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 .
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
Priority
This application is a continuation of U.S. Patent Application of 17/823,924 filed on 08/31/2022 which is a continuation of U.S. Patent Application of 17/216,510 filed on 03/29/2021 which is a continuation of international Patent Application of PCT/US2020/024426 filed on 03/24/2020 which claims priority to U.S. Provisional Application No. 62/824,279 filed on 03/26/2019 and U.S. Provisional Application No. 62/824,284 filed on 03/26/2019.
The initial priority of this application is restored to 03/26/2019 in light of Applicant’s amendments of claims and arguments of 10/09/2025.
Claim Status
The Applicant amended claims 1, 11, 14, 18, and 20; and noted that no new matter is added. Claims 2-10, 12-13, 15-17, 19 and 21-27 are original. Thus, claims 1-27 are pending and are under examination.
Withdrawn Objections and Rejections
The previous objection to claim 14, regarding informalities, is withdrawn in response to Applicant’s amendments of the claim.
The previous rejection of claim 11 under 35 U.S.C. 112(b), as being indefinite, is withdrawn in response to Applicant’s amendments of the claim.
The previous rejection of claims 1-27 under 35 U.S.C. 103, regarding obviousness, is withdrawn in response to Applicant’s amendments of claims.
New Rejections necessitated by Amendments
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 (PHOSITA) 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.
Claims 1-23 and 27 are rejected under 35 U.S.C. 103 as being unpatentable over Soldo et al. (US 2021/0302416 A1, effective filing date of 07/27/2018) in view of Shi et al. (Methods 56 (2012) 246–253) and Dawson et al. (US 2012/0046184 A1).
Regarding claim 1, Soldo teaches a method of using a plurality of particles to isolate and characterize biomarkers for analysis by mass spectrometry (Abstract; page 6, [0066] and [0070]; page 15, Examples 4-5).
In Example 5, Soldo pre-treated a sample to first deplete sample interferences, using particle reagent A (magnetic microparticles with a capture moiety that does not have specificity for the biomarker to be enriched). See [0188]-[0189]. The reagent A beads are then magnetically removed from the sample. Next, the interference-depleted sample is mixed with reagent B, in order to capture and enrich the biomarker of interest from the sample. Reagent B is then magnetically separated from the sample supernatant, and tested in order to measure capture biomarker. The biomarker may be cleaved, eluted, or selectively released from the Reagent B magnetic particles [0189] step 9.
Soldo teaches mass spectrometry detection (Example 4, [0094]-[0095], [0231]).
Soldo teaches depleting the biofluid sample to form a depleted biofluid sample (Page 2, [0016]).
Soldo teaches that the biofluid is plasma or serum (Page 9, [0089]).
Soldo teaches contacting the biofluid sample with a first plurality of particles to allow the first plurality of proteins to bind to the first plurality of particles (Page 15, [0169]; page 18, claim 2).
Soldo teaches separating the first plurality of particles from the biofluid sample (Page 5, [0053]; page 7, [0072]; page 16, [0188]).
Soldo teaches that the separation of particles from the biofluid comprises centrifugation or magnetic separation (Page 5, [0052-0054]; page 16, [0188])
Soldo teaches forming a second plurality of proteins from the depleted biofluid sample onto a second plurality of particles (Page 16, [0188], [0194]).
Soldo teaches separating the second plurality of proteins from the depleted biofluid sample (Page 16, [0188], [0196]).
Soldo teaches that one or more of the first plurality of particles and the second plurality of particles are in a mixture with the target molecules (Pages 17-18, claims 1-2).
Regarding claim 3, Soldo teaches that the depleting enables the detection of a low abundance protein among the second plurality of proteins (Page 6, [0057]; pages 17-18, claims 1-2).
Regarding claim 12, Soldo teaches forming the second plurality of proteins on a second plurality of particles (Page 16, [0188], [0194]).
Regarding claim 17, Soldo teaches that the first plurality of particles comprises nanoparticles (Page 15, [0169]; page 18, claim 2).
