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 .
Election/Restrictions
Applicant’s election without traverse of claims 1-4 (Group I) in the reply filed on 05/22/2026 is acknowledged.
Claims 5-18 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 05/22/2026.
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 1-4 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.
Claim 1 recites “the relative protein abundances” in line 4. There is insufficient antecedent basis for this limitation in the claim.
Claim 1 recites “the proteomic profile” in line 8. There is insufficient antecedent basis for this limitation in the claim.
Claim 1 recites “the ratio of the relative abundances for each protein” in lines 8-9. There is insufficient antecedent basis for this limitation in the claim.
Claim 1 recites “said protein in the non-pathological tissue” in line 10. There is insufficient antecedent basis for this limitation in the claim.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-4 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
In claim 1 the steps of “determining” the proteomic profile of said sample and “determining” a reference proteomic profile for the previously diagnosed pathological condition.
While the claims recite a computer-implemented method, under a broadest reasonable interpretation, the “determination” is not precluded from being performed mentally in which case it is an abstract idea and a judicial exception.
The claimed subject manner is not integrated into a practical application since neither the proteomic profile of said sample nor the reference proteomic profile are used for any claimed purpose.
The step of obtaining a sample by macrodissection or laser microdissection of a formalin-fixed paraffin-embedded or frozen tissue in claim 2 are routine and conventional steps of sample collection/preparation.
The step quantification of the relative protein abundances mass spectrometry in claim 3 is a routine and convention analysis step of data acquisition.
The pathological conditions recited in claim 4 are merely sample choices.
None of claims 2-4 integrated the subject manner of claim 1 into a practical application.
Thus, in light of the above considerations the claims remain non-statutory, and are thus not patent eligible under 35 U.S.C. 101.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries 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.
1. Claims 1-4 are rejected under 35 USC 103 as being unpatentable over Henriet et al. (“A combined laser microdissection and proteomic analysis method,” JOURNAL OF HEPATOLOGY, vol. 68, 1 April 2018). (cited by applicant)
for identification of liver tumors signatures
Henriet et al. discloses combining laser microdissection and mass spectrometry analysis to compare the proteomic profiles of tumors and for identification of liver tumors signatures. (under “Method”)
Henriet et al. discloses comparing tumoral and non-tumoral proteins expression levels in HCA, H-HCA, IHCA. b-HCA, and UHCA. Using the Oncoprot's process. (http://www.tbmcore.u-bordeaux.fr/oncoprot/). (under “Method” and “Results”)
Henriet et al. disclose that the authors searched for proteins specifically deregulated in UHCA. First, we demonstrated that proteomic profiles allow them to discriminate between known HCA subtypes by the identification of classical biomarkers of each HCA subgroup. (under “Results”)
Henriet et al. does not teach label free quantification; however, Henriet et al. does not teach labels. Otherwise it would have been obvious to one of ordinary skill in the art before applicant’s effective filing date to practice the method of Henriet et al. using label free quantification.
Henriet et al. does not teach determining a proteomic profile of a sample by calculating the ratio of relative abundances, for each protein, of a protein in the pathological tissue with respect to a protein in the non-pathological tissue.
It would have been obvious to one of ordinary skill in the art before applicant’s effective filing date to determine a proteomic profile of a sample by calculating the ratio of relative abundances, for each protein, of a protein in the pathological tissue with respect to a protein in the non-pathological tissue, for purposes of using conventional statical date manipulation to determine amounts of proteins for comparison purposes.
Henriet et al. does not teach determining a reference proteomic profile for the previously diagnosed pathological condition, by means of a statistical test established between at least two groups of subjects.
Henriet et al. teaches research efforts concentrated on the identification of genomic abnormalities in tumors offering the prospect of personalized treatments and thus a better management of patients. (under “Background and Aims”)
It would have been obvious to one of ordinary skill in the art before applicant’s effective filing date to modify Henriet et al. by determining a reference proteomic profile for the previously diagnosed pathological condition, for purposes of comparison to determine pathological conditions of a subject for identifying and determining suitable treatment.
The claimed use of using statistical test established between at least two groups of subjects is an obvious and known means to average data using multiple data sets.
While Henriet et al, does not specifically teach a computer-implemented method, the use of a computer to process data is conventional and obvious to those skilled in the art.
I.) As noted above, Henriet et al. renders all the limitations of claim 1 obvious.
Therefore, Henriet et al. renders claim 1 obvious
II.) Regarding applicant’s claim 2, as noted above Henriet et al. renders all the limitations of claim 1 obvious from which claim 2 depends.
Claim 2 recites that sample is obtainable by macrodissection or laser microdissection of a formalin-fixed paraffin-embedded or frozen tissue.
As noted above, Henriet et al. teaches microdissection. (under “Method”)
As to microdissection of a formalin-fixed paraffin-embedded or frozen tissue, it is conventional or otherwise obvious to use formalin-fixed paraffin-embedded or frozen tissues for microdissection to allow cutting tissue samples.
Therefore, Henriet et el. renders claim 2 obvious.
III.) Regarding applicant’s claim 3, as noted above Henriet et al. renders all the limitations of claim 1 obvious from which claim 3 depends.
Claim 3 recites that label free quantification of the relative protein abundances is realized by mass spectrometry.
As noted above, Henriet et al, teaches mass spectrometry. (under “Method”)
Therefore, Henriet et al. renders claim 3 obvious.
IV.) Regarding applicant’s claim 4, as noted above Henriet et al. renders all the limitations of claim 1 obvious from which claim 4 depends.
Claim 4 recites that the pathological condition is chosen among a cancer, an autoimmune disease, a thrombosis, an inflammatory disease, an infection, a graft or prosthesis rejection, or a benign tumor.
Henriet et al. discloses investigating liver tumors, including cancerous liver tumors. (Title)
Therefore, Henriet et al. renders claim 4 obvious
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
U.S. Patent Application Publication No. 2018/0259533 to Gold et al. teaches comparing protein expression level in tumor tissue of an individual versus protein expression level in normal or healthy tissue from the same individual. [0166]
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/MICHAEL STANLEY GZYBOWSKI/Examiner, Art Unit 1798
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