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 without traverse of the chemokine biomarker panel in Table A in the reply filed on 12/15/2025 is acknowledged.
Claims 1-12 are pending. Claims 5, 7-9 are withdrawn as being drawn to a nonelected panel.
An action on the merits for claims 1-4, 6, and 10-12 is set forth below.
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 1-4, 6, and 10-12 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for measuring expression, does not reasonably provide enablement for classifying and assigning subtypes. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make or use the invention commensurate in scope with these claims.
Factors to be considered in determining whether a disclosure meets the enablement requirement of 35 USC 112, first paragraph, have been described by the court in In re Wands, 8 USPQ2d 1400 (CA FC 1988). Wands states at page 1404,
“Factors to be considered in determining whether a disclosure would require undue experimentation have been summarized by the board in Ex parte Forman. They include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.”
The breadth of the claims
Claims 1-4, 6, and 10-12 are drawn to a method of selecting a therapeutic treatment for a high-risk HER2+ or HER2- Stage II or Stage III breast cancer that is hormone receptor+ or hormone receptor-, the method comprising: classifying the Stage II or Stage III breast cancer as having a positive or negative immune response profile for responding to an immunotherapy treatment, wherein a positive immune response profile is assigned by determining that the expression pattern of at least one panel of immune status genes reaches or exceeds a threshold that is associated with a high pathology complete response (pCR) rate for patients treated with an immune pathway-targeted therapy compared to patients treated with therapies that do not target the immune response; and a negative immune response profile is assigned by determining that the expression pattern is lower than the threshold; classifying the Stage II or Stage III breast cancer as having a positive or negative DNA Repair Defect (DRD) profile for responding to a DNA repair treatment, wherein a positive DRD response profile is assigned by determining that the expression pattern of at least one panel of DRD status reaches or exceeds a threshold that is associated with a high pathology complete response (pCR) rate for patients treated with a DNA repair-targeted therapy compared to patients treated with therapies that do not target DNA repair; and a negative DRD response profile is assigned by determining that the expression pattern is lower than the threshold; and assigning the breast cancer to a treatment subtype selected from the group consisting of HER2-/Immune-/DRD-, HER2-/Immune-/DRD+, HER2-/Immune+, HER2+/BP-HER2-type or Basal-type, and HER2+/BP-Luminal-type
The claims encompass a correlation of any expression level of these genes in any sample from any species and the determination of subtypes. As discussed below the specification has not provided sufficient guidance for correlation to subtype assignment based on the breadth of the claims.
Nature of the Invention
The invention is in a class of invention which the CAFC has characterized as “the unpredictable arts such as chemistry and biology.” Mycogen Plant Sci., Inc. v. Monsanto Co., 243 F.3d 1316, 1330 (Fed. Cir. 2001).
Guidance in the Specification and Working Examples
The specification teaches that immune status or immune profile comprises analyzing biomarker panels comprising immune response genes (p. 13-14). The specification teaches that this includes genes that regulate Tcell, Bcell, dendritic cell, natural killer immune functions, genes that regulate immune functions compared to alternative therapy (p. 13). As such the specification suggests a very large list of genes that could be used for immune status. However, the specification does not provide which of these genes would functionally provide the assignment of the subtypes. The specification provides in table A particular chemokine genes for data analysis, however, the specification does not provide any particular combinations to determine particular subtypes. The claims are drawn to classifying based upon exceeding or being lower than a threshold, however, the specification does not provide a limiting threshold. Depending on the threshold used a profile could be considered positive or negative.
The specification discloses DRD genes include any gene included in DNA repair defect including the genes in table B (p. 18-19). However, the specification does not provide which of these genes would functionally provide the assignment of the subtypes. The claims are drawn to classifying based upon exceeding or being lower than a threshold, however, the specification does not provide a limiting threshold. Depending on the threshold used a profile could be considered positive or negative.
On page 23-24, the specification provides particular treatments for particular pathways. However, the specification has not provided that these subtypes are limited to the particular treatments set forth. Further these treatment selection and phenotypes appear to be based upon particular thresholds whereas the claims are drawn to any thresholds.
The specification provides particular subtypes based on data (p. 29-31), however, but these do not provide support for applying any of the expression data encompassed to the recited subtypes.
The specification does not define the term “subject” to limit it to a particular species type and therefore the claims can encompass any mammalian species including, for example, gorillas, platypuses, and dogs. The art (Enard et al) discussed below teaches that expression levels between species are distinct to the species. As such a correlation observed in one species would not be directly extrapolated to any other species. Herein in the instant case, the data provided by the specification is based upon the analysis of human subjects. The specification provides no guidance that the same genetic associations would be observable in any other species. Furthermore as discussed by Cobb et al (see below) expression levels between samples differ and that correlations therefore between samples are not predictable.
