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
Claims 6-7, 9-20 and 22 are cancelled. Claims 23-28 are withdrawn.
Claims 1-5, 8, 21 are under examination.
Response to Amendment dated 2/19/2025
The objection to claim 21 is withdrawn in light of the amendment correcting the informality.
The rejection of claims 1-5, 8 and 21 under 35 U.S.C. 101 as being directed to a judicial exception is withdrawn in light of the amendment to claims 1 and 21 incorporating the judicial exception into a practical application to amount to sufficiently more than the judicial exception, by amending claims 1 and 21 to include a step of “administering a therapeutic agent or a dental procedure to the human patient, or a combination of the therapeutic agent and the dental procedure to the human patient” following the diagnosing step.
The previous rejection of claims 1-5 and 21 under 35 U.S.C. 102(a)(1) as being anticipated by Ebersole et al. is withdrawn in light of the amendment to claim 1 requiring detecting the combination of proteins A1AGP, MMP8, MMP9 and Hb-beta in the sample of saliva. Ebersole does not teach detecting A1AGP or Hb-beta in a saliva sample.
Priority
This application is a 371 of PCT/EP2019/059041 filed on April 10, 2019, which claims benefit of EPO 18166943.3 filed on 4/12/2018.
Acknowledgment is made of applicant's claim for foreign priority based on an application filed in European Patent Office on April 12, 2018.
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
The effective filing date of the instant application is April 10, 2018.
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 for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Modified rejection necessitated by amendment: Claims 1-2, 4-5 and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Chapple et al. (WO 2014/037924 A2, published on March 13, 2014; previously cited) in view of Ebersole et al. (“Targeted salivary biomarkers for discrimination of periodontal health and disease(s)”, Frontiers in Cellular and Infection Microbiology, 2015, Vol. 5, Article 62, 12 pages; previously cited).
Regarding claims 1 and 21, Chapple teaches the analysis of saliva proteome for biomarkers of gingivitis and periodontitis using FT-ICR-MS/MS (relevant to claim 1: an in vitro method for diagnosing gingivitis; relevant to claim 21: a method of diagnosing whether a human patient has gingivitis) (title). Chapple teaches collecting saliva samples non-invasively from the mouths of several patients (relevant to in a human patient; relevant to claim 1(a): obtaining a sample of saliva from the human patient) (description p.11, lines 3-4). Chapple teaches using liquid chromatography techniques coupled with Fourier Transform – tandem Mass Spectrometry (FT MS/MS) to separate protein biomarkers from within the samples and to identify the protein biomarkers (relevant to claim 1(b): detecting, in the sample of saliva from said human patient, the concentrations of proteins; relevant to claim 21: detecting in a sample of saliva of the human patient) (description p.11, lines 4-6). Chapple teaches the samples were analyzed in triplicate by LC-MS/MS; the CID spectra were used to identify the peptides and the HCD spectra were used to quantify them (description p.16, lines 4-15). Chapple teaches the data were analyzed and used for protein quantification and protein grouping (relevant to (c) determining a testing value reflecting the concentrations of said proteins detected in the sample of saliva) (description p.16, lines 17-31). Chapple teaches a method for diagnosing severe periodontitis includes selecting at least one protein biomarker from the group consisting of: S100-A8 (calgranulin-A), alpha-1-acid glycoprotein 1 and 2, and matrix metalloproteinase-9 (relevant to alpha-1-acid glycoprotein (A1AGP), and matrix metalloproteinase-9) (description p.23, lines 1-5). Chapple further teaches that the set of biomarkers can be selected from haemoblogin chains alpha and beta (relevant to hemoglobin subunit beta (Hb-beta)) (description p.9. lines 20-21). Chapple teaches that the nineteen proteins identified as cluster 2 show an increase in abundance with gingivitis before returning to baseline like levels in periodontitis (relevant to (d) diagnosing the human patient with gingivitis when said value exceeds a threshold value) (description p.17 line 35 – p.18 line 1). Chapple teaches that patients were recruited and sampled, and volunteers with periodontitis were then treated non-surgically in order to remove the periodontal inflammation and restore improved health (relevant to administering of a dental procedure to the human patient) (p.12, lines 18-20). Chapple teaches the quantification values are expressed as a ratio between healthy subjects and subjects with gingivitis (description p.19, line 11; Supplementary Table 1 and Table 4; A column header in Supplementary Table 1 is 114/113, where 113 corresponds to healthy state and 114 corresponds to gingivitis state). While the prior art does not expressly state “threshold”, the instantly claimed threshold is so broad, it encompasses the values expressed in a healthy patient. Therefore, since Chapple clearly teaches looking at values of the healthy subject and comparing those values to subjects with gingivitis, it suggests obtaining the threshold (i.e. values in healthy patients) and comparing those values.
Chapple is silent about a testing value reflecting the joint concentrations determined for said proteins. Chapple does not teach matrix metalloproteinase-8.
However, Ebersole teaches subjects expectorated at least 5mL of unstimulated whole saliva into sterile tubes (relevant to (a) obtaining a saliva sample from the human patient using a measurement device) (p.3, 1st column – Salivary Samples). Ebersole teaches the MILLIPLEX MAP Kit was used to detect IL-1β, IL-6, MMP-8 and MIP-1α, and the kit was used to analyze individual saliva samples for the four biomarkers using a Luminex 100IS instrument (relevant to (b) detecting the concentration of Matrix metalloproteinase-8 (MMP-8)) (p.3, 2nd column – Salivary Molecular Biomarkers; Figure 1). Ebersole teaches first threshold cutoff values for each analyte were based upon the population distribution and selected to optimize sensitivity for detection of periodontitis (relevant to a threshold value) (p.4, 1st column – last paragraph; Figure 1). Ebersole teaches that combinations of these biomarkers improved the sensitivity, specificity, and accuracy of the identification of periodontitis vs. either health or gingivitis subjects when compared to the performance of the individual biomarkers (relevant to (c) determining a testing value reflecting the joint concentrations of said proteins detected in the sample of saliva; (d) diagnosing a patient with gingivitis when said testing value exceeds a threshold value) (p.4, 2nd column – 3rd paragraph; Table 5).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Chapple to include MMP-8 protein, and further determine a testing value reflecting the joint concentrations of A1AGP, MMP9 and Hb-beta, because Ebersole teaches that higher salivary levels of several proteins were detected in disease groups compared to healthy. One of ordinary skill in the art would have been motivated to determine a joint concentration of the proteins because Ebersole teaches that the combination of sensitivity, specificity, and accuracy was improved by exploring combinations of the biomarkers. One of ordinary skill in the art would have found it beneficial to obtain a testing value reflecting the joint concentrations of the proteins to more accurately determine whether a human subject had gingivitis.
Regarding claim 2, Chapple teaches in the case of periodontitis, oral fluid diagnostics methods should be able to distinguish at least between healthy patients and those that have developed gingivitis, milder forms of periodontitis, and/or more severe forms of periodontitis (relevant to wherein the human patient is suspected to have gingivitis) (description p.1, line 30 – p.2, line 2).