Regarding claim 18, Soldo teaches that the second plurality of particles comprises magnetic nanoparticles (Page 7, [0079]; Page 11, [0112]; page 16, [0188-0189] and [0192]).
Regarding claims 19, Soldo teaches that the first plurality of magnetic particles comprises iron oxide (Page 11, [0112]; page 16, [0188-0189] and [0192]).
Regarding claim 20, Soldo teaches that the second plurality of particles comprises iron oxide (Page 11, [0112]; page 16, [0188-0189] and [0194-0196]).
Regarding claim 21, Soldo teaches that separating the first plurality of particles from the biofluid sample comprises magnetic separation (Page 16, [0188-0189] and [0192-0196]).
Regarding claim 22, Soldo teaches that separating the first plurality of particles from the biofluid sample comprises centrifugation (Page 6, [0058] and [0067]).
Regarding claim 23, Soldo teaches that the mass spectrometry comprises LC-MS/MS (Page 6, [0066] and [0070]; page 15, Example 4, “LC-MS/MS”).
Regarding claim 1, Soldo does not teach depleting the set of high abundance proteins which contributes at least 95% of the protein mass and wherein the high abundance proteins comprise albumin and IgG.
Soldo does not teach that the depleting reduces at least 50% of the set of high abundance proteins in the biofluid sample.
Soldo does not specifically teach resuspending the second plurality of proteins to prepare the second plurality of proteins for mass spectrometry.
Regarding claim 1, Shi teaches that depleting the biofluid sample comprises reducing levels of a first plurality of proteins in the biofluid sample such as reducing the high abundant proteins (Abstract; page 247, right column, third paragraph).
Shi teaches that the first plurality of proteins comprises a set of high abundance proteins (Abstract; page 247, right column, third paragraph).
Shi teaches that the set of high abundance proteins contributes at least 95% of the protein mass in the biofluid sample such as in human plasma (Abstract; page 247, right column, third paragraph).
Shi teaches that the set of high abundance proteins comprises albumin and IgG (Fig. 1., The top 14 HAP are targeted by the IgY14 column (A), “Albumin”, “IgG”)
Shi et al. teaches that IgY14 removes the 14 most abundant proteins in human plasma that constitute 90-95% of the total protein mass of a sample (Page 247, left column, second paragraph).
Shi teaches that the method yields a reduced dynamic range of the second plurality of proteins (Page 248, left column, first paragraph, “dynamic range of protein concentrations in the depleted fraction is reduced by at least 10-fold.”; page 248, left column, second paragraph, “Collectively, tandem IgY14 and SuperMix separations provide ~100-fold enrichment of LAP in the flow-through fraction and at least two orders magnitude reduction in the dynamic range of protein concentrations.”).
Regarding claim 3, Shi teaches that the low abundance protein (LAP) is otherwise not detected using mass spectrometry (MS) without depleting (Page 247, right column, second paragraph, “All analytical detection technologies including LC–MS have a limited dynamic range of detection. The range of protein concentrations in the human blood plasma spans >10 orders of magnitude, which is far greater than the dynamic range of detection afforded by LC–MS technologies (typically 4–5 orders of magnitude).As a result, strategies are necessary to reduce the range of protein concentrations and enhance the ability to detect LAP”).
Regarding claim 4, Shi teaches that the dynamic range of the biofluid sample is compressed by at least 2 orders of magnitude (Page 248, left column, second paragraph, “Collectively, tandem IgY14 and SuperMix separations provide … and at least two orders magnitude reduction in the dynamic range of protein concentrations.”).
Regarding claim 8, Shi teaches that the depleting comprises using immunodepletion (Page 248, right column, second paragraph, “The IgY immunodepletion column is prepared …”).
Regarding claim 9, Shi teaches the depletion is performed with a total cycle of almost sixty minutes (Page 249, end of left column and start of right column, “The IgY14 LC10 separation consists of five steps … The total cycle time … is ~60 min”).
