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 .
The examiner of your application in the PTO has changed. To aid in correlating any papers for this application, all further correspondence regarding this application should be directed to Brian Whiteman, Art Unit 1636.
Election/Restrictions
Claims 8-15 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12/5/24.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Priority
It is noted that Example 1b in the instant application was not described in provisional 62/930,367 filed on 11/4/16, but at this time no pending claims appear to be directed to example 1b set forth in PCT/US20/058958 11/4/20.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The use of the term MAXQUANT, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term. Please review the entire specification for any other trademarks or names.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claims 1-3, 7, 18 and 20 are objected to because of the following informalities: the insertion of the new limitation “the value of a normalized proteome codon count divided by the tRNA profile value for a particular tRNA is in the top 5% of values for normalized proteome codon count divided by the tRNA profile value for all codons measured” does not appear to have a nexus between the con-rare codon and the value of a normalized proteome codon. Claim 3 lists one or more following factors for the value and it is not apparent how the new limitation is connected to the value, which is a function of the more or more following factors (1)-(5).
Appropriate correction is required.
Response to Arguments
Applicant’s arguments, see pages 5-7, filed 10/16/25, with respect to the rejection(s) of claims 1-3, 7, and 17-22 under 112a, b, and d have been fully considered and are persuasive. Therefore, the rejections have been withdrawn because of the amendments to claims 1-3. However, upon further consideration, a new ground(s) of rejection is made in view of the amendment to claims 1-3 and reviewing the instant claims under the 101 guidelines set forth in MPEP 2106.
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 1-3. 7, 18 and 20 are rejected under 35 U.S.C. 101 because the claimed invention is directed to using an abstract idea (a mental process and/or with a mathematical calculation) without significantly more. The claimed invention is directed to a process comprising steps, which is one of the four statutory categories. There is no nexus between the target cell or tissue in the pre-amble of the instant claims and the method steps. In addition, there appears to be no nexus between the rare codon and a value of a normalized proteome codon count divided by the tRNA profile value for a particular tRNA is the top 5% of values.
Claims 1 and 7: The claimed method embraces a) acquiring the identity of or replacing a contextually rare codon ("con-rare codon") for the nucleic acid sequence in the target cell or tissue, wherein for the con-rare codon, the value of a normalized proteome codon count divided by the tRNA profile value for a particular tRNA is in the top 5% of values for normalized proteome codon count divided by the tRNA profile value for all codons measured; b)(i) replacing a con-rare codon in the nucleic acid sequence with a contextually abundant ("con-abundant") codon for the nucleic acid sequence, wherein the con-abundant codon comprises the most contextually frequent codon that encodes the same amino acid as the con-rare codon; and/or (ii) replacing a con-abundant codon in the nucleic acid sequence with a con-rare codon for the nucleic acid sequence. thereby providing a modified nucleic acid sequence which is contextually modified ("con-modified").
The specification discloses ‘proteome codon count’ refers to the sum (for all of the proteins of a set of reference proteins in a target cell (or tissue)) of the number of times the codon is used in a protein of the reference set multiplied by the value of that protein's abundance.
Example 1 of the specification provides examples of how to determine tRNA profile value, but the specification does not appear to provide a definition for the term. The broadest reasonable interpretation of the term embraces the amount of a tRNA in a cell or tissue.
This judicial exception is not integrated into a practical application because in view of the broadest reasonable interpretation (BRI) of the claimed invention and the description in the specification (pages 58-60 and examples 1-7); steps a) and b)i) and/or ii) encompass a mental process of evaluating nucleic acid sequences performing mathematical calculations and/or a mental step of replacing a con-rare codon or con-abundant codon in the nucleic acid sequence with another codon. See MPEP 2106.04(a)(2)III states: "The courts consider a mental process (thinking) that 'can be performed in the human mind, or by a human using a pen and paper' to be an abstract idea." Acquiring a value can be done mentally by observing experimental outputs visually and therefor reads on an abstract idea. Furthermore, step a) is directed to a data gathering step based on a value of a normalized proteome codon count divided by tRNA profile value for a particular tRNA and step b) is a mental step (or using the data to carry out the method step which would be directed to an insignificant extra-solution activity (See MPEP 2106.05(g)).
The ‘wherein’ clause directed to the value of a normalized proteome codon count divided by the tRNA profile value for a particular tRNA is in the top 5% of values normalized proteome codon count divided by the tRNA profile value for all codons measured encompasses a mental process of calculating con-rare codon. The BRI of carrying out step 2)i) and/or ii), as claimed, encompasses writing out sequences with pen and paper.
