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 .
Interview Summary
The Examiner would like to note the inclusion of the Applicant’s interview summary regarding the video conference interview on April 6th, 2026. With the inclusion of this summary, the interview record is complete.
Response to Amendment
The amendment filed April 30th, 2026 is acknowledged. Regarding the Office Action mailed December 4th, 2025:
The objections to the claims are withdrawn in view of the amendments.
The rejections of claims 1-3, 6, 8-9, 11, 14-15, 17-20, 24, and 26 as set forth under 35 U.S.C. 112(b) are withdrawn in view of the amendments and cancellation of claims 6, 15, and 18. The rejection of claim 10 has been modified as necessitated by amendment (see below).
The rejections of claims 1-3, 6, 8-9, 11, 14-15, 17-20, 24, and 26 as set forth under 35 U.S.C. 112(a) are withdrawn in view of the amendments and cancellation of claims 6, 15, and 18. The rejection of claim 10 has been modified as necessitated by amendment (see below).
The double patenting rejection is withdrawn in view of the cancellation of the relevant claims in the reference application.
Maintained, modified, or new rejections are set forth below, as necessitated by the amendments. Responses to arguments, if necessary, follow their respective rejection sections.
Claim Summary
Claims 1, 3, 8-11, 14, 17, and 19-20 have been amended. Claims 4-7, 12-13, 15-16, 18, 21-23, 25, 27, and 30 have been canceled. Claims 1-3, 8-11, 14, 17, 19-20, 24, 26, 28-29, and 31 are pending. Claims 28-29 and 31 are withdrawn from consideration as being drawn to a non-elected invention/species. Claims 1-3, 8-11, 14, 17, 19-20, 24, and 26 are under examination and discussed in this Office action.
Claim Objections
Claim 14 is objected to because of the following informalities:
Claim 14 contains an unnecessary “and” at the end of step (b). This should be removed.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b) - Modified - Necessitated by Amendment
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.
Claim 10 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 10 recites the limitation “sequencing the one or more amplification products to identify the isolated ribosome-bound RNA fragment and determine the translation rate of the RNA in the biological sample”. There is insufficient antecedent basis for this limitation in the claim. No claim from which claim 10 depends introduces “translation rate of the RNA in the biological sample”. Therefore, claim 10 is found indefinite.
Response to Arguments
As has been noted above, the rejections of claims 1-3, 6, 8-9, 11, 14-15, 17-20, 24, and 26 as set forth under 35 U.S.C. 112(b) are withdrawn in view of the amendments and cancellation of claims 6, 15, and 18. However, because of these amendments, claim 10 is still indefinite and the rejection has been modified to reflect this indefiniteness.
Claim Rejections - 35 USC § 112(a) - Modified - Necessitated by Amendment
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 10 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
In making a determination of whether the application complies with the written description requirement under 35 U.S.C. 112(a) or 35 U.S.C. 112, first paragraph, it is necessary to understand what Applicant is claiming and what Applicant has possession of. To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. See, e.g., Moba, B.V, v. Diamond Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed. Cir. 2003); Vas-Cath, Inc. v. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116. Possession may be shown in a variety of ways including description of an actual reduction to practice, or by showing that the invention was “ready for patenting” such as by the disclosure of drawings or structural chemical formulas that show that the invention was complete, or by describing distinguishing identifying characteristics sufficient to show that the applicant was in possession of the claimed invention. See, e.g., Pfaff v. Wells Eiees., Inc., 525 U.S. 55, 68, 119 S.Ct. 304, 312, 48 USPQ2d 1641,1647 (1998); Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406; Amgen, Inc. v. Chugai Pharm., 927 F. 2d 1200, 1206, 18 USPQ2d 1016, 1021 (Fed. Cir. 1991). See MPEP § 2163.
Claim 10 recites the limitation “[t]he method of claim 9, further comprising ligating a DNA adapter to a 3' end of the cDNA fragment; amplifying the cDNA fragment to generate one or more amplification products; and sequencing the one or more amplification products to identify the isolated ribosome-bound RNA fragment and determine the translation rate of the RNA in the biological sample.” The claim as written embraces a method wherein sequencing of cDNA amplification products identifies RNA of interest and determines a translation rate of the RNA of interest. However, determining a translation rate is not further defined or described in the claims.
