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 .
Claims 1-11, 13, 16, 18, 21-23, 34-35, 40, and 42-43 are currently pending and under examination. Claims 12, 14-15, 17, 19-20, 24-33, 36-39, and 41 are canceled.
Priority
The instant application 18/714,670 filed on 5/30/24 is a 371 US national phase of PCT/GB2022/053048 filed on 12/1/22, and claims foreign priority to GB2117404.0 filed on 12/2/21. The priority date is determined to be 12/2/21.
Receipt is acknowledged of GB2117404.0 certified copies of papers required by 37 CFR 1.55. Priority Documents were electronically retrieved by USPTO from participating IP office on 5/30/24.
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 1-11, 13, 16, 18, 21-23, and 42-43 are rejected under 35 U.S.C. 101 because the claimed invention is directed to judicial exception without significantly more. The claims have been evaluated using the 2019 Revised Patent Subject Matter Eligibility Guidance (see Federal Register Vol. 84, No. 4 Monday, January 7, 2019).
Step 1: The claim is directed to the statutory category of a process.
Step 2A, prong one: The claim recites a judicial exception.
Claim 1 recitation of “classifying a patient’s cancer”; claim 7 recitation of “compared to or correlated with”; claim 9 recitations of “determine the cancer proliferation status” and “classify the cancer”; and claim 10 recitation of “prognosing or predicting” are all abstract ideas. These limitations are abstract mental processes (see MPEP 2106.04(a)). The abstract mental processes of classifying, comparing/correlation, determination, and prognosing/predicting are concepts performed in the human mind.
Additionally, the claims are directed towards laws of nature and natural phenomena through the correlations of biomarker expression levels (genotype) and cancer (phenotype) (see MPEP 2106.04(b)).
Step 2A, prong two: The judicial exception is not integrated into a practical application.
Claims 1-11, 13, 16, 18, 21-23, and 42-43 recite insignificant extra-solution activities directed towards mere data gathering at high levels of generality (see MPEP 2106.05(g)). It is further noted that the claims are not directed to a particular treatment or prophylaxis (see MPEP 2106.04(d)(2)).
Claim 1 recites data gathering activities of “determining the expression level of at least one biomarker” with a high level of generality; claim 2 ends with the law of nature/natural phenomena of biomarker expression level (genotype) correlated with proliferation status of the cancer (phenotype); claim 3 recites biomarkers for data gathering activities; claims 4-6 recite cancer limitations unrelated to integrating the judicial exceptions; claim 7 ends with the judicial exceptions; claim 8 recites limitations for the data gathering activities; claim 9 ends with the judicial exceptions; claim 10 recites data gathering activities of “determining the expression level of at least one biomarker” with a high level of generality; claim 11 recites biomarkers for data gathering activities; claim 13 recites cancer limitations unrelated to integrating the judicial exceptions; claims 16 and 18 recite limitations for the data gathering activities at a high level of generality; claims 21-22 recite limitations for the cancer sample input of the data gathering activities; claim 23 recites biomarkers for data gathering activities; claim 42 recites limitations for the data gathering activities at a high level of generality; and claim 43 recites biomarkers for data gathering activities.
Step 2B: The claim does not provide an inventive concept.
MPEP 2106.05(d)):
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:
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);
ii. Using polymerase chain reaction to amplify and detect DNA, Genetic Techs.
Ltd. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir.
2016); Ariosa Diagnostics, Inc. v. Sequenom, Inc., 788 F.3d 1371, 1377, 115
USPQ2d 1152, 1157 (Fed. Cir. 2015);
iii. Detecting DNA or enzymes in a sample, Sequenom, 788 F.3d at 1377-78,
115 USPQ2d at 1157); Cleveland Clinic Foundation 859 F.3d at 1362, 123
USPQ2d at 1088 (Fed. Cir. 2017);
iv. Immunizing a patient against a disease, Classen Immunotherapies, Inc. v.
Biogen IDEC, 659 F.3d 1057, 1063, 100 USPQ2d 1492, 1497 (Fed. Cir. 2011);
v. Analyzing DNA to provide sequence information or detect allelic
variants, Genetic Techs. Ltd., 818 F.3d at 1377, 118 USPQ2d at 1546;
vi. Freezing and thawing cells, Rapid Litig. Mgmt. 827 F.3d at 1051, 119
USPQ2d at 1375;
vii. Amplifying and sequencing nucleic acid sequences, University of Utah
Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d
1241, 1247 (Fed. Cir. 2014); and
viii. Hybridizing a gene probe, Ambry Genetics, 774 F.3d at 764, 113 USPQ2d
at 1247.
The claims end with the judicial exceptions. Additionally, methods of classifying a patient’s cancer and prognosing or predicting clinical outcomes are not inventive (Abba et al. (2010; NPL citation CA in IDS filed 5/30/24; “Breast cancer biomarker discovery in the functional genomic age: a systematic review of 42 gene expression signatures”. Biomark Insights. 2010 Oct 27;5:103-18. doi: 10.4137/BMI.S5740)).
