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 .
Information Disclosure Statement
The IDSs filed 3/11/2025, 3/12/2025, and 9/1/2026 have been considered by the Examiner.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. Priority of US application 62/571,414 filed 10/12/2017 is acknowledged.
Claim Status
Claims 1-17 are pending and are examined on the merits.
Claim Objections
Claim 10 recites “wherein the presence of the mutation in the cancer-specific gene weighs more than the presence of the mutation in the cancer-related genes other than the cancer-specific gene”, which should read as “wherein the presence of the mutation in the cancer-specific gene weighs more than the presence of the mutation in the cancer-related genes.”
Claims 12, 13 and 14 are all objected to because of the following informalities: claims 12, 13 and 14 all recite “at least one of the plurality of cancer gene”, which is not grammatically correct. “plurality of cancer gene” should read as “plurality of cancer genes” Appropriate correction is required.
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 1-17 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 1 recites “wherein the first and cancer gene scores correspond to the omics data before and after the treatment, respectively”. It is not clear what “the first and cancer gene scores” means here.
It is suspected that a “second” is missing so the clause should read as “the first and second cancer gene scores”. Applicant can amend claim 1 accordingly. To advance compact prosecution, claim 1 is interpreted as “wherein the first and second cancer gene scores correspond to the omics data before and after the treatment, respectively”.
Claim 2 recites “wherein the plurality of cancer-related genes comprises at least one of a cancer-related gene…”. It is not clear the metes and bounds among a cancer-related gene, a cancer-specific gene, a DNA-repair gene, a neoepitope. A cancer-specific gene can be a cancer-related genes, a DNA-repair gene can be a cancer-specific gene. A neoepitope is probably a cancer specific gene (suggested by claim 3). Particularly, the difference between “cancer-related genes” and “cancer-specific genes” are not clear. The disclosure provides no definition. Similar indefiniteness also exist in claim 10.
Claim 4 recites “copy number data duplication”. It sounds odd because the other items are about “data” while this item is about “data duplication”, and it is not clear whether Applicant wants to claim “copy number data,” and “duplication data,” or Applicant wants to claim “copy number duplication data”.
Claims 12, 13 and 14 all recite the limitation “the plurality of cancer gene” in their second line. There is insufficient antecedent basis for this limitation in the claim.
“Plurality of cancer-related genes” has an antecedent in claim 1, but not “the plurality of cancer gene”.
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 1-17 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
Step 1: Process, Machine, Manufacture or Composition
claims 1-17 are to a method of evaluating an effectiveness of a treatment for a cancer patient, with a series of functional steps. So a process.
Step 2A Prong One: Identification of Abstract Ideas
The claim(s) recite(s):
Obtaining from the blood omics data of the cancer patient before and after the treatment for a plurality of cancer-related genes, wherein the omics data comprise at least one of DNA sequence data, RNA sequence data, and RNA expression level;
This step does not specify how “obtaining” is performed, but it recites “obtaining” itself. Under a broadest reasonable interpretation (BRI), “Obtaining” encompasses data analysis which leads to “at least one of DNA sequence data, RNA sequence data, and RNA expression level”. This process can be achieved in the human mind, with the help of a pen and paper. Therefore this step equals to an abstract idea of mental processes.
Analyzing the omics data to generate first and second cancer gene scores, wherein the first and cancer gene scores correspond to the omics data before and after the treatment, respectively; and
This step recites analyzing the omics data in a general way, with a purpose to generate cancer gene scores from omics data as input. Under a broadest reasonable interpretation (BRI), this step can be achieved in the human mind using reasoning, analyzing and judging. Therefore this step equates to an abstract idea of mental processes.
Providing the effectiveness of the treatment based on a comparison of the first and second cancer gene scores.
This step recites comparing two cancer gene scores to an opinion or judgement of effectiveness. Under a BRI, this step can be achieved in the human mind using reasoning, analyzing and judging. Therefore this step equates to an abstract idea of mental processes.
Dependent claims further describe data, treatments and data analyzing processes, which are still part of the abstract ideas.
Step 2A Prong Two: Consideration of Practical Application
The claims result in a process of “providing the effectiveness of the treatment”, which is an abstract idea of mental processes. The claims do not recite any additional elements that integrate the abstract idea/judicial exception into a practical application.
This judicial exception is not integrated into a practical application because the claims do not meet any of the following criteria:
An additional element reflects an improvement in the functioning of a computer, or an improvement to other technology or technical field;
an additional element that applies or uses a judicial exception to effect a particular treatment or prophylaxis for a disease or medical condition;
an additional element implements a judicial exception with, or uses a judicial exception in conjunction with, a particular machine or manufacture that is integral to the claim;
an additional element effects a transformation or reduction of a particular article to a different state or thing; and
an additional element applies or uses the judicial exception in some other meaningful way beyond generally linking the use of the judicial exception to a particular technological environment, such that the claim as a whole is more than
a drafting effort designed to monopolize the exception.