Turning to the specification, there is no description that clearly defines or describes how a translation rate is determined. Page 10, lines 30-21 state, “the normalized Ribo-eCLIP enrichment correlates with translation rate estimates from independent approaches”. This passage does not describe what enrichment or normalization entails, nor how normalized Ribo-eCLIP enrichment correlates or is equivalent to determining translation rate. Page 13, lines 22-26 state, “profiling includes sequencing of a nucleic acid (e.g., DNA or RNA), wherein the gene expression profile includes information of active translation at a point in time. As used herein, the term "translation rate" can refer to the level of translation of an mRNA in a cell, wherein translation is the process in which ribosomes synthesize proteins after the process of transcription of DNA to RNA. In some embodiments, genetic differences and their subsequent expression as mRNAs impact the translation rate in an RNA-specific matter”. This passage appears to indicate that, at most, translation rate is related to expression of mRNA. However, this passage also does not further describe how translation rate is determined. Finally, Page 18, lines 20-28 state, “[n]ext, it was tested whether Ribo-eCLIP accurately quantitates ribosome-associated RNAs and it was also tested whether per-gene enrichments in Ribo-eCLIP (quantitated as fold-enrichment in IP versus paired input) corresponded to independent measurement of ribosome-associated RNAs obtained by isolation of polysomes followed by RNA-seq. By binning all expressed RNAs into 10 bins based on the ratio of polysome-associated to monosome- or non-ribosome-associated expression, it was observed that Ribo-eCLIP enrichments indeed significantly correlated with polysome-associated RNA enrichments (FIG. 3C). Thus, Ribo-eCLIP recapitulates independent assessments of ribosome-associated RNAs.” This passage from the examples appears to be the most relevant in terms of calculating outcomes from Ribo-eCLIP data. However, it addresses quantification of RNAs and per-gene enrichments, and not specifically determining a rate of translation. Without any further explanation provided, it cannot be clearly determined whether one of these quantifications is actually for determining a translation rate. The cited figure (Figure 3C) appears to relate a translation rate estimate to IP versus input ratio, but it is unclear from this axis label or the figure description what these compared values entail, or even if they are the same as the similar values described in the specification (fold-enrichment in IP versus paired input). Furthermore, even if what is seen in the specification and on the figure was how translation rate is calculated, it would be improper for the Examiner to read limitations from the specification into the claims (See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993)). Overall, there is no description that clearly defines or describes how a translation rate is determined.
Based on the above analysis, the Applicant does not have possession of the method as claimed. Claim 10 does not present possession of the method as claimed and does not have support based on the specification.
Response to Arguments
Applicant's arguments filed April 30th, 2026 have been fully considered but they are not persuasive.
The Applicant indicates that as discussed for the 112(b) rejections, claims 1 and 14 no longer refer to determining RNA translation rate, and as currently amended are clear and sufficiently described (Pages 9-10 of the Remarks filed April 30th, 2026). The Examiner acknowledges the adequate description of these claims and most dependent claims given the presented amendments. However, claim 10 still recites “determine the translation rate of the RNA in the biological sample”, which lacks description as analyzed above. Therefore, the rejection has been modified to reject only claim 10 and is maintained.
Claim Rejections - 35 USC § 101 - New - Necessitated by Amendment
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 1-3, 8-11, 24, and 26 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. While the claims are directed to a process, and therefore meet step 1 of the subject matter eligibility test (see MPEP 2106.03), the claims recite the mathematical calculation of calculating fold-enrichment of the immunoprecipitation sample compared to the paired input sample. As covered in MPEP 2106.04(a)(2)(I)(C), mathematical calculations are considered abstract ideas.
Step 2A of the subject matter eligibility test requires a two-pronged analysis. Prong One asks: does the claim recite an abstract idea, law of nature or natural phenomenon? As discussed in MPEP 2106.04(II)(A)(1), the meaning of “recites” is “set forth” or “describes”. That is, a claim recites a judicial exception when the judicial exception is “set forth” or “described” in the claim. In the instant case, the claims describe an abstract idea: the mathematical calculation of calculating fold-enrichment of the immunoprecipitation sample compared to the paired input sample.
