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 .
Information Disclosure Statement
The information disclosure statement (IDS) submitted on June 18, 2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1 – 13 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1 – 13 are drawn to a method for quantifying a target protein, however fails to claim active steps for quantifying the protein. Rather, the claims appear drawn to preparing a sample for quantification. Although the claims recite a step c, “quantifying the target protein,” the step recites “using a mass spectroscopy method” and fails to clearly delineate steps required for quantification. Clarification is required.
Claim Rejections - 35 USC § 102
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.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1 - 3 and 6 – 13 are rejected under 35 U.S.C. 102a1 as being anticipated by Li et al. (2019, IDS 06.18.2024 NPL #2).
Regarding claims 1 – 3 and 13, Li teaches methods for quantifying a fusion protein (target protein) in a serum sample, the method comprising incubating the sample with PNGaseF (amidase) and Asp-N (protease) for a period of time followed by chromatography and mass spectrometry (title, abstract, page 3).
Regarding claims 6 – 8, Li teaches quantification perform on Acquity UPLC system coupled to an AB Sciex API; or Agilent 1200 PHLC coupled to API 6500 QTrap mass spectrometer equipped with electrospray ionization (p.3) which are ion exchange systems coupled with UV detection (see Waters product summaries).
Regarding claims 9 – 11, the samples are incubated with enzymes for 1 – 2 hours (60 – 120 minutes) at 37°C (p.3).
Regarding claim 12, the method further comprises a change in buffers, which occurs prior to mass spectrometry (p.3).
The reference anticipates the claimed subject matter.
Claims 1 – 4, 6 – 11 and 13 are rejected under 35 U.S.C. 102a1 and 102a2 as being anticipated by Magnelli et al. (US 2015/0346194, IDS 06.18.2024 USPD #1).
Regarding claims 1 – 4, Magnelli teaches methods for quantifying glycosylated antibodies (target protein) in a sample, the method comprising incubating the sample with PNGaseF (amidase) and trypsin (protease) for a period of time followed by chromatography and mass spectrometry (example 21, figure 20). Other amidases are disclosed useful in the methods to include PNGaseA, exoglycosidase, endoglycosidase F and H (0010, 0092); while other proteases are disclosed to include Lys-C, Lys-N, Arg-C, Glu-C, Asp-N and chymotrypsin (0009).
Regarding claim 6, Magnelli teaches various methods of mass spectrometry can be used to include MALDI-TOF and ESI (0080).
Regarding claims 7 – 8, Magnelli teaches various methods of chromatography can be used to include HPLC (affinity separation with UV detection) and anion-exchange (0080).
Regarding claims 9 – 11, the samples are incubated with enzymes for 30 minutes to 3 hours (30 – 180 minutes) at 37°C or 5 – 30 minutes at 50°C (example 21).
Regarding claim 13, the sample may be serum, plasma, blood, body fluids or derivatives thereof (0084).
The reference anticipates the claimed subject matter.
Claim Rejections - 35 USC § 103
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.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1 and 5 are rejected under 35 U.S.C. 103 as being unpatentable over Li et al. (2019, IDS 06.18.2024 NPL #2) OR Magnelli et al. (US 2015/0346194, IDS 06.18.2024 USPD #1), in view of Zhang et al., (2014, IDS 06.18.2024 NPL #3).
Regarding claim 1, Li teaches methods for quantifying a fusion protein (target protein) in a serum sample, the method comprising incubating the sample with PNGaseF (amidase) and Asp-N (protease) for a period of time followed by chromatography and mass spectrometry (title, abstract, page 3). Li teaches the digestion approach for measuring proteins proves more sensitive than whole protein quantification (abstract).
Magnelli teaches methods for quantifying glycosylated antibodies (target protein) in a sample, the method comprising incubating the sample with PNGaseF (amidase) and trypsin (protease) for a period of time followed by chromatography and mass spectrometry (example 21, figure 20).
Regarding claim 5, the references do not teach the methods wherein the target protein is cancer antigen 125 or carcinoembryonic antigen. However, at the time the claims were filed, cancer antigen 125 (CA125) and carcinoembryonic antigen (CEA) were known clinical biomarkers for various cancers. In support, Zhang teaches that glycosylated proteins such as CA125 and CEA were clinical biomarkers (abstract, p.1) that are advantageously digested with trypsin and PNGase F for quantification with mass spectrometry and chromatography (p.2-3, 5, 10). Specifically, Zhang teaches the combination of proteomics and glycomics allows for “unique contributions to the discovery of biomarkers of cancer” (p.1-2) which is accomplished by tryptic digestion to remove non-glycosylated peptides and PNGaseF to remove glycosylated peptides (p.5). At the time the claims were filed, one of ordinary skill in the art would have been motivated to practice the methods of Li or Magnelli to quantify CA125 and/or CEA because of their known status as cancer biomarkers, for their glycosylated structure which was known to benefit from the combined treatment with protease and amidase and with a reasonable expectation for successfully quantifying the target proteins.
Thus, the invention as a whole is prima facie obvious over the references, especially in the absence of evidence to the contrary.
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RUTH A DAVIS whose telephone number is (571)272-0915. The examiner can normally be reached Monday - Friday (8am - 4pm).
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Fereydoun Sajjadi can be reached at 571-272-3311. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/RUTH A DAVIS/Primary Examiner, Art Unit 1699