Step 2B: Consideration of Additional Elements and Significantly More
The claimed method also recites "additional elements" that are not limitations drawn to an abstract idea. The recited additional elements are drawn to:
obtaining blood from a patient having a cancer;
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because obtaining patient blood samples and obtaining blood omics data are in-significant extra-solution activities (MPEP 2106.05(g))
The claims do not include additional elements that are sufficient to amount of significantly more than the judicial exception because it is routine and conventional to perform the acts of obtaining patient blood samples and obtaining blood omics data in the clinical industry. For example, the courts have recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity (MPEP 2106.05(d).II):
i. Determining the level of a biomarker in blood by any means, Mayo, 566 U.S. at 79, 101 USPQ2d at 1968; Cleveland Clinic Foundation v. True Health Diagnostics, LLC, 859 F.3d 1352, 1362, 123 USPQ2d 1081, 1088 (Fed. Cir. 2017);
v. Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs. Ltd., 818 F.3d at 1377; 118 USPQ2d at 1546;
Viewed as a whole, these additional claim element(s) do not provide meaningful limitation(s) to transform the abstract idea recited in the instantly presented claims into a patent eligible application of the abstract idea such that the claim(s) amounts to significantly more than the abstract idea itself. Therefore, the claim(s) are rejected under 35 U.S.C. 101 as being directed to non-statutory subject matter.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims (1,3), 2, 4-10 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 3-9 of U.S. Patent No. US11810672B2 in view of Oxnard et al., Noninvasive detection of response and resistance in EGFR-mutant lung cancer using quantitative next-generation genotyping of cell-free plasma DNA. Clinical cancer research (2014). The instant claim 3 is part of the reference claim 1. Although the reference claim 1 does not recite “analyzing the omics data to generate first and second cancer gene scores, wherein the first and cancer gene scores correspond to the omics data before and after the treatment, respectively”, the reference claim 1 recites “associating the digital score with at least one of a health status, an omics error status, a cancer prognosis, a therapeutic recommendation, an effectiveness of a treatment”.
Oxnard provides (page 1698, Section “Abstract/Experimental Design”) “Serial assessment of response and resistance was studied in patients with EGFR-mutant lung cancer on a prospective trial of erlotinib”. Serial plasma specimens over therapy teach before/after treatment molecular data, and pretreatment detection and serial response/resistance. Therefore, instant claim 1 plus instant claim 3 are obvious over reference claim 1 combined with Oxnard.
a side-by-side claim mapping is provided here:
18/465.868
US11810672B2
1
3
A method of evaluating an effectiveness of a treatment for a cancer patient, comprising:
obtaining blood from a patient having a cancer;
obtaining from the blood omics data of the cancer patient before and after the treatment for a plurality of cancer-related genes, wherein the omics data comprise at least one of DNA sequence data, RNA sequence data, and RNA expression level;
analyzing the omics data to generate first and second cancer gene scores, wherein the first and cancer gene scores correspond to the omics data before and after the treatment, respectively; and
providing the effectiveness of the treatment based on a comparison of the first and second cancer gene scores.
The method of claim 2, wherein the neoepitope is tumor specific and patient specific.
1
A method of analyzing omics data and treating a patient having a cancer, the method comprising: obtaining blood from the patient having or suspected to have the cancer;
obtaining, from the blood, omics data for a plurality of cancer-related genes, wherein the omics data comprise at least one of DNA sequence data, RNA sequence data, and RNA expression level data; providing an omics record computer system that includes at least one processor and at least one computer readable memory coupled to the processor and configured to digitally store the omics data for the plurality of cancer-related genes in the at least one memory;
calculating, in silico, a digital score from the digital omics data, wherein the digital score is calculated in silico by the sum of (i) counting the number of mutations of cancer-related genes, inflammation-related genes, and DNA-repair genes, (ii) counting changes in methylation or modifications in DNA of cancer-related genes and DNA-repair genes, (iii) counting upregulation or downregulation in expression levels of RNA of cancer-related genes, inflammation-related genes, and DNA-repair genes, (iv) counting the number of tumor- and patient-specific neoepitopes, (v) counting splice variants of cancer-related genes and DNA-repair genes, and (vi) counting changes in length of poly A tail of any cancer-related genes, inflammation-related genes, and DNA-repair genes;
associating the digital score with at least one of a health status, an omics error status, a cancer prognosis, a therapeutic recommendation, an effectiveness of a treatment; and
upon the digital score reaching a threshold value and a majority portion of the digital score is highly weighted as an overexpression of a specific neoepitope;
generating a personalized treatment option for the patient, wherein the personalized treatment option comprises a recombinant nucleic acid encoding one or more tumor- and patient-specific neoepitopes; and
treating the cancer by administering the personalized treatment option to the patient.