Regarding claim 10, Shi teaches that separating the second plurality of proteins from the depleted biofluid sample comprises filtering by using Amicon®Ultra-15 centrifugal filter unit (Page 249, right column, second paragraph, “Following the IgY14 separations, the flow-through and bound
fractions can be concentrated using Amicon®Ultra-15”).
Regarding claim 12, Shi teaches digesting the second plurality of proteins (Page 250, right column, “Protein samples in the collected bound and flow-through fractions are amenable to downstream processing and proteomics analyses with various technologies. In the case of LC–MS/MS proteomics profiling, protein samples are typically subjected to trypsin digestion, and the resulting peptide samples are analyzed by LC–MS/MS”).
Regarding claim 16, Shi teaches that the set of high abundance proteins comprises at most 14 most abundant proteins in the biofluid sample (Page 247, right column, third paragraph, “The IgY14 column is designed to remove the 14 most abundant proteins in human plasma that constitute 90–95% of the total protein mass”).
Regarding claim 23, Shi teaches that the mass spectrometry comprises LC-MS/MS (Page 250, right column, “In the case of LC–MS/MS proteomics profiling, protein samples are typically subjected to trypsin digestion, and the resulting peptide samples are analyzed by LC–MS/MS”).
Regarding claim 27, Shi teaches that depleting comprises using affinity-based depletion (Abstract; page 247, right column, first paragraph, “Herein, we present a brief overview of single-stage IgY14 and tandem IgY14-SuperMix immunoaffinity separations”).
Regarding claim 1, Dawson teaches resuspending a second plurality of proteins from the depleted biofluid sample onto a second plurality of particles by implementing “selective concentration” (Page 2, [0016-0018]).
Dawson showed how to concentrate low abundance proteins onto particles by what is referred to as “selective concentration”(Page 2, [0016]). In this process a first pass is made to concentrate the 3700 plasma proteins to a more limited panel of 20 proteins including the protein(s) of interest, and a second step in which the protein of interest is further concentrated with respect to the other 19 proteins using the same or another (more tailored) nanoparticle (Page 2, [0017]). Thus, Dawson teaches a method of selective concentration of a specific biomolecule using two different nanoparticle preparations to selectively concentrate specific low abundance biomolecule, from a complex biological system (Page 2, [0018]).
Dawson teaches resuspending the second plurality of proteins to prepare for mass spectrometry (Page 2, [0018]; page 15, [0130-0132]).
Regarding claim 2, Dawson describes how to precipitate a protein (Page 16-17, [0147]).
Dawson teaches separating the second plurality of proteins from the depleted biofluid sample based on the nature of the biomolecule to be recovered or its binding affinity to a panel of nanoparticles with different physicochemical and surface properties (Page 3, [0019]).
Regarding claim 11, Dawson teaches that the filtering removes the second plurality of magnetic particles from the second plurality of proteins such as with apoA1 (Page 1, [0006]; page 16, [0139], “Urea fractions ( eluates form the nanoparticles) were pooled and passed through a 0.45 μm syringe filter”, “The apoA1 were eluted”).
Regarding claim 12, Dawson teaches digesting the second plurality of proteins after precipitating or concentrating (Page 16, [0144]).
Regarding claim 13, Dawson teaches resuspending the pellet after precipitation and centrifugation (Page 2, [0018]; page 15, [0130-0132]).
Regarding claim 14, Dawson teaches that at least one physiochemical property of the nanoparticle surface is modified to generate different particle surface types (Page 1, [0005]; page 2, [0013-0014]; page 4, [0030]).
Regarding claim 15, Dawson teaches that at least one physiochemical property of the nanoparticle surface is modified to generate different particle surface types (Page 1, [0005]; page 9, [0095]). An artisan will be able to change different physiochemical property of the nanoparticle surface to generate different nanoparticle surfaces.
