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 .
Election/Restrictions
Applicant’s election of Group I in the reply filed on 02/25/2026 is acknowledged. Applicant states that the claims have been amended and that claims 29 and 34 properly belong in Group I, as opposed to Group II. This is not found persuasive because this application is a national stage application and thus, where a group of inventions is claimed in a national stage application, the requirement of unity of invention shall be fulfilled only when there is a technical relationship among those inventions involving one or more of the same or corresponding special technical features. The expression “special technical features” shall mean those technical features that define a contribution which each of the claimed inventions, considered as a whole, makes over the prior art. Claims 29 and 34 do not share the same or corresponding special technical feature as claims 1-5, 7, 8, 10, 12, 13, 16, and 18 of Group I. Instead, claims 29 and 34 share a technical feature with claims 36, 37, and 41-43 of Group II. The requirement is still deemed proper and is therefore made FINAL.
Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 29, 34, 36, 37, and 41-43 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claims Status
Claim 14 is canceled.
Claims 29, 34, 36, 37, and 41-43 are withdrawn from consideration.
Claims 1-5, 7, 8, 10, 12, 13, 16, and 18 are examined on the merits herein.
Priority
The instant application is a national stage application of PCT/US20/55093, filed 10/09/2020, which claims priority to US provisional application No. 62/912727, filed 10/09/2019. Therefore, the Effective Filing Date (EFD) assigned to each of the claims 1-5, 7, 8, 10, 12, 13, 16, and 18 is the provisional filing date of application No. 62/912727, filed 10/09/2019.
Information Disclosure Statement
The Information Disclosure Statements filed 07/06/2022, 03/07/2024, and 01/17/2025 are in compliance with the provisions of 37 CFR 1.97 and have therefore been considered. Signed copies of the IDS documents are included with this Office Action.
It is noted that a duplicate of the IDS document filed 03/07/2024 was submitted. Furthermore, the foreign references of the IDS document filed 07/06/2022 are not considered as no copy of the foreign documents was submitted herein.
Drawings
The drawings filed 04/11/2022 are accepted.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code, such as in paragraphs [0041] and [0042]. 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.
The disclosure is further objected to because of the following informalities:
On page 1, the paragraph numbers incorrectly transition from [0001] and [0002], to [0010]
In paragraph [0098], “classify the two lung cancer histologies was evalutated” should read “classify the two lung cancer histologies was evalu
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 1-5, 7, 8, 10, 12, 13, 16, and 18 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.
With respect to claim 1, the claim recites in the preamble, “by using copy number alteration (CNA) data alone”. The claim is indefinite because in step (b), the claim recites that the mathematical model is “based on mRNA expression data, protein expression, somatic mutations, clinical features, and/or molecular subtypes”. Thus, it is unclear what data is required by the claim and if the method is supposed to be performed only using CNA data or if the preamble is not limiting to the claim because step (b) requires other forms of data.
The remaining claims are rejected for being dependent upon independent claim 1 without remedying the indefiniteness.
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 1-5, 7, 8, 10, 12, 13, 16, and 18 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to an abstract idea of mental steps, mathematic concepts, or a natural law without significantly more.
The MPEP at MPEP 2106.03 sets forth steps for identifying eligible subject matter:
(1) Are the claims directed to a process, machine, manufacture or composition of
matter?
(2A)(1) Are the claims directed to a judicially recognized exception, i.e. a law of nature,
a natural phenomenon, or an abstract idea?
(2A)(2) If the claims are directed to a judicial exception under Prong One, then is the
judicial exception integrated into a practical application?
(2B) If the claims are directed to a judicial exception and do not integrate the judicial
exception, do the claims provide an inventive concept?
With respect to step (1): Yes, the claims recite a method.
With respect to step (2A)(1): The claims are directed to abstract ideas of mental processes and mathematical concepts.
“Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection” (MPEP 2106.04). Abstract ideas include mathematical concepts (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (procedures for observing, evaluating, analyzing/judging and organizing information (MPEP 2106.04(a)(2)). Laws of nature or natural phenomena include naturally occurring principles/relations that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature (MPEP 2106(b)).
