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 .
Status of the Claims
Claims 49-68 are pending and examined herein.
Drawings
The drawings are objected to because:
Figs. 2, 3, 5, 8, 9, 13, 14, 18A, 18B, and 19-21 have low resolution and insufficient quality. Some labels and values are illegible.
Rows and columns in Fig. 10 table are not labeled.
Figs. 22-24 have insufficient quality and axis labels are barely legible. The Spearman correlation code cannot be read because positive and negative values look identical in the drawings.
There are two drawings labeled as Fig. 23B.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification
The Specification is objected to because:
The specification states that “FIG. 1 presents Table 1, which sets forth the novel protein biomarkers, Nos. 1-82. The protein biomarkers set forth in Table 1 and amino acid sequences in the sequence listing filed herewith” ([0056]). However, no sequence listing has been filed with this application and there are no SEQ ID NOs and/or actual sequences present in the specification. Listed accession NOs in Table 1 is not a proper way for disclosing amino acid sequences. Therefore, it is unclear whether or not Applicant wants to disclose the biomarkers by their amino acid sequences.
Example 10 refers to Table 5 for the diagnostic values of the biomarkers to mTBI, but Table 5 is not present in the specification ([0270]).
Claim Objections
Claims 52 and 62 are objected to because of the following informalities:
Claims 52 and 62 recite PEA-15, PEA15, and PEA 15. Terminology should be consistent.
Appropriate correction is required.
Claim Interpretation
Claims 49 and 59 recite measuring the levels of protein biomarkers or peptide biomarkers derived therefrom in a biomarker panel comprising soluble Suppression of Tumorigenicity 2 protein (sST2), Glial Fibrillary Acidic Protein (GFAP), and Neurogranin (NRGN). In step (B) the claims recite diagnosing a neurological or brain injury in the subject or stratifying the risk of the patient based on the measured levels of one or more of the biomarkers are. As such, the diagnosing/stratifying decision is based on individual biomarker measurement, but not on the combined result of the entire panel.
Therefore, claims 49 and 59 are interpreted as measuring the levels of individual biomarkers: soluble Suppression of Tumorigenicity 2 protein (sST2), Glial Fibrillary Acidic Protein (GFAP), or Neurogranin (NRGN). Correspondingly, claims 51 and 61 are interpreted as the measured levels of sST2, GFAP, or NRGN are higher or lower in the biological sample compared to the respective control sample.
Claims 50 and 60 recite further comprising measuring levels of one or more biomarkers selected from Aldolase C (ALDOC), Brain Derived Neurotrophic Factor (BDNF), Calcitonin Gene Related Peptide (CGRP), Endothelin 1 (ET1), Eotaxin (CCL11), Fatty Acid Binding Protein 7 (FABP7), Growth Associated Protein 43 (GAP-43), Intercellular Adhesion Molecule 5 (ICAM-5), Interleukin 6 (IL-6), Interleukin 8 (IL-8), Interleukin 10 (IL-10), Metallothionein 3 (MT3), Neurofilament heavy chain (NF-H), Neurofilament light chain (NF-L), Neurofilament medium chain (NF-M), Neuron Specific Enolase (ENO2/NSE), Oligodendrocyte Myelin Glycoprotein (OMG), Reticulon (RTN1), Synuclein alpha (SNCA), Synuclein beta (SNCB), Tau microtubule binding protein (TAU/MAPT), and Vascular Endothelial Growth Factor (VEGF-A, B, C or D homo or heterodimers). The claims do not recite any diagnosing/stratifying decision based on the additional biomarkers of the claims.
Therefore, claim 50 is interpreted as measuring the levels of protein biomarkers of claims 49 and 50, and diagnosing based on the measured levels of one or more of the biomarkers, wherein the one or more of the biomarkers are selected from the combined list of the biomarkers of claims 49 and 50.
Therefore, claim 60 is interpreted as measuring the levels of protein biomarkers of claims 59 and 60, and stratifying based on the measured levels of one or more of the biomarkers, wherein the one or more of the biomarkers are selected from the combined list of the biomarkers of claims 59 and 60.
