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 .
This action is in response to papers filed 4/30/2026.
Applicant’s election without traverse of ALK, APC, BRAF, BRCA1, BRCA2, EGFR, IDH1, KIT, KRAS, MYC, MYCN, NRAS, PDGFRA, PIK3CA in the reply filed on 10/28/2025 is acknowledged. It is noted that the claim list the term “PGFRA”, however, it appears that the gene should be “PDGFRA” and as such this gene is used in the art provided below.
CLiams 1-8 are pending.
The following rejections are newly applied or modified necessitated by amendment. Response to arguments follows.
This action is FINAL.
Withdrawn Objections and Rejections
The objection is to the claims made in the previous office action is withdrawn based upon amendments to the claims.
The previous 35 USC 112(b) rejection made in the previous office action is withdrawn based upon amendments to the claims.
The 35 USC 102(b) rejection made in the previous office action is withdrawn based upon amendments to the claims.
Newly Applied 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 1-8 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.
The newly applied steps in claim 1 are considered new matter. The reply points to examples, figure 2, 4-6 and paragraphs 32-44. The recitation of Tier 0-V! is provided only in figure 6 and paragraphs 44-53 which states “[0044] FIG. 6 is a schematic view showing tiers for screening patient-specific variants. Tiers are biological characteristics used to increase the probability of detecting ctDNA in a sample of interest, since cells present in tumor tissue are genetically very heterogeneous. As a result of the previous variant screening and categorization, final patient-specific variants are selected through seven tiers (tier 0 to tier VI) for patient-specific variants corresponding to somatic variants. Description of each tier is as follows.
“[0045] Tier 0: variants that occur frequently in tumors or have been frequently reported in tumor databases.
[0046] Tier I: variants detected in a clonal tumor cell population.
[0048] Tier II: variants whose variant allele frequency (VAF) passes the desired threshold.
[0050] Tier III: variants whose variant function score (Tier I) passes the threshold, among the genes involved in the generation/development of tumors.
[0051] Tier IV: variants whose variant function score (Tier II) passes the threshold, among the genes involved in the generation/development of tumors.
[0052] Tier V: variants whose variant function score (Tier II) does not pass the threshold, among the genes involved in the generation/development of tumors.
[0053] Tier VI: variants found in genes other than those involved in the generation/development of tumors.” Although the specification recite these tiers, the specification does not describe the use of these with the steps a-c of the claims. Further, the recitation is limited to somatic variants however the claims are drawn to variant information. The claims are drawn to cancer recurrence, however, there is no description in the claims as to comparing information of the patient specific panel to determine cancer recurrence.
The claims are drawn to identifying patient specific variants from the captured regions by removing false positive variant and selecting variants through a stratification of Tier 0 to Tier VI based on biological characteristics of a tumor.
However the specification does not describe this methodology in such a way that the skilled artisan would be able to determine the patient of interest has cancer recurrence. The specification describes that the tiers are based upon somatic variants, in such a way that each type of variant is measured in distinct methods. For examples tier 0 requires that the variants occur frequently in tumors or databases, however, the specification has not described the methodology of tier 0 nor the use of this with any cancer recurrence. A similar issue is applied to each of the tiers which require analysis in clonal tumor cell population, VAF, generation or development of tumors, and variant not involved in these tumors. The specification has not described any of these steps and further the claims are drawn to any variants.
Newly Applied Claim Rejections - 35 USC § 112
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 1-8 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.
Claims 1-8 are indefinite over step b and “frequently appear in tumor patient groups or variants. The term “frequently” in claim 1 and 8 is a relative term which renders the claim indefinite. The term “frequently” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. In particular it is not clear the metes and bounds of the term “frequently” as such it is not clear which variants would be encompassed.
Claims 1-8 are indefinite over step c of claim 1 and 8. The claims recites the limitation "the blood derived" in step c. There is insufficient antecedent basis for this limitation in the claim. In particular the variant information from a tissue and as such it is not clear where the blood sample is recited.
Claims 1-8 are indefinite over the step of d of claim 1 and 8. In particular the claims are drawn to any patient specific genomic variant, however, step d requires stratification of tiers that based upon the specification would require particular variants methodologies which are not required by the claim steps.
Maintained 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 1-8 are rejected under 35 U.S.C. 101 are rejected under 35 U.S.C. 101 because the claimed invention is directed to the judicial exception of a natural phenomenon, and/or an abstract idea without significantly more. The judicial exception is not integrated into a practical application and the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception for the reasons that follow.
Note that the unpatentability of laws of nature was confirmed by the U.S. Supreme Court in Mayo Collaborative Services v. Prometheus Laboratories, Inc., No. 10-1150 (March 20, 2012).
The unpatentability of abstract ideas was confirmed by the U.S. Supreme court in Bilski v. Kappos, No. 08-964, 2010 WL 2555192 (June 28, 2010) and in Alice Corp. v. CLS Bank Int’l, 134 S. Ct. 2347, 2354 (2014).
