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
Application Status
Claim 1 is drawn to a method for monitoring the effect of an environmental factor on the proteome or parts thereof of a cell, the method comprising the steps of:(a) selecting introns to be targeted in the genome of a cell; (b) identifying guide RNA (gRNA) sequences suitable for inserting a tag in the selected introns in the genome of the cell; (c) cloning identified gRNA sequences and tag sequence into transduction vectors; (d) contacting a population of the cell with said vectors of (c) to integrate the tag of (b) into selected introns; (e) exposing cell population to environmental factor; and (f) monitoring the effect of the environmental factor on the proteome based on the detection of the tag prior to exposure of the cell population to the environmental factor and subsequent to exposure of the cell population to the environmental factor.
This application is a 371 of PCT/EP2020/082295, filed on 05/23/2022.
Claims 1-3, 5-7, 9, 11-12, 16, 18-19 and 20-27 are currently pending in the instant application, and under consideration.
The preliminary amendment filed on 08/14/2023, amending claims 3, 5-7, 9, 11-12, and 16, and adding new claims 20-27 is acknowledged.
Election/Restriction
Applicant's election without traverse of Group I, Claims 1, 3, 5-7, 9, 11-12, and 16, drawn to a method for monitoring the effect of an environmental factor on the proteome or parts thereof of a cell, the method comprising the steps of:(a) selecting introns to be targeted in the genome of a cell; (b) identifying guide RNA (gRNA) sequences suitable for inserting a tag in the selected introns in the genome of the cell; (c) cloning identified gRNA sequences and tag sequence into transduction vectors; (d) contacting a population of the cell with said vectors of (c) to integrate the tag of (b) into selected introns; (e) exposing cell population to environmental factor; and (f) monitoring the effect of the environmental factor on the proteome based on the detection of the tag prior to exposure of the cell population to the environmental factor and subsequent to exposure of the cell population to the environmental factor, in the response filed on 08/15/2025 is acknowledged.
Claims 2, 18-19 and 20-27 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Applicants request for rejoinder is noted. However, current claims of elected Group I are not allowable at this time. When Group I would be allowable, rejoinder request would be evaluated at that time.
The requirement is still deemed proper and is therefore made FINAL.
Claims 1, 3, 5-7, 9, 11-12, and 16 are present for examination.
Priority
Acknowledgement is made of applicants claim for foreign priority under 35 U.S.C. 119(a)-(d) to a foreign patent application EPO 19211077.3, filed on 11/22/2019.
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on 09/22/2023 and 12/22/2025 are acknowledged. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is considered by the examiner. The signed copies of 1449 are enclosed herewith.
Drawings
Drawings submitted on 05/23/2022 are accepted by the Examiner.
Claim Objections
Claim 1 is objected to in the recitation “Method”, which should be changed to “A method”. Appropriate correction is required.
Claim 6 is objected to in the recitation “at least 3000 at least 10000 tagged introns”, which should be changed to “at least 3000 and at least 10000 tagged introns”. Appropriate correction is required.
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.
The claimed invention is directed to a naturally-occurring nucleic acid or fragment thereof, whether isolated or not, that is not patent-eligible pursuant to the Supreme Court decision in Association for Molecular Pathology v. Myriad Genetics, Inc., -- U.S. -- (June 13, 2013).
Claims 1, 3, 5-7, 9, 11-12, and 16 are rejected under 35 U.S.C. 101 because the claimed invention is not directed to patent eligible subject matter. The instant rejection is issued because of recent "Guidance for Determining Subject Matter Eligibility of Claims Reciting or Involving Laws of Nature, Natural Phenomena, & Natural Products or Abstract ideas" (see, MPEP 2106, and updated Guidance of 2019-PEG).
In the instant case, when a claim is determined to recite or involve one or more judicial exceptions, the key inquiry becomes whether the claim as a whole recites something significantly different than the judicial exception. The Guidance provides weighing factors for determining whether a claim recites something that is significantly different than the judicial exception. If the totality of the relevant factors weighs toward eligibility, the claim qualifies as eligible subject matter. However, if the totality of the relevant factors weighs against eligibility, the claim should be rejected.
Based upon consideration of all of the relevant factors with respect to the claims as a whole, the factors weigh against something that is significantly more than a law of nature or product of nature, or abstract ideas and therefore the claims do not qualify as eligible subject matter. The rationale for this determination is explained below:
Claim 1 is drawn to under Broadest Reasonable Interpretation (BRI) – “a method for monitoring the effect of an environmental factor on the proteome or parts thereof of a cell, the method comprising the steps of: (a) selecting introns to be targeted in the genome of a cell; (b) identifying guide RNA (gRNA) sequences suitable for inserting a tag in the selected introns in the genome of the cell; (c) cloning identified gRNA sequences and tag sequence into transduction vectors; (d) contacting a population of the cell with said vectors of (c) to integrate the tag of (b) into selected introns; (e) exposing cell population to environmental factor; and (f) monitoring the effect of the environmental factor on the proteome based on the detection of the tag prior to exposure of the cell population to the environmental factor and subsequent to exposure of the cell population to the environmental factor”.
