor concentrations of each individual in the mixture… In-silico mixtures may be modelled to calculate the expected mean number of minor alleles for a two-person mixture and the minor contributor's average mAR plateau to compare against the unknown mixtures to estimate the number of contributors and contributor concentrations, respectively” (see instant disclosure page 7 lines 14-27). However, it is unclear what the steps of the Unknown Concentration Estimation method are, and it is further unclear what steps are performed for calculating the minor contributors average mAR plateau and what steps are performed for comparing this minor contributor’s average mAR plateau against the unknown mixtures which leads to an estimate of contributor concentrations. Dependent claims 2- 14 are rejected by virtue of their dependency on a rejected claim without alleviating the indefiniteness. For the sake of furthering examination, the structure (i.e., associated algorithm) for this component will be interpreted as encompassing any algorithm which can predict the concentration of contributors in a DNA mixture.
Therefore, the claim is indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph.
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;
(b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)).
If applicant is of the opinion that the written description 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 by either:
(a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181.
Claims 2 and 16 recite the limitation “wherein the one or more forensic genealogy databases…” in line 1 of the claims. There is insufficient antecedent basis for this limitation in the claim. The indefiniteness arises because the claim does not make clear what “the one or more forensic genealogy databases” is referring to in the claims. Further, it is unclear what active step of the method or part of the system this limitation is meant to further limit. For the sake of furthering examination, this limitation in the system (claim 2) will be interpreted as wherein the system is configured to use a database comprising DNA markers and this limitation in the method (claim 16) is interpreted as using a database comprising DNA markers.
Claim 5 recites “applying a threshold responsive to a predicted DNA marker at each genetic location and the estimated concentrations”, Claim 7 recites “wherein the random forest model is operated to deconvolve two-person mixture”, claim 8 recites “wherein the processing component is used within an identification pipeline”, and claim 9 recites “wherein the processing component is used to identify and select two-person mixtures for processing through the identification pipeline” which renders the metes and bounds of the claims indefinite. The indefiniteness arises because claims 5, 7, 8, and 9 recite a single claim which claims both a system and method steps of using the system. The MPEP states “A single claim which claims both an apparatus and the method steps of using the apparatus is indefinite under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. See In re Katz Interactive Call Processing Patent Litigation, 639 F.3d 1303, 1318, 97 USPQ2d 1737, 1748-49 (Fed. Cir. 2011) (see MPEP 2173.05(p)). For the sake of furthering examination, claim 5 will be interpreted as wherein the system is configured to apply a threshold responsive to a predicted DNA marker at each genetic location and the estimated concentrations”, claim 7 is interpreted as “wherein the random forest model is configured to deconvolve two-person mixture”, and claims 8 and 9 are interpreted as being intended uses of the processing component.
Claim 22 recites “wherein the processing an input DNA mixture is performed within an identification pipeline” and claim 23 recites “wherein the processing an input DNA mixture comprises identifying and selecting two-person mixtures for processing through the identification pipeline” which renders the metes and bounds of the claim indefinite. The indefiniteness arises because it is unclear if these limitations are meant to further limit the active steps of the method or if these limitations are meant to be intended uses of the method. For the sake of furthering examination these limitations will be interpreted as being intended uses of the method claims.
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 1-28 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
(Step 1)
Claims 1-14 fall under the statutory category of a machine and claims 15-28 fall under the statutory category of a process.
(Step 2A Prong 1)
Under the BRI, the instant claims recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mental process”, such as procedures for evaluating, analyzing or organizing information, and forming judgement or an opinion. The instant claims further recite judicial exceptions that are an abstract idea of the type that is in the grouping of a “mathematical concept”, such as mathematical relationships and mathematical equations.
Independent claims 1 and 15 recite a mental process of identifying a number of contributors in the DNA mixture and select mixtures comprising two DNA contributors, identifying a sex of the two DNA contributors, identifying a concentration of the two DNA contributors, and determining an individual DNA profile for the two DNA contributors.