Claims 52 and 62 recite further comprising measuring the levels of one or more biomarkers selected from brain lipid binding protein (BLBP/ FABP7), a trauma-specific breakdown product (BDP) of ALDOCL, a trauma-specific BDP of BLBP/FABP7, glutamine synthetase (GS), astrocytic phosphoprotein PEA-15 (PEA15), aB-crystallin (CRYAB), a trauma-specific proteolytic cleavage product of ALDOC, a trauma-specific proteolytic cleavage product of GS, a trauma-specific proteolytic cleavage product of PEA 15, a trauma-specific proteolytic cleavage product CRY AB, and a 20-30 kDa trauma-specific BDP of GFAP. The claims do not recite any diagnosing/stratifying decision based on the additional biomarkers of the claims.
Therefore, claim 52 is interpreted as measuring the levels of protein biomarkers of claims 49 and 52, and diagnosing based on the measured levels of one or more of the biomarkers, wherein the one or more of the biomarkers are selected from the combined list of the biomarkers of claims 49 and 52.
Therefore, claim 62 is interpreted as measuring the levels of protein biomarkers of claims 59 and 62, and stratifying based on the measured levels of one or more of the biomarkers, wherein the one or more of the biomarkers are selected from the combined list of the biomarkers of claims 59 and 62.
Claim 68 recites optionally bind to one or more additional protein biomarkers.
MPEP 2143.03 instructs that “Language that suggests or makes a feature or step optional but does not require that feature or step does not limit the scope of a claim under the broadest reasonable claim interpretation”. Therefore, additional biomarkers of claim 68 that have “optionally” indication are not given patentable weight.
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 53 and 59-67 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 49 and 67 recite methods for measuring levels of biomarkers. Corresponding dependent claims 53 and 67 recite the biological sample and/or respective control sample is obtained from blood, serum, plasma, cerebrospinal fluid (CSF), saliva, urine, sputum, secretions, tears, or tissue. The prior art is silent on measuring the levels of the recited biomarkers in saliva, urine, sputum, secretions, tears, or tissue.
The specification discloses only serum as the biological sample.
One of ordinary skill in the art would conclude that Applicant did not have possession of all recited biological samples at the time the application was originally filed.
Claims 59, 60, and 62 recite a method for measuring levels of biomarkers, stratifying the risk of the patient, and administering an effective amount of therapy or drug to the patient.
The prior art is silent on measuring the levels of protein biomarkers or peptide biomarkers recited in claims 59, 60, and 62 and using the measured levels for stratifying the risk of the patient with post TBI disorders recited in claim 59.
The following examples are disclosed in the specification:
Example 1 - Discovery of Biomarkers for Neurological Injury and Disease;
Example 2 - Detection of Autoantibodies to Proteins to Specific Candidate TBI Biomarkers;
Example 3 - Increased Citrullination of TBI Biomarkers;
Example 4 - Increased Citrullination of Biomarker Proteins;
Example 5 - Discrimination of TBI from Control Subjects without Injury or with Orthopedic Injury;
Example 6 - Biomarker Panels and Correlations;
Example 7 - Discriminating mTBI Based on Specific CT Features and sST2;
Example 8 - Discriminating TBI Based on vWF and Age at the Acute Stage of TBI;
Example 9 - Discriminating TBI Based on GFAP, vWF, and sST2 at Acute and Late Stages of TBI;
Example 10 - Discrimination of TBI by Single and Combinations of Features;
Example 11 - Monitoring sST2 Levels Predicts Recovery;
Example 12 - Correlation of Biomarkers to mTBI;
Example 13 - Performance of Risk Stratification Models for Post-Concussive Syndrome 3 Months Post-Injury;
Example 14 - Performance of Risk Stratification Models for Clinically Significant Depressive Symptoms 3 Months Post-Injury;
Example 15 - Performance of Risk Stratification Models Clinically Significant Depressive Symptoms 6 Months Post-Injury.