It would have been obvious to one of ordinary skill in the art before the effective filing date to combine the immunoaffinity separation method of Shi with the nanoparticles of Soldo to increase the detection of low abundance proteins by mass spectrometry because Shi teaches how to couple the immunoaffinity separation method with any downstream proteomics technologies for biomarker discovery or for candidate verification (Page 247, right column, first paragraph), and notes that the removal of high abundance proteins (HAP) and medium abundance proteins (MAP) from human biofluids is a powerful tool for biomarker discovery studies (Page 252, left column, last paragraph) because it will unmask low abundance proteins for biomarker discovery and allow for better detection of a potential biomarker without any interference from HAP or MAP proteins.
Furthermore, a skilled artisan would have been motivated to combine the nanoparticles of Dawson with the combined invention of Shi and Soldo because Dawson teaches the advantages of using nanoparticles with different surface types to isolate proteins from different cellular compartments or from biological fluids (Page 3, [0021]) and further teaches using nanoparticles to look for low abundance proteins that serve as biomarkers of different diseases (Page 1, [0003] and [0005-0006]). As Soldo teaches automating the capture and characterization of nanoparticles, Dawson teaches using different surface types of nanoparticles to isolate different proteins and thus offers further flexibility in the choice of nanoparticles to use for isolating a particular protein (Page 3, [0021). A skilled artisan would have been motivated to combine the above methods and protocols to ease the identification and detection of a potential biomarker in different biofluids.
Given that Soldo’s particle-based methods follow the same general format of first depleting unwanted, abundant proteins from a sample followed by enrichment, it would have been obvious to one of ordinary skill in the art to deplete known abundant proteins including albumin and IgG in order to achieve the same purpose. One of ordinary skill in the art would have had a reasonable expectation of success in combining the methods of Dawson, Shi and Soldo because the methods are directed to isolating and detecting different protein compositions. When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation, § 103 may bar its patentability. When considering obviousness of a combination of known elements, the operative question is thus “whether the improvement is more than the predictable use of prior art elements according to their established functions.” (MPEP 2141. I). Thus, such a combination of references would generate a predictable outcome.
It would have been obvious to one of ordinary skill in the art to combine the different methods and protocols of Dawson, Shi and Soldo in one method to achieve a reproducible identification of a biomarker from a biofluid for differential diagnosis and monitoring of a disease.
Claims 24-26 are rejected under 35 U.S.C. 103 as being unpatentable over Soldo et al. (US 2021/0302416 A1, effective filing date of 07/27/2018), Shi et al. (Methods 56 (2012) 246–253) and Dawson et al. (US 2012/0046184 A1) as applied to claim 1 above, and further in view of Borg et al. (Clinical Proteomics, 2011, 8: 6).
Regarding claims 24-26, the teachings and suggestions of Dawson, Shi and Soldo are discussed previously, but Soldo fails to teach the following limitations:
Regarding claim 24, Soldo does not teach performing the mass spectrometry to identify at least 500 proteins in the second plurality of proteins.
Regarding claim 25, Soldo does not teach performing the mass spectrometry to identify at least 900 proteins in the second plurality of proteins.
Regarding claim 26, Soldo does not teach performing the mass spectrometry to identify at least 500 low abundance proteins in the second plurality of proteins
Regarding claim 24, Borg teaches performing the mass spectrometry to identify at least 500 proteins in the second plurality of proteins (Page 10 of 14, first paragraph, “When this method was adapted to small volumes, the total number of identified proteins was reduced to 530”).
Regarding claim 25, Borg teaches performing the mass spectrometry to identify at least 900 proteins in the second plurality of proteins (Page 8 of 14, second paragraph, “CSF immunodepletion with IgYHSA column and analysis with 2DLC-MS/MS of one of the replicates led to the identification of 913 proteins”).
Regarding claim 26, Borg teaches performing the mass spectrometry to identify at least 500 low abundance proteins in the second plurality of proteins (Page 10 of 14, first paragraph, “When this method was adapted to small volumes, the total number of identified proteins was reduced to 530”).