Dependent claims 5 and 19 recite a mental process of applying a threshold response to a predicted DNA marker at each genetic location and the estimated concentration. Dependent claims 7 and 21 recite a mental process of deconvolve two-person mixtures. Dependent claims 11 and 25 recites a mental process of deconvolving input DNA mixture comprising at least two DNA contributors into at least two distinct DNA profiles. Dependent claims 12 and 26 recite a mental process of determining the at least two distinct DNA profiles without performing a comparison with one or more DNA reference profiles.
The claims recite a mental process of identifying a number of contributors in the DNA mixture and select mixtures comprising two contributors (which encompasses analyzing DNA sequence data by counting the number of loci with a minor allele, comparing the number of loci with a minor allele to a mean of an expected number of minor alleles for a number of contributors, and selecting mixtures comprising two contributors for further analysis), identifying a sex of the two DNA contributors (which encompasses analyzing DNA sequence data by making an observation of y-sex markers to determine the presence/absence of male in the mixture and determining a ratio of male to female presence using a signal ratio of the y to x-sex markers in the DNA sequence data), identifying a concentration of the two DNA contributors (which encompasses analyzing sequence count data with difference alleles to determine the amount of certain differing sequences in the DNA mixture), determining an individual DNA profile for the two DNA contributors (which encompasses utilizing differences in sequencing data to determine difference to separate individual profiles of DNA in a mixture which is a process of deconvolution), and applying a threshold responsive to a predicted DNA marker at each genetic location and estimated concentrations (which encompasses analyzing DNA sequence data by comparing a DNA marker at each location and estimated concentrations to a threshold).
Dependent claims 2, 4, 8-10, 14, 16, 18, 22-24, 28 further limit the mental process/mathematical concept recited in the independent claim but do not change their nature as a mental process/mathematical concept. Thus, the claims recite abstract ideas.
(Step 2A Prong 2)
Claims found to recite a judicial exception under Step 2A, Prong 1 are then further analyzed to determine if the claims as a whole integrate the recited judicial exception into a practical application or not (Step 2A, Prong 2). Integration into a practical application is evaluated by identifying whether there are any additional elements recited in the claim and evaluating those additional elements to determine whether they integrate the exception into a practical application.
The additional element in claim 1 of a system comprising components configured to perform judicial exceptions (which is interpreted as being a generic computer comprising processors programed to perform the judicial exceptions see interpretation above and instant disclosure page 17) does not integrate the judicial exceptions into a practical application because this is applying the judicial exceptions to a generic computer without an improvement to computer technology (see MPEP 2106.04(d)(1)). This generic computer system only interacts with judicial exceptions in a manner which the computer is invoked as a tool to perform the judicial exceptions.
The additional element in claim 3 of a supervised learning model, the additional element in claims 6 and 7 of a random forest model, the additional element in claim 17 of training a supervised learning model, the additional element in claims 20 and 21 of the supervised learning model includes a random forest model, the additional element in claim 27 of training a learning model on a plurality of classification features does not integrate the judicial exceptions into a practical application because this generally linking the judicial exceptions of analyzing classification features (which falls under the abstract idea as being abstract data derived from DNA mixture data) and generating analysis outputs of deconvoluting two person mixtures, generating a probability for each possible genotypes, generating a predicted genotype with a highest probability score, predicting DNA profiles and corresponding prediction probabilities for each of the at least two DNA contributors, and identifying a sex of the two DNA contributors (which falls under the abstract idea of solutions of an abstract analysis performed on the abstract data) to the technological environment of supervised learning models, random forest models, and training models (see MPEP 2106.05(h)). The recited claims do not provide an improvement to these models through training, rather the models and training of the models are generally linked to the judicial exceptions of recited in the claims.
(Step 2B)
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself (Step 2B). The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because:
The additional element in claim 1 of using a generic computer to perform judicial exceptions is conventional as shown by MPEP 2106.05(b) and 2106.05(d)(II).
The additional element in claim 3 of a supervised learning model, the additional element in claims 6 and 7 of a random forest model, the additional element in claim 17 of training a supervised learning model, the additional element in claims 20 and 21 of the supervised learning model includes a random forest model, the additional element in claim 27 of training a learning model are conventional as shown by Singh et al. (2016 3rd international conference on computing for sustainable global development (INDIACom). Ieee, 2016).