For the reasons set forth above, claims 1-11, 13, 16, 18, 21-23, and 42-43 are not directed to patent eligible subject matter.
Claim Rejections - 35 USC § 102
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.
Claims 1-11, 13, 16, 18, 21-23, 34-35, 40, and 42-43 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Abba et al. (2010; NPL citation CA in IDS filed 5/30/24; “Breast cancer biomarker discovery in the functional genomic age: a systematic review of 42 gene expression signatures”. Biomark Insights. 2010 Oct 27;5:103-18. doi: 10.4137/BMI.S5740).
Relevant to claim 1, Abba et al. Abstract teaches “a systematic analysis of transcriptomic signatures derived from 42 breast cancer gene expression studies, in an effort to identify the most relevant breast cancer biomarkers using a meta-analysis method… In addition, the identified meta-signature improves breast cancer patient stratification independently of traditional prognostic factors in a multivariate Cox proportional-hazards analysis.”
Further relevant to claim 1, Abba et al. Figure 1 includes expression biomarkers KIF23, AURKA, MCM2, CCNA2, and PCNA.
Relevant to claim 2, Abba et al. teaches “In a wide range of tumor types compared with essentially non-proliferating matched normal tissue, AURKA is strongly expressed at high frequency” (page 113, left column). This teaching links the AURKA biomarker expression with proliferation status.
Relevant to claim 3, Abba et al. Figure 1 includes expression biomarkers MKI67, KIF23, AURKA, MCM2, CCNA2, and PCNA.
Relevant to claims 4-6, Abba et al. Figure 4 teaches classification of luminal A, luminal B, and hormone receptor positive and her2 negative breast cancer.
Relevant to claim 7, Abba et al. Figure 4 compares biomarker expression levels with values attributed to luminal A and luminal B breast cancer subtypes.
Relevant to claim 8, Abba et al. Figure 1 includes expression biomarkers KIF23, AURKA, MCM2, CCNA2, and PCNA (5 biomarkers).
Relevant to claim 9, Abba et al. Figure 4 includes a hierarchical clustering of biomarker expression (weighted expression) and classification of the cancer as being a luminal A or luminal B subtype.
Relevant to claim 10, Abba et al. teaches “To further investigate the prognostic value of the gene expression meta-signature, we did survival analyses in a publicly available breast cancer microarray study… In an unsupervised analysis, 295 tumor samples were grouped by similarity of the 117 gene list meta-signature by complete linkage clustering by using the Multi Experiment Viewer software. The samples were segregated into three classes (from Cluster 1 to Cluster 3) based on the second bifurcation of the clustering dendrogram. In addition, we integrated the gene expression meta-signature with four prognostic or predictive gene signatures (Intrinsic subtype, Poor-prognosis, Recurrence Score and Wound Response signatures) to evaluate the data set” (Materials and Methods section “Gene expression meta-signature and survival analysis”; pages 105-106).
Further relevant to claim 10, Abba et al. Figure 1 includes expression biomarkers KIF23, AURKA, MCM2, CCNA2, and PCNA.
Relevant to claim 11, Abba et al. Figure 1 includes expression biomarkers MKI67, KIF23, AURKA, MCM2, CCNA2, and PCNA.
Relevant to claim 13, Abba et al. Title teaches “Breast Cancer Biomarker Discovery in the Functional Genomic Age: A Systematic Review of 42 Gene Expression Signatures”.
Relevant to claims 16 and 18, Abba et al. Figure 2 teaches that the biomarker expression levels were determined based on the amount of the RNA transcript level and that the expression level for each measured biomarker is determined quantitatively through the depicted platforms.
Relevant to claims 21-22, Abba et al. teaches analysis from “295 tumor samples” (Materials and Methods section “Gene expression meta-signature and survival analysis”; page 106).
Relevant to claim 23, Abba et al. Figure 1 includes expression biomarkers MKI67, KIF23, AURKA, MCM2, CCNA2, and PCNA.
Relevant to claims 34-35, Abba et al. Figure 2 teaches various platforms (microarrays, RT-PCR, multiple platforms, etc.) that contributed to the 42 breast cancer gene expression studies used to provide their systematic analysis of transcriptomic signatures. Notably, several commercially available platforms are depicted within Figure 2, which would include the instantly claimed kit of parts.
Relevant to claim 40, Abba et al. Figure 4 teaches that the gene meta-signature was used to determine whether a breast cancer is luminal A or luminal B status.
Relevant to claim 42, Abba et al. Figure 2 teaches that the biomarker expression levels were determined based on the amount of the RNA transcript level through the depicted platforms.
Relevant to claim 43, Abba et al. Figure 1 includes expression biomarkers MKI67, KIF23, AURKA, MCM2, CCNA2, and PCNA.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Sarah J Kennedy whose telephone number is (571)272-1816. The examiner can normally be reached Monday - Friday 8a - 5p.
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/SARAH JANE KENNEDY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682
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