Prong Two of the analysis under step 2A asks: does the claim recite additional elements that integrate the judicial exception into a practical application of the judicial exception? As discussed in MPEP 2106.04(II)(A)(2), “Because a judicial exception is not eligible subject matter, Bilski, 561 U.S. at 601, 95 USPQ2d at 1005-06 (quoting Chakrabarty, 447 U.S. at 309, 206 USPQ at 197 (1980)), if there are no additional claim elements besides the judicial exception, or if the additional claim elements merely recite another judicial exception, that is insufficient to integrate the judicial exception into a practical application. See, e.g., RecogniCorp, LLC v. Nintendo Co., 855 F.3d 1322, 1327, 122 USPQ2d 1377 (Fed. Cir. 2017) ("Adding one abstract idea (math) to another abstract idea (encoding and decoding) does not render the claim non-abstract"); Genetic Techs. v. Merial LLC, 818 F.3d 1369, 1376, 118 USPQ2d 1541, 1546 (Fed. Cir. 2016) (eligibility "cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself."). For a claim reciting a judicial exception to be eligible, the additional elements (if any) in the claim must "transform the nature of the claim" into a patent-eligible application of the judicial exception, Alice Corp., 573 U.S. at 217, 110 USPQ2d at 1981, either at Prong Two or in Step 2B.” The considerations to be used are set forth at MPEP 2106.05(a) through (c) and (e) through (h). Turning to those sections of the MPEP:
MPEP 2106.05(a) has to do with improvements to the functioning of a computer or to any other technology or technical field. The claims at issue do not improve the functioning of a computer or other technology. While the instant claims recite steps of crosslinking a ribosomal protein to an RNA in a biological sample via UV, the biological sample being a tissue sample or a fresh frozen tissue sample cryoground into a powder; fragmenting the RNA; performing immunoprecipitation with an anti-ribosomal protein antibody to generate a library of ribosome bound RNA fragments; depleting rRNA from the library; sequencing the library via high-throughput sequencing; mapping sequence reads and quantifying per-gene read counts in sample versus paired input; calculating fold-enrichment of the sample compared to paired input to determine ribosome association for target mRNA, thereby quantifying ribosome-associated RNA in the sample; lysing the sample and fragmenting with a nuclease; dephosphorylating 3’ and 5’ ends of ribosome bound RNA fragments and ligating an RNA adapter to the 3’ end; isolating a ribosome-bound RNA fragment and reverse transcribing cDNA; and ligating a DNA adapter to the 3’ end of the cDNA, amplifying, and sequencing the amplification products to identify isolated ribosome-bound RNA and determine translation rate, the claims do not improve upon crosslinking, fragmenting RNA, immunoprecipitation, sequencing, mapping reads, lysing, reverse transcription, or ligation of adapters. The claims merely use existing methods for these steps. Note that MPEP 2106.05(a) indicates that “[u]sing well-known standard laboratory techniques to detect enzyme levels in a bodily sample” is an example that the courts have indicated may not be sufficient to show an improvement to technology. That the above steps were known in the prior art will be shown below.
MPEP 2106.05(b) has to do with whether the claims involve the use of a particular machine. In this case, the claims do not involve the use of a particular machine. While instant claims recite steps of crosslinking a ribosomal protein to an RNA in a biological sample via UV, the biological sample being a tissue sample or a fresh frozen tissue sample cryoground into a powder; fragmenting the RNA; performing immunoprecipitation with an anti-ribosomal protein antibody to generate a library of ribosome bound RNA fragments; depleting rRNA from the library; sequencing the library via high-throughput sequencing; mapping sequence reads and quantifying per-gene read counts in sample versus paired input; calculating fold-enrichment of the sample compared to paired input to determine ribosome association for target mRNA, thereby quantifying ribosome-associated RNA in the sample; lysing the sample and fragmenting with a nuclease; dephosphorylating 3’ and 5’ ends of ribosome bound RNA fragments and ligating an RNA adapter to the 3’ end; isolating a ribosome-bound RNA fragment and reverse transcribing cDNA; and ligating a DNA adapter to the 3’ end of the cDNA, amplifying, and sequencing the amplification products to identify isolated ribosome-bound RNA and determine translation rate, no such machines are required by the claim, and certainly no particular machines. Even if some conventional machine were recited in the claims, such as a particular sequencing device, further considerations such as the particularity or generality of the recited machine must be taken into account, as well as whether the involvement of the machine is merely extra-solution activity. MPEP 2106.05(g) describes “extra-solution activity”, noting that “[d]etermining the level of a biomarker in blood” is an example of “mere data gathering” which the courts have found to be insignificant extra-solution activity.
MPEP 2106.05(c) has to do with whether the claims involve a particular transformation. Here, none of the limitations of the claims involve a particular transformation. For example, sequencing does not transform the nucleic acid of interest into something else during the sequencing process.
MPEP 2106.05(e) has to do with “other meaningful limitations”. The additional limitations imposed upon the mathematical calculation of calculating fold-enrichment of the immunoprecipitation sample compared to the paired input sample in the instant case have to do with crosslinking a ribosomal protein to an RNA in a biological sample via UV, the biological sample being a tissue sample or a fresh frozen tissue sample cryoground into a powder; fragmenting the RNA; performing immunoprecipitation with an anti-ribosomal protein antibody to generate a library of ribosome bound RNA fragments; depleting rRNA from the library; sequencing the library via high-throughput sequencing; mapping sequence reads and quantifying per-gene read counts in sample versus paired input; lysing the sample and fragmenting with a nuclease; dephosphorylating 3’ and 5’ ends of ribosome bound RNA fragments and ligating an RNA adapter to the 3’ end; isolating a ribosome-bound RNA fragment and reverse transcribing cDNA; and ligating a DNA adapter to the 3’ end of the cDNA, amplifying, and sequencing the amplification products to identify isolated ribosome-bound RNA and determine translation rate. These limitations are not considered “meaningful limitations”. MPEP 2106.05(e) states: “The phrase "meaningful limitations" has been used by the courts even before Alice and Mayo in various contexts to describe additional elements that provide an inventive concept to the claim as a whole.” In addition, as has been discussed, they represent insignificant extra-solution activity, i.e. “data gathering”.