2
The method of claim 1, wherein the plurality of cancer-related genes comprises at least one of a cancer-related gene, a cancer-specific gene, a DNA-repair gene, a neoepitope, and a gene not associated with a disease.
2
The method of claim 1, wherein the plurality of cancer-related genes comprises at least one of a cancer-related gene, a cancer-specific gene, a DNA-repair gene, a neoepitope, and a gene not associated with a disease.
4
The method of claim 1, wherein the DNA sequence data are selected from the group consisting of mutation data, copy number data duplication, loss of heterozygosity data, and epigenetic status.
3
The method of claim 1, wherein the DNA sequence data is selected from the group consisting of mutation data, copy number data duplication, loss of heterozygosity data, and epigenetic status.
5
The method of claim 1, wherein the RNA sequence data are selected from the group consisting of mRNA sequence data and splice variant data.
4
The method of claim 1, wherein the RNA sequence data is selected from the group consisting of mRNA sequence data and splice variant data.
6
The method of claim 1, wherein the RNA expression level data are selected from the group consisting of a quantity of RNA transcript and a quantity of a small noncoding RNA.
5
The method of claim 1, wherein the RNA expression level data is selected from the group consisting of a quantity of RNA transcript and a quantity of a small noncoding RNA.
7
The method of claim 1, wherein DNA sequence data are obtained from circulating free DNA.
6
The method of claim 1, wherein DNA sequence data is obtained from circulating free DNA.
8
The method of claim 1, wherein the RNA sequence data are obtained from the group consisting of circulating tumor RNA and circulating free RNA.
7
The method of claim 1, wherein the RNA sequence data is obtained from the group consisting of circulating tumor RNA and circulating free RNA.
9
The method of claim 4, wherein the plurality of cancer-related genes includes a cancer-specific gene, and the score is calculated based on a presence or an absence of a mutation in the cancer-specific gene.
8
The method of claim 3, wherein the plurality of cancer-related genes includes a cancer-specific gene, and the digital score is calculated based on a presence or an absence of a mutation in the cancer-specific gene.
10
The method of claim 9, wherein the presence of the mutation in the cancer-specific gene weighs more than the presence of the mutation in the cancer-related genes other than the cancer-specific gene.
9
The method of claim 8, wherein the presence of the mutation in the cancer-specific gene weighs more than the presence of the mutation in the cancer-related genes other than the cancer-specific gene.
Hence, instant claims (1,3), 2, 4-10 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 3-9 of U.S. Patent No. US11810672B2 in view of Oxnard et al.
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.
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.
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.
Claims 1, 5, 7-8, 12 and 15-17 are rejected under 35 U.S.C. 103 as being unpatentable over Oxnard et al.: (“Noninvasive detection of response and resistance in EGFR-mutant lung cancer using quantitative next-generation genotyping of cell-free plasma DNA”. Clinical cancer research (2014)), in view of Best et al.: (“RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics”. Cancer cell (2015)), and Newman et al.: (“An ultrasensitive method for quantitating circulating tumor DNA with broad patient coverage”. Nature medicine (2014)).
Claim 1 is interpreted as a method for evaluating the effectiveness of a cancer patient treatment. Regarding claim 1, Oxnard provides (page 1698, Section “Abstract/Experimental Design”) “plasma collected from patients with advanced lung cancer or melanoma of a known tumor genotype”, which teaches obtaining blood from a patient having cancer.
Oxnard provides (page 1698, Section “Abstract/Experimental Design”) “Serial assessment of response and resistance was studied in patients with EGFR-mutant lung cancer on a prospective trial of erlotinib”. Serial plasma specimens over therapy teach before/after treatment molecular data, and pretreatment detection and serial response/resistance.
Oxnard does not teach DNA sequence data or RNA sequence data.
Newman provides (page 548, section Abstract) “we introduce cancer personalized profiling by deep sequencing (CAPP-Seq), an economical and ultrasensitive method for quantifying ctDNA. We implemented CAPP-Seq for non-small-cell lung cancer (NSCLC) with a design covering multiple classes of somatic alterations that identified mutations in >95% of tumors.” Somatic alteration/mutation data from ctDNA/cfDNA is DNA-sequence omics data.