Regarding claims 4 and 5, Chapple teaches that GCF and saliva samples were collected from 10 volunteers in each of five clearly defined phenotypic groups: healthy, gingivitis, mild periodontitis, severe periodontitis, and edentulous patients as a negative control group, where the phenotypic groups are defined based on predefined clinical data thresholds (relevant to wherein the threshold is based on concentrations in one or more reference samples, each sample associated with the presence or absence of gingivitis) (description p.12, lines 16-18). Chapple teaches clinical data was collected at a time of baseline and post therapy obtained from 50 patients representing five phenotypic groups (relevant to claim 4: wherein the threshold value is based on concentrations determined for the proteins in one or more reference samples, each sample associated with the presence of gingivitis or the absence of gingivitis; relevant to claim 5: wherein the threshold value is based on the concentrations of the proteins in a set of samples, including samples from subjects that have gingivitis and samples from subjects not having gingivitis) (p.12, lines 23-27).
Maintained rejection: Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Chapple et al. (WO 2014/037924 A2, published on March 13, 2014; previously cited) in view of Ebersole et al. (“Targeted salivary biomarkers for discrimination of periodontal health and disease(s)”, Frontiers in Cellular and Infection Microbiology, 2015, Vol. 5, Article 62, 12 pages; previously cited) as applied to claim 1 above, and further in view of Eke et al. (“Prevalence of Periodontitis in Adults in the United States: 2009 and 2010”, Journal of Dental Research, 2012, Vol. 91, Issue 10, pp.914-920; previously cited).
The teachings of Chapple and Morelli are discussed above.
Regarding claim 3, Chapple teaches that gingivitis is a non-destructive form of periodontal disease involving soft tissue inflammation of the gums (description p.1, lines 5-6).
Chapple is silent on determining the age of the human patients, and does not teach that the testing value reflects the concentration of the proteins in combination with the age of the subject.
Ebersole teaches the cohort included 65 subjects in the healthy group, 43 subjects in the gingivitis group, and 101 subjects in the periodontitis group, with some differences in age, gender, race/ethnicity and smoking across the groups (relevant to wherein the age of the human patient is determined) (p.3, 2nd column – Distribution of Analytes in Saliva; Table 1). Ebersole is silent on whether the testing value reflects the concentration of proteins in combination with the age of the subject.
However, Eke teaches the prevalence of periodontitis in adults in the United States (title). Eke teaches that total periodontitis is 70.1% in adults age 65 years and older compared to 24.4% in adults 30-34 years old (relevant to the age of the subject is determined) (p.915, right column, “Results” paragraph 1). Eke teaches that gingivitis is a form of periodontal disease (p.919, left column, bottom of second full paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Chapple by including the age of the patient in the determination of the gingivitis state of the patient, because Ebersole teaches determining the age of the patient, and Eke teaches that gingivitis was a demographic risk factor for periodontal disease. One of ordinary skill in the art would have had a reasonable expectation of success that combining age of the patient with concentrations of proteins would predictably result in a correlation with risk for periodontitis, because Eke taught that age correlated with risk for periodontitis, and Chapple taught that an abundance of A1AGP and S100A8 proteins were biomarkers for gingivitis.
Maintained rejection: Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Chapple et al. (WO 2014/037924 A2, published on March 13, 2014; previously cited) in view of Ebersole et al. (“Targeted salivary biomarkers for discrimination of periodontal health and disease(s)”, Frontiers in Cellular and Infection Microbiology, 2015, Vol. 5, Article 62, 12 pages; previously cited) as applied to claim 1 above, and further in view of Baliban et al. (“Discovery of biomarker combinations that predict periodontal health or disease with high accuracy from GCF samples based on high-throughput proteomic analysis and mixed-integer linear optimization”, Journal of Clinical Periodontology, 2013, Vol. 40, Issue 2, pp.131-139; previously cited).
The teachings of Chapple and Ebersole are discussed above.
Regarding claim 8, Chapple and Ebersole are silent regarding wherein the testing values of the joint concentrations are arithmetically processed into a number between 0 and 1.
However, Baliban teaches identifying combinations of biomarkers that predict periodontal health or disease (title). Baliban teaches collecting GCF samples from chronic periodontitis patients and healthy patients, and analyzing the samples using high-throughput liquid chromatography, tandem mass spectrometry and the PILOT_PROTEIN algorithm (abstract). Baliban teaches predicting the periodontal status of a gingival crevicular fluid (GCF) sample based on a list of identified proteins within the sample, wherein the periodontal status is inferred based on a score determined by a weighted sum for each protein using a scoring function, where the matrix A contains the protein information about the sample; Aij = 1 if protein i exists in sample j, and Aij = 0 otherwise (relevant to wherein the testing values of the joint concentrations determined are arithmetically processed into a number between 0 and 1) (p.4, last paragraph “Scoring Function”).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to improve the method of Chapple by determining a testing value reflecting the joint concentrations determined for IL-1 and MMP-8 taught by Ebersole and comparing the testing value with a threshold value using the method of Baliban. One of ordinary skill in the art would have been motivated to process the testing values into a number between 0 and 1 based on the teaching of Baliban, which suggested a predictive formula that could be used to predict periodontal status based on protein biomarkers. One of ordinary skill in the art would have had a reasonable expectation of success that improving the method of Chapple and Ebersole using the formula of Baliban would predictably result in an improved assessment of gingivitis in a patient, because each of Chapple, Ebersole and Baliban’s methods were intended to determine periodontal status.
Response to Arguments
Applicant argues that claims 1 and 21 have been amended to recite “detecting the concentrations of the proteins: Alpha-1-acid glycoprotein (A1AGP), Matrix metalloproteinase-8 (MMP8), Matrix metalloproteinase-9 (MMP9), and Hemoglobin subunit beta (Hb-beta)”, and having reviewed Chapple et al. and Ebersole et al., applicant has failed to uncover the disclosure of the detection of all three substances as set forth in claim 1 (See Remarks dated 2/19/2025, p.10 – Rejections under 35 U.S.C. §103).
Applicant's arguments filed February 19. 2025 have been fully considered but they are not persuasive. Chapple teaches the detection of A1AGP, MMP-9 and Hb-beta proteins in saliva. Ebersole teaches MMP-8 in saliva, and the detection of combined protein concentrations. Chapple teaches a method of determining the concentration of individual proteins known in the art as saliva protein markers related to gingivitis. Ebersole teaches combining concentrations of proteins to determine concentrations in diseased groups compared to healthy groups, and further that the combination of sensitivity, specificity and accuracy was improved by exploring combinations of the biomarkers. Thus, Chapple in view of Ebersole teaches all the elements required of the instantly claimed method, and one of ordinary skill in the art would have been motivated to combine concentrations of biomarkers to obtain a more sensitive, specific and accurate method of discriminating periodontitis from health and gingivitis.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Modified rejection necessitated by amendment: Claims 1-2, 4-5, 8 and 21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2 of U.S. Patent No. 12,050,223 (previously copending Application No. 16/615,420) in view of Chapple et al. (WO 2014/037924 A2, published on March 13, 2014; previously cited) and Ebersole et al. (“Targeted salivary biomarkers for discrimination of periodontal health and disease(s)”, Frontiers in Cellular and Infection Microbiology, 2015, Vol. 5, Article 62, 12 pages; previously cited).
