Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
2. References have been lined-through on the attached IDS forms because the required publication year is not included.
ELECTION
3. Applicant's election with traverse of Group I in the reply filed on 04/21/26 is acknowledged. The traversal is on the ground(s) that Groups I-IV fall within CPC class C12Q 1/68 and are directed to a general inventive concept of identifying a homologous recombination deficiency status, and as such there would be no serious burden on the Examiner to search and examine all the claims. This is not found persuasive because the restriction is based on PCT Rules 13.1 and 13.2 regarding lack of same or corresponding special technical feature, which does not take into consideration CPC class. The restriction points out why the Groups lack unity of invention, and the traverse does not point to any error in the restriction. Due to the different special technical features of each of the Groups, different key word searches using different search terms would be required to examine more than one group, imposing a serious burden on the Examiner.
The requirement is still deemed proper and is therefore made FINAL.
4. Claims 17-25, 38-40, 44-46, and 48-50 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 04/21/26.
5. Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
OBJECTIONS
6. Applicant is reminded of the proper content of an abstract of the disclosure.
A patent abstract is a concise statement of the technical disclosure of the patent and should include that which is new in the art to which the invention pertains. The abstract should not refer to purported merits or speculative applications of the invention and should not compare the invention with the prior art.
If the patent is of a basic nature, the entire technical disclosure may be new in the art, and the abstract should be directed to the entire disclosure. If the patent is in the nature of an improvement in an old apparatus, process, product, or composition, the abstract should include the technical disclosure of the improvement. The abstract should also mention by way of example any preferred modifications or alternatives.
Where applicable, the abstract should include the following: (1) if a machine or apparatus, its organization and operation; (2) if an article, its method of making; (3) if a chemical compound, its identity and use; (4) if a mixture, its ingredients; (5) if a process, the steps.
Extensive mechanical and design details of an apparatus should not be included in the abstract. The abstract should be in narrative form and generally limited to a single paragraph within the range of 50 to 150 words in length.
See MPEP § 608.01(b) for guidelines for the preparation of patent abstracts.
7. Claim 43 is objected to because of the following informality: ‘interval’ at the end of line 4 should be ‘intervals’. Correction is required.
NON-PRIOR ART REJECTIONS
8. 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 1-16, 26-37, 41-43, 47, and 51 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.
A) Claims 1-16, 26-37, and 41-42 are indefinite because it cannot be determined what is encompassed by ‘identifying a HRD status based on the LOH score’ in independent claims 1 and 37. As the claims do not recite any correlation between any HRD status and any particular LOH score, it cannot be determined how HRD status is to be identified. Clarification is required.
B) Claim 35 is further indefinite because ‘a tumor purity of the sample’ lacks proper antecedent basis, as claim 1 does not recite a sample comprising a tumor. Correction is required.
C) Claims 41-42 are further indefinite because they depend from claim 37 which is drawn to a system comprising a data storage device, but the further limitations are method steps, so it is unclear how the system of claim 37 is to be further limited. Correction is required.
D) Claims 43, 47, and 51 are indefinite because it cannot be determined what is encompassed by ‘instructions to identify a HRD status’ in independent claim 43, as there is no basis in the claim for correlating HRD status with any particular LOH score; thus, it cannot be determined what instructions are contemplated. In addition, the claims are indefinite because a kit cannot comprise a ‘computer program’, which is not a physical object, but information comprising computer code. Clarification is required.
E) Claim 47 is further indefinite because the further limitation relates to HRD status, but is cannot be determined how this is intended to further limit the claimed kit which comprises a reagent and a computer program. Clarification is required.
9. 35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-16, 26-37, 41-43, 47, and 51 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon or correlation without significantly more. The claims recite a correlation between HRD status and LOH score, or in the case of kit claims 43, 47, and 51, a set of oligonucleotides corresponding to nucleic acid sequences found naturally in the human genome and a computer program. These judicial exceptions are not integrated into a practical application because data gathering steps required to use the correlation do not add a meaningful limitation to the method as they are insignificant extra-solution activity, and because merely placing multiple oligonucleotide judicial exceptions into proximity in a kit in no way alters their individual structures and properties. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the only additional physical limitation involves sequencing SNPs, which was well-understood, routine, and conventional in the prior art, as evidenced by Abkevich et al. (US 2017/0283879), see pages 1-43.
According to the 2019 Revised Patent Subject Matter Eligibility Guidance, an initial two step analysis is required for determining statutory eligibility.
According to the Manual of Patent Examination Procedure (MPEP) sections 2103 through 2106.07(c), which now incorporates the 2019 Revised Patent Subject Matter Eligibility Guidance (2019 PEG), October 2019 Patent Eligibility Guidance Update (October 2019 Update), and the Berkheimer Memo, an initial two step analysis is required for determining statutory eligibility.
Step Analysis
Step 1 requires a determination of whether the claims are directed to a process, machine,
manufacture, or a composition of matter. In the instant case, the Step 1 requirement is satisfied as the claims are directed towards a process.
Step 2 The Step 2 analysis is a two-part analysis, Step 2A and Step 2B.
Step 2A. prong 1 Step 2A, prong 1 requires a determination of whether the claims are directed towards a judicial exception, i.e. a law of nature, natural phenomenon, or an abstract idea, while step 2A, prong 2 requires an analysis of whether the judicial exception integrated into a practical application if the claim recites a judicial exception under Prong 1.
Step 2A. prong 2
Step 2A, prong 2 requires an analysis of whether the judicial exception is integrated into a practical application if the claim recites a judicial exception under Prong 1.