MPEP 2106.05(f) raises the question as to whether the additional elements recited in the claim represent “mere instructions to apply an exception”. Here, the judicial exception is the mathematical calculation of calculating fold-enrichment of the immunoprecipitation sample compared to the paired input sample. The additional elements recited in the claims (i.e. crosslinking a ribosomal protein to an RNA in a biological sample via UV, the biological sample being a tissue sample or a fresh frozen tissue sample cryoground into a powder; fragmenting the RNA; performing immunoprecipitation with an anti-ribosomal protein antibody to generate a library of ribosome bound RNA fragments; depleting rRNA from the library; sequencing the library via high-throughput sequencing; mapping sequence reads and quantifying per-gene read counts in sample versus paired input; lysing the sample and fragmenting with a nuclease; dephosphorylating 3’ and 5’ ends of ribosome bound RNA fragments and ligating an RNA adapter to the 3’ end; isolating a ribosome-bound RNA fragment and reverse transcribing cDNA; and ligating a DNA adapter to the 3’ end of the cDNA, amplifying, and sequencing the amplification products to identify isolated ribosome-bound RNA and determine translation rate) does amount to mere instructions to apply the judicial exception, since the crosslinking, fragmenting, immunoprecipitation, sequencing mapping reads, lysing, introducing adapters via ligation, and using particular samples serve as mere conventional steps taken for the purpose of gathering data to calculate the fold-enrichment of immunoprecipitation, which any practical use of the mathematical calculation would require.
MPEP 2106.05(g) has to do with whether the additional elements of the claim amount to insignificant extra-solution activity. MPEP 2106.05(g) notes that “[d]etermining the level of a biomarker in blood” is an example of “mere data gathering” which the courts have found to be insignificant extra - solution activity. Likewise, MPEP 2106.05(g) notes that “[p]erforming clinical tests on individuals to obtain input for an equation” also represents insignificant extra-solution activity. This aligns closely with the instant claims, where the additional elements of the claims amount to collecting data from a biological sample via crosslinking, fragmenting, immunoprecipitation, sequencing, mapping reads, lysing, and ligating adapters.
MPEP 2106.05(h) has to do with whether the additional elements amount to more than generally linking the use of a judicial exception to a particular technological environment or field of use. Here, the recitation of the methods being used to quantify ribosome-associated RNAs in a biological sample is considered a “field of use”. However, as MPEP 2106.05(h) indications, such limiting to a particular “field of use” does not confer patentability on otherwise ineligible subject matter.
In addition, the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception (as set forth in step 2B of the subject matter eligibility test; see MPEP 2106-III) because it was routine and conventional in the prior art to quantify RNAs bound to proteins of interest, where those proteins may be ribosomes; immunoprecipitate ribosomes with specific antibodies; deplete rRNA before sequencing; and use the particular types of samples as claimed.
For example, Van Nostrand (Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP), Nature Methods, March 2016, 13, 508-514 plus Online Methods; cited on the IDS filed October 20th, 2022; previously cited) teaches a method of quantifying RNA binding protein-associated RNAs in a biological sample, the method comprising: (a) crosslinking an RNA binding protein to an RNA in a biological sample (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); (b) fragmenting the RNA (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); (c) performing immunoprecipitation on the biological sample with an anti-RNA binding protein specific antibody to generate a library of ribosome-bound RNA fragments (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); (e) sequencing the library to produce a plurality of sequence reads (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); (f) mapping the plurality of sequence reads and quantifying per-gene read counts in the immunoprecipitation sample versus a paired input sample (Online Methods, Page 1 column 2 to Page 2, column 1, Normalization of eCLIP signal against SMInput); and (g) calculating fold-enrichment of the immunoprecipitation sample compared to the paired input sample to determine RNA binding protein association for at least one target mRNA, thereby quantifying RNA binding protein-associated RNAs in the biological sample (Online Methods, Page 1 column 2 to Page 2, column 1, Normalization of eCLIP signal against SMInput). Van Nostrand further teaches wherein the crosslinking comprises UV crosslinking (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation). Van Nostrand further teaches wherein the method further comprises lysing the biological sample, thereby producing a lysate comprising a plurality of RNA fragments, wherein the fragmenting of the RNA comprises using a nuclease (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation). Van Nostrand further teaches the method further comprising dephosphorylating a 3' and a 5' end of an RNA binding protein-bound RNA fragment and ligating an RNA adapter to the 3' end of the RNA binding protein-bound RNA fragment (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation). Van Nostrand further teaches the method further comprising isolating a RNA binding protein-bound RNA fragment and producing a cDNA fragment by reverse transcription (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation). Van Nostrand further teaches the method further comprising ligating a DNA adapter to a 3' end of the cDNA fragment (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); amplifying the cDNA fragment to generate one or more amplification products (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); and sequencing the one or more amplification products to identify the isolated RNA binding protein-bound RNA fragment and determine the translation rate of the RNA in the biological sample (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation; see 112(b) interpretation). Van Nostrand further teaches wherein the sequencing comprises high-throughput sequencing (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation).
