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 .
Priority
This application was filed on 08/10/2023.
Election/Restrictions
Applicant’s election with traverse of group II (claims 29-34: drawn to a microarray or a kit comprising one or more probes predictive of FOLFIRI, or FOLFOX chemotherapy response) in the reply filed on 07/17/2026 is acknowledged.
Applicant did not provide the grounds for the traversal.
The requirement is still deemed proper and is therefore made FINAL.
Concerning the species election requirement,
As it relates to species A: Response markers for treatment with FOLFOX for any stage of colorectal cancer: Applicant elects the combination consisting of CFAP92, LTA4H, SH3GLR1, AP5Z1, CARM1, TRIM3, PPDPF, GPN3, GTF2A1, HELZ2.
As it relates to species B: Response markers for treatment with FOLFOX in early-stage colorectal cancer: Applicant elects the combination consisting of FOXA 1, KRT23, GRM8, HOXA 11, HOXA 10, ABCB1, LEFTYl, CHRM3, OLMF4, LYZ.
As it relates to species C: Response markers for treatment with FOLFOX in metastatic stage colorectal cancer: Applicant elects the combination consisting of IF144L, WIF1, L Y6G6D, SFRP2, RETNLB, CMPK2, ACSL6, RSAD2, LOC 100507477, IFITI, MXI, HUNK.
As it relates to species D: Response markers for treatment with FOLFIRI for any stage of colorectal cancer, Applicant elects the combination consisting of AMOTL 1, CTHRC1, FNDC1, COL 1A2, DDR2, SLIT2, CDH11, COL3A1, AKAP12, SFRP2, PTGR2, CD36.
As it relates to species E: the type of biomarker for prognosing FOLFOX or FOLFIRI response, Applicant hereby elects nucleic acid transcripts.
Claims 23-28, 31 and 34-35 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention(s), there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 07/17/2026.
Status of the claims
Claims 23-35 are pending. Claims 29-30 and 32-33 and currently under examination.
Claim Objections
Claim 29 is objected to because of the following informalities: For step (iii), claim 29 recites the limitation “(iii): Interferon Induced Protein 44 Like (IFI44L)”.
A semicolon symbol is recited as following “(iii)” and should be deleted to maintain clarity in claim 29. Appropriate correction is required.
Claim Interpretation
Prior to analysis of the art, the claims must be construed. As noted in MPEP 2111, citing Phillips v. AWH Corp., 415 F.3d l303, 75 USPQ2d l321 (Fed. Cir. 2005), "During patent examination, the pending claims must be 'given their broadest reasonable interpretation consistent with the specification.' ".
The preamble of claim 29 and claim 32 each recite the limitations “FOLFIRI” and “FOLFOX”.
Based on the disclosure of the specification, the limitation “FOLFIRI” is construed as corresponding to FOL= Leucovorin Calcium (Folinic Acid), F = Fluorouracil and IRI = Irinotecan Hydrochloride).
Based on the disclosure of the specification, the limitation “FOLFOX” is construed as (corresponding to FOL= Leucovorin Calcium (Folinic Acid), F = Fluorouracil and OX= Oxaliplatin).
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 29-30 and 32-33 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 29-30 each recites the limitation “RNASeq” which is indefinite as it is confusing as to which statutory category (process or product) this limitation belongs.
Claim 32 is indefinite as this claim omits a concluding period. It is unclear what limitations beyond the limitation of step (iv), that are encompassed within claim 32. Claim 33 is further rejected as it depends from claim 32.
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 29-30 and 32-33 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to a judicial exception (i.e., a law of nature, a natural phenomenon, an abstract idea, or a natural product) without significantly more.
Claims 29-30 and 32-33 are broadly directed to nucleic acids that appear to encompass one or more natural product(s) which falls within the law of nature exception. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
The unpatentability of natural products was confirmed by the U.S. Supreme Court in Association for Molecular Pathology v. Myriad Genetics, Inc., No. 12-398 (June 13, 2013) - “A naturally occurring DNA segment is a product of nature and not patent eligible merely because it has been isolated”, and “Myriad’s DNA claim falls within the law of nature exception”.
The following inquiries are used to determine whether a claim is drawn to patent-eligible subject matter:
Step 1. Is the claim directed to a process, machine, article of manufacture, or composition of matter?
Yes- the claims are clearly directed to nucleic acids/nucleotide sequence(s) which are a composition of matter.
Step 2A, prong one. Does the claim recite a law of nature, a natural phenomenon, or an abstract idea (recognized judicial exceptions)?
Yes- the claims are directed one or more polynucleotides or nucleic acid transcripts selected from CFAP92, LTA4H, AP5Z1, SH3GLR1, CARM1, TRIM3, PPDPF, GPN3, GTF2A1, HELZ2, FOXA1, HOXA10, GRM8, ARBCR1, HOXA11, LEFTYJ, KRT23, CHRM3, OLMF4, LYZ, IFI44L, WIF1, LY6G6D, SFRP2, RETNLB, CMPK2, ACSL6, RSAD2, LOC100507477, MXI, IFITI , HUNK, AMOTLI, CTHRC1, COLJA2, DDR2, FNDC1, SLIT2, CDH11, COL3A1, AKAP12, SFRP2, PTGR2, CD36.
The polynucleotides of claims 29-30 and 32-33 are not markedly different than their naturally occurring counterparts.
