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 .
DETAILED ACTION
Status of Claims
Claims 1-22 and 24 are pending. Claims 1-13 and 15-19 are the subject of this NON-FINAL Office Action. This is the first office action on the merits.
Election/Restrictions
Applicants’ election with traverse of Group I (claims 1-13 and 15-19) in the reply filed on 07/13/2026 is acknowledged. The requirements for election of species are withdrawn. Claims 14, 20-22 and 24 are withdrawn. Applicants argue that “the claims do not use ‘generic methylation markers’ but require specific methylation markers selected from Tables 2 and 3.” Applicants are encouraged to read their claims in light of Tables 1 and 2. The claims broadly encompass methylation ay any site of any two genes (kilobases in length), and any site within large DNA locations of many kilobases from Tables 1 and 2 (not Table 3). This is generic and encompasses millions of possible methylation sites, encompasses a huge swath of any organisms’ genome. The claims are indeed broad and generic. There is no unity here.
This is proven by the prior art below.
Claim Interpretation
The claims are broad indeed. For example, claim 1 encompasses any and all “neurodegenerative disease or disorder.” This is a massive genus. And it ranges widely. For example, it ranges from Alzheimer’s to Batten Disease, to Multiple System Atrophy, to merely memory loss. These are very different diseases and disorders. Yet, claim 1 states the ability to “[indicate] . . . the diagnosis of . . . , . . . the probability of develop[ing] . . . and/or . . . the probability of progression of” any and all of these vastly different “neurodegenerative diseases or disorders” using methylation status of any two genes or genome locations from Tables 1 and/or 2 (which list hundreds of options). All that is required to do this is any generic score (e.g. 1). The claims are clearly not allowable.
Claim Rejection - 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 1-13 and 15-19 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Specifically, the claims are directed to the natural correlation between certain gene methylation levels and Alzheimer’s (AD) and all other “neurodegenerative disease or disorders,” without significantly more.
First, under Step 1, the claims are directed to a method to predict AD and all other “neurodegenerative disease or disorders.” Thus, the claims are directed to statutory methods.
Under step 2A, prong one, the claims are clearly directed to a “method for determining a score indicative of the diagnosis of a neurodegenerative disease or disorder of a subject, of the probability of a subject to develop a neurodegenerative disease or disorder and/or of the disease progression of a neurodegenerative disease or disorder,” by detecting gene methylation status, which is a natural correlation. See MPEP § 2106.04(b).
As to step 2A, prong two, none of the claims integrate the natural correlation into a practical application. The claims simply begin and end with the natural correlation, thus monopolizing the correlation itself. Although the claims require “c) determining a score indicative of the diagnosis of a neurodegenerative disease or disorder of the subject, of the probability of the subject to develop a neurodegenerative disease or disorder and/or of the disease progression of a neurodegenerative disease or disorder based on the comparison obtained in (b),” yet no actual score much less scoring technique is claimed. The “score” is any subjective score such as 1, or 0.1, or 20, or 1,000. In other words, the claim is so broad in scope that it encompasses any and all scores, such as yes/no, or any numerical value, resulting from any possible scoring method. Moreover, adding another abstract judicial except recited at such a high level of generality (“determining a score”) fails to add significantly more to another judicial exception. Finally, the sample can be any sample from any organism. This is monopolization indeed.
At best, claim 1 recites “a) obtaining at least one methylation status of two or more genes selected from Table 1 and/or two or more regions selected from Table 2 from a sample of a subject; b) comparing the methylation status obtained in (a) to a reference pattern,” which is the epitome of routine and conventional techniques (prior art below; spec., para. 0126). In addition, these steps are recited at such a high level of generality that they encompass all possible methylation detection techniques.
As to step 2B, nor do any claims contain additional elements other than the natural correlation that yield improvements in a technology or technical field. The claims simply recite a natural correlation at a high level of generality such that the claims encompass the use of any and all routine and conventional methylation analyses (e.g. qPCR, sequencing, etc.). The claims lack any specificity whatsoever in the methylation assay. Without such specificity, the claims fail to recite any additional elements that amount to a specific improvement in an assay or analysis.
Thus, the claims fail to pass muster under Section 101.
As to claim 4, cfDNA is routinely used in methylation detection; it fails to add significantly more to the natural correlation.
As to claim 13, this merely layers in the routine and conventional monitoring of diseases/disorders, which requires time points; thus, this is simply the monopolization of disease/disorder monitoring using methylation status.