Culver (Meanderings of the mRNA through the Ribosome, Structure, September 2001, 9, 751-758; previously cited) teaches that ribosomal proteins can bind to RNA, necessarily indicating that they are RNA binding proteins (whole document, but noted at Page 751, Summary and Page 756, column 1, paragraph 4 for specific examples).
Friedman (US 20150141274 A1) teaches on isolating mRNA from cell populations via contacting cell lysate with a reagent and allowing the reagent to bind to a ribosome protein (Page 1, paragraph [0003]). This reagent may be an antibody against ribosomal protein S6 (Page 1, paragraph [0005]; Page 1, paragraph [0008]). Friedman also teaches that the isolating can be accomplished by affinity methods, including immunoprecipitation (Page 13, paragraph [0073]).
Derisi (US 20180051320 A1; previously cited) teaches on depleting rRNA-containing sequencing library products before sequencing by a method called DASH (Page 7, paragraph [0065]), which uses Cas9 proteins combined with gRNAs to cleave unwanted species before sequencing (Page 1, paragraph [0006]).
Darnell (US 20140378316 A1; previously cited) teaches on a CLIP method wherein the biological sample is a tissue sample (Page 1536, column 2, paragraph 3).
Ingolia (The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments, Nature Protocols, July 2012, 7, 1534-1550; previously cited) teaches wherein the biological sample for a similar technique regarding ribosome footprinting can be a fresh, frozen tissue sample that is cryoground into powder (Page 1536, column 2, paragraph 3).
Therefore, the additional elements beyond the mathematical calculation do not represent an inventive concept because quantifying RNAs bound to proteins of interest, where those proteins may be ribosomes; immunoprecipitating ribosomes with specific antibodies; depleting rRNA before sequencing; and using the particular types of samples as claimed was routine, well-known, and conventional
Having considered the factors discussed in MPEP 2106.05 (a)-(c) and (e)-(h), as well as the prior art of Van Nostrand, Culver, Friedman, Derisi, Darnell, and Ingolia, it is clear that the additional elements recited in the claims, whether considered individually or as a combination, do not integrate the judicial exception into a practical application of that exception in such a way as to provide meaningful limits on the use of the judicial exception. Therefore, claims 1-3, 8-11, 24, and 26 are rejected under 35 U.S.C. 101.
Claim Rejections - 35 USC § 103 - Modified - Necessitated by Amendment
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.
Claims 1-3 and 8-11 are rejected under 35 U.S.C. 103 as being unpatentable over Van Nostrand (Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP), Nature Methods, March 2016, 13, 508-514 plus Online Methods; cited on the IDS filed October 20th, 2022; previously cited), in view of Culver (Meanderings of the mRNA through the Ribosome, Structure, September 2001, 9, 751-758; previously cited), Friedman (US 20150141274 A1), and Derisi (US 20180051320 A1; previously cited).
Regarding instant claim 1, Van Nostrand teaches a method of quantifying RNA binding protein-associated RNAs in a biological sample, the method comprising: (a) crosslinking an RNA binding protein to an RNA in a biological sample (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); (b) fragmenting the RNA (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); (c) performing immunoprecipitation on the biological sample with an anti-RNA binding protein specific antibody to generate a library of ribosome-bound RNA fragments (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); (e) sequencing the library to produce a plurality of sequence reads (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); (f) mapping the plurality of sequence reads and quantifying per-gene read counts in the immunoprecipitation sample versus a paired input sample (Online Methods, Page 1 column 2 to Page 2, column 1, Normalization of eCLIP signal against SMInput); and (g) calculating fold-enrichment of the immunoprecipitation sample compared to the paired input sample to determine RNA binding protein association for at least one target mRNA, thereby quantifying RNA binding protein-associated RNAs in the biological sample (Online Methods, Page 1 column 2 to Page 2, column 1, Normalization of eCLIP signal against SMInput).
Van Nostrand does not teach on the RNA binding protein being a ribosome.