Thus, the additional elements are not sufficient to amount to significantly more than the judicial exception because they are conventional.
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, 2, 5, 8, 9, 11, 12, 15, 16, 19, 22, 23, 25, and 26 are rejected under 35 U.S.C. 103 as being unpatentable over Ricke et al. (US 20210017592 A1) in view of Allen (US 20140147849 A1; cited in IDS received 18 August 2023).
Independent claim 1 is directed to a system comprising a processing component configured to process an input DNA mixture, a component configured to identify the number of contributors in the DNA mixture and select mixtures comprising two DNA contributors;
Ricke et al. shows a computer system for processing DNA mixture data (Ricke et al. [0288]). Ricke et al. shows calculating a predictive value for a number of contributors in a DNA sample (Ricke et al. [0288], [0292]-[0294], and Fig. 11). Ricke et al. shows analyzing mixtures comprising two DNA contributors for the process of deconvoluting the mixture into individual profiles (Ricke et al. [0548]).
a component configured to identify a concentration of the two DNA contributors;
Ricke et al. shows identifying a concentration of the DNA contributors in a mixture of two contributors using computational methods for analyzing DNA sequence data (Ricke et al. [0283]-[0286]).
a component adapted to determine an individual DNA profile for the two DNA contributors.
Ricke et al. shows direct deconvolution of a complex DNA mixture to individual contributors and/or components by calculating a minor allele ratio (mAR) at each locus (Ricke et al. [0435]). Ricke et al. further shows that within mixtures, the observed mAR values directly correlate with the number of contributing individuals and their relative DNA molar concentrations and that these correlations can be leveraged to identify the presence of and/or separate individual contributors DNA profiles (Ricke et al. [0435]).
Ricke et al. shows that a gender of an individual can be predicted for signal contributor samples by examining SNP and STR loci on the X and Y chromosomes but does not explicitly show a component configured to identify a sex of the two DNA contributors
Like Ricke et al., Allen shows analyzing DNA information from forensic samples which contain mixtures. Allen shows using DNA sequence information on X and Y chromosomes specific genes to determine the sex of the sample and the possible existence of male and female mixtures in extracts (Allen [0004] and [0010]). Allen shows the gender of the DNA donor(s) can be determined by comparing X and Y amplicons of amelogenin and the X chromosome version of amelogenin is shorter than the Y chromosome version, and the two can thus be readily distinguished from each other (Allen [0009]).
Independent claim 15 is directed to a method comprising: processing an input DNA mixture, identifying the number of contributors in the DNA mixture and select mixtures comprising two DNA contributors
Ricke et al. shows processing input DNA mixture data (Ricke et al. [0288]). Ricke et al. shows calculating a predictive value for a number of contributors in a DNA sample (Ricke et al. [0288]). Ricke et al. shows analyzing mixtures comprising two DNA contributors for the process of deconvoluting the mixture into individual profiles (Ricke et al. [0548]).
identifying a concentration of the two DNA contributors
Ricke et al. shows identifying a concentration of the DNA contributors in a mixture of two contributors (Ricke et al. [0283]-[0286]).
determining an individual DNA profile for the two DNA contributors.
Ricke et al. shows determining an individual DNA profile for a major and a minor contributor from a complex DNA mixture (Ricke et al. [0059]). Ricke et al. shows direct deconvolution of a complex DNA mixture to individual contributors and/or components by calculating a minor allele ratio (mAR) at each locus (Ricke et al. [0435]). Ricke et al. further shows that within mixtures, the observed mAR values directly correlate with the number of contributing individuals and their relative DNA molar concentrations and that these correlations can be leveraged to identify the presence of and/or separate individual contributors DNA profiles (Ricke et al. [0435]).
Ricke et al. shows that a gender of an individual can be predicted for signal contributor samples by examining SNP and STR loci on the X and Y chromosomes but does not explicitly show identifying a sex of the two DNA contributors.