Neither Oxnard nor Newman teaches RNA sequence data
Best provides (page 666, Section “Summary”) “We determined the diagnostic potential of TEPs by mRNA sequencing of 283 platelet samples”, which teaches blood-based mRNA sequencing and expression profiling.
Oxnard provides (page 1698, Section “Abstract/Results”) “We identified a reference range for EGFR L858R and exon 19 deletions in specimens from KRAS-mutant lung cancer, allowing identification of candidate thresholds with high sensitivity and 100% specificity. Received operative characteristic curve analysis of four assays demonstrated an area under the curve in the range of 0.80 to 0.94”. Oxnard teaches quantified molecular levels/signatures used for assessment; “cancer gene score” is not the prior-art label but would have been a routine composite score implementation.
Oxnard provides (page 1698, Section “Abstract/Conclusions”) “Noninvasive genotyping of cfDNA using ddPCR demonstrates assay qualities that could allow effective translation into a clinical diagnostic. Serial quantification of plasma genotype allows noninvasive assessment of response and resistance”. Oxnard teaches comparison of serial quantitative biomarkers to infer response/effectiveness.
Regarding claim 5, Oxnard does not teach RNA sequencing. Best provides (page 667, col 1, 2nd para) “The combination of specific splice events in response to external signals and the capacity of platelets to directly ingest (spliced) circulating mRNA can provide TEPs with a highly dynamic mRNA repertoire, with potential applicability to cancer diagnostics”, which suggests the RNA sequence data comprising of mRNA sequence data and splice variant data.
Regarding claim 7, Oxnard provides (page 1698, Section “Abstract/Conclusions”) “Noninvasive genotyping of cfDNA using ddPCR demonstrates assay qualities that could allow effective translation into a clinical diagnostic”. Oxnard teaches cfDNA/cell-free tumor DNA.
Regarding claim 8, Oxnard does not teach RNA sequencing. Best provides (page 667, col 1, 2nd para) “The combination of specific splice events in response to external signals and the capacity of platelets to directly ingest (spliced) circulating mRNA can provide TEPs with a highly dynamic mRNA repertoire, with potential applicability to cancer diagnostics”, which suggests blood RNA/mRNA liquid-biopsy of circulating tumor RNA.
Regarding claim 12, Oxnard provides (page 1698, Section “Abstract/Experimental Design”) “patients with EGFR-mutant lung cancer on a prospective trial of erlotinib”. which teaches drug/targeted therapy selection using actionable mutation status.
Regarding claim 15, Oxnard provides (page 1698, Section “Abstract/Results”) “We identified a reference range for EGFR L858R and exon 19 deletions in specimens from KRAS-mutant lung cancer, allowing identification of candidate thresholds with high sensitivity and 100% specificity”. Oxnard teaches threshold-based quantitative mutation measurement.
Regarding claims 16-17, Oxnard provides (page 1698, Section “Abstract/ Results”) “identified a reference range for EGFR L858R and exon 19 deletions in specimens from KRAS-mutant lung cancer, allowing identification of candidate thresholds with high sensitivity and 100% specificity. Received operative characteristic curve analysis of four assays demonstrated an area under the curve in the range of 0.80 to 0.94. Sensitivity improved in specimens with optimal cfDNA concentrations”, which teaches effectiveness determined by difference between before/after cancer gene score, and a thresholded difference rule; exact difference threshold is a routine implementation detail.
It would have been prima facie obvious to modify Oxnard’s noninvasive assessment of tumor biology through quantitative genotyping of cell-free plasma DNA (ddPCR assays for EGFR, KRAS, and BRAF mutations), with Best’s mRNA sequencing of Tumor-educated blood platelets (TEPs), because Best’s method offers higher accuracy.
One would reasonably expect success as both Oxnard and Best are work on cancer molecular diagnosis through blood-based liquid biopsies, and mRNA sequencing is a proven industrial method.
It would have been prima facie obvious to combine the combined noninvasive assessment of tumor biology using mRNA sequencing of Tumor-educated blood platelets (TEPs) by Oxnard and Best, with Newman’s method of cancer personalized profiling by deep sequencing (CAPP-Seq) of circulating tumor DNA (ctDNA), because Newman’s method is economical and ultrasensitive for quantifying ctDNA.
One would reasonably expect success as Oxnard, Best and Newman are all work on cancer molecular diagnosis through blood-based liquid biopsies, and ctDNA sequencing in addition to mRNA sequencing offers better sensitivity.
Conclusion
No claims are allowed.
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/GL/
Patent Examiner
Art Unit 1686
/Anna Skibinsky/
Primary Examiner, AU 1635