The unpredictability of the art and the state of the prior art
The art of Cobb et al (Crit Care Med 2002 Vol. 30 p. 2711) teaches the unpredictability in analysis of gene expression in spleen and liver sample from septic mice. Notably, the reference teaches that, when compared to a non-septic sample, the relevant expression profiles of the septic mouse spleen and the septic mouse liver contain different nucleic acids at different levels (Table 1; p.2714, middle col., lns.2-8). As such the art teaches that expression levels of the same nucleic acids in different tissue samples differ. Therefore the art indicates that an association of expression level to a subtype in one sample would not be correlative to an association to any other sample type.
Enard et al. (Science 2002 Vol 296 p. 340) teaches that even between closely related species gene expression patterns differ (abstract). Enard et al. teaches that mRNA expression levels are different between humans, chimpanzees, orangutans and rhesus marcques (p. 340 1st column last sentence-2nd column 1st paragraph). Enard et al. teaches that there are a large number of quantitative differences in gene expression in closely related mammals (p. 342 2nd column last paragraph). Therefore the art teaches that even between very closely related mammals there is a divergence of gene expression. As such a correlation of expression and disease in one species would not be directly correlative to any other species without further experimentation. This experimentation would be unpredictable as there is no expectation of success that expression patterns observed in one species would be similar to any other species.
Level of Skill in the Art
The level of skill in the art is deemed to be high.
Quantity of Experimentation and Conclusion
The quantity of experimentation in this area would be extremely large since there is significant number of parameters that would have to be studied. The claims are drawn the association of any expression in any sample from any species and determination phenotypes. The specification has not provided a correlation of each of these possible combinations with any particular phenotype.
The skilled artisan would need to perform undue experimentation to determine such an associations as the specification has not provided guidance that these associations are predictable. Therefore to use the invention as presented would require a large amount of inventive effort, with each of the many intervening steps, upon effective reduction to practice, not providing any guarantee of success in the succeeding steps.
The art indicates that expression levels are further species and sample specific (Cobb et al. and Enard et al). As such the breadth of the claims towards any sample or any mammalian subject would require a large amount of inventive effort without a guarantee of success as the art teaches that even if an association between expression level and a diagnosis could be determined this association would be species and sample specific.
Therefore the method as claimed would require a large amount of inventive effort, with each of the many intervening steps, upon effective reduction to practice, not providing any guarantee of success in the succeeding steps. Thus given the broad claims in an art whose nature is identified as unpredictable, the unpredictability of that art, the large quantity of research required to define these unpredictable variables, the negative teachings in the art, and the lack of guidance provided in the specification balanced only against the high skill level in the art, it is the position of the examiner that it would require undue experimentation for one of skill in the art to perform the method of the claim as broadly written.
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 1-4, 6, and 10-12 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.
Claims 1-4, 6, and 10-12 are drawn to a method of selecting a therapeutic treatment for a high-risk HER2+ or HER2- Stage II or Stage III breast cancer that is hormone receptor+ or hormone receptor-, the method comprising: classifying the Stage II or Stage III breast cancer as having a positive or negative immune response profile for responding to an immunotherapy treatment, wherein a positive immune response profile is assigned by determining that the expression pattern of at least one panel of immune status genes reaches or exceeds a threshold that is associated with a high pathology complete response (pCR) rate for patients treated with an immune pathway-targeted therapy compared to patients treated with therapies that do not target the immune response; and a negative immune response profile is assigned by determining that the expression pattern is lower than the threshold; classifying the Stage II or Stage III breast cancer as having a positive or negative DNA Repair Defect (DRD) profile for responding to a DNA repair treatment, wherein a positive DRD response profile is assigned by determining that the expression pattern of at least one panel of DRD status reaches or exceeds a threshold that is associated with a high pathology complete response (pCR) rate for patients treated with a DNA repair-targeted therapy compared to patients treated with therapies that do not target DNA repair; and a negative DRD response profile is assigned by determining that the expression pattern is lower than the threshold; and assigning the breast cancer to a treatment subtype selected from the group consisting of HER2-/Immune-/DRD-, HER2-/Immune-/DRD+, HER2-/Immune+, HER2+/BP-HER2-type or Basal-type, and HER2+/BP-Luminal-type
The claims are therefore drawn to analysis of any immune response profiles of expression pattern of at least one panel of immune status genes and a DRD profile of expression pattern of at least one panel of DRD status. The claims further provide the functionality of assigning based upon the classifying particular treatment subtypes. The claims further limit the immune response genes to chemokine genes set forth in Table A.