Claims 15-16 merely pay lip service to a generic “storage device” or generic “server,” without significantly more. This fails to transform the natural correlation, or generic “storage device” or generic “server,” into significantly more.
Claim Rejections - 35 USC § 112- Indefiniteness
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.
Claims 2, 4, 6-8 and 10 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 pre-AIA the applicant regards as the invention.
Claims 2 and 6-8 are littered with the word “preferably,” and the phrase “more preferably,” which renders the scope of the claims confusing because it is not clear if what follows is required are only optional.
Claim 4 recites “cell free-DNA,” which is an unknown phrase. Specifically, free-DNA is nonsensical, much less free-DNA that is a cell. The Examiner believes the phrase should be “cell-free DNA.”
In claim 8, “nucleotide width” is confusing. Specifically, this phrase is never defined in the specification, nor ever used in the art. It is completely unknown. Thus, one cannot determine the metes and bounds of this phrase.
Moreover, the claim fails to state the “nucleotide width” of what. Thus, it is also unclear what this measures.
In claim 10, a conjunction is missing for the Markush group. The claim states “marker selected from the group of subject background data, cognitive performance marker, autonomic nervous system biomarker.”
Claim Rejection - 35 USC § 112 – Written Description
The following is a quotation 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.
Claims 1-13 and 15-19 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claims contain 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, at the time the application was filed, had possession of the full scope of the claimed invention.
The specification fails to demonstrate possession of any method to “[indicate] . . . the diagnosis of . . . , . . . the probability of develop[ing] . . . and/or . . . the probability of progression of” any and all of vastly different “neurodegenerative diseases or disorders” by a generic score using methylation status of any two genes or genome locations from Tables 1 and/or 2 (which list hundreds of options). In fact, the specification never actually performs this, much less provides any proof-of-principle. Instead, the specification merely wishes or plans to do so. At best, Applicants have merely slapped together various known methylation markers, with various known neurodegenerative diseases or disorders, then merely asserted that a score can be developed to “[indicate] . . . the diagnosis of . . . , . . . the probability of develop[ing] . . . and/or . . . the probability of progression of” any and all of vastly different “neurodegenerative diseases or disorders.” The specification even states that there is nothing technically new in the claimed invention: “The general methods and techniques described herein may be performed according to conventional methods well known in the art and as described in various general and more specific references that are cited and discussed throughout the present specification unless otherwise indicated” (para. 0126).
The only possible invention disclosed here is described in Example 1.
Example 1
Project Objectives and Design
Hypothesis and Primary Objective
Our working hypothesis is that an ongoing neurodegenerative process leads to detectable brain-derived cfDNA circulating in the plasma carrying an epigenetic signature precisely reflecting the origin as well as the pathogenic mechanisms causing and resulting from AD [Alzheimer’s Disease].
The primary objective of this observational pilot study is to reach a proof of concept of an in vitro diagnosis for AD based on the analysis of cfDNA
(paras. 0139-40). In other words, detection of methylation in cfDNA in AD patients. To do this, Applicants state the following:
Primary Endpoint
The primary endpoint is the difference in total amount of cfDNA in plasma and its epigenetic signature between patients with AD and healthy subjects.
The total amount of cfDNA present in plasma as well as its epigenetic signature are expected to significantly differ between age- and gender-matched healthy controls and patients with clinically diagnosed AD in a phase of the disease displaying a significant rate of neuronal and synaptic loss. This will allow obtaining an epigenetic signature of AD that can be used for in vitro diagnostics (IVD) diagnosis.
Project Design
This observational pilot study is based on a single collection of blood samples from two cohorts of participants, one with an AD diagnosis and the other of age- and gender matched healthy subjects. The blood samples are utilized for the purification of cfDNA from plasma and the analysis of epigenetic status at a whole genome level.
[ . . . ]
Study Procedures
One visit for blood draws at the “Unita disturbi cognitivi e logopedia Neurocentro”, Istituto di Neuroscienze Cliniche della Svizzera Italiana, Ente Ospedaliero Cantonale.