Like Ricke et al., Allen shows analyzing DNA information from forensic samples which contain mixtures. Allen shows using DNA sequence information on X and Y chromosomes specific genes to determine the sex of the sample and the possible existence of male and female mixtures in extracts (Allen [0004] and [0010]). Allen shows the gender of the DNA donor(s) can be determined by comparing X and Y amplicons of amelogenin and the X chromosome version of amelogenin is shorter than the Y chromosome version, and the two can thus be readily distinguished from each other (Allen [0009]).
Claim 2 is directed to wherein the system is configured to use a database comprising DNA markers and claim 16 is directed to using a database comprising DNA markers.
Ricke et al. shows using a database comprising DNA markers (Ricke et al. [0049], [0055], and [0063]).
Claims 5 and 19 are directed to further comprising applying a threshold responsive to a predicted DNA marker at each genetic location and the estimated concentrations.
Ricke et al. shows applying a threshold responsive to a predicted DNA maker and the estimated concentrations to determine if a minor allele is present in the mixture by using estimated concentrations to determine sequencing signal variability for filtering (Ricke et al. [0741]-[0743] and [0745]-[0747]).
Claims 8 and 22 are directed to wherein the processing an input DNA mixture is performed within an identification pipeline. Claims 9 and 23 are directed to wherein the processing an input DNA mixture comprises identifying and selecting two-person mixtures for processing through the identification pipeline.
These limitations are interpreted as being an intended use of the system and intended use of the method. Ricke et al. shows the system and the method may be used for determining individuals from complex mixtures (e.g., an identification pipeline) (Ricke et al. [0043]).
Claims 11 and 25 are directed to deconvolving input DNA mixture comprising at least two DNA contributors into at least two distinct DNA profiles. Claims 12 and 26 are directed to determining the at least two distinct DNA profiles without performing a comparison with one or more DNA reference profiles.
Ricke et al. shows determining individual profiles from mixtures utilizing a multiple methods (Ricke et al. [0547] – [550]). Ricke et al. shows applying these methods to a mixture of two individuals (Ricke et al. [0548]). Ricke et al. further shows that these methods for deconvolving DNA mixtures identify individuals in mixtures without known reference samples (Ricke et al. [0547]).
An invention would have been obvious to one or ordinary skill in the art if some motivation in the prior art would have led that person to modify reference teachings to arrive at the claimed invention. It would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have modified the gender determination prediction of Ricke et al. to incorporate the use of comparing X and Y amplicons of amelogenin of Allen because this would allow for the ability of distinguishing X and Y versions of the amplicons to make a determination of gender in mixed samples which is useful in forensic cases (Allen [0009]). One would have a reasonable expectation of success because both Ricke et al. and Allen show analyzing DNA mixture samples and gender determination utilizing information of X and Y sequence markers while Allen shows utilizing a particular marker which is distinguished by amplicon length to make a determination of gender of DNA donors/contributors to a sample.
Claims 3, 4, 10, 17, 18, and 24 are rejected under 35 U.S.C. 103 as being unpatentable over Ricke et al. in view of Allen as applied to claims 1 and 15 above, and further in view of Scheffler et al. (US 20220262460 A1).
Claim 3 is directed to the system further comprising a supervised learning model, the model being trained on a plurality of classification features relating to the input DNA mixture. Claim 17 is directed to further comprising training a supervised learning model on a plurality of classification features relating to the input DNA mixture.
Ricke et al. in view of Allen does not show a supervised learning model, the model being trained on a plurality of classification features relating to the input DNA mixture or training a supervised learning model on a plurality of classification features relating to the input DNA mixture.
Like Ricke et al. in view of Allen, Scheffler et al. shows analyzing DNA mixture samples utilizing computational methods. Scheffler et al. shows a probabilistic mixture model for which analyzes allele counts for each of the alleles at the polymorphism loci to determine a probability that a specific contributor among the one or more contributors has a specific genotype (Scheffler et al. abstract and [0007]). Scheffler et al. further shows performing numerical optimization for adjusting the parameters of the probabilistic mixture model which analyzes the DNA mixture data which is interpreted as a process of training the probabilistic mixture model (Scheffler et al. [0086] and [0265]-[0270]).