Culver, in a reasonably pertinent field, teaches that ribosomal proteins can bind to RNA, necessarily indicating that they are RNA binding proteins (whole document, but noted at Page 751, Summary and Page 756, column 1, paragraph 4 for specific examples).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the RNA binding protein of Van Nostrand with ribosomal proteins from Culver. Since Culver teaches on RNA binding with ribosomal proteins as it relates to the ribosome, which is reasonably pertinent to the RBPs of Van Nostrand, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because it is known that ribosomal proteins bind to mRNA (Culver, whole document, but noted at Page 751, Summary and Page 756, column 1, paragraph 4 for specific examples). This would amount to simple substitution of one element for another to obtain predictable results (see MPEP 2141(III)).
Neither of these references teach on immunoprecipitating with an anti-ribosomal protein specific antibody.
Friedman, in a reasonably pertinent field, teaches on isolating mRNA from cell populations via contacting cell lysate with a reagent and allowing the reagent to bind to a ribosome protein (Page 1, paragraph [0003]). This reagent may be an antibody against ribosomal protein S6 (Page 1, paragraph [0005]; Page 1, paragraph [0008]). Friedman also teaches that the isolating can be accomplished by affinity methods, including immunoprecipitation (Page 13, paragraph [0073]).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Van Nostrand with the antibody of Friedman. Since Friedman teaches on immunoprecipitating RNA using an anti-ribosomal specific antibody, which is reasonably pertinent to the method of Van Nostrand, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because it amounts to simple substitution of one known element for another to obtain predictable results (see MPEP 2141(III)). Van Nostrand teaches on using antibodies against RNA binding proteins, which can easily be substituted with the antibody against ribosomal proteins of Friedman.
None of these references teaches on depleting ribosomal RNA from the library.
Derisi, in a reasonably pertinent field, teaches on depleting rRNA-containing sequencing library products before sequencing by a method called DASH (Page 7, paragraph [0065]), which uses Cas9 proteins combined with gRNAs to cleave unwanted species before sequencing (Page 1, paragraph [0006]).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Van Nostrand, in view of Culver, with the rRNA depletion step of Derisi. Since Derisi teaches on manipulation of sequencing libraries, which is reasonably pertinent to the sequencing libraries of Van Nostrand, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because DASH cleaves unwanted species, preventing them from consuming sequencing space (Derisi, Page 1, paragraph [0006]). Furthermore, applying DASH after library generation means the depletion can be performed on any library without regard to starting RNA amount (Page 14, paragraph [0120]).
Regarding instant claim 2, Van Nostrand, in view of Culver, Friedman, and Derisi, teaches the method of claim 1. Van Nostrand further teaches wherein the crosslinking comprises UV crosslinking (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation).
Regarding instant claim 3, Van Nostrand, in view of in view of Culver, Friedman, and Derisi, teaches the method of claim 1. Van Nostrand further teaches wherein the method further comprises lysing the biological sample, thereby producing a lysate comprising a plurality of RNA fragments, wherein the fragmenting of the RNA comprises using a nuclease (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation).
Regarding instant claim 8, Van Nostrand, in view of Culver, Friedman, and Derisi, teaches the method of claim 1. Van Nostrand further teaches the method further comprising dephosphorylating a 3' and a 5' end of an RNA binding protein-bound RNA fragment and ligating an RNA adapter to the 3' end of the RNA binding protein-bound RNA fragment (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation). As made obvious in the analysis of claim 1, Culver, teaches that ribosomal proteins can bind to RNA, necessarily indicating that they are RNA binding proteins (whole document, but noted at Page 751, Summary and Page 756, column 1, paragraph 4 for specific examples).
Regarding instant claim 9, Van Nostrand, in view of Culver, Friedman, and Derisi, teaches the method of claim 1. Van Nostrand further teaches the method further comprising isolating a RNA binding protein-bound RNA fragment and producing a cDNA fragment by reverse transcription (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation). As made obvious in the analysis of claim 1, Culver, teaches that ribosomal proteins can bind to RNA, necessarily indicating that they are RNA binding proteins (whole document, but noted at Page 751, Summary and Page 756, column 1, paragraph 4 for specific examples).
Regarding instant claim 10, Van Nostrand, in view of Culver, Friedman, and Derisi, teaches the method of claim 9. Van Nostrand further teaches the method further comprising ligating a DNA adapter to a 3' end of the cDNA fragment (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); amplifying the cDNA fragment to generate one or more amplification products (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); and sequencing the one or more amplification products to identify the isolated RNA binding protein-bound RNA fragment and determine the translation rate of the RNA in the biological sample (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation; see 112(b) interpretation). As made obvious in the analysis of claim 1, Culver, teaches that ribosomal proteins can bind to RNA, necessarily indicating that they are RNA binding proteins (whole document, but noted at Page 751, Summary and Page 756, column 1, paragraph 4 for specific examples).
Regarding instant claim 11, Van Nostrand, in view of Culver, Friedman, and Derisi, teaches the method of claim 1. Van Nostrand further teaches wherein the sequencing comprises high-throughput sequencing (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation).