Claim 1 of ‘223 is drawn to a method for treating mild or advanced periodontitis, wherein the method comprises:
detecting, in a sample of saliva from a human patient, the concentrations of proteins consisting of: Interleukin-1β (IL-1β), Matrix metalloproteinase-9 (MMP-9), and at least one of Interleukin-6 (IL-6) and Matrix metalloproteinase-3 (MMP-3);
determining a testing value reflecting the joint concentrations detected for said proteins;
determining a mild periodontitis threshold value based upon a joint concentration of IL-1β, MMP-9, and at least one of IL-6 and MMP-3 from at least one subject known to have mild periodontitis;
determining an advanced periodontitis threshold value based upon a joint concentration value of IL-1β, MMP-9, IL-6, and MMP-3 from at least one subject known to have advanced periodontitis;
wherein the joint concentration value that determines the mild periodontitis threshold value and the joint concentration value that determines the advanced periodontitis threshold value are both determined in the same manner as the joint concentrations that determine the testing value; and
comparing said testing value with said mild periodontitis threshold value and said advanced periodontitis threshold value, so as to assess whether the testing value is indicative for mild periodontitis or for advanced periodontitis in said patient;
calculating a periodontal severity score between 0 and 1 for said human patient based on the comparison, wherein a periodontal severity score of 0 indicates a low probability of said human patient having either mild or advanced periodontitis and a periodontal severity score of 1 indicates a high probability of said human patient having advanced periodontitis, the periodontal severity score being calculated from a sigmoid function with coefficients determined from sample testing values taken from a plurality of patients known to have mild periodontitis and a plurality of subjects known to have advanced periodontitis; and
selecting for treatment said patient when said testing value exceeds either said mild periodontitis threshold value or said advanced periodontitis value; and
administering therapeutic agents to and/or performing a dental procedure on said human patient;
wherein said therapeutic agents comprise at least one of an antibiotic or an enzyme suppressant; and
wherein said dental procedure is at least one of scaling, root planing, surgical pocket reduction, flap surgery, gum grafts, or bone graft (relevant to instant claims 1 and 21).
Claim 2 of ‘223 is drawn to the method of claim 1, wherein the human patient is known to have periodontitis (relevant to instant claim 2).
Claims 1-2 of ‘223 do not recite the proteins Alpha-1-acid glycoprotein (A1AGP), Matrix metalloproteinase-8 (MMP8) or Hemoglobin subunit beta (Hb-beta).
Chapple teaches the analysis of saliva proteome for biomarkers of gingivitis and periodontitis using FT-ICR-MS/MS (title). Chapple teaches collecting saliva samples non-invasively from the mouths of several patients (description p.11, lines 3-4). Chapple teaches using liquid chromatography techniques coupled with Fourier Transform – tandem Mass Spectrometry (FT MS/MS) to separate protein biomarkers from within the samples and to identify the protein biomarkers (description p.11, lines 4-6). Chapple teaches the samples were analyzed in triplicate by LC-MS/MS; the CID spectra were used to identify the peptides and the HCD spectra were used to quantify them (description p.16, lines 4-15). Chapple further identifies protein biomarkers as haemoglobin subunit beta (Hb-beta), S100-A8, alpha-1-acid glycoprotein 1 and 2 (A1AGP), and matrix metalloproteinase-9 (MMP9) (description p.23, lines 1-5). Chapple teaches the quantification values are expressed as a ratio between healthy subjects and subjects with gingivitis (description p.19, line 11; Supplementary Table 1 and Table 4; A column header in Supplementary Table 1 is 114/113, where 113 corresponds to healthy state and 114 corresponds to gingivitis state) (relevant to claims 1-2, 4-5, 8 and 21).
Ebersole teaches subjects expectorated at least 5mL of unstimulated whole saliva into sterile tubes (p.3, 1st column – Salivary Samples). Ebersole teaches the MILLIPLEX MAP Kit was used to detect IL-1β, IL-6, MMP-8 and MIP-1α, and the kit was used to analyze individual saliva samples for the four biomarkers using a Luminex 100IS instrument (p.3, 2nd column – Salivary Molecular Biomarkers; Figure 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of detection in ‘223 to further detect A1AGP and Hb-beta taught by Chapple and MMP-8 taught by Ebersole. Each of ‘223, Chapple and Ebersole teach sets of proteins that were known in the art as biomarkers for gingivitis.
Modified rejection necessitated by amendment: Claims 1-3 and 21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,768,207 (previously co-pending Application No. 16/615,429 in view of Chapple et al. (WO 2014/037924 A2, published on March 13, 2014; previously cited).
Claim 1 of ‘207 is drawn to a method for treating a human subject diagnosed with periodontitis, comprising:
determining the age of the human subject and detecting, in a sample of saliva from said human subject, the concentration of proteins consisting of Hepatocyte Growth Factor (HGF) and Matrix Metalloproteinase 8 (MMP-8);
determining a single testing value for the human subject comprising a combination of the determined concentrations of HGF and MMP-8 and the age as associated with periodontitis;
comparing the determined testing value with a threshold value, the threshold value reflecting in the same manner the joint combined concentrations of HGF and MMP-8 and the age as associated with periodontitis;
determining, based on the comparison, that the testing value is indicative for periodontitis in said human subject; and
administering, in response to determining that the human subject has periodontitis, a treatment comprising a dental procedure and/or administration of an anti-periodontitis therapeutic agent.
Claim 1 of ‘207 does not recite the proteins Alpha-1-acid glycoprotein (A1AGP), Matrix metalloproteinase-9 (MMP9) or Hemoglobin subunit beta (Hb-beta).
Chapple teaches the analysis of saliva proteome for biomarkers of gingivitis and periodontitis using FT-ICR-MS/MS (title). Chapple teaches collecting saliva samples non-invasively from the mouths of several patients (description p.11, lines 3-4). Chapple teaches using liquid chromatography techniques coupled with Fourier Transform – tandem Mass Spectrometry (FT MS/MS) to separate protein biomarkers from within the samples and to identify the protein biomarkers (description p.11, lines 4-6). Chapple teaches the samples were analyzed in triplicate by LC-MS/MS; the CID spectra were used to identify the peptides and the HCD spectra were used to quantify them (description p.16, lines 4-15). Chapple further identifies protein biomarkers as haemoglobin subunit beta (Hb-beta), S100-A8, alpha-1-acid glycoprotein 1 and 2 (A1AGP), and matrix metalloproteinase-9 (MMP9) (description p.23, lines 1-5). Chapple teaches the quantification values are expressed as a ratio between healthy subjects and subjects with gingivitis (description p.19, line 11; Supplementary Table 1 and Table 4; A column header in Supplementary Table 1 is 114/113, where 113 corresponds to healthy state and 114 corresponds to gingivitis state) (relevant to claims 1-2, 4-5, 8 and 21).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of detection in ‘207 to further detect A1AGP, MMP-9 and Hb-beta taught by Chapple. Both ‘207 and Chapple teach sets of proteins that were known in the art as biomarkers for gingivitis.