The polynucleotides of claims 29-30 and 32-33 have no functional differences relative to their naturally occurring counterparts since both the claimed and naturally occurring molecules hybridize to complementary nucleic acids.
MPEP 2106.04(b)(i) identifies nucleic acid sequence(s) having no structural or functional differences from naturally occurring nucleic acids as an example of a patent-ineligible natural product.
In addition, as discussed in MPEP 2016.04(b)(II), “[P]roduct of nature exceptions include both naturally occurring products and non-naturally occurring products that lack markedly different characteristics from any naturally occurring counterpart.” See Ambry Genetics, 774 F.3d at 760, 113 USPQ2d at 1244.
Step 2A, prong two. Does the claim as a whole integrate the recited judicial exception into a practical application of the exception?
No - This evaluation is performed by identifying whether there are any additional elements recited in the claim beyond the judicial exception and evaluating those additional elements individually and in combination to determine whether the claim as a whole integrates the exception into a practical application.
In the instant case, the claims do not appear to recite any additional elements beyond those that may reasonably be consider part of a naturally occurring nucleic acid transcripts.
Here it is noted the none of the claims recite elements other than standard DNA elements (e.g. fluorophore labels that are non-naturally occurring nucleotides, naturally occurring elements) nor do they have functions not possessed by naturally occurring nucleic acids.
Step 2B. Does the claim recite additional elements that amount to significantly more than the judicial exception?
No- In the instant case, as detailed above, claims 29-30 and 32-33 are directed to one or more polynucleotides or nucleic acid transcripts encompassing partial or full-length sequence(s) of naturally occurring DNA sequences. This part of the eligibility analysis evaluates whether the claim as a whole amount to significantly more than the recited exception, i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim. MPEP 2106.05.
Concerning claims are drawn to nucleic acids that encompass a product that is naturally occurring (i.e.: a claimed primer pair/probe may be the same as a portion of a natural genome), it is noted that in Association for Molecular Pathology et al v. Myriad Genetics, Inc. et al, (569 U.S. (2013)), the Supreme Court provides:
Myriad did not create or alter either the genetic information encoded in the BCRA1 and BCRA2 genes or the genetic structure of the DNA. It found an important and useful gene, but groundbreaking, innovative, or even brilliant discovery does not by itself satisfy the §101 inquiry. See Funk Brothers Seed Co. v. Kalo Inoculant Co., 333 U. S. 127. Finding the location of the BRCA1 and BRCA2 genes does not render the genes patent eligible “new . . . composition[s] of matter,” §101. Myriad’s patent descriptions highlight the problem with its claims: They detail the extensive process of discovery, but extensive effort alone is insufficient to satisfy §101’s demands. Myriad’s claims are not saved by the fact that isolating DNA from the human genome sever the chemical bonds that bind gene molecules together.
Further, where claims 29-30 and 32-33 are directed to a collection of polynucleotides or nucleic acid transcripts, the nucleic acid transcripts possess no structural or functional difference to and do not have any markedly different characteristic as a collection than each nucleic acid transcript has individually.
In view of the foregoing, claims 29-30 and 32-33 are rejected under 35 U.S.C. 101 for being directed to ineligible subject matter.
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 29-30 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Lin et al. (Sept 2018, Onco Targets Ther. 11:5943-5955).
Regarding claims 29-30, Lin et al. provides measurements of gene expression profiles of colorectal cancer patients with FOLFOX therapy collected with Affymetrix Human Genome U133 Plus 2.0 Array (pg 5944, left col., text of section entitled Methods and pg 5944, right col., 1st and 2nd para).
On pg 5948, Fig. 3, Lin et al. teach 138 genes in the responder and non-responder colorectal cancer patients. On pg 5954 in Table S2, Lin et al. teach LTA4H (order 15) and HOXA11 (order 81) probe(s).
Accordingly, Lin et al. meet the current limitations of claims 29-30 by teaching a microarray comprising one or more nucleic acid probes as recited in claim 29, groups (i) through (iv).
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 32-33 are rejected under 35 U.S.C. 103 as being unpatentable over Lin et al. (Sept 2018, Onco Targets Ther. 11:5943-5955) as applied to claim 29, further in view of Polansky (US2004/0023207).
The teachings of Lin et al. as it relates to claim 29 from above are applied here. Lin et al. do not teach a kit.
Polansky (claims 32-33)
Polansky (US2004/0023207) taught (paragraph [0919]): “Well known advantages of commercial kits include convenience and reproducibility due to manufacturing standardization, quality control and validation procedures.”
It would have been prima facie obvious before the effective filing date of the invention to provide a microarray as taught by Lin et al. and other components for methods taught by Lin et al., into a kit for practicing the methods, for benefits taught or suggested by Polansky e.g. convenience of having elements of practicing a detection method in one place.
In view of the combined teachings of all of the cited reference(s), the instant claims 32-33 are prima facie obvious.
Conclusion
No claims are currently allowed.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to OLAYINKA A OYEYEMI whose telephone number is (571)270-5956. The examiner can normally be reached Monday -Thursday: 9:00 am - 5:00 pm, EST.
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OLAYINKA A. OYEYEMI
Examiner
Art Unit 1681
/OLAYINKA A OYEYEMI/Examiner, Art Unit 1681
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684
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