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 .
Priority
Acknowledgment is made of Applicant's claim for priority to the following application(s):
* PCT/US2023/072035 filed on 10 August 2023
* 63398496 filed 16 August 2022
Information Disclosure Statement
The information disclosure statement(s) (IDS) submitted on the following date(s) is/are entered and considered by Examiner:
* 12 February 2025
Response to Amendment
The preliminary amendment filed on 12 February 2026 is hereby entered and considered.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim(s) 1-6,8-10,12-18,21-22 and 24-25 is/are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract idea without significantly more.
Claim 1 recites:
A method for determining a DNA mismatch repair deficiency (MMRD) status comprising:
receiving, at one or more processors, sequence read data for a plurality of sequence reads derived from a sample from an individual;
extracting, using the one or more processors, two or more genomic features of the sample based on the sequence read data;
determining, using the one or more processors, a MMRD probability score for the sample based on the two or more extracted genomic features and a machine learning model configured to process genomic feature input data and output MMRD probability scores; and
comparing the MMRD probability score, using the one or more processors, to one or more predetermined thresholds to determine a MMRD status for the sample from the individual.
Step 1:
The claim as a whole falls within at least one statutory category, i.e. a process, machine, manufacture, or composition of matter.
Step 2A Prong One:
The highlighted portion, as drafted, is a process that, under its broadest reasonable interpretation, falls under “Certain methods of organizing human activity” because determining a user’s risk for DNA mismatch copy is traditionally performed by a physician when treating a patient, i.e. managing personal behavior or relationships or interactions between people (including social activities, teaching, and following rules or instructions). MPEP 2106.04(a)(2)(II)
The highlighted portion, as drafted, is a process that, under its broadest reasonable interpretation, falls under “Mental processes”.
But for a generic computer recited with a high level of generality in a post hoc manner to implement the abstract idea, the steps above may be practically performed in the human mind.
Accordingly, these limitations have been found to be directed towards concepts performed in the human mind (including an observation, evaluation, judgment, opinion). MPEP 2106.04(a)(2)(III)
The different categories of abstract ideas are being considered together as one single abstract idea. MPEP 2106.04(II)(B)
Dependent claim(s) recite(s) additional subject matter which further narrows or defines the abstract idea embodied in the claims (such as claim(s) 2-6,8-10,12-18,21-22 reciting limitations further defining the abstract idea, which may be performed in the mind but for recitation of generic computer components, and/or may be a method of managing relationship or interactions between people).
Step 2A Prong Two:
This judicial exception is not integrated into a practical application. In particular, the claim recites the following additional element(s), if any:
receiving, at one or more processors, sequence read data for a plurality of sequence reads derived from a sample from an individual;
using the one or more processors,
The additional element(s) do(es) not integrate the abstract idea into a practical application, other than the abstract idea per se.
The generic processor amount(s) to mere instructions to apply an exception (invoking computers as a tool to perform the abstract idea). MPEP 2106.05(f))
The receiving step merely add(s) insignificant extra-solution activity to the abstract idea (mere data gathering, selecting a particular data source or type of data to be manipulated, insignificant application). MPEP 2106.05(g))
Dependent claim(s) recite(s) additional subject matter which amount to limitation(s) consistent with the additional element(s) in the independent claims).
Looking at the limitations as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely provide conventional computer implementation and do not impose a meaningful limit to integrate the abstract idea into a practical application.
Accordingly, the additional elements do not integrate the judicial exception into a practical application because it does not impose any meaningful limits on practicing the abstract idea.
Accordingly, the claim recites an abstract idea.
Step 2B:
The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception. As discussed above with respect to integration of the abstract idea into a practical application, the additional elements amount to no more than mere instructions to apply an exception, add insignificant extra-solution activity to the abstract idea, and/or generally link the abstract idea to a particular technological environment or field of use.
The additional elements, as discussed above and incorporated herein, amount to no more than mere instructions to apply an exception, add insignificant extra-solution activity to the abstract idea, and/or generally link the abstract idea to a particular technological environment or field of use, as discussed above and incorporated herein.
Mere instructions to apply an exception, insignificant extra-solution activity, and linking to a particular technological environment using a generic computer component cannot provide an inventive concept.