Therefore the claims are drawn to a genus of the measurement of any of the genes that would be considered immune response or DNA repair Defects. Further the claims are drawn to assigning these sample to a particular subtype without any analysis of particular types of subtypes (e.g. Basal and luminal).
The specification teaches that immune status or immune profile comprises analyzing biomarker panels comprising immune response genes (p. 13-14). The specification teaches that this includes genes that regulate Tcell, Bcell, dendritic cell, natural killer immune functions, genes that regulate immune functions compared to alternative therapy (p. 13). As such the specification suggests a very large list of genes that could be used for immune status. However, the specification does not provide which of these genes would functionally provide the assignment of the subtypes. The specification provides in table A particular chemokine genes for data analysis, however, the specification does not provide any particular combinations to functionally determine any particular subtypes.
The specification discloses DRD genes include any gene included in DNA repair defects including the genes in table B (p. 18-19). However, the specification does not provide which of these genes would functionally provide the assignment of the subtypes.
On page 23-24, the specification provides particular treatments for particular pathways. However, the specification has not provided that these subtypes are limited to the particular treatments set forth and has not provided any critical structures to functionally correlate subtypes and expression analysis.
As shown below, the art teaches that this is a very large genus wherein merely being expressed in one sample is not sufficient to describe the critical features in any other sample.
In analyzing whether the written description requirement is met for genus claims, it is first determined whether a representative number of species have been described by their complete structure. However, as discussed above, the specification provides on particular species and does not provide critical structures for the breadth of the claims.
Further, the art, as recited below, teaches that expression of biomarkers differ in different species. However, the specification has not provided identifying characteristics or functional attributes that would distinguish different members of the claimed genus. Rather, the art teaches that changes in the structure of nucleic acids between species can have an effect on expression. Enard et al. (Science 2002 Vol 296 p. 340) teaches that even between closely related species gene expression patterns differ (abstract). Enard et al. teaches that mRNA expression levels are different between humans, chimpanzees, orangutans and rhesus marcques (p. 340 1st column last sentence-2nd column 1st paragraph). Enard et al. teaches that there are a large number of quantitative differences in gene expression in closely related mammals (p. 342 2nd column last paragraph).
The art of Cobb et al (Crit Care Med 2002 Vol. 30 p. 2711) teaches the in analysis of gene expression in spleen and liver sample from septic mice. Notably, the reference teaches that, when compared to a non-septic sample, the relevant expression profiles of the septic mouse spleen and the septic mouse liver contain different nucleic acids at different levels (Table 1; p.2714, middle col., lns.2-8). As such the art teaches that expression levels of the same nucleic acids in different tissue samples differ. Therefore the art indicates that the identifying characteristics or functional attributes that would distinguish different members of the claimed genus will differ depending on the sample type.
In the instant case the specification does not provide the skilled artisan with an adequate written description of particular nucleic acids suitable for performing the claimed method as generically encompassed in the claims.
In analysis of the claims for compliance with the written description requirement of 35 U.S.C. 112, first paragraph, the written description guidelines note regarding genus/species situations that "Satisfactory disclosure of a ``representative number'' depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features of the elements possessed by the members of the genus in view of the species disclosed." (See: 'Written Description" Requirement, Federal Register, Vol. 66, No. 4, pages 1099-1111, Friday January 5, 2001.) In the instant case, the specification fails to teach the necessary common attributes or features of the biomarkers across species and samples and functionally determining breast cancer associated disease state in view of the species disclosed. As such, one of skill in the art would not recognize that applicant was in possession of the genus encompassed by the broadly claimed invention.
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 1-4, 6, and 10-12 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 1-4, 6, and 10-12 are indefinite over the step of assigning in claim 1. Although it is clear that the classifying steps provide information on positive or negative immune are DRD, it is not clear how to obtain the assignment of “HER2+/BP-HER2- type or basal type and HER2+. BP luminal type”. The claims do not appear to provide a step of classifying these groups.
Claim 2 is unclear over the recitation of table A. MPEP 2173.05(s) addresses the use of such limitations in claims:
Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table "is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience."
In the instant case the claims may be amended to recite particular gene symbols from the relevant table as presented in the specification as originally filed.
Claim 10 contains the trademark/trade name MammaPrint. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe classifying and, accordingly, the identification/description is indefinite.
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 1-4, 6, and 10-12 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (e.g.: a law of nature, a natural phenomenon, or an abstract idea) without significantly more. The claim(s) is/are directed to a judicial exception encompassing an abstract idea and a law of nature. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception as set forth below. The judicial exception is not integrated into a practical application of the judicial exception.
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 law of nature. The claims recite relationship between assigning treatment subtype and classifying immune response profile and DNA repair defect profile.