In this case, the recited “a method for monitoring the effect of an environmental factor on the proteome or parts thereof of a cell, is not markedly different in structure from a naturally occurring environmental factors” molecule because the words “monitoring the effect of an environmental factors” does not add anything unless provided with specific environmental factors and its effect on the proteome of a cell. See Association for Molecular Pathology v. Myriad
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Genetics Inc. 106 USPQ2d 1972 (U.S. Supreme Court 2013). As such, the claimed recited “monitoring the effect of an environmental factors,” is not markedly different in structure from a naturally occurring factors (product) and thus the claimed “monitoring the effect of an environmental factors is not patent eligible subject matter.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because of the following analysis:
Step 1) Are the claims directed to a process, machine, manufacture or composition of matter?
Yes, the claims are drawn to a composition of matter or manufacture (a product).
Step 2a, Prong 1) Does the claim recite an Abstract Idea, Law of Nature or Natural Phenomenon?
Yes, the claim 1 is drawn to an Abstract idea, Natural Phenomenon and Law of Nature, “monitoring the effect of an environmental factors on the proteome or parts thereof of a cell”. Thus, monitoring and effect of an environmental factors would meet the defined claim and render it non-patent eligible.
Step 2a, Prong 2) Does the claim recite additional elements that integrate the Judicial Exception into a Practical Application?
No, the claimed composition doesn’t improve any technology or technical field, apply or use the JE to effect to a particular application or apply/use the JE in some other meaningful way.
Step 2B) Does the claim recite additional elements that amount to significantly more than the Judicial Exception?
The answer is No, therefore, the recited “monitoring the effect of an environmental factors on the proteome or parts thereof of a cell”, is not patent eligible.
Claims 3, 5-7, 9, 11 and 16 are also not patent eligible for the same reason as discussed above for claim 1.
Claim 12 recites specific environmental factors and thus, claim 12 is patent eligible.
Claim Rejections - 35 USC § 112(b)
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.
Claims 1, 3, 5-7, 9, 11-12, and 16 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 pre-AIA the applicant regards as the invention.
Claim 1 is indefinite and vague in the recitation “part thereof” in the context of proteome, which is confusing, wherein the phrase “part” is a relative term, which renders the claim indefinite because there is no boundary of said phrase “part” of a proteome. The term is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Clarification is required.
Claim 5 is 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 pre-AIA the applicant regards as the invention.
Claim 5 is indefinite and vague in the recitation “part thereof” in the context of gRNA insert, which is confusing, wherein the phrase “part” is a relative term, which renders the claim indefinite because there is no boundary of said phrase “part” of a gRNA insert. The term is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Clarification is required.
Claim 6 is rejected under 35 U.S.C. 112(b), as being indefinite and vague for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 6 is indefinite in the recitation “preferably”, in the context of sequencing vector, wherein the phrase “preferably”, is unclear as to the scope of the claim. The phrase "preferably" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. Does “preferably” mean a Crop-Seq vector or something else? See MPEP § 2173.05(d). Clarification is required.
Claim 9 is rejected under 35 U.S.C. 112(b), as being indefinite and vague for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 9 is indefinite in the recitation “preferably”, in the context of occurrence, wherein the phrase “preferably”, is unclear as to the scope of the claim. The phrase "preferably" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. Does “preferably” mean an occurrence 1 or something else? See MPEP § 2173.05(d). Clarification is required.
Claim 12 is rejected under 35 U.S.C. 112(b), as being indefinite and vague for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 12 is indefinite in the recitation “preferably or preferentially”, in the context of adherent, non-migratory cell line, or GFP, EGFP ----- or a Tag, wherein the phrase “preferably or preferentially”, is unclear as to the scope of the claim. The phrase "preferably or preferentially " renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. Does “preferably or preferentially” mean an adherent cell, GFP, or something else? See MPEP § 2173.05(d). Clarification is required.
Claim 16 is rejected under 35 U.S.C. 112(b), as being indefinite and vague for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 16 is indefinite in the recitation “preferably”, in the context of cells separation, wherein the phrase “preferably”, is unclear as to the scope of the claim. The phrase "preferably" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. Does “preferably” mean separation of cells by using FACS, or something else? See MPEP § 2173.05(d). Clarification is required.
Claim 12 is rejected under 35 U.S.C. 112(b), as being indefinite and vague for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 12 is indefinite in the recitation “e.g.”, in the context of Tag or microscopy, wherein the phrase “e.g.”, is unclear as to the scope of the claim. The phrase "e.g." renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d). Clarification is required.