None of these examples disclose using measured biomarker levels and/or stratifying the risk of the patient. No biomarker levels are matched to patients with post-TBI seizures, post-TBI depression, post-TBI anxiety, post-TBI post-traumatic stress disorder (PTSD), post-TBI sleep disorder, post-TBI headache, post-TBI chronic pain, post-TBI oculomotor deficits, post-TBI attention and cognitive defects, and/or post-TBI balance and gait problems.
Therefore, the specification fails to disclose any evidence for stratifying the risk of the patient with post TBI disorders.
Claims 60-67 are rejected because they depend from rejected claim 59.
Based on the above findings, one of ordinary skill in the art would conclude that Applicant did not have possession of the claimed invention at the time the application was originally filed.
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 58, 60, 65, and 68 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 58 and 65 contain parenthetical subject matter (step (B)(ii)) which is vague because it is unclear if the parenthetical subject matter are positive limitations of the claim.
Claims 60 and 68 contain parenthetical subject matter (Vascular Endothelial Growth Factor (VEGF-A, B, C or D homo or heterodimers) which is vague because it is unclear if the parenthetical subject matter are positive limitations of the claim.
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 49-67 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a naturally occurring correlation, without significantly more.
Claims 49 and 59 are directed to a process, which belongs to the four statutory categories.
The claims are related to methods of establishing relationships between changes in biomarker levels in a biological sample taken from a subject and diagnosing of a neurological or brain injury or stratifying the risk of the patient. These relationships are categorized as a naturally occurring correlation, and therefore it is a judicial exception.
The claims also recite additional steps of measuring (A) and diagnosing/stratifying (B).
The additional step of “measuring” is an insignificant extra-solution activity that amounts to mere data gathering necessary to apply the judicial exception.
The additional step of “diagnosing” amounts to making a conclusion based on the results from step (A) that the subject has a neurological or brain injury. The step of “diagnosing” amounts to a mental process, performed in the human mind, since diagnosing is considered an evaluation, and/or a judgement. The limitation of “diagnosing” falls into the mental process groupings of abstract ideas and therefore is a judicial exception.
The additional step of “stratifying” amounts to making a conclusion based on the results from step (A). The step of “stratifying” amounts to a mental process, performed in the human mind, since stratifying is considered an evaluation, and/or a judgement. The limitation of “stratifying” falls into the mental process groupings of abstract ideas and therefore is a judicial exception.
The claims recite an additional step of treating the neurological or brain injury in the subject with an effective amount of therapy or drug (claim 49); and administering an effective amount of therapy or drug to the patient (claim 59). Although this limitation indicates that a treatment is to be administered, it does not provide any information as to how the subject is to be treated, or what the treatment is, but instead covers any possible treatment that a doctor decides to administer to the subject. This limitation is recited at a high level of generality, it tells the doctors about the naturally occurring correlation, and at most adds a suggestion that the doctors take this correlation into account when treating their patients. The limitation of treating/administering thus fails to meaningfully limit the claim because it does not require any particular medication or treatment, and is at best the equivalent of merely adding the words “apply it” to the judicial exception. Accordingly, the limitation of treating/administering does not integrate the recited judicial exception into a practical application and the claims are therefore directed to the judicial exception.
When considering the elements in combination, the claims as a whole do not integrate the recited exceptions into a practical application.
Additional elements of measuring the biomarkers levels are recited at a high level of generality: claims 49 and 59 do not recite any specific measurement methods and dependent claims 55 and 66 broadly recite well-known methods for measuring any biomarker levels. Such measurements have been recognized as routine laboratory techniques.
The techniques for measuring a level of sST2 protein are known in the art. It was routine and conventional to measure sST2 levels in patients’ serum using an ELISA kit (pg. 147, col. 2, section “2.3. Immunoassay methods”), see Du et al. (IDS; Clin Chim Acta. 2018 Dec; 487:145-152).
Therefore, the claims as a whole do not amount to significantly more than the recited exception, because there are no additional elements, or combination of additional elements, that add an inventive concept to the claims and are not routine and conventional.
The dependent claims 50-58 and 60-67 fail to add additional elements, or combination of additional elements, that contribute to an inventive concept to the claim.
For these reasons, claims 49-67 are ineligible under 35 U.S.C. 101.