Modified rejection necessitated by amendment: Claims 1-2, 4 and 21 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 9-11 of U.S. Patent No. 12,111,323 (previously copending Application No. 16/758,902) in view of Chapple et al. (WO 2014/037924 A2, published on March 13, 2014; previously cited).
Claim 9 of ‘323 is drawn to a method for assessing whether a human subject has mild periodontitis or advanced periodontitis, the method comprising:
measuring in a sample of oral fluid from said subject concentrations of proteins HGF, MMP8, and MMP9 to obtain measurement results;
comparing, using a processing unit, the measurement results with cluster centres to determine whether the measurement results for the subject fit with a first cluster or a second cluster, wherein the cluster centres are obtained by (i) determining concentrations of the proteins HGF, MMP8, and MMP9 in oral fluid samples of patients known to have periodontitis; (ii) subjecting the determined concentrations for said patients to a clustering technique to obtain the first cluster and the second cluster, wherein the first cluster is a defined cluster and the second cluster is a non-defined cluster;
when the measurement results fit with the second cluster, further measuring in a sample of oral fluid of said subject concentration of TIMP1, thereby obtaining a second testing value reflecting joint concentrations measured for said TIMP1 and the earlier measured concentration of the protein HGF;
comparing, using a processor, the first testing value or the second testing value with a threshold value reflecting corresponding joint concentrations associated with advanced periodontitis, so as to assess whether the first testing value or the second testing value is indicative of mild periodontitis or advanced periodontitis in said subject; and
determining of a treatment of the subject based on the indication of mild periodontitis or advanced periodontitis. (relevant to instant claims 1 and 21).
Claim 9 of ‘323 does not recite the proteins Alpha-1-acid glycoprotein (A1AGP) or Hemoglobin subunit beta (Hb-beta).
Chapple teaches the analysis of saliva proteome for biomarkers of gingivitis and periodontitis using FT-ICR-MS/MS (title). Chapple teaches collecting saliva samples non-invasively from the mouths of several patients (description p.11, lines 3-4). Chapple teaches using liquid chromatography techniques coupled with Fourier Transform – tandem Mass Spectrometry (FT MS/MS) to separate protein biomarkers from within the samples and to identify the protein biomarkers (description p.11, lines 4-6). Chapple teaches the samples were analyzed in triplicate by LC-MS/MS; the CID spectra were used to identify the peptides and the HCD spectra were used to quantify them (description p.16, lines 4-15). Chapple further identifies protein biomarkers as haemoglobin subunit beta (Hb-beta), S100-A8, alpha-1-acid glycoprotein 1 and 2 (A1AGP), and matrix metalloproteinase-9 (MMP9) (description p.23, lines 1-5). Chapple teaches the quantification values are expressed as a ratio between healthy subjects and subjects with gingivitis (description p.19, line 11; Supplementary Table 1 and Table 4; A column header in Supplementary Table 1 is 114/113, where 113 corresponds to healthy state and 114 corresponds to gingivitis state) (relevant to instant claims 1-2, 4 and 21).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of detection in ‘323 to further detect A1AGP and Hb-beta taught by Chapple. Both ‘323 and Chapple teach sets of proteins that were known in the art as biomarkers for gingivitis.
Claim 10 of ‘323 is drawn to the method of claim 9, wherein the human subject is suspected to have periodontitis (relevant to instant claim 2).
Claim 11 of ‘323 is drawn to the method of claim 9, wherein the threshold value is based on concentrations determined for HGF, MMP8, MMP9, IL1-b, IL6 and Collagen Telopeptide in a reference sample associated with the presence of advanced periodontitis (relevant to instant claim 4).
Modified rejection necessitated by amendment: Claims 1-5, 8 and 21 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-2 and 5 of copending Application No. 16/962,246 (reference application) in view of Chapple et al. (WO 2014/037924 A2, published on March 13, 2014; previously cited) and Ebersole et al. (“Targeted salivary biomarkers for discrimination of periodontal health and disease(s)”, Frontiers in Cellular and Infection Microbiology, 2015, Vol. 5, Article 62, 12 pages; previously cited).
Claim 1 of ‘246 is drawn to an in vitro method for assessing whether a human patient is free from periodontal disease, has gingivitis, has mild periodontitis or has advanced periodontitis, wherein the method comprises:
detecting, in a sample of saliva from said human patient, the concentrations of the proteins: Alpha-1-acid glycoprotein (A1AGP) and Pyruvate Kinase (PK), and at least one of the proteins Matrix metalloproteinase-9 (MMP-9) and S100 calcium binding protein A8 (S100A8);
determining at least one testing value reflecting the joint concentrations determined for said proteins;
determining that the testing value is indicative for one or more of gingivitis, mild periodontitis, and advanced periodontitis in said patient; and
administering, based on determining that the testing value is indicative for one or more of gingivitis, mild periodontitis, and advanced periodontitis in said patient, a treatment for the gingivitis and/or periodontitis in the human patient, wherein the administered treatment comprises one or more of an administered therapeutic agent and an administered dental procedure (relevant to instant claims 1 and 21).
Claim 1 of ‘246 does not recite the proteins Matrix metalloproteinase-8 (MMP8) or Hemoglobin subunit beta (Hb-beta).
Chapple teaches the analysis of saliva proteome for biomarkers of gingivitis and periodontitis using FT-ICR-MS/MS (title). Chapple teaches collecting saliva samples non-invasively from the mouths of several patients (description p.11, lines 3-4). Chapple teaches using liquid chromatography techniques coupled with Fourier Transform – tandem Mass Spectrometry (FT MS/MS) to separate protein biomarkers from within the samples and to identify the protein biomarkers (description p.11, lines 4-6). Chapple teaches the samples were analyzed in triplicate by LC-MS/MS; the CID spectra were used to identify the peptides and the HCD spectra were used to quantify them (description p.16, lines 4-15). Chapple further identifies protein biomarkers as haemoglobin subunit beta (Hb-beta), S100-A8, alpha-1-acid glycoprotein 1 and 2 (A1AGP), and matrix metalloproteinase-9 (MMP9) (description p.23, lines 1-5). Chapple teaches the quantification values are expressed as a ratio between healthy subjects and subjects with gingivitis (description p.19, line 11; Supplementary Table 1 and Table 4; A column header in Supplementary Table 1 is 114/113, where 113 corresponds to healthy state and 114 corresponds to gingivitis state) (relevant to claims 1-2, 4-5, 8 and 21).
Ebersole teaches subjects expectorated at least 5mL of unstimulated whole saliva into sterile tubes (p.3, 1st column – Salivary Samples). Ebersole teaches the MILLIPLEX MAP Kit was used to detect IL-1β, IL-6, MMP-8 and MIP-1α, and the kit was used to analyze individual saliva samples for the four biomarkers using a Luminex 100IS instrument (p.3, 2nd column – Salivary Molecular Biomarkers; Figure 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of detection in ‘246 to further detect Hb-beta taught by Chapple and MMP-8 taught by Ebersole. Each of ‘246, Chapple and Ebersole teach sets of proteins that were known in the art as biomarkers for gingivitis.