Applicant’s attention is directed to the USPTO January 7, 2019 Revised Patent Subject Matter Eligibility Guidance (i.e., “PEG”) available at URL:
<https://www.govinfo.gov/content/pkg/FR-2019-01-07/pdf/2018-28282.pdf>.
Regarding Step 1 of the PEG, the claims are directed to the statutory category of a process.
Regarding Step 2A, prong one, the claims recite the judicial exception of a natural phenomenon. The claims recite relationship between predicting cancer recurrence and information of sequencing information. As in Mayo Collaborative Services v. Prometheus, the recited relationship is a natural phenomenon that exists apart from any human action.
The claims also recite the judicial exception of an abstract idea and particularly mental processes. In particular the step of “analyzing”, which would encompass a step of looking at data. Further, the step of “generating” a panel of information (data) and comparing that information is considered abstract steps of providing data and comparing. Note that the Courts have held that steps that can be performed by a human using mental processes or basic critical thinking, or intangible verbal communication are types of activities that represent abstract ideas.
Regarding abstract mental processes, Applicant’s attention is directed to the Association for Molecular Pathology (AMP) and ACLU v. USPTO and Myriad Genetics (Fed. Cir. 2012)) wherein it is stated at 56-57:
Having determined that steps ii-iv are abstract ideas, we move to the second step of Alice and ask whether the particular mechanism for the detection renders the claims patent-eligible. For this step, Alice dictates that we ask whether the remaining elements, either in isolation or combination with the other non-patent-ineligible elements, are sufficient to “‘transform the nature of the claim’ into a patent-eligible application.” Alice, 134 S. Ct. at 2355 (quoting Mayo, 132 S. Ct. at 1297). There must be a further inventive concept to take the claim into the realm of patent-eligibility. Id. at 2355. In particular these steps merely produce a score.
Thus, the claims recite and are directed to the patent-ineligible concepts of abstract processes and a natural phenomenon.
Regarding Step 2A, prong two, having determined that the claims recite a judicial exception, it is then determined whether the claims recite additional elements that integrate the judicial exception into a practical application.
Herein, the claims do not recite additional steps or elements that integrate the recited judicial exceptions into a practical application of the exception(s). The steps of obtaining, is not method considered an integration as rather, it is using any routine and conventional hybridization methods. Further, the dependent steps merely limit the types of samples/genes detected but do not limit the steps themselves to integrate the method and the judicial exception.
Regarding Step 2B, the next question is whether the remaining elements/steps – i.e., the non-patent-ineligible elements/steps - either in isolation or combination, amount to significantly more than the judicial exception.
Herein, the claims as a whole are not considered to recite any additional steps or elements that amount to significantly more than routine and conventional activity and do not add something “significantly more” so as to render the claims patent-eligible. The additionally recited steps are routine in the prior art.
The claims are using a known method of NGS. Further, DeLaVega (US Patent Application 20190050530 Feb 14, 2019) system for cancer recurrence (para 78). DeLaVega obtaining genomic variant information and genomic sequences (clinically actionable target information) from tissue samples (para 31). DeLaVega comparing these to sequence information from blood from the individual (para 31).
For the reasons set forth above, when the claims are considered as a whole, the claims are not considered to recite something significantly more than a judicial exception and thereby are not directed to patent eligible subject matter.
Response to arguments
The reply traverses the rejection. A summary of the arguments made in the reply is provided below with response to arguments following. The reply asserts that the claims have been amended to require a customized panel that includes a hybridization capture method and use of stratification algorithm and false positive elimination (p. 6). These arguments have been reviewed but have not been found persuasive. These arguments have been reviewed but have not been found persuasive.
The step of hybridization capture method is a well known assay method that is routine and conventional in the prior art that would encompass any hybridization assay commercially known. The step of stratification algorithm and false positive elimination is considered abstract judicial exceptions of applying mathematical algorithms which would also be considered a mental step.
Newly Applied Claim Rejections - 35 USC § 102
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 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.
Claim(s) 8 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by DeLaVega (US Patent Application 20190050530 Feb 14, 2019).
It is noted that claim 8 has been modified from method to a product. The product requires a processor and a memory storing instructions.
With regard to claims 8, DeLaVega teaches a processor and a memory module configured to execute machine readable instructions (para 5-6). The inclusion of instructions is not considered to provide a patentable limitation on the claims because the instructions merely represent a statement of intended use in the form of instructions in a kit. See In re Ngai, 367 F.3d 1336, 70 U.S.P.Q.2d 1862 (Fed. Cir. 2004) (holding that an inventor could not patent known kits by simply attaching new set of instructions to that product). The limitation of “with instructions for …” is considered printed instructions and does not limit the required structures.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KATHERINE D SALMON whose telephone number is (571)272-3316. The examiner can normally be reached 9-530.
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, Wu Cheng (Winston) Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KATHERINE D SALMON/Primary Examiner, Art Unit 1682
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