The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because other than the mental steps or using a generic computer with a mental step the claimed method does not recite any active method steps for modifying the cell. There are no additional steps to impose any meaningful limitation on practicing the abstract idea.
Dependent claim 7 is directed to a ‘wherein’ clause for the target cell in the pre-amble of claim 1 and does not add any patentable weight to the claimed method because the method steps do not require expression the modified sequence in a cell or tissue.
Claims 2 and 18: The claimed invention embraces a) replacing a contextually con-rare codon with a different codon, wherein for the con-rare codon, the value of a normalized proteome codon count divided by the tRNA profile value for a particular tRNA is in the top 5% of values for normalized proteome codon count divided by the tRNA profile value for all codons measured; and/or b) replacing a con-abundant codon with a different codon, wherein the con-abundant codon comprises the most contextually frequent codon that encodes the same amino acid as the con-rare codon, thereby providing a modified nucleic acid sequence which is con-modified.
This judicial exception is not integrated into a practical application because in view of the BRI and specification (pages 56-60 and examples 1-7), the claimed method encompass a mental process or data gathering step of evaluating sequences for similarity, performing mathematical calculations and a mental step of replacing a con-rare codon or con-abundant codon in the nucleic acid sequence with another codon. Page 56 indicates that proteome codon count is a mathematical equation. Merely reciting that a mental process or mathematical calculations are being performed does not preclude the steps from being an abstract idea. See also MPEP 2106.04(a)(2)III.
Furthermore, step a) is directed to a data gathering step based on a value of a normalized proteome codon count divided by tRNA profile value for a particular tRNA and step b) is a mental step or using the data to carry out the method step a) (or using the data to carry out the method step which would be directed to an insignificant extra-solution activity (See MPEP 2106.05(g)).
One of skill in the art carrying out the method steps under BRI, as claimed, encompasses writing out sequences with pen and paper and/or using a computer to collect the data.
The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because other than the mental steps or using a generic computer with a mental step the claimed method does not recite any active method steps for modifying the cell. There are no additional steps to impose any meaningful limitation on practicing the abstract idea.
Dependent claim 18 is directed to a ‘wherein’ clause for the target cell in the pre-amble of claim 2 and does not add any patentable weight to the claimed method because the method steps do not require expression the modified sequence in a cell or tissue.
Claims 3 and 20: The claimed invention embraces (a) acquiring a value for a con-rare codon, wherein for the con-rare codon, the value of a normalized proteome codon count divided by the tRNA profile value for a particular tRNA is in the top 5% of values for normalized proteome codon count divided by the tRNA profile value for all codons measured, wherein the value is a function of one or more of the following factors: (1) the sequence of the codon; (2) the availability of a corresponding tRNA for that con-rare codon in a target cell or tissue; (3) the expression profile (or proteomic properties) of the target cell or; (4) the proportion of the tRNAs corresponding to the con-rare codon which are charged; and (5) the iso-decoder isotype of the tRNA corresponding to the con-rare codon, (b) replacing the con-rare codon with a different codon.
This judicial exception is not integrated into a practical application because in view of the BRI and specification (pages 58-60 and examples 1-7) step a) encompasses a mental process of evaluating sequences for similarity, performing mathematical calculations and a mental step of replacing a con-rare codon or con-abundant codon in the nucleic acid sequence with another codon. See MPEP 2106.04(a)(2)III.
Furthermore, step a) is directed to a data gathering step based on a value of a normalized proteome codon count divided by tRNA profile value for a particular tRNA and step b) is a mental step or using the data to carry out the method step (or using the data to carry out the method step which would be directed to an insignificant extra-solution activity (See MPEP 2106.05(g)).
The ‘wherein’ clause directed to the value of a normalized proteome codon count divided by the tRNA profile value for a particular tRNA is in the top 5% of values normalized proteome codon count divided by the tRNA profile value for all codons measured encompasses a mental process of calculating con-rare codon. The meaning of carrying out step a) under BRI, as claimed, encompasses writing out sequences with pen and paper.
The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because other than the mental steps or using a generic computer with a mental step the claimed method does not recite any active method steps for modifying the cell. There are no additional steps to impose any meaningful limitation on practicing the abstract idea.
Dependent claim 20 is directed to a ‘wherein’ clause for the target cell in the pre-amble of claim 3 and does not add any patentable weight to the claimed method because the method steps do not require expression the modified sequence in a cell or tissue.
Claim Rejections - 35 USC § 112
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.
Claims 2, 3, 18 and 20 are 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(s) 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.