Blood samples will be collected in 5×10 ml_(50 ml) PAXgene Blood ccfDNA Tubes, Qiagen. cfDNA will next be purified from plasma using QlAamp Circulating Nucleic Acid Kit and its quantity determined by fluorescence-based commercial kits. cfDNA will be sequenced according to standard protocols of methylated DNA (e.g. chemistry-basted methylation sequencing and enzyme-based methylation sequencing) (Illumina)
(paras. 0141-43 & 0150-51). Yet, Applicants fail to present the data in understandable form. Specifically, it is entirely unclear which methylation markers or sites were used, and what score was developed. And it is entirely unclear if anything other than AD was assessed, or any other samples from any other organisms used. Paragraphs 0224-26 report some conclusions, but completely fail to explain any of the details (neurodegenerative diseases or disorders, methylation markers/sites, specific scores and meanings, how the scores are calculated, scope of sample types used, etc.) critical to showing possession of the claimed invention:
Differential Methylation Analysis
Raw sequencing data in FastQ file format were aligned to the human genome (GRCh38 version) using the Bismark software (version 0.23.1). The software was run using default parameters except for the following parameters: —L 28—D 3—R 0. Using the deduplicate_bismark command (default parameters), alignments to the same position in the genome from the Bismark mapping output, which can arise by PCR amplification were removed. In the next step we used bismark_methylation_extractor to extracts the methylation call for every single C analysed. The following arguments were set: —no_overlap—comprehensive—merge_non_CpG.
Evaluation of differences in methylation status between cases and controls was performed using the dmrseq package (version 1.16.0) for R/Bioconductor (version 4.1) environment. CpG coverage and methylation status data, stored in the “*.bismark.cov.gz”, one file per patient, were imported and merged using read.bismark( ) function. CpGs were filtered selecting 19715509 loci with a coverage >=8× in all 50 samples.
From the study cohort, a training set (80%, 24 cases and 16 controls) and a validation set (20% 6 cases and 4 controls) were identified. Differential analysis was performed on the training set using the dmrseq( ) function. Default parameters were used expect for: cutoff=0.02, minNumRegion=20, maxPerms=50. 9149 regions were identified genome wide with 14 having a p-value<0.001. Those regions became the input for the training of a classifier able to accurately discriminate between cases and controls using the most relevant subset of CpG regions. We used a regularized logistic regression model as implemented in the glmnet R/Bioconductor package (version 4.1-4). All 9149 regions previously identified in 40 samples were used as candidate features. By varying the penalization parameter lambda between 10-15 and 1, the optimal subset of features required was selected, by optimizing the prediction performance (measured as area under the ROC curve or AUC) in a 4-fold cross-validation setting. We used the cv.glmnet( ) function, additionally setting: alpha=0.5, keep=T, grouped=FALSE. The fully trained model was applied to the 10 samples of the independent validation set not used for the development of the classifier. The whole cross-validation procedure was repeated 100 times to quantify the variability caused by the sampling procedure. For each iteration, the optimal number of features included (median=274), the cross-validated AUC (median=0.99) and the AUC for the independent validation set (median=0.83) were collected.
From this single, limited example, the specification clearly fails to provide written description support for any and all neurodegenerative diseases or disorders, any and all methylation markers/sites, any and all scores, any and all sample types from any and all organisms, and any and all methods of calculating scores. The results fail to show diagnosis or prediction of any neurodegenerative diseases or disorders, or any scoring system correlated thereto.
In sum, the specification reads as a plan to determine methylation scores in order to diagnose neurodegenerative diseases or disorders in any and all organisms, not an actual methylation scoring system for an actual disease for an actual organism using an actual sample.
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:
Novelty; Prior Art.—A person shall be entitled to a patent unless—
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; or
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 1-2, 5-13 and 15-19 are rejected under 35 U.S.C. § 102(a)(2) as being anticipated by SINGH (US20220002808).
As to claim 1, 11-12 and 17-19, SINGH teaches a method for determining a score indicative of the diagnosis of a neurodegenerative disease or disorder of a subject, of the probability of a subject to develop a neurodegenerative disease or disorder and/or of the disease progression of a neurodegenerative disease or disorder (AD; Abstract), the method comprising the steps of:
a) obtaining at least one methylation status of two or more genes selected from Table 1 and/or two or more regions selected from Table 2 from a sample of a subject (Creb5, Gtf2h4/vars2, Hoxa7; Table 5 and Abstract);
b) comparing the methylation status obtained in (a) to a reference pattern (Abstract); and
c) determining a score indicative of the diagnosis of a neurodegenerative disease or disorder of the subject, of the probability of the subject to develop a neurodegenerative disease or disorder and/or of the disease progression of a neurodegenerative disease or disorder based on the comparison obtained in (b) (methylation levels= scores/values; e.g. Claim 1 and para. 0091).
As to claim 2, SINGH teaches the sample is a body fluid sample (blood; Abstract).