Step 2B
The second part, Step 2B of the two-step analysis is drawn to determining whether any element or combination of elements, in the instant claims is/are sufficient to ensure that the claims as a whole amount to significantly more than the judicial exception.
Following the analysis below the claims are not patent eligible under 35 U.S.C. 101.
Concerning Step 1: YES. Claims 1-16, 26-37, 41-43, 47, and 51 are directed to a method, system, or kit, therefore the claims are directed to a statutory category.
Concerning Step 2A: NO. Claims 1-16, 26-37, and 41-42 rely on abstract steps to determine if a patient is suitable for treatment based on a natural correlation between HRD status and LOH score. In other words, these claims rely on a judicially excluded abstract idea without significantly more. Claims 43, 47, and 51 involve a kit which relies on placing into physical proximity oligonucleotides which correspond to naturally-occurring nucleotide sequences and a computer program which is code or information, and thus not statutory subject matter. In other words, these claims rely on a judicially excluded natural product and a non-statutory element without significantly more.
Concerning Step 2A, prong 1, claims 1-16, 26-37, 41-43, 47, and 51 are directed towards a judicial exception, i.e., a natural correlation or oligonucleotides corresponding to natural nucleotide sequences, as noted above. These claims recite abstract ideas of comparing and parsing data, as these claims recite steps of identifying LOH and calculating HRD status in a manner that could be achieved as a mental step.
Concerning Step 2A, prong 2, the judicial exception of claims 1-16, 26-37, 41-43, 47, and 51 is not integrated into a practical application because of the following.
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, such that the claim is more than a drafting effort designed to monopolize the judicial exception. When the exception is so integrated, then the claim is not directed to a judicial exception.
Claims 1-16, 26-37, and 41-42 do not recite steps beyond the recited steps of sequencing SNPs and identifying HRD status based on LOH score. Claims 43, 47, and 51 do not include elements or components other than judicial exceptions.
Claims 1-16, 26-37, 41-43, 47, and 51 do not recite steps/elements that are construed to be a practical application that apply, rely on, or use the judicial exceptions. The step of sequencing certain SNPs is not a practical application as this step must be applied to realize the judicial exception.
Only claim 27 requires administering a treatment, but this treatment is recited with a high level of generality (simply administering a treatment) which therefore does not add any meaningful limitation to practicing the natural correlation or abstract idea. Claims 26, 28, and 29 only require identifying a treatment, and not administering a treatment.
Concerning Step 2B, claims 1-16, 26-37, 41-43, 47, and 51 do not recite any additional elements that ensure that the claims as a whole amount to significantly more than the judicial exception.
As a result of this analysis, the claims are rejected as being ineligible under 35 U.S.C. 101.
10. 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.
11. 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.
12. 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.
13. This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
14. Claims 1-16, 26-37, 41-43, 47, and 51 are rejected under 35 U.S.C. 103 as being unpatentable over Abkevich et al. (US 2017/0283879).
Regarding independent claim 1, Abkevich discloses a method comprising: sequencing a plurality of SNPs, identifying LOH, calculating an LOH score, and identifying HRD status based on the LOH score. See entire document on pages 1-43.
Regarding independent claim 37, Abkevich discloses a system comprising a data storage device for performing the method. See paragraphs 0016, 0083-0084, and 0127-0148.
Regarding independent claim 43, Abkevich discloses a kit comprising a set of oligonucleotides targeting a plurality of SNPs, and a computer program. See paragraphs 0014, 0017, 0082, and 0085.
Abkevich does not disclose the exact manner of identifying HRD status based on LOH score; that is, targeting SNPs at certain length intervals, identifying both number of LOH SNP loci and number of nonhomozygous SNP loci, and calculating the LOH score as the ratio of LOH SNP loci to nonhomozygous SNP loci.
One of ordinary skill in the art would have been motivated to modify the method, system, and kit of Abkevich in the manner of the independent as well as dependent claims because, in the absence of evidence to the contrary, the limitations not explicitly disclosed by Abkevich would have been determined either by straightforward, logical scientific reasoning based on conventional genomics bioinformatics knowledge, or else determined merely by routine optimization of known-important reaction parameters, which as well established in U.S. patent practice does not support unobviousness (M.P.E.P. 2144.05). For example, Abkevich discusses spacing between SNPs in general in paragraphs 0089 and 0092. The skilled artisan considering Abkevich would have been well versed in knowledge of genomics bioinformatics, and would have been aware that HRD status and LOH score could be calculated in alternative or optimized ways using alternative or optimized algorithms, depending on the desired application and information. It would have been prima facie obvious to one of ordinary skill in the art at the time the application was filed to make the claimed system and kit, and to carry out the claimed method.
If this rejection is traversed, it is requested that Applicant point out in detail why one of ordinary skill in the art considering Abkevich would not have arrived at the claimed method, system, and kit only through straightforward, logical scientific reasoning or routine optimization relating to genomics bioinformatics, or point out a surprising or unexpected result compared with the method of Abkevich.
CONCLUSION
15. No claims are free of the prior art.
16. Na et al. (US 2022/0186322) and Abkevich et al. (US 10,400,287, US 12,221,656, and US 12,421,555) are made of record by the Office as references of interest.
17. Any inquiry concerning this communication or earlier communications from the examiner should be directed to KENNETH R HORLICK whose telephone number is (571)272-0784. The examiner can normally be reached Mon. - Thurs. 8:30 - 6:30.
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, Gary Benzion can be reached at 571-272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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06/11/26
/KENNETH R HORLICK/ Primary Examiner, Art Unit 1681
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