Claims 4 and 18 are directed to wherein the plurality of classification features comprises at least one of a group comprising: a plurality of autosomal loci, estimated concentrations for minor and major contributors, minor allele counts ratio for each autosomal loci within the input DNA mixture, number of loci with a minor allele within the input DNA mixture, and global allele frequencies for each of the plurality of autosomal loci.
Ricke et al. shows utilizing DNA concentrations of contributors to deconvolve the mixture (Ricke et al. [0066]). Scheffler et al. shows the probabilistic mixture model utilizes a concentration parameter (Scheffler et al. [0017]).
Claims 10 and 24 are directed to wherein the supervised learning model includes at least one output from a group comprising: a probability for each possible genotype combination contained in the mixture, a predicted genotype with a highest probability score, and predicted DNA profiles and corresponding prediction probabilities for each of the at least two DNA contributors.
Scheffler et al. shows that the probabilistic mixture model reports plausible genotype configurations and associated probabilities for the DNA mixture sample (which is interpreted as predicted DNA profiles and corresponding prediction probabilities for each of the at least two DNA contributors) (Scheffler et al. [0274]).
An invention would have been obvious to one or ordinary skill in the art if some motivation in the prior art would have led that person to modify reference teachings to arrive at the claimed invention. It would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have modified the determination of the DNA profile of individuals in the DNA mixture of Ricke et al. to incorporate the use of the probabilistic mixture model for determining genotype probabilities of Scheffler et al. because this model allows for the ability of determining individual contributor DNA profiles when the genotype of both contributors are unknown (Scheffler et al. [0004] and [0010]). One would have a reasonable expectation of success because Ricke et al. in view of Allen show analyzing DNA mixture samples to determine individual DNA profiles while Scheffler et al. shows a particular model for which predicts DNA profiles of individual contributors when both contributors genotypes are unknown.
Claims 6, 7, 20, and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Ricke et al. in view of Allen in view of Scheffler et al. as applied to claims 3 and 17 above, and further in view of Alotaibi (International Journal of Advanced Computer Science and Applications 12.11 (2021)).
Claims 6 and 20 are directed to wherein the supervised learning model includes a random forest model. Claims 7 and 21 are directed to wherein the random forest model is operated to deconvolve two-person mixtures.
Ricke et al. in view of Allen in view of Scheffler et al. do not show random forest model.
Like Ricke et al. in view of Allen in view of Scheffler et al., Alotaibi et al. shows analyzing DNA mixtures utilizing computational models. Alotaibi et al. shows analyzing DNA mixture data for DNA profiling utilizing a Random forest model (Alotaibi et al. page 131 right col.).
It would have been obvious to one of ordinary skill in the art before the effective filling date of the invention to have substituted the model for determination of individual DNA profiles for a DNA mixture which leverages classification features from the data of Ricke et al. in view of Allen in view of Scheffler et al. with the use of a random forest model of Alotaibi et al. because Alotaibi et al. shows the ability of the random forest model be trained to analyze DNA mixtures and would lead to predictable results of utilizing a random forest model for determining individual DNA profiles of contributors by training the random forest model with the classification features informative for this prediction task.
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 action.
Claims 13, 14, 27, and 28 are free of the prior art of record. Ricke et al. (US 20210017592 A1) is the closest prior art of record which shows identifying contributors in a mixed sample, identifying a concentration of contributors in the mixed sample, and determining individual DNA profiles for two contributors. However, the prior art of record does not show “a learning model, the model being trained on a plurality of classification features relating to the input DNA mixture”, “wherein the plurality of classification features comprises a total number of counts of non-autosomal loci of the input DNA mixture at each sex genetic location”, “wherein the identifying a sex of the two DNA contributors comprises training a learning model on a plurality of classification features relating to the input DNA mixture”, or “wherein the plurality of classification features comprises a total number of counts of non-autosomal loci of the input DNA mixture at each sex genetic location”. Thus, claims 13, 14, 27, and 28 are free of the prior art of record.
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/JONATHAN EDWARD HAYES/Examiner, Art Unit 1685
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