Claim 2 of ‘246 is drawn to the method of claim 1, wherein a testing value is generated for one, two or three of (i) the probability of periodontitis versus health or gingivitis, (ii) the probability of gingivitis versus health, and (iii) the probability of advanced periodontitis versus mild periodontitis; and
further comprising the step of comparing said at least one testing value with at least one threshold value reflecting in the same manner the joint concentrations associated with gingivitis, periodontitis or advanced periodontitis, wherein the threshold value is based on the concentrations of the proteins in a set of samples, including samples from subjects with healthy gums, samples from subjects that have gingivitis, samples from subjects that have mild or moderate periodontitis, and samples from subjects having advanced periodontitis.
Claim 5 of ‘246 is drawn to method of claim 2, wherein the human patient is known to have periodontal disease and the method assesses whether the patient has gingivitis, mild periodontitis, or has advanced periodontitis;
wherein the age of the subject is determined and the testing value reflects the joint concentrations determined for said proteins in combination with the determined age of the subject;
wherein the threshold value is based on the concentrations determined for the proteins in one or more reference samples each sample associated with the presence of healthy gums, gingivitis, mild periodontitis, or advanced periodontitis; and
wherein the concentration values determined are arithmetically processed into a number between 0 and 1 (relevant to instant claims 2-5 and 8).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Modified rejection necessitated by amendment: Claims 1-4, 8 and 21 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-4 and 6-7 of copending Application No. 17/045,312 (reference application) in view of Chapple et al. (WO 2014/037924 A2, published on March 13, 2014; previously cited) and Ebersole et al. (“Targeted salivary biomarkers for discrimination of periodontal health and disease(s)”, Frontiers in Cellular and Infection Microbiology, 2015, Vol. 5, Article 62, 12 pages; previously cited).
Claim 1 of ‘312 is drawn to method performed in vitro for assessing whether a human patient has mild periodontitis or advanced periodontitis, the method comprising:
detecting, in a sample of saliva from said human patient, joint concentrations of proteins Pyruvate Kinase (PK) and at least two of Haemoglobin-beta (Hb-beta), Haemoglobin-delta (Hb-delta), S100 calcium-binding protein A8 (S100A8) or S100 calcium-binding protein A9 (S100A9);
determining a testing value based on the detected joint concentrations of the proteins;
comparing the testing value with a threshold value reflecting joint concentrations of the same proteins associated with advanced periodontitis to determine when the testing value is indicative for mild periodontitis or advanced periodontitis in the human patient, and
determining to administer at least one of a therapeutic agent or a dental procedure to the human patient when the comparing of the testing value to the threshold value indicates advanced periodontitis (relevant to instant claim 1 and instant claim 21).
Claim 2 of ‘312 is drawn to a method according to claim 1, further comprising: determining age of the human patient, wherein the testing value is further based on the age of the subject (relevant to instant claim 3).
Claim 6 of ‘312 is drawn to the method according to claim 2, wherein the proteins consist of PK, S100A8 and S100A9; PK, Hb-beta and Hb-delta; PK, S100A8 and Hb-beta; PK, S100A8, Hb-beta and Hb-delta; Pk, S100A9, Hb-beta and Hb-delta; PK, S100A8, S100A9 and Hb-beta; A1AGP, PK, S100A8 and S100A9; A1AGP, HB-beta, Hb-delta and PK; A1AGP, PK, S100A8 and S100A9; Profilin, Hb-beta, Hb-delta and PK; or Profilin, Hb-beta, PK and S100A8 (relevant to instant claims 1-2 and instant claim 21).
Claims 1 and 6 of ‘312 do not recite the proteins MMP8 or MMP9.
However, Chapple teaches the analysis of saliva proteome for biomarkers of gingivitis and periodontitis using FT-ICR-MS/MS (title). Chapple teaches collecting saliva samples non-invasively from the mouths of several patients (description p.11, lines 3-4). Chapple further identifies protein biomarkers as haemoglobin subunit beta (Hb-beta), S100-A8, alpha-1-acid glycoprotein 1 and 2 (A1AGP), and matrix metalloproteinase-9 (MMP9) (description p.23, lines 1-5). Chapple teaches the quantification values are expressed as a ratio between healthy subjects and subjects with gingivitis (description p.19, line 11; Supplementary Table 1 and Table 4; A column header in Supplementary Table 1 is 114/113, where 113 corresponds to healthy state and 114 corresponds to gingivitis state).
Ebersole teaches subjects expectorated at least 5mL of unstimulated whole saliva into sterile tubes (p.3, 1st column – Salivary Samples). Ebersole teaches the MILLIPLEX MAP Kit was used to detect IL-1β, IL-6, MMP-8 and MIP-1α, and the kit was used to analyze individual saliva samples for the four biomarkers using a Luminex 100IS instrument (p.3, 2nd column – Salivary Molecular Biomarkers; Figure 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of detection in ‘312 to further detect MMP-9 taught by Chapple and MMP-8 taught by Ebersole. Each of ‘312, Chapple and Ebersole teach sets of proteins that were known in the art as biomarkers for gingivitis.
Claim 3 of ‘312 is drawn to a method according to claim 1, wherein the threshold value is based on the joint concentrations of the same proteins in one or more reference samples associated with presence of advanced periodontitis (relevant to instant claim 3).
Claim 4 of ‘312 is drawn to a method according to claim 1, wherein the threshold value is based on the joint concentrations of the same proteins in a set of samples, including samples from subjects having mild or moderate periodontitis and samples from subjects having advanced periodontitis (relevant to instant claim 4).
Claim 7 of ‘312 is drawn to a method according to claim 1, wherein the concentration values determined are arithmetically processed into a number between 0 and 1 (relevant to instant claim 8).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Modified rejection necessitated by amendment: Claims 1, 3-4, 8 and 21 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4 and 7 of copending Application No. 17/045,344 (reference application) in view of in view of Chapple et al. (WO 2014/037924 A2, published on March 13, 2014; previously cited).
Claim 1 of ‘344 is drawn to an in vitro method for treating periodontal disease in a human patient based on assessing or predicting a response of the human patient to treatment of the periodontal disease, wherein the method comprises:
detecting, in a sample of saliva from said human patient suffering from periodontal disease, a concentrations of proteins:
(i) Alpha-1-acid glycoprotein (A1AGP), Interleukin-1-beta (IL-13), Matrix metalloproteinase-8 (MMP-8) and Matrix metalloproteinase-9 (MMP-9); or
(ii) Alpha-1-acid glycoprotein (A1AGP) and Interleukin-1-beta (IL-13), and at least one of Matrix metalloproteinase-8 (MMP-8), Matrix metalloproteinase-9 (MMP-9) and Keratin-4 (K-4); or
(iii) Matrix metalloproteinase-9 (MMP-9) and S100 calcium binding protein A9 (S100A9);
determining at least one testing value reflecting the concentration determined for said proteins;
comparing said testing value with a threshold value reflecting in the same manner the concentration associated with successful treatment of periodontal disease, so as to assess whether the testing value is indicative for predicted successful treatment of periodontal disease in said patient, and
administering, based on the assessed predicted successful treatment, a treatment for the periodontal disease in said treatment (relevant to instant claim 1, instant claim 21).