Regarding the receiving step, this limitation amount(s) to element(s) that have been recognized as well-understood, routine, and conventional activity in particular fields (e.g., receiving or transmitting data over a network, Symantec, MPEP 2106.05(d)(II)(i)). MPEP 2106.05(d)(II)(ii))
Dependent claims recite additional subject matter which amount to limitations consistent with the independent claim. MPEP 2106.05(d)(II)(ii))
Looking at the limitations as an ordered combination adds nothing that is not already present when looking at the elements taken individually. There is no indication that the combination of elements improves the functioning of a computer or improves any other technology. Their collective functions merely provide conventional computer implementation.
The claim is not patent eligible.
Claim(s) 24-25 recite(s) substantially similar limitations as those of claim(s) 1 above, and are therefore rejected for substantially similar rationale as applied above, and incorporated herein.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1-6, 8-10, 12-18, 22, 24-25 is/are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Berger (20210155992).
Claim 1: Berger discloses:
A method (Title illustrating a method) for determining a DNA mismatch repair deficiency (MMRD) (Abstract illustrating detecting microsatellite instability in nucleic acid sequence reads) status comprising:
receiving, at one or more processors (Figure 1A illustrating a processor), sequence read data for a plurality of sequence reads derived from a sample from an individual (paragraph 0117 illustrating receiving the recited data from a patient);
extracting, using the one or more processors, two or more genomic features of the sample based on the sequence read data (paragraph 0125-127 illustrating extracting the genetic sequence, paragraph 0142 illustrating a plurality of genes disclosed in the Specification’s exemplary embodiments);
determining, using the one or more processors, a MMRD probability score for the sample based on the two or more extracted genomic features and a machine learning model configured to process genomic feature input data and output MMRD probability scores (paragraph 0137 illustrating determining a probability using ML model); and
comparing the MMRD probability score, using the one or more processors, to one or more predetermined thresholds to determine a MMRD status for the sample from the individual (paragraph 0159-0161 illustrating comparing the score to a threshold to determine the likelihood of a gene permutation).
Claim 2, Berger discloses:
wherein the MMRD probability score is compared to a first predetermined threshold, and wherein a MM RD-positive status is determined if the MMRD probability score is greater than the first predetermined threshold, or a MM RD-negative status is determined if the MMRD probability score is less than or equal to the first predetermined threshold (para [0158]-[0161] illustrating comparing the value to the threshold to determine the status of the patient’s genomic mutation).
Claim 3, Berger discloses:
wherein the MMRD probability score is compared to a first predetermined threshold and to a second predetermined threshold, and wherein a MMRD positive status is determined if the MMRD probability score is greater than the first predetermined threshold, a MMRD-negative status is determined if the MMRD probability score is less than the second predetermined threshold, or a MMRD-ambiguous status is determined if the MMRD probability score is less than or equal to the first predetermined threshold but greater than or equal to the second predetermined threshold (para [0139], [0158]-[0161] illustrating determining that the patient has a lower value than the threshold value to indicate mutation).
Claim 4: Berger discloses:
further comprising making a treatment decision for the individual based on a determination of MMRD positive status (para [0134]-[0135], [0145], [0160]-[0163] illustrating suggesting a treatment).
Claim 5: Berger discloses:
wherein the treatment decision comprises treating the individual with an immune checkpoint inhibitor (para [0134]-[0135], [0145], [0160]-[0163] illustrating providing immune-deficient patients with a treatment recommendation).
Claim 6: Berger discloses:
further comprising making a recommendation for follow-up germ line testing of the subject based on a determination of MMRD-positive status (para [0137] illustrating germline mutations).
Claim 8: Berger discloses:
wherein the two or more genomic features comprise two or more of a fraction unstable score, a composite COSMIC single-base substitution signature, a COSMIC indel signature, a copy number signature, a tumor mutational burden score, a blood-based tumor mutational burden score, a germline status for a mutation in one or more genes associated with DNA mismatch repair (MMR), a methylation status for one or more genes associated with DNA mismatch repair (MMR), a methylation status for one or more promoters associated with the one or more genes associated with DNA mismatch repair (MMR), or any combination thereof (para [0126]-[0127], [0134]-[0142] illustrating determining the comparison status of the recited genes).