Claim 12 is rejected under 35 U.S.C. 112(b), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
In the present instance, claim 12 recite “another” in the context of cell line. The metes and bounds of the term “another” are not clear to the Examiner. It is not clear what applicants reason by “another” because there are thousands cell lines exits in the world. Clarification is required.
Claim Rejections – 35 USC § 112(b)
The following is a quotation of the second paragraph of 35 U.S.C. 112:
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.
Claim 7 is rejected under the judicially approved “improper Markush grouping” doctrine. See Supplementary Examination Guidelines for Determining Compliance with 35 U.S.C. §112 and for Treatment of Related Issues in Patent Applications, 76 FR 7162 (Feb. 9, 2011), page 7166.
Claim 7 is rejected as reciting an improper Markush group (i.e., wherein the introns to be tagged are comprised in genomic sequence of – metabolic enzymes, chromatin proteins, kinases, ------- or one intron per protein coding gene as the species of the recited Markush group do not all share a disclosed structural similarity essential to the common use of the species. Although both species share a common use, the species do NOT share any structural similarity at all as each are genes of distinct pathways. Note that the species of the Markush Group must end with “and” not “or” before last species. Clarification is required.
Claim 12 is rejected under the judicially approved “improper Markush grouping” doctrine. See Supplementary Examination Guidelines for Determining Compliance with 35 U.S.C. §112 and for Treatment of Related Issues in Patent Applications, 76 FR 7162 (Feb. 9, 2011), page 7166.
Claim 12 is rejected as reciting an improper Markush group (i.e., wherein the environmental factor selected from radiation, chemical compound, biological compound ------ ion concentration before last species as the species of the recited Markush group do not all share a disclosed structural similarity essential to the common use of the species. Although all species share a common use, the species do NOT share any structural similarity at all as each are distinct species sch as radiation, chemical compound, temperature. Note that the species of the Markush Group must end with “and” not “or” before last species. Clarification is required.
Claim 12 is rejected under the judicially approved “improper Markush grouping” doctrine. See Supplementary Examination Guidelines for Determining Compliance with 35 U.S.C. §112 and for Treatment of Related Issues in Patent Applications, 76 FR 7162 (Feb. 9, 2011), page 7166.
Claim 12 is rejected as reciting an improper Markush group (i.e., wherein the effect on the proteome is selected from protein expression, protein localization, ----- protein mobility, before last species as the species of the recited Markush group do not all share a disclosed structural similarity essential to the common use of the species. Although all species share a common use, the species do NOT share any structural similarity at all as each are distinct species. Note that the species of the Markush Group must end with “and” not “or” before last species. Clarification is required.
Claim 12 is rejected under the judicially approved “improper Markush grouping” doctrine. See Supplementary Examination Guidelines for Determining Compliance with 35 U.S.C. §112 and for Treatment of Related Issues in Patent Applications, 76 FR 7162 (Feb. 9, 2011), page 7166.
Claim 12 is rejected as reciting an improper Markush group (i.e., wherein the cell is a HAP1 cell, K562 cell , HeLa cell ---------- or another cell line, before last species as the species of the recited Markush group do not all share a disclosed structural similarity essential to the common use of the species. Although all species share a common use, the species do NOT share any structural similarity at all as each are distinct species. Note that the species of the Markush Group must end with “and” not “or” before last species. Clarification is required.
Claim 12 is rejected under the judicially approved “improper Markush grouping” doctrine. See Supplementary Examination Guidelines for Determining Compliance with 35 U.S.C. §112 and for Treatment of Related Issues in Patent Applications, 76 FR 7162 (Feb. 9, 2011), page 7166.
Claim 12 is rejected as reciting an improper Markush group (i.e., wherein the tag is a fluorescence tag, GFP, EGFP ------ or a tag suitable for detection, before last species as the species of the recited Markush group do not all share a disclosed structural similarity essential to the common use of the species. Although all species share a common use, the species do NOT share any structural similarity at all as each are distinct species. Note that the species of the Markush Group must end with “and” not “or” before last species. Clarification is required.
Relevant reference of interest: Serebrenik et al. Efficient and flexible tagging of endogenous genes by homology-independent intron targeting. Genome Research (June 25, 2019), 29(8): 1322-1328.
Conclusion
Status of the claims:
Claims 1, 3, 5-7, 9, 11-12, and 16 are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to IQBAL H CHOWDHURY whose telephone number is (571)272-8137. The examiner can normally be reached on M-F, at 9:00-5:00 PM.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Manjunath N. Rao, can be reached on 571-272-0939. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Iqbal H. Chowdhury, PhD.
Primary Patent Examiner
Iqbal H. Chowdhury, Primary Examiner
Art Unit 1656 (Recombinant Enzymes and Protein Crystallography)
US Patent and Trademark Office (USPTO)
Ph. (571)-272-8137 and Fax (571)-273-8137
/IQBAL H CHOWDHURY/
Primary Examiner, Art Unit 1656