Claim 1 of ‘344 does not recite the protein Hemoglobin subunit beta (Hb-beta).
Chapple teaches the analysis of saliva proteome for biomarkers of gingivitis and periodontitis using FT-ICR-MS/MS (title). Chapple teaches collecting saliva samples non-invasively from the mouths of several patients (description p.11, lines 3-4). Chapple further identifies protein biomarkers as haemoglobin subunit beta (Hb-beta), S100-A8, alpha-1-acid glycoprotein 1 and 2 (A1AGP), and matrix metalloproteinase-9 (MMP9) (description p.23, lines 1-5).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of detection in ‘344 to further detect Hb-beta taught by Chapple. Each of ‘344 and Chapple teach sets of proteins that were known in the art as biomarkers for gingivitis.
Claim 4 of ‘344 is drawn to a method according to claim 1, wherein: an age of the human patient is determined and the testing value reflects the concentration determined for said proteins in combination with the determined age of the subject;
and/or
the threshold value is based on a concentration determined for the proteins in one or more reference samples, each reference sample associated with successful treatment of periodontitis or unsuccessful treatment of periodontitis; and/or
the proteins consist of A1AGP, MMP-9, and K-4 or MMP-8 (relevant to instant claims 1, 3-4 and 21).
Claim 7 of ‘344 is drawn to a method according to claim 1, wherein the concentration values determined are arithmetically processed into a number between 0 and 1 (relevant to instant claim 8).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Modified rejection necessitated by amendment: Claims 1, 3-4, 8 and 21 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 7-10 of copending Application No. 17/046,361 (reference application) in view of Chapple et al. (WO 2014/037924 A2, published on March 13, 2014; previously cited).
Claim 1 of ‘361 is drawn to an in vitro method for assessing or predicting the response of a human patient suffering from periodontal disease to treatment of that periodontal disease, wherein the method comprises:
detecting, at a first point in time, in a sample of saliva from said human patient suffering from periodontal disease, concentrations for each of the proteins:
Hemoglobin subunit delta (Hb-delta) and Pyruvate kinase (PK); or
Keratin-4 (K-4) and at least two of Alpha-1-acid glycoprotein (A1AGP), Pyruvate Kinase (PK) and Matrix metalloproteinase-8 (MMP-8); or
Alpha-1-acid glycoprotein (A1AGP), Pyruvate Kinase (PK) and S100 calcium binding protein A8 (S100A8);
determining at least one pre-treatment testing value reflecting a joint concentration of the proteins based on the concentrations determined for each of said proteins at the first point in time;
determining, in a sample of saliva from said human patient, concentrations for each of the proteins used to determine the pre-treatment testing value at a second point in time after said human patient has been provided with one or more treatments for periodontal disease;
determining at least one post-treatment testing value reflecting a joint concentration of the proteins based on the concentrations determined for each of said proteins, at the second point in time;
determining a treatment efficacy value associated with the human patient based on a comparison between the pre-treatment testing value and the post-treatment testing value; and
comparing said treatment efficacy value with a threshold value reflecting in the same manner a change in joint protein concentrations associated with successful treatment of periodontal disease, so as to assess whether the treatment efficacy value is indicative for successful treatment of periodontal disease in said patient (relevant to instant claim 1; instant claim 21).
Claim 1 of ‘361 does not recite the protein metalloproteinase-9 (MMP9).
Chapple teaches the analysis of saliva proteome for biomarkers of gingivitis and periodontitis using FT-ICR-MS/MS (title). Chapple teaches collecting saliva samples non-invasively from the mouths of several patients (description p.11, lines 3-4). Chapple further identifies protein biomarkers as haemoglobin subunit beta (Hb-beta), S100-A8, alpha-1-acid glycoprotein 1 and 2 (A1AGP), and matrix metalloproteinase-9 (MMP9) (description p.23, lines 1-5).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of detection in ‘361 to further detect Hb-beta taught by Chapple. Each of ‘361 and Chapple teach sets of proteins that were known in the art as biomarkers for gingivitis.
Claim 7 of ‘361 is drawn to a method according to claim 1, wherein the age of the subject is determined and the testing value reflects the joint concentrations determined for said proteins in combination with the age of the subject (relevant to instant claim 3).
Claim 8 of ‘361 is drawn to a method according to claim 1, wherein the threshold value is based on the concentration or concentrations determined for the proteins in one or more reference samples each sample associated with the successful treatment of periodontitis or the unsuccessful treatment of periodontitis (relevant to instant claim 4).
Claim 9 of ‘361 is drawn to a method according to claim 1, wherein the concentrations of the proteins:
Hemoglobin subunit delta (Hb-delta) and Pyruvate kinase (PK); or
Alpha-1-acid glycoprotein (A1AGP), Pyruvate Kinase (PK), and S100 calcium binding protein A8 (S100A8); or
Keratin-4 (K-4), Alpha-1-acid glycoprotein (A1AGP), and Pyruvate Kinase (PK); or
Keratin-4 (K-4), Alpha-1-acid glycoprotein (A1AGP), and Matrix metalloproteinase-8 (MMP-8); or
Keratin-4 (K-4), Pyruvate Kinase (PK), and Matrix metalloproteinase-8 (MMP-8); or
Keratin-4 (K-4), Alpha-1-acid glycoprotein (A1AGP), Pyruvate Kinase (PK) and Matrix metalloproteinase-8 (MMP-8);
are detected (relevant to instant claims 1 and 21).
Claim 10 of ‘361 is drawn to a method according to claim1, wherein the concentration values determined are arithmetically processed into a number between 0 and 1 (relevant to instant claim 8).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Modified rejection necessitated by amendment: Claims 1-5, 8 and 21 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-10 and 23 of copending Application No. 17/046,430 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the reference claims 1-10 and 23 anticipate the instant claims 1-5, 8 and 21.
Claim 1 of ‘430 is drawn to a method performed in vitro for assessing whether a human patient has periodontitis, the method comprising:
detecting, in a sample of saliva from the human patient, the concentrations of at least three proteins, including Matrix metalloproteinase-8 (MMP-8) and two or more of Matrix metalloproteinase-9 (MMP-9), Pyruvate Kinase (PK) and S100 calcium-binding protein A8 (S100A8);
determining a testing value based on a combination of the detected concentrations of the at least three proteins;
comparing the testing value with a threshold value reflecting joint concentrations of the same at least three proteins associated with periodontitis to determine when the human patient has periodontitis; and
administering at least one of a therapeutic agent or a dental procedure to the human patient when the human patient is determined to have periodontitis (relevant to instant claim 1, instant claim 21).
Claim 8 of ‘430 is drawn to the method according to claim 1, wherein the at least three proteins additionally comprise one or more of IL-1 HGF, FLC Kappa, FLC Lambda, A1AGP, Hb-beta, Hb-delta, Keratin 4, Profilin, and S100A9 (relevant to instant claims 1 and 21).
Claim 2 of ‘430 is drawn to the method according to claim 1, wherein the human patient is suspected to have periodontitis (relevant to instant claim 2).
Claim 3 of ‘430 is drawn to the method according to claim 1, wherein the testing value reflects the joint concentrations for the at least three proteins, in combination with an age of the human patient (relevant to instant claim 3).