Claim 9: Berger discloses:
wherein the mutation in one or more genes associated with MMR is a mutation in MSH2, MSH6, PMS2, or MLH1 (para [0126]-[0127], [0139]-[0142] illustrating the recited genes).
Claim 10: Berger discloses:
wherein the machine learning model comprises a supervised learning model (para [0160] illustrating training with known samples [considered to be a form of “supervised” learning]).
Claim 12: Berger discloses:
wherein the machine learning model has been trained using a training data set comprising data for the two or more genomic features for a plurality of training samples (para [0148], [0159]-[0166] illustrating using training data).
Claim 13: Berger discloses:
wherein the plurality of training samples comprises only MMRD positive and MMRD-negative training samples (para [0148], [0159]-[0166] illustrating using training data).
Claim 14: Berger discloses:
wherein the plurality of training samples comprises MMRD positive, MM RD-negative, and MMRD ambiguous training samples (para [0148], [0159]-(0166] illustrating using the recited genes as training data ).
Claim 15: Berger discloses:
wherein the MMRD-positive training samples comprise samples having an identified alteration in a gene known to be associated with DNA mismatch repair (MMR) (para [0148], [0159]-(0166] illustrating identifying DNA mismatch).
Claim 16: Berger discloses:
wherein the identified alteration is in MSH2, MSH6, PMS2, or MLH1 (para (0126]-[0127], [0139]-(0142] disclosing the recited genes).
Claim 17: Berger discloses:
wherein the training data set is periodically or continuously updated, and used to periodically or continuously retrain the machine learning model (para [0148]-[0149], [0159]-(0166] illustrating updating the training [considered to be a form of “periodically”] data).
Claim 18: Berger discloses:
wherein the MMRD probability score comprises a real-valued number ranging from 0.0 to 1.0 (para (0158]-[0160] illustrating the values within the recited range).
Claim 22: Berger discloses:
wherein the determination of MMRD status is used to diagnose or confirm a diagnosis of disease in the individual (para [0056], [0158]-(0161] illustrating confirming the diagnosis of the patient’s DNA copy mismatch).
Claim(s) 24-25 recite(s) substantially similar limitations as those of claim(s) 1 above, and are therefore rejected for substantially similar rationale as applied above, and incorporated herein.
In particular, Berger discloses a computer and associated CRM (see at least Figure 1A illustrating a computer and associated hardware components).
Claim Rejections - 35 USC § 103
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claim(s) 21 is/are rejected under 35 U.S.C. 103 as being unpatentable over Berger in view of Danaher (20210198748).
Claim 21: Berger does not disclose:
further comprising determining a gene expression score for one or more genes associated with MMR and using the one or more determined gene expression scores as input for the machine learning model, wherein the machine learning model has been trained using a training data set that further comprises gene expression data for the one or more genes associated with MMR.
Danaher discloses:
further comprising determining a gene expression score for one or more genes associated with MMR and using the one or more determined gene expression scores as input for the machine learning model, wherein the machine learning model has been trained using a training data set that further comprises gene expression data for the one or more genes associated with MMR (para [0072], [0133] illustrating using gene expression to determine the gene mismatch).
Before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill in the art to include the algorithm of Danaher within the gene calculation system of Berger with the motivation of improving patient care by using a known algorithm to improve the accuracy of gene mutation determination (Danaher; page 1 paragraph 0004).
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Bell (11043283) discloses identifying a DNA mutation for a patient (Abstract) in a manner similar to those disclosed in the instant pending Specification as originally filed.
Eun (20210027896) discloses processing patient data to determine a genetic condition (Abstract) in a manner similar to those disclosed in the instant pending Specification as originally filed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TRAN N NGUYEN whose telephone number is (571)272-0259. The examiner can normally be reached Monday-Friday 9AM-5PM Eastern.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, KAMBIZ ABDI can be reached on (571)272-6702. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/T.N.N./ Examiner, Art Unit 3685 /KAMBIZ ABDI/Supervisory Patent Examiner, Art Unit 3685
Prosecution Insights