Mental processes recited in claim 1:
measuring, or having measured, a plurality of CNAs over a plurality of locations on a plurality of chromosomes
Mathematical concepts recited in claim 1:
analyzing the measured CNAs using a mathematical model based on mRNA expression data, protein expression, somatic mutations, clinical features, and/or molecular subtypes, wherein the mathematical model has been statistically validated so as to generate the calculated cancer signature for the sample
Dependent claims 2-5, 7, 8, 10, 12, 13, and 16 recite additional steps that either are directed to abstract ideas or further limit the judicial exceptions in independent claim 1, and as such, are further directed to abstract ideas. Hence, the claims explicitly recite numerous elements that individually and in combination constitute abstract ideas. The relevant recitations are:
Claim 2: “wherein greater than 50 CNAs are measured”
Claim 3: “wherein greater than 100 CNAs are measured”
Claim 4: “wherein between about 250 and about 400 CNAs are measured”
Claim 5: “wherein the calculated cancer signature corresponds to a somatic mutation signature”
Claim 7: “wherein the calculated cancer signature corresponds to an mRNA expression signature”
Claim 8: “wherein the calculated cancer signature is a signature of a breast cancer subtype”
Claim 10: “wherein the calculated cancer signature corresponds to a protein expression signature”
Claim 12: “wherein the protein expression signature is an immunohistochemistry (IHC) signature”
Claim 13: “wherein the IHC signature is an estrogen receptor (ER), an epidermal growth factor receptor (EGFR), a human epidermal growth factor receptor 2 (HER2), a progesterone receptor (PR), or a retinoblastoma (RB) signature”
Claim 16: “wherein the calculated cancer signature is a…”
The abstract ideas in the claims are evaluated under Broadest Reasonable Interpretation (BRI) and determined herein to each cover mental processes and mathematic concepts because the claims recite no more than analyzing performing statistical analysis.
With respect to step (2A)(2): The claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d)). The claimed additional elements are analyzed alone or in combination to determine if the judicial exception is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exception, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
Dependent claim 18 is directed to a data gathering steps or a step limiting the data gathered on which the judicial exceptions are performed. Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application (MPEP 2106.05(g)).
None of the claims recite additional elements, alone or in combination, which would integrate a judicial exception into a practical application.
Lastly, the claims have been evaluated with respect to step (2B): Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims lack a specific inventive concept. Under said analysis, Applicant is reminded that the judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements described above do not rise to the level of significantly more than the judicial exception. As set forth in the MPEP at 2106.05(d).I, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rests in whether or not the additional elements (or combination of elements) represents well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to claim 18: The additional element of the plurality of CNAs are obtained from whole genome sequencing (WGS), whole exome sequencing (WES), or a combination thereof do not rise to the level of significantly more than the judicial exception. The prior art to Lipson et al. (US 9340830, patented 05/17/2016, IDS reference) discloses that methods of isolating and preparing libraries from whole genomic fragments obtaining are known in the art (column 91, line 21). As such, it is recognized that these additional limitations are routine, well understood, and conventional in the art. These limitations do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not affect a transformation of matter, nor do they provide a non-conventional or unconventional step. As such, these limitations fail to rise to the level of significantly more.
The claims have all been examined to identify the presence of one or more judicial exceptions. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether the additional limitations integrate the judicial exception into a practical application. Each additional limitation in the claims has been addressed, alone and in combination, to determine whether those additional limitations provide an inventive concept which provides significantly more than those exceptions. Individually, the limitations of the claims and the claims as a whole have been found lacking.
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.
(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.
Claims 1-3, 5, 7, 8, 10, 12, 13, 16, and 18 are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Vaske et al. (US 2018/00446752, published 02/15/2018, IDS reference).
Regarding claim 1, Vaske et al. teaches a method of generating a calculated cancer signature associated with a cancer phenotype (paragraph [0032]), for a sample obtained from a patient (paragraphs [0023]; [0024]; [0026]), which comprises:
measuring, or having measured, a plurality of CNAs over a plurality of locations on a plurality of chromosomes (paragraphs [0026], [0035]; [0107]; [0137]; [0271); and
analyzing the measured CNAs using a mathematical model (paragraph [0026]) based on mRNA expression data, protein expression, somatic mutations, clinical features, and/or molecular subtypes (paragraphs [0032]; [0083]; [0111]; claim 12), wherein the mathematical model has been statistically validated so as to generate the calculated cancer signature for the sample (paragraphs [0173]; [0199]).