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.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
Determining the scope and contents of the prior art.
Ascertaining the differences between the prior art and the claims at issue.
Resolving the level of ordinary skill in the pertinent art.
Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 49-58 are rejected under 35 U.S.C. 103 as being unpatentable over Du et al. (IDS; Clin Chim Acta. 2018 Dec; 487:145-152) in view of Kimberly (IDS; PGPub 20200339674) and as evidenced by Kay et al. (J Head Trauma Rehabil. 1993; 8(3):86–87).
Regarding claims 49, 50, and 52, Du teaches a method of using sST2 as a prognostic biomarker for traumatic brain injury (Title and Abstract). Specifically, Du teaches a method comprising:
measuring sST2 levels in patients’ serum using an ELISA kit (pg. 147, col. 2, section “2.3. Immunoassay methods”). The claim recites a panel of biomarkers comprising sST2, GFAP, and NRGN. However, diagnosing step (B) recites that only one biomarker is sufficient for diagnosing purposes (see Claim Interpretation above for details). Therefore, the teaching of sST2 by Du meets the claim;
diagnosing posttraumatic cerebral infarction (PTCI) (Fig. 1, right column) when the measured levels of sST2 was higher in the subject's sample relative to the corresponding level in non-PTCI control samples.
Du does not specifically teach treating the neurological or brain injury in the subject diagnosed in step (B) with an effective amount of therapy or drug.
Regarding claims 49, 50, and 52, Kimberly teaches methods and compositions for treating a brain injury (Title). Specifically, the reference teaches that soluble suppression of tumorigenicity 2 (sST2) serves as a prognostic biomarker for the functional outcome of a patient having suffered an ischemic stroke; increased levels of sST2 in a plasma sample were associated with poor outcome and mortality ([0005]); and treatments can range from rest, medication, to surgery, and can be administered or performed by a skilled practitioner ([0107]).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have combined the method of Du with treatments as taught by Kimberly, in order to provide comprehensive health care to the patients, as an obvious matter of combining prior art elements according to known methods to yield predictable results.
One having ordinary skill in the art would have had a reasonable expectation of success of combining the prior art references because diagnostics and therapy are independent methods and their combination is expected to yield predictable results.
Regarding claim 51, Du teaches the increased levels of sST2 were determined in comparison with 106 healthy controls (Abstract), meeting the limitation reciting the measured levels of sST2 is higher in the biological sample compared to the respective control sample.
Regarding claim 53, Du teaches measuring sST2 levels in patients’ serum using an ELISA kit (pg. 147, col. 2, section “2.3. Immunoassay methods”), meeting the limitation reciting the biological sample and/or respective control sample is obtained from serum.
Regarding claim 54, Du teaches the increased levels of sST2 were determined in comparison with 106 healthy controls (Abstract), meeting the limitation reciting control samples are obtained from a subject not having a neurological or brain injury.
Regarding claim 55, Du teaches measuring sST2 levels in patients’ serum using an ELISA kit (pg. 147, col. 2, section “2.3. Immunoassay methods”), meeting the limitation reciting one or more of the biomarkers are measured by an immunoassay.
Regarding claim 56, Du teaches the relationship between serum soluble ST2 concentrations, inflammation, severity, and prognosis following traumatic brain injury (TBI), meeting the limitation (iii) reciting a concussion or traumatic brain injury (TBI).
Regarding claim 57, Du in view of Kimberly teaches diagnosing mild traumatic injury “Symptoms of a mild traumatic brain injury include, but are not limited to, brief loss of consciousness (e.g., seconds to a few minutes), headache, fatigue, vomiting, problems with speech, dizziness, and/or loss of balance” ([0100]), meeting the limitation reciting the TBI is a mild TBI (mTBI).