Claim 4 of ‘430 is drawn to the method according to claim 1, wherein the threshold value is based on joint concentrations determined for the at least three proteins in one or more reference samples, wherein each reference sample of the one or more proteins is associated with presence of periodontitis or absence of periodontitis (relevant to instant claim 4).
Claim 5 of ‘430 is drawn to the method according to claim 1, wherein the threshold value is based on joint concentrations of the at least three proteins in a set of samples, including samples from subjects that have periodontitis and samples from subjects not having periodontitis (relevant to instant claim 5).
Claim 6 of ‘430 is drawn to the method according to claim 1, wherein the at least three proteins comprise MMP-8 and/or MMP-9 (relevant to instant claim 1).
Claim 7 of ‘430 is drawn to the method according to claim 1, wherein the at least three proteins comprise: MMP-8 and MMP-9; MMP-8 and PK; MMP-8 and S100A8; or MMP-9 and Pyruvate kinase (relevant to instant claim 1).
Claim 10 of ‘430 is drawn to the method according to claim 1, wherein the testing value is arithmetically processed into a number between 0 and 1 (relevant to instant claim 8).
Claim 23 of ‘430 is drawn to a method of diagnosing whether a human patient has periodontitis, the method comprising
detecting, in a sample of saliva of the human patient, at least three proteins including Matrix metalloproteinase-8 (MMP-8) and two or more of Matrix metalloproteinase-9 (MMP-9), Pyruvate Kinase (PK) and S100 calcium-binding protein A8 (S100A8);
assessing presence of periodontitis in the human patient based on a combination of the detected concentrations of the at least three proteins in the sample of saliva; and
administering at least one of a therapeutic agent or a dental procedure to the human patient when the presence of periodontitis is determined in the human patient (relevant to instant claim 21).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Modified rejection necessitated by amendment: Claims 1-5, 8 and 21 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-6, 8 and 21 of copending Application No. 17/046,473 (reference application) in view of Chapple et al. (WO 2014/037924 A2, published on March 13, 2014; previously cited) and Ebersole et al. (“Targeted salivary biomarkers for discrimination of periodontal health and disease(s)”, Frontiers in Cellular and Infection Microbiology, 2015, Vol. 5, Article 62, 12 pages; previously cited).
Claim 1 of ‘473 is drawn to a method for treating periodontitis in a human patient based on assessing that the human patient has periodontitis, wherein the method comprises:
detecting, in a sample of saliva from said human patient, a concentration of the proteins: Alpha-1-acid glycoprotein (A1AGP), Profilin, and S100 calcium-binding protein A9 (S100A9);
determining a testing value reflecting a joint concentration determined for said proteins;
comparing said testing value with a threshold value reflecting in a same manner the joint concentration associated with periodontitis, so as to assess that the testing value is indicative for periodontitis in said patient; and
administering, based on the assessed testing value being indicative for periodontitis, a treatment for the periodontitis (relevant to instant claim 1, instant claim 21).
Claim 1 of ‘473 does not recite the proteins Matrix metalloproteinase-8 (MMP8), Matrix metalloproteinase-9 (MMP9) or Hemoglobin subunit beta (Hb-beta).
Chapple teaches the analysis of saliva proteome for biomarkers of gingivitis and periodontitis using FT-ICR-MS/MS (title). Chapple teaches collecting saliva samples non-invasively from the mouths of several patients (description p.11, lines 3-4). Chapple further identifies protein biomarkers as haemoglobin subunit beta (Hb-beta), S100-A8, alpha-1-acid glycoprotein 1 and 2 (A1AGP), and matrix metalloproteinase-9 (MMP9) (description p.23, lines 1-5).
Ebersole teaches subjects expectorated at least 5mL of unstimulated whole saliva into sterile tubes (p.3, 1st column – Salivary Samples). Ebersole teaches the MILLIPLEX MAP Kit was used to detect IL-1β, IL-6, MMP-8 and MIP-1α, and the kit was used to analyze individual saliva samples for the four biomarkers using a Luminex 100IS instrument (p.3, 2nd column – Salivary Molecular Biomarkers; Figure 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of detection in ‘473 to further detect A1AGP and Hb-beta taught by Chapple and MMP-8 taught by Ebersole. Each of ‘473, Chapple and Ebersole teach sets of proteins that were known in the art as biomarkers for gingivitis.
Claim 2 of ‘473 is drawn to a method according to claim 1, wherein the human patient is suspected to have periodontitis prior to assessing that the testing value is indicative for periodontitis (relevant to instant claim 2).
Claim 3 of ‘473 is drawn to a method according to claim 1, wherein the age of the subject is determined and the testing value reflects the joint concentrations determined for said proteins, in combination with the age of the subject (relevant to instant claim 3).
Claim 4 of ‘473 is drawn to a method according to claim 1, wherein the threshold value is based on the concentrations determined for the proteins in one or more reference samples each sample associated with the presence of periodontitis or absence of periodontitis (relevant to instant claim 4).
Claim 5 of ‘473 is drawn to a method according to claim 1, wherein the threshold value is based on the concentrations of the proteins in a set of samples, including samples from subjects that have periodontitis and samples from subjects not having periodontitis (relevant to instant claim 5).
Claim 6 of ‘473 is drawn to a method according to claim 1, wherein the step of detecting comprises detecting the concentration of three or more of A1AGP, hemoglobin-subunit delta (Hb-delta), hemoglobin-subunit beta (Hb-beta), keratin 4 (K-4), profilin, pyruvate kinase (PK), S100 calcium-binding protein A8 (S100A8), and S100A9 (relevant to instant claims 1 and 21).
Claim 8 of ‘473 is drawn to a method according to claim 1, wherein the concentration values determined are arithmetically processed into a number between 0 and 1 (relevant to instant claim 8).
Claim 21 of ‘473 is drawn to a method of diagnosing that a human patient has periodontitis and treating the patient’s periodontitis, comprising:
detecting in a sample of saliva of the human patient a joint concentration value representing a concentration of proteins: Alpha-1-acid glycoprotein (A1AGP), Profilin, and S100 calcium-binding protein A9 (S100A9);
comparing the detected joint concentration value to joint concentration values from patients known to have periodontitis;
determining, based on the comparison, a presence of periodontitis in the patient; and administering, based on the determined presence of periodontitis in the patient, a treatment for the periodontitis (relevant to instant claim 21).
Claim 21 of ‘473 does not recite the proteins Matrix metalloproteinase-8 (MMP8), Matrix metalloproteinase-9 (MMP9) or Hemoglobin subunit beta (Hb-beta).
Chapple teaches the analysis of saliva proteome for biomarkers of gingivitis and periodontitis using FT-ICR-MS/MS (title). Chapple teaches collecting saliva samples non-invasively from the mouths of several patients (description p.11, lines 3-4). Chapple further identifies protein biomarkers as haemoglobin subunit beta (Hb-beta), S100-A8, alpha-1-acid glycoprotein 1 and 2 (A1AGP), and matrix metalloproteinase-9 (MMP9) (description p.23, lines 1-5).