Regarding claim 2, the claim is directed to greater than 50 CNAs being measured. Vaske et al. teaches the method of claim 1. Vaske et al. also teaches measuring 63 regions of focal amplification (paragraph [0193]).
Regarding claim 3, the claim is directed to greater than 100 CNAs being measured. Vaske et al. teaches the method of claim 1. Vaske et al. also teaches measuring 113 CNAs, comprising focal amplifications and focal deletions (paragraphs [0193] and [0194]).
Regarding claim 5, the claim is directed to the calculated cancer signature corresponding to a somatic mutation signature. Vaske et al. teaches the method of claim 1. Vaske et al. also teaches the calculated cancer signature corresponding to a somatic mutation signature (paragraph [0192]).
Regarding claim 7, the claim is directed to the calculated cancer signature corresponding to an mRNA expression signature. Vaske et al. teaches the method of claim 1. Vaske et al. also teaches the calculated cancer signature corresponding to an mRNA expression signature (paragraphs [0256], [0271], [0272], [0274]).
Regarding claim 8, the claim is directed to the calculated cancer signature being a signature of a breast cancer subtype. Vaske et al. teaches the method of claim 1. Vaske et al. also teaches the calculated cancer signature being a signature of a breast cancer subtype (paragraphs [0177], [0178], and Table 1).
Regarding claim 10, the claim is directed to the calculated cancer signature corresponding to a protein expression signature. Vaske et al. teaches the method of claim 1. Vaske et al. also teaches the calculated cancer signature corresponding to a protein expression signature, such as an EGFR signature (paragraphs [0182], [0225]).
Regarding claim 12, the claim is directed to the protein expression signature being an immunohistochemistry (IHC) signature. Vaske et al. teaches the method of claim 10. Vaske et al. also teaches the protein expression signature being an IHC signature, such as an EGFR signature (paragraphs [0023], [0109], [0110], [0182], [0196]).
Regarding claim 13, the claim is directed to the IHC signature being an estrogen receptor (ER), an epidermal growth factor receptor (EGFR), a human epidermal growth factor receptor 2 (HER2), a progesterone receptor (PR), or a retinoblastoma (RB) signature. Vaske et al. teaches the method of claim 12. Vaske et al. also teaches the IHC signature being an EGFR signature (paragraphs [0182], [0225]).
Regarding claim 16, Vaske et al. teaches the method of claim 1. Vaske et al. also teaches the calculated cancer signature being a lung cancer, adenocarcinoma, sarcoma, melanoma, bladder, breast, gastrointestinal tract, etc. cancer signature (paragraph [0032]).
Regarding claim 18, the claim is directed to the plurality of CNAs being obtained from whole genome sequencing (WGS), whole exomes sequencing (WES), or a combination thereof. Vaske et al. teaches the method of claim 1. Vaske et al. also teaches the CNAs being obtained through whole genome amplification (paragraph [0271]) and exome capture and sequencing (paragraph [0188]).
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.
Claim 4 is rejected under 35 U.S.C. 103 as being unpatentable over Vaske et al., as applied to claims 1-3, 5, 7, 8, 10, 12, 13, 16, and 18 in the 102 rejection above.
The claim is directed to between about 250 and about 400 CNAs being measured. Vaske et al. teaches the method of claim 1. Although Vaske et al. does not explicitly teach measuring between about 250 and about 400 CNAs, Vaske et al. teaches expression measurements for 11864 genes (paragraph [0195]). Thus, it would be prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have measured between about 250 and about 400 CNAs because Vaske et al. measured the expression levels of 11864 genes, and thus has the potential to measure between 250 and 400 CNAs.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Emilie A Smith whose telephone number is (571)272-7543. The examiner can normally be reached 9am - 5pm.
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, Larry D Riggs can be reached at (571)270-3062. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/E.A.S./Examiner, Art Unit 1686
/LARRY D RIGGS II/Supervisory Patent Examiner, Art Unit 1686
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