It would have been obvious to one of ordinary skill in the art before the effective filing date to combine plasma-designed immunoaffinity columns of Borg with the combined invention of Dawson, Shi and Soldo to increase the detection of low abundance proteins by mass spectrometry because Borg used plasma-designed immunoaffinity columns to find ways to improve the reproducible detection and isolation of low abundance proteins that serve as potential biomarkers of disease by mass spectrometry (Abstract) and noted that the presence of high abundance proteins in a biological sample could hinder the detection of biomarkers that are present at low concentrations as compared to high abundance proteins (Page 2 of 14, first paragraph). A skilled artisan would have been motivated to combine the above methods and protocols to identify a potential biomarker in different biofluids. One of ordinary skill in the art would have had a reasonable expectation of success in combining the methods of Borg, Dawson, Shi and Soldo because the methods are directed to isolating and detecting different protein compositions. It would have been obvious to one of ordinary skill in the art to combine the different methods and protocols of Borg, Dawson, Shi and Soldo to increase the number of detected low abundance proteins and for expediating the discovery of a biomarker from a biofluid.
Response to Arguments
Applicant's arguments filed 10/09/2025 have been fully considered but they are not persuasive for the following reasons:
The Applicant alleged that Reference Soldo has a publication date of September 30, 2021, which is later than the claimed priority date of 03/26/2019, and therefore Soldo is not available as prior art under 35 U.S.C. § 103.
This argument is not persuasive because Soldo claims priority to US provisional application No. 62/711,415 filed on July 27, 2018, and thus Reference Soldo has an effective filing date of 07/27/2018 which is before the claimed priority date of 03/26/2019 of the instant application.
The Applicant alleged that even with the benefit of an earlier date, Soldo would not be anticipatory or make obvious the present claims at least because Soldo fails to teach, on a second plurality of magnetic particles, forming protein coronas comprising a second plurality of proteins from the supernatant of the depleted biofluid sample.
This argument is not persuasive because Soldo teaches forming a second plurality of proteins from the depleted biofluid sample onto a second plurality of particles (Page 16, [0188], [0194]).
The Applicant alleged that Borg, Shi, Dawson, Sigma Aldrich and Millipore, alone or in combination, fail to establish a prima facie case of obviousness because they do not disclose, "on a second plurality of magnetic particles, forming protein coronas comprising a second plurality of proteins from the depleted supernatant of the biofluid sample" as recited in independent claim 1.
This argument is not persuasive because Soldo teaches the forming of a second plurality of proteins from the depleted biofluid sample onto a second plurality of particles as discussed above. Furthermore, Applicant’s arguments with respect to claim 1 have been considered but are moot because the new ground of rejection does not rely on any of the references of Borg, Sigma Aldrich or Millipore applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
The Applicant alleged that combining the immunoaffinity-based method of Borg with a magnetic-based separation method such as that of Dawson would change the principle of operation of Borg. The Applicant further alleged that Borg discloses that "the objective of the study was to compare two
immunodepletion methods with a simple and efficient procedure rather than identifying the
largest number of proteins" of a CSF sample (p. 9 of Borg, emphasis added), and modifying Borg
in the manner stated by the Office (i.e. by introducing multiple subsequent steps using magnetic
particles), would render Borg unsatisfactory for its purpose.
This argument is not persuasive because Borg is teaching how to reduce the presence of high abundance proteins and Dawson is teaching how to deal with low abundance proteins and the two references are used as advantageous additives to the method of Soldo.
Thus, the previous rejection of claims 1-27 under 35 U.S.C. 103, regarding obviousness, is maintained and is made final.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to OMAR RAMADAN whose telephone number is (571)270-0754. The examiner can normally be reached Monday-Friday 8:30 am - 5:00 pm.
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/OMAR RAMADAN/Examiner, Art Unit 1678
/GREGORY S EMCH/Supervisory Patent Examiner, Art Unit 1678