As to claim 5, SINGH teaches obtaining at least one methylation status comprises genome methylation profiling (paras. 0076, 0091).
As to claim 6, SINGH teaches the at least one methylation status comprises the methylation status of at least 100 regions selected from Table 2 (para. 0091).
As to claim 7, SINGH teaches the at least one methylation status comprises the methylation status of at least 80% of the regions selected from Table 3 (id.)
As to claim 8, the claim and specification state an inherent characteristics of all the listed methylation sites; thus the prior, which teaches the same sites, will have the same characteristics.
As to claims 9-10, SINGH teaches at least one further marker is obtained in (a) compared in (b), wherein the at least one further marker is a marker selected from the group of subject background data, cognitive performance marker, autonomic nervous system biomarker (e.g. para. 0091).
As to claim 13, SINGH teaches monitoring a neurodegenerative disease or disorder using the method of claim 1 (e.g. para. 0116).
As to claim 15, SINGH teaches storage device comprising computer-readable program instructions to execute the method according to claim 1 (paras. 0014 & 0048).
As to claim 16, SINGH teaches server comprising the storage device of claim 15, at least one processing device, and a network connection for receiving data indicative of at least one methylation status (id.)
Claim Rejections - 35 USC § 103
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.
Claim(s) 3-4 is/are rejected under 35 U.S.C. 103 as being unpatentable over SINGH (US20220002808), in view of KR20160080165A, KR20100034832A, US 20120208711, US 20140080715.
The prior art as a whole demonstrates that it would have been obvious to a skilled artisan in methylation detection analyses to use cfDNA or frozen samples in order to non-invasively detect methylation with a reasonable expectation of success.
SINGH does not explicitly teach frozen sample; or cfDNA sample.
However, these sample types for DNA methylation analyses were routinely used in the art in order to non-invasively test subjects with success. For example, KR20160080165A teaches “diagnosing degenerative brain diseases and a method for diagnosing degenerative brain diseases using the composition, and more particularly, to a composition for measuring a methylation level of a gene related to a degenerative brain disease and a method for diagnosing Alzheimer's disease” by “(a) obtaining genomic DNA of cell-free DNA and mononuclear cells from a biological sample of a patient; (b) transforming unmethylated cytosine bases of the cell-free DNA and the genomic DNA obtained in step (a); (c) PCR using the cell-free DNA modified from unmethylated cytosine base from the step (b) as a template and using at least one primer pair selected from SEQ ID NO: 1 to SEQ ID NO: 132.” “The supernatant containing pure DNA was recovered and stored frozen (-20 ° C) until the next analysis step.” KR20100034832A teaches “analyzing circulating free DNA in plasma, and to diseases or phenomena related to gene regulation CpG island methylation using the same, particularly cancer. A method, kit, and composition for diagnosing or detecting a gene), wherein the plasma free-circulating DNA can be analyzed for the amount of gene-regulated CpG island methylation.” The “plasma was separated and stored frozen at -20 ° C.” US 20120208711 teaches “a method for analyzing DNA methylation profiles of cell-free DNA in body fluids by enriching a methylated or unmethylated fraction of DNA from cell-free DNA and subjecting the enriched DNA to microarray based methylome profiling and bioinformatics data analysis” (Abstract). And US 20140080715 teaches “methylation profile can be deduced for fetal/tumor tissue based on a comparison of plasma methylation (or other sample with cell-free DNA) to a methylation profile of the mother/patient” (Abstract). These references are cited to demonstrate that cfDNA is routinely used with success to non-invasively detect methylation status of genes and DNA sies in order to diagnose diseases such as neurodegenerative diseases or disorders. Thus, a skilled artisan would have been familiar with cfDNA and frozen samples as a well-known, routine sample type to detect methylation status of genes and DNA sites non-invasively.
Prior Art
The following prior art, among many, also teaches methylation profiles for AD and other ND diseases: Zhang et al, Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer’s disease, Nature Communications volume 11, Article number: 6114 (2020); Konki et al, Plasma cell-free DNA methylation marks for episodic memory impairment: a pilot twin study, Scientific Reports volume 10, Article number: 14192 (2020); Robichaud et al, Circulating cell-free DNA as potential diagnostic tools for amyotrophic lateral sclerosis, Neuroscience Letters, Date: 17 April 2021, Article: 135813, Volume: Volume 750.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Aaron Priest whose telephone number is (571)270-1095. The examiner can normally be reached 8am-6pm.
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/AARON A PRIEST/Primary Examiner, Art Unit 1681
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