New Matter:
Claims 3 and 20:
The limitation '(a) acquiring a value for a con-rare codon, wherein for the con-rare codon, the value of a normalized proteome codon count divided by the tRNA profile value for a particular tRNA is in the top 5% of values for normalized proteome codon count divided by the tRNA profile value for all codons measured, wherein the value is a function of one or more of the following factors: (1) the sequence of the codon; (2) the availability of a corresponding tRNA for that con-rare codon in a target cell or tissue; (3) the expression profile (or proteomic properties) of the target cell or; (4) the proportion of the tRNAs corresponding to the con-rare codon which are charged; and (5) the iso-decoder isotype of the tRNA corresponding to the con-rare codon, (b) replacing the con-rare codon with a different codon' in amended claim 3 and 20 is not supported by the as-filed specification. Applicant has not pointed out where the amended claim is supported, nor does there appear to be a written description of the claim limitation in the application as filed. See MPEP § 2163.06. Claim 3 embraces acquiring the value for a contextually con rare codon wherein the value is based on proteome codon count divided by the tRNA profile value for a particular tRNA and wherein the value is a function of one or more following factors (1)-(5); and it is not apparent how the new limitation is connected to when the value is a function of the more or more following factors (1)-(5). The specification contemplates either or but does not disclose method using both values to acquire the con-rare codon.
Thus, claims 3 and 20 do not appear to have written support.
Written Description:
The claimed method in claims 2 and 18 embraces replacing a con-rare codon with a different codon and/or replacing a con-abundant codon with a different codon, wherein the con-abundant codon comprises the most contextually frequence codon that encodes the same amino acid as the con-rare codon. Pages 46-48 of the specification provide definitions for the terms con-rare codon and con-abundant codon.
The method reads on a very large genus of nucleic acid sequences from any tissue or cell from a genus of organisms (animals, humans, prokaryotes, plants).
The pre-amble of the claim “modifying a nucleic acid sequence for a target cell or a tissue” is not required because the method steps to complete the pre-amble are not recited in the method steps.
The limitation ‘wherein for the con-rare codon, the value of a normalized proteome codon count divided by the tRNA profile value for a particular tRNA is in the top 5% of values for normalized proteome codon count divided by the tRNA profile value for all codons measured’ does not provide written description for the limitation ‘wherein the con-abundant codon comprises the most contextually frequent codon that encodes the same amino acid as the con-rare codon.’ It is not apparent how this limitation is connected to the con-rare codon. To expedite prosecution of the instant claims, the Office will consider the limitation to be the calculation used to obtain a con-rare codon. The specification contemplates this limitation, but does not provide any con-rare codons meeting this limitation. The contemplation and working examples in the as-filed specification do not appear to describe any con-rare codons meeting this limitation. The applicant discovered that the codon identity and function is highly contextual and varied with an organism (page 6 of the specification).
The prior art does not appear to teach that this limitation was routine in the prior art. Torres et al. (PNAS 2019, 116, 8451-8456) teach that there is a variation amongst species of tRNA in human nucleic acids sequences. The specification does not provide a representative sample of nucleic acid sequences to provide written description for the claimed genus of sequences.
While the specification describes an assay for acquiring a con-rare codon using a mathematical calculation process involving a normalized proteome codon count divided by the tRNA profile value for a particular tRNA, the specification does not provide written support for the product embraced by the claimed method.
Furthermore, since the specification does not provide written support for the con-rare codon, the specification does not provide written description for the limitation ‘wherein the con-abundant codon comprises the most contextually frequence codon that encodes the same amino acid as the con-rare codon’ in instant claim 2.
Thus, instant claims 2 and 18 do not have written support because the skilled artisan cannot envision that the instant disclosure had possession of the a con-rare codon, wherein for the con-rare codon has a value of a normalized proteome codon count divided by the tRNA profile value for a particular tRNA is in the top 5% of values for normalized proteome codon count divided by the tRNA profile value for all codons measured and a con-abundant codon having the most contextually frequent codon that encodes the same amino acid as the con-rare codon.
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 1-3, 7, 18 and 20 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 1-3 recite the limitation "the value of a normalized proteome codon count divided by the tRNA profile value for a particular tRNA is in the top 5% of values normalized proteome codon count divided by the tRNA profile value for all codons measured encompasses a mental process of calculating con-rare codon" in line 3. There is insufficient antecedent basis for this limitation in the claim. The new limitation does not appear to have a nexus between the con-rare codon and the value of a normalized proteome codon.
Claim 2 recites the limitation "the con-rare codon" in line 9. There is insufficient antecedent basis for this limitation in the claim because of “the and/or” clause indicating if the “or” clause is read the limitation lacks antecedent basis.