Regarding claim 58, Du and Kimberly do not specifically teach symptoms of mTBI recited in the claim. However, Kay provides evidence for a definition of mTBI “A patient with mild traumatic brain injury is a person who has had a traumatically induced physiological disruption of brain function, as manifested by at least one of the following:
any period of loss of consciousness;
any loss of memory for events immediately before or after the accident;
any alteration in mental state at the time of the accident (eg, feeling dazed, disoriented,
or confused); and
focal neurological deficit(s) that may or may not be transient;
but where the severity of the injury does not exceed the following:
loss of consciousness of approximately 30 minutes or less;
after 30 minutes, an initial Glasgow Coma Scale (GCS) of 13-15; and
posttraumatic amnesia (PTA) not greater than 24 hours (pg. 86, Section “Definition”).
The definition meets the limitations of claim 58.
Claim 68 is rejected under 35 U.S.C. 103 as being unpatentable over Du in view of Van Meter et al. (WO 2018/217792).
Regarding claim 68, Du teaches sST2 as a prognostic biomarker for traumatic brain injury (Title and Abstract). Specifically, Du teaches a method comprising: measuring sST2 levels in patients’ serum using an ELISA kit (pg. 147, col. 2, section “2.3. Immunoassay methods”). As such, Du teaches a composition comprising a solid substrate and a binding agent immobilized on the substrate, and the binding agent specifically bind to soluble Suppression of Tumorigenicity 2 protein (sST2).
Du does not specifically teach a composition comprising a solid substrate and binding agents immobilized on the substrate, and the binding agents specifically bind to biomarkers GFAP and NRGN.
Regarding claim 68, Van Meter teaches compositions useful in the detection of brain injuries (Abstract). Van Meter also teaches a composition comprising a solid substrate and binding agents immobilized on the substrate, and the binding agents specifically bind to biomarkers GFAP and NRGN. Specifically, the reference teaches “embodiments of the invention provide compositions including a solid substrate and a plurality of polypeptide biomarkers disclosed herein immobilized on the substrate, wherein each of the polypeptide biomarkers is immobilized at a different, indexable, location on the substrate. In certain embodiments, the plurality of polypeptide biomarkers include ALDOC or GFAP and one of more of NRGN” (pg. 51, lines 14-18).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Du and Van Meter for a composition comprising a solid substrate and a plurality of binding agents immobilized on the substrate, and the binding agents specifically bind to a plurality of protein biomarkers comprising sST2, GFAP, and NRGN, in order to aid in diagnosis, prognosis and/or treatment of brain injuries.
It is prima facie obvious to combine elements, each of which is taught by the prior art to be useful for the same purpose. See MPEP 2144.06.
One having ordinary skill in the art would have had a reasonable expectation of success in combining the prior art references because the binding agents specifically bind biomarkers sST2, GFAP, and NRGN independently from each other.
Subject Matter Free of the Prior Art
Claims 59-67 are free of the prior art.
The prior art neither teaches nor suggests measuring the levels of sST2, GFAP, or NRGN biomarkers and stratifying the risk of the patient at one or more time points for post-TBI seizures, post-TBI depression, post-TBI anxiety, post-TBI post-traumatic stress disorder (PTSD), post-TBI sleep disorder, post-TBI headache, post-TBI chronic pain, post-TBI oculomotor deficits, post-TBI attention and cognitive defects, and/or post-TBI balance and gait problems.
The closest prior art teaches:
Du et al. (IDS; Clin Chim Acta. 2018 Dec; 487:145-152) - measuring sST2 levels in patients’ serum using an ELISA kit (pg. 147, col. 2, section “2.3. Immunoassay methods”) and diagnosing posttraumatic cerebral infarction, but fail to teach stratifying the risk of the patient;
Kimberly (IDS; PGPub 20200339674) - methods and compositions for treating a brain injury (Title), but fails to teach stratifying the risk of the patient;
Van Meter et al. (WO 2018/217792) - methods, compositions, and kits useful in the detection, assessment, diagnosis, prognosis, and/or treatment of brain injuries (Abstract), but fail to teach stratifying the risk of the patient.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Alexander Volkov whose telephone number is (571) 272-1899. The examiner can normally be reached M-F 9:00AM-5:00PM (EST).
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bao-Thuy Nguyen can be reached on (571) 272-0824. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ALEXANDER ALEXANDROVIC VOLKOV/
Examiner, Art Unit 1677
/REBECCA M GIERE/Primary Examiner, Art Unit 1677
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