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 steps of “classifying” and “analyzing”, which would encompass a step of looking at data. 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 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 there are no further steps in the independent claim.
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).
Further, the dependent steps merely limit the judicial exception. For claim 10, the claim is drawn to using a commercially produced analysis and therefore would be considered routing and conventional. CLiams 11-12 are drawn to a further abstract idea of “selecting”, which would encompass choosing from a list.
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.
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.
Claim(s) 1, 3-4, 6, and 10-12 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Pusztal et al. (Cancer Cell Vol 39 July 2021 p. 989 cited on IDS) .
The applied reference has a common Laura van’t Veer with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2). This rejection under 35 U.S.C. 102(a)(2) might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B) if the same invention is not being claimed; or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed in the reference and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement.
With regard to claim 1, Pusztal discloses a method of selecting a therapeutic treatment for a high-risk HER2+ or HER2- Stage II or Stage III breast cancer that is hormone receptor+ or hormone receptor- (investigating (method of selecting) the combination of durvalumab/olaparib/paclitaxel (a therapeutic treatment) for stage II/III HR (hormone receptor)-positive/HER2-negalive breast cancer;abstract), the method comprising: classifying the Stage II or Stage III breast cancer as having a positive or negative immune response profile for responding to an immunotherapy treatment, wherein a positive immune response profile is assigned by determining that the expression pattern of at least one panel of immune status genes reaches or exceeds a threshold that is associated with a high pathology complete response or pCR rate for patients treated with an Immune pathway-targeted therapy compared to patients treated with therapies that do not target the immune response; and a negative immune response profile is assigned by determining that the expression pattern is lower than the threshold (durvalumab/olaparib/pacitaxel increased pCR rates (positive immune response profile) in all
HR-positive/HER2-negative and triple-negative stage II or III breast cancer, wherein the pCR rates are determined based on expression of a panel of immune biomarker panel (determining that the expression pattern of at least one panel of immune status genes reaches or exceeds a threshold that is associated with a high pathology complete response or pCR rate for patients treated with an immune pathway-targeted therapy compared to patients treated with therapies that do not target the immune response), and wherein decreased pCR rates would intrinsically involve determining that the expression pattern is lower than the threshold, indicating a negative immune response profile; abstract; page 990, 2nd column, 2nd paragraph; page 991, 1st column, 5th paragraph); classifying the Stage II or Stage III breast cancer as having a positive or negative DNA Repair Defect or DRD profile for responding to a DNA repair treatment, wherein a positive DRD response profile is assigned by determining that the expression pattern of at least one panel of DRD status reaches or exceeds a threshold that is associated with a high pathology complete response or pCR rate for patients treated with a DNA repair-targeted therapy compared to patients treated with therapies that do not target DNA repair; and a negative DRD response profile is assigned by determining that the expression pattern is lower than the threshold (DNA repair deficiency signature biomarkers were assessed and were positively associated with pCR for stage II or III breast cancer subjects treated with durvalumab/olaparib/paclitaxel (a positive DRD response profile is assigned by determining that the expression pattern of at least one panel of DRD status reaches or
exceeds a threshold that is associated with a high pathology complete response or pCR rate for patients treated with a DNA repair-targeted therapy compared to patients treated with therapies that do not target DNA repair), wherein a DNA repair signature expression pattern lower than the threshold would intrinsically indicate a negative DRD response profile; abstract; page 990, 2nd column, 2nd paragraph; page 991, 1st column, 5th paragraph); and assigning the breast cancer to a treatment subtype selected from the group consisting of HER2-/Immune-/DRD-, HER2-/Immune-/DRD+, HER2-/immune+, HER2+/BP-HER2-type or Basal-type, and HER2+/BP-Luminal-type (the cancers are classified as HER2-/immune+ since the trial was conducted In HER2-negative stage II/III breast cancer patients and the Immune response profile was determined to have a high pCR rate; abstract; page 990, 2nd column, 2nd
paragraph; page 991, 1st column, 5th paragraph).
With regard to claim 3, Pusztal further discloses wherein the breast cancer is hormone receptor-positive or HR+ (the breast cancer is hormone receptor-positive or HR+; abstract).
With regard to claim 4, Pusztal further discloses wherein the breast cancer is HER2- (the breast cancer is HER2-; abstract).
With regard to claim 6, Pusztal teaches a method of using triple negative breast cancer (abstract).
With regard to claim 10. Pusztal teaches use of Mammaprint (p 990 table 1).
With regard to claims 11-12, Pusztal teaches selecting therapies including PARP inhibitions (p. 990).
Conclusion
No Claims are allowed.
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/KATHERINE D SALMON/ Primary Examiner, Art Unit 1682