Claim 3 recites the limitation "the sequence of the codon" in item (1) of step (a). There is insufficient antecedent basis for this limitation in the claim because is the limitation referring to the rare codon or all codons measured in the new limitation.
Claims 7, 18 and 20 are also rejected because they depend on claims 1-3.
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.
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 2 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Mauro et al. (Trends in Molecular Medicine 2014, Vol. 20, pages 604-613) taken with Mignon et al. (FEBS Letters, 592:1554-1564, 2018, of record).
In view of the “and/or” clause in instant claim 2, the only method step required is replacing an abundant codon with a different codon, wherein the con-abundant codon comprise the most contextually frequent codon that encodes the same amino acid as a rare codon.
Dependent claim 18 is directed to a ‘wherein’ clause for the target cell in the pre-amble of claim 2 and does not add any patentable weight to the claimed method because the method steps do not require expression the modified sequence in a cell or tissue.
Mauro provided a review of codon optimization for protein production, including replacing rare codons with frequently used ones for increased protein production.
Mauro does not specifically teach replacing a con-abundant that is the most contextually frequent codon that encodes the same amino acid as a con-rare codon with a different codon.
Mignon teach using Codon Adaptation Index (CAI) that analyzes the codon usage bias in organisms (pages 1554-64). The process involves differences in frequency of occurrence of synonymous codons in coding DNA sequence in a specific organism.
It would have been prima facie obvious to a person of ordinary skill in the art before the time of the effective filing date to combine the teaching of Mauro taken with Mignon to use CAI optimization to determine the most frequent and rare codon and replace the most frequent codon with a different codon in a sequence to study protein yield, namely to arrive at the claimed invention. See MPEP 2143(I)B.
Therefore the invention as a whole would have been prima facie obvious to one ordinary skill in the art before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains.
The prior art teaches that one of ordinary skill in the art can estimate differential expression of tRNA expression from tRNA-Seq databases by well-established statistical methods see page 8451 of Torres (supra).
In view of the prior art of record, one of ordinary skill in the art could determine a specific tRNA in a cell or tissue; determine proteome codon count in a cell or tissue; and determine if a rare codon was present in the cell or tissue. However, the prior art does not appear to teach or suggest a step of determining a rare codon in a cell or tissue comprising using a proteome codon count divided by the tRNA profile for a specific tRNA (known as PCC-tF on page 56) and the limitation ‘wherein for the con-rare codon, the value of a normalized proteome codon count divided by the tRNA profile value for a particular tRNA is in the top 5% of values for normalized proteome codon count divided by the tRNA profile value for all codons measured’ recited in the instant claims. Furthermore, the claims and the specification do not make readily apparent what the value calculated by the a normalized proteome codon divided by the tRNA profile value for a particular tRNA is in the top 5% of values for normalized proteome count divided by the tRNA profile value for all codons measured corresponds to acquiring a value for con-rare codon. In view of a search of the prior art, it does not appear that a con-rare codon exists, wherein the con-rare codon was identified by calculating the value by using normalized proteome codon divided by the tRNA profile value for a particular tRNA is in the top 5%.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claim 3 and 20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 51-55, 57, and 59-60 of copending Application No. 17928450 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because both set of claims embrace acquiring a value for a con-rare codon in the nucleic acid sequence, wherein the value is a function of one or more of the following factors: (1) the sequence of the codon; (2) the availability of a corresponding tRNA for that con-rare codon in a target cell or tissue; (3) the expression profile (or proteomic properties) of the target cell or tissue; (4) the proportion of the tRNAs corresponding to the con-rare codon which are charged; and (5) the iso-decoder isotype of the tRNA corresponding to the con-rare codon, wherein (1) comprises determining the presence or absence of a con-rare codon. The only different is the new limitation in claim 3 which is not recited in the claims of ‘411. However, when a person of ordinary skill in the art looks at the disclosure of the ‘411 to determine how to carry out the steps in claims 51-55, 57, 59-60 for acquiring a value for a con-rare codon, they would arrive at pages 37-38 which discloses this new limitation for evaluating con-rarity recited in instant claim 3. A person of ordinary skill in the art would use this method step recited on these pages to carry out the method step in claim 51 and arrive at the new limitation. Thus, the instant claims are considered an obvious variation of the claims of ‘411.
Dependent claim 20 is directed to a ‘wherein’ clause for the target cell in the pre-amble of claim 3 and does not add any patentable weight to the claimed method because the method steps do not require expression the modified sequence in a cell or tissue.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
See attached PTO-326 for disposition of claims.
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/BRIAN WHITEMAN/ Primary Examiner, Art Unit 1636
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