Claims 14, 17, and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Van Nostrand (Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP), Nature Methods, March 2016, 13, 508-514 plus Online Methods; cited on the IDS filed October 20th, 2022; previously cited), in view of Culver (Meanderings of the mRNA through the Ribosome, Structure, September 2001, 9, 751-758; previously cited) and Friedman (US 20150141274 A1).
Regarding instant claim 14, Van Nostrand teaches a method of generating a library of RNA binding protein-bound RNA fragments from a biological sample, the method comprising: (a) crosslinking an RNA binding protein to an RNA in the biological sample (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); (b) fragmenting the RNA (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); and (c) performing immunoprecipitation on the biological sample with an anti-RNA binding protein specific antibody (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); (d) isolating an RNA binding protein-bound RNA fragment and producing a cDNA fragment by reverse transcription (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); and (e) performing PCR amplification to generate one or more amplification products, thereby generating a library of RNA binding protein-bound RNA fragments (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation).
Van Nostrand does not teach on the RNA binding protein being a ribosome.
Culver, in a reasonably pertinent field, teaches that ribosomal proteins can bind to RNA, necessarily indicating that they are RNA binding proteins (whole document, but noted at Page 751, Summary and Page 756, column 1, paragraph 4 for specific examples).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the RNA binding protein of Van Nostrand with ribosomal proteins from Culver. Since Culver teaches on RNA binding with ribosomal proteins as it relates to the ribosome, which is reasonably pertinent to the RBPs of Van Nostrand, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because it is known that ribosomal proteins bind to mRNA (Culver, whole document, but noted at Page 751, Summary and Page 756, column 1, paragraph 4 for specific examples). This would amount to simple substitution of one element for another to obtain predictable results (see MPEP 2141(III)).
Neither of these references teach on immunoprecipitating with an anti-ribosomal protein specific antibody.
Friedman, in a reasonably pertinent field, teaches on isolating mRNA from cell populations via contacting cell lysate with a reagent and allowing the reagent to bind to a ribosome protein (Page 1, paragraph [0003]). This reagent may be an antibody against ribosomal protein S6 (Page 1, paragraph [0005]; Page 1, paragraph [0008]). Friedman also teaches that the isolating can be accomplished by affinity methods, including immunoprecipitation (Page 13, paragraph [0073]).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Van Nostrand with the antibody of Friedman. Since Friedman teaches on immunoprecipitating RNA using an anti-ribosomal specific antibody, which is reasonably pertinent to the method of Van Nostrand, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because it amounts to simple substitution of one known element for another to obtain predictable results (see MPEP 2141(III)). Van Nostrand teaches on using antibodies against RNA binding proteins, which can easily be substituted with the antibody against ribosomal proteins of Friedman.
Regarding instant claim 17, Van Nostrand, in view of Culver and Friedman, teaches the method of claim 14. Van Nostrand further teaches the method further comprising dephosphorylating a 3' and a 5' end of the RNA binding protein-bound RNA fragment and ligating an RNA adapter to the 3' end of the RNA binding protein-bound RNA fragment (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation). As made obvious in the analysis of claim 14, Culver, teaches that ribosomal proteins can bind to RNA, necessarily indicating that they are RNA binding proteins (whole document, but noted at Page 751, Summary and Page 756, column 1, paragraph 4 for specific examples).
Regarding instant claim 19, Van Nostrand, in view of Culver and Friedman, teaches the method of claim 14. Van Nostrand further teaches the method further comprising ligating a DNA adapter to a 3' end of the cDNA fragment (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation); and sequencing the one or more amplification products (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation).
Claims 20 is rejected under 35 U.S.C. 103 as being unpatentable over Van Nostrand (Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP), Nature Methods, March 2016, 13, 508-514 plus Online Methods; cited on the IDS filed October 20th, 2022; previously cited), Culver (Meanderings of the mRNA through the Ribosome, Structure, September 2001, 9, 751-758; previously cited) and Friedman (US 20150141274 A1), as applied to claims 14, 17, and 19, and further in view of Derisi (US 20180051320 A1; previously cited).
Regarding instant claim 20, Van Nostrand, in view of Culver and Friedman, teaches the method of claim 19. Van Nostrand further teaches wherein the sequencing comprises high-throughput sequencing (Figure 1A; Online Methods, Page 1, column 1, eCLIP-seq library preparation).
Neither reference teaches the method further comprising depleting rRNA-containing amplification products before sequencing the one or more amplification products.