Ebersole teaches subjects expectorated at least 5mL of unstimulated whole saliva into sterile tubes (p.3, 1st column – Salivary Samples). Ebersole teaches the MILLIPLEX MAP Kit was used to detect IL-1β, IL-6, MMP-8 and MIP-1α, and the kit was used to analyze individual saliva samples for the four biomarkers using a Luminex 100IS instrument (p.3, 2nd column – Salivary Molecular Biomarkers; Figure 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of detection in ‘473 to further detect A1AGP and Hb-beta taught by Chapple and MMP-8 taught by Ebersole.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Modified rejection necessitated by amendment: Claims 1-5, 8 and 21 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-5, 8 and 21 of copending Application No. 17/046,882 (reference application) in view of Chapple et al. (WO 2014/037924 A2, published on March 13, 2014; previously cited) and Ebersole et al. (“Targeted salivary biomarkers for discrimination of periodontal health and disease(s)”, Frontiers in Cellular and Infection Microbiology, 2015, Vol. 5, Article 62, 12 pages; previously cited).
Claim 1 of ‘882 is drawn to a method for treating a human patient who has mild periodontitis or advanced periodontitis, wherein the method comprises:
detecting, in a sample of saliva from said human patient, the concentrations of the proteins: Pyruvate Kinase (PK) and at least one of Matrix metalloproteinase-9 (MMP9), S100 calcium-binding protein A8 (S100A8), and Hemoglobin subunit beta (Hb-beta);
determining a testing value reflecting the joint concentrations determined for said proteins; and
comparing said testing value with a threshold value reflecting in the same manner the joint concentrations associated with advanced periodontitis, so as to assess whether the testing value is indicative for mild periodontitis or for advanced periodontitis in said patient; and
administering, to the human patient for which the testing value is indicative for mild periodontitis or for advanced periodontitis, an anti-microbial therapeutic agent to the gum tissue of the patient (relevant to instant claim 1, instant claim 21).
Claim 1 of ‘882 does not recite the proteins Alpha-1-acid glycoprotein (A1AGP) or Matrix metalloproteinase-8 (MMP8).
Chapple teaches the analysis of saliva proteome for biomarkers of gingivitis and periodontitis using FT-ICR-MS/MS (title). Chapple teaches collecting saliva samples non-invasively from the mouths of several patients (description p.11, lines 3-4). Chapple further identifies protein biomarkers as haemoglobin subunit beta (Hb-beta), S100-A8, alpha-1-acid glycoprotein 1 and 2 (A1AGP), and matrix metalloproteinase-9 (MMP9) (description p.23, lines 1-5).
Ebersole teaches subjects expectorated at least 5mL of unstimulated whole saliva into sterile tubes (p.3, 1st column – Salivary Samples). Ebersole teaches the MILLIPLEX MAP Kit was used to detect IL-1β, IL-6, MMP-8 and MIP-1α, and the kit was used to analyze individual saliva samples for the four biomarkers using a Luminex 100IS instrument (p.3, 2nd column – Salivary Molecular Biomarkers; Figure 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of detection in ‘882 to further detect A1AGP taught by Chapple and MMP-8 taught by Ebersole. Each of ‘882, Chapple and Ebersole teach sets of proteins that were known in the art as biomarkers for gingivitis.
Claim 2 of ‘882 is drawn to the method of claim 1, wherein the human patient is known to have periodontitis (relevant to instant claim 2).
Claim 3 of ‘882 is drawn to the method of claim 1, wherein an age of the subject is determined and the testing value reflects the joint concentrations determined for said proteins, in combination with the age of the subject (relevant to instant claim 3).
Claim 4 of ‘882 is drawn to the method of claim 1, wherein the threshold value is based on the concentrations determined for the proteins in one or more reference samples each sample associated with the presence of advanced periodontitis (relevant to instant claim 4).
Claim 5 of ‘882 is drawn to the method of claim 1, wherein the threshold value is based on the concentrations of the proteins in a set of samples, including samples from subjects that have mild or moderate periodontitis and samples from subjects having advanced periodontitis (relevant to instant claim 5).
Claim 8 of ‘882 is drawn to the method of claim 1, wherein the concentration values determined are arithmetically processed into a number between 0 and 1 (relevant to instant claim 8).
Claim 21 of ‘882 is drawn to a method of treating a human patient who has mild periodontitis or advanced periodontitis, comprising:
detecting in a sample of saliva of the human patient the proteins: Pyruvate Kinase (PK) and at least one of Matrix metalloproteinase-9 (MMP9), S100 calcium-binding protein A8 (S100A8), and Hemoglobin subunit beta (Hb-beta);
determining a testing value reflecting joint concentrations determined for said proteins; and
assessing the presence of mild periodontitis or advanced periodontitis in the patient on the basis of the concentrations of said proteins in said sample, comprising comparing said determined testing value with a threshold value reflecting in the same manner the joint concentrations associated with advanced periodontitis, so as to assess whether the testing value is indicative for mild periodontitis or for advanced periodontitis in said patient; and
administering, to the human patient for which the assessment is indicative for mild periodontitis or for advanced periodontitis, an anti-microbial therapeutic agent to the gum tissue of the patient (relevant to instant claims 1 and 21).
Claim 21 of ‘882 does not recite the proteins Alpha-1-acid glycoprotein (A1AGP) or Matrix metalloproteinase-8 (MMP8).
Chapple teaches the analysis of saliva proteome for biomarkers of gingivitis and periodontitis using FT-ICR-MS/MS (title). Chapple teaches collecting saliva samples non-invasively from the mouths of several patients (description p.11, lines 3-4). Chapple further identifies protein biomarkers as haemoglobin subunit beta (Hb-beta), S100-A8, alpha-1-acid glycoprotein 1 and 2 (A1AGP), and matrix metalloproteinase-9 (MMP9) (description p.23, lines 1-5).
Ebersole teaches subjects expectorated at least 5mL of unstimulated whole saliva into sterile tubes (p.3, 1st column – Salivary Samples). Ebersole teaches the MILLIPLEX MAP Kit was used to detect IL-1β, IL-6, MMP-8 and MIP-1α, and the kit was used to analyze individual saliva samples for the four biomarkers using a Luminex 100IS instrument (p.3, 2nd column – Salivary Molecular Biomarkers; Figure 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of detection in ‘882 to further detect A1AGP taught by Chapple and MMP-8 taught by Ebersole. Each of ‘882, Chapple and Ebersole teach sets of proteins that were known in the art as biomarkers for gingivitis.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
Applicant argues that when these rejections remain the only obstacles to allowance, applicant will duly file terminal disclaimers (See Remarks dated 2/19/2025, p.9 paragraphs 1-2).
Applicant's arguments filed February 19, 2025 have been fully considered but they are not persuasive. A terminal disclaimer is required to overcome a non-statutory double patenting rejection. See MPEP §804.02.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DEEPA MISHRA whose telephone number is (571) 272-6464. The examiner can normally be reached Monday - Friday 9:30am - 3:30pm EST.
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/DEEPA MISHRA/Examiner, Art Unit 1657
/MELENIE L GORDON/Supervisory Patent Examiner, Art Unit 1657