Derisi, in a reasonably pertinent field, teaches on depleting rRNA-containing sequencing library products before sequencing by a method called DASH (Page 7, paragraph [0065]), which uses Cas9 proteins combined with gRNAs to cleave unwanted species before sequencing (Page 1, paragraph [0006]).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the method of Van Nostrand, in view of Culver, with the rRNA depletion step of Derisi. Since Derisi teaches on manipulation of sequencing libraries, which is reasonably pertinent to the sequencing libraries of Van Nostrand, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because DASH cleaves unwanted species, preventing them from consuming sequencing space (Derisi, Page 1, paragraph [0006]). Furthermore, applying DASH after library generation means the depletion can be performed on any library without regard to starting RNA amount (Page 14, paragraph [0120]).
Claim 24 is rejected under 35 U.S.C. 103 as being unpatentable over Van Nostrand (Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP), Nature Methods, March 2016, 13, 508-514 plus Online Methods; cited on the IDS filed October 20th, 2022; previously cited), in view of Culver (Meanderings of the mRNA through the Ribosome, Structure, September 2001, 9, 751-758; previously cited), Friedman (US 20150141274 A1), and Derisi (US 20180051320 A1; previously cited), as applied to claims 1-3, 6, 8-10, 14-15, and 17-19 above, and further in view of Darnell (US 20140378316 A1; previously cited).
Regarding instant claim 24, Van Nostrand, in view of Culver, Friedman, and Derisi, teaches the method of claim 1.
Neither reference teaches wherein the biological sample is a tissue sample.
Darnell, in the same field of endeavor, teaches on a CLIP method wherein the biological sample is a tissue sample (Page 1536, column 2, paragraph 3).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the biological sample of Van Nostrand with the tissue sample of Darnell. Since Van Nostrand and Darnell are in the same field of endeavor (e.g. CLIP techniques for RNA-protein interaction), one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because it amounts to simple substitution of one known element for another to obtain predictable results (see MPEP 2141(III)).
Claim 26 is rejected under 35 U.S.C. 103 as being unpatentable over Van Nostrand (Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP), Nature Methods, March 2016, 13, 508-514 plus Online Methods; cited on the IDS filed October 20th, 2022; previously cited), Culver (Meanderings of the mRNA through the Ribosome, Structure, September 2001, 9, 751-758; previously cited), Friedman (US 20150141274 A1), and Derisi (US 20180051320 A1; previously cited), as applied to claims 1-3, 6, 8-10, 14-15, and 17-19 above, and further in view of Ingolia (The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments, Nature Protocols, July 2012, 7, 1534-1550; previously cited).
Regarding instant claim 26, Van Nostrand, in view of Culver, Friedman, and Derisi, teaches the method of claim 1.
Neither reference teaches wherein the biological sample is a fresh, frozen tissue sample that is cryoground into powder.
Ingolia, in a reasonably pertinent field, teaches wherein the biological sample for a similar technique regarding ribosome footprinting can be a fresh, frozen tissue sample that is cryoground into powder (Page 1536, column 2, paragraph 3).
It would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the biological sample of Van Nostrand with the tissue sample of Ingolia. Since Ingolia teaches on downstream applications regarding ribosome associated mRNAs, which is reasonably pertinent to the method of Van Nostrand, in view of Culver, where ribosomal proteins are binding to RNA, one of ordinary skill in the art would combine the two teachings with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to make this modification because cryogenic pulverization of frozen tissue produces effective lysis and homogenization under conditions that block biological responses (Ingolia, Page 1536, column 2, paragraph 3).
Response to Arguments
Applicant's arguments filed April 30th, 2026 have been fully considered but they are not persuasive.
The Applicant first summarizes the Examiner’s previous references and claim rejections (Page 10 of the Remarks filed April 30th, 2026). The Applicant states that they disagree with these rejections, but without conceding the basis of the rejections, claims 1 and 14 have been amended (Page 10 of the Remarks filed April 30th, 2026). The Applicant argues that Van Nostrand does not teach the amended claim 1, particularly newly amended steps (c) and (d), directed to immunoprecipitation and depleting ribosomal RNA respectively (Page 11 of the Remarks filed April 30th, 2026). The Applicant further argues that Culver, Derisi, Darnell, and Ingolia also do not teach newly amended steps (c) and (d), directed to immunoprecipitation and depleting ribosomal RNA respectively (Pages11-12 of the Remarks filed April 30th, 2026). The Applicant argues that for these reasons, the cited references alone or in combination fail to describe or otherwise render obvious all of the features of the amended claims 1 and 14 (Page 12 of the Remarks filed April 30th, 2026).
In response to these arguments, it is noted that as currently presented in the above rejection, it is found that the cited references in combination teach all recited limitations of amended claims 1 and 14 (see modified 103 rejections above). Therefore, the arguments presented by the Applicant are not found persuasive.
Conclusion
All claims stand rejected.
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.
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/ALLISON E SCHLOOP/Examiner, Art Unit 1683
/Robert T. Crow/Primary Examiner, Art Unit 1683
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