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 .
Claim Status
Claims were amended prior to examination in paper dated 12/15/2022.
Claims 3-10 and 13-20 were amended.
Claims 1-20 are being examined.
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.
Drawings
The drawings (e.g., Figs 7a-b) are objected to under 37 CFR 1.83(a) because they fail to show the flow diagram depicting an exemplary process for detecting and replacing a sequence which may cause an undesired variant in a gene construct nor flow diagram depicting an exemplary process for creating a gene therapy product used in cell therapy (e.g., spec paras 022-023, 0162, 0166) as described in the specification. Any structural detail that is essential for a proper understanding of the disclosed invention should be shown in the drawing. MPEP § 608.02(d). Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claims 5 and 7 are objected to because of the following informalities:
Claim 5: missing an article before “plurality of alternative sequences increase…”.
Claim 7: because the listed optional components of the claim are conditional phrases, rather than objects, the lack of punctuation at the beginning of the list leads to a lack of clarity in the sentence. Appropriate correction is required.
Claim Rejections - 35 USC § 112 - indefiniteness
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 2, 4, 5, 12 and 15 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 2 recites the limitation "the gap-aware alignment" in claim 1. There is insufficient antecedent basis for this limitation in the claim.
Claim 4 is unclear over the recitation “calculating a matrix”. It is unclear what is being calculated, as the matrix contains nucleotides but no specific values are otherwise described.
Claim 5 recites the limitation "the matrix" in claim 1. There is insufficient antecedent basis for this limitation in the claim.
Claim 5 is unclear over the recitation “increases a sum over the matrix”. It is unclear what value the sequences have that would increase and over what sum they are increasing.
Claim 12 recites the limitation "the gap-aware alignment" in claim 11. There is insufficient antecedent basis for this limitation in the claim.
Claim 15 recites the limitation "the matrix" in claim 11. There is insufficient antecedent basis for this limitation in the claim.
Claim Interpretation
Regarding claims 4 and 5, neither the claim nor specification describe what is meant by “calculating” a matrix nor “increasing a sum over the matrix”, however, the specification describes creating a matrix (e.g., Spec page 30, line 1-2, para 0135). It does not describe exactly what is summed to derive the sequence similarity, but the Hamming distance was acquired for each subsection combinations in the matrix, so Examiner interprets the sum to be that of the Hamming distances acquired. Examiner further interprets that the “increases a sum over the matrix” to mean that the random synonymous codon substitutions of claim 5 has a higher sum of Hamming distances than that of the matrix of claim 4 as interpreted from specification para 0135.
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.
Claims 1-3, and 6-10 are rejected under 35 U.S.C. 103 as being unpatentable over Sather (US PG PUB 2019/0161553, published 05/30/2019, US PAT DOC AA on IDS dated 12/15/2022) in view of Hong et al (2018, published 02/07/2018).
Regarding claim 1, Sather teaches a method of performing an in silico analysis (e.g., Sather para 0346) comprising detecting splice sites, including cryptic splice sites (e.g., Sather para 0343), removing and replacing undesired variants with synonymous codons (e.g., Sather para 0337, 0354) reading on the limitation “performing an in-silico analysis of the gene construct to detect a presence of the sequence which may cause the undesired variant; replacing the detected sequence which may cause the undesired variant with an alternative sequence, wherein the alternative sequence is derived comprising synonymous codon substitution” of the instantly rejected claim 1. Sather teaches that the in silico analysis and steps of modification can be repeated until heterogeneity of modified transcript is reduced compared to the heterogeneity of the initial transcript, and where the frequency percentage of expression is determined through in vivo methods (e.g., Sather paras 0355, 0314, 0316) reading on the limitation “repeating the in-silico analysis and replacing steps if the frequency percentage of the undesired variant in the gene product from the in-vivo analysis is greater than a predetermined value of acceptable frequency percentage of the undesired variant” of the instantly rejected claim 1.
Sather does not teach an in vivo analysis where the frequency percentage is determined by using RNA sequencing and at least two splice aware aligners, but these were known in the art and were taught by Hong et al.
Hong et al teaches a method of in vivo analysis of RNA variant analysis via RNA sequencing (e.g., Hong abstract; page 2, last para; page 3, first para), where frequency of RNA variants are determined by spice-aware aligners (i.e., HISAT2, STAR, STAR2, Subread and Subjunc) (e.g., Hong et al., Fig 4b; abstract) reading on the limitation “performing a RNA-sequencing analysis of an RNA product transcribed from the gene construct, wherein the frequency percentage of the undesired variant is determined at least in part by using a splice-aware aligner from the RNA- sequencing analysis” of the instantly rejected claim 1.
It would have been prima facie obvious before the effective filing date of the claimed invention for a person having ordinary skill in the art to have performed the method of in vivo RNA sequencing and splice-aware aligner analysis of Hong et al with the in silico detection and replacement of undesired variants of Sather. The skilled artisan would have been motivated to use the in vivo RNA sequencing and splice-aware aligner analysis of Hong et al based on the teachings Hong et al, that they followed the multi-step analysis method for identifying RNA variants, and found that selection of alignment tool was the most important factor (e.g., Hong et al., page 3, last para; page 4, first para) and that identification of RNA variants is highly dependent on alignment algorithm, highlighting the importance of alignment tool selection (e.g., Hong et al., page 5, para 3). Thus, the addition of the in vivo RNA sequencing and splice-aware aligner of Hong et al to the in silico undesired variant detection and replacement of Sather would have been a simple combination of known methods to yield predicable results.
Regarding claim 2, Hong et al teaches a method of using five separate splice-aware aligners (i.e., HISAT2, STAR, STAR2, Subread and Subjunc) (e.g., Hong et al., Fig 4).
Regarding claim 3, Sather teaches a method that includes repeating the steps of identifying splice sites (e.g., Sather paras 0340, 0355), including identical sites (e.g., Sather para 1313) and replacing them with synonymous codons (e.g., Sather para 0354-0355).
Regarding claim 6, Sather teaches a method wherein the gene construct comprises a sequence encoding a chimeric antigen receptor (e.g., Sather abstract; para 0005).
Regarding claim 7, Sather teaches a method of eliminating undesired splice sites to improve or optimize expression of a particular product, such as a chimeric antigen receptor (CAR), at a specific degree of RNA heterogeneity (i.e., or RNA homogeneity) (e.g., Sather para 0313), and that the undesired splice sites negatively impacts expression on cell surfaces or reduces protein expression or function in CAR (e.g., Sather para 0313).
Regarding claim 8, Sather teaches a method wherein the predetermined value of desired RNA homogeneity for CAR expression on cell surfaces and the antigen binding domain is 95-100%(e.g., Sather para 0313, 0100), meaning expression of undesired splice sites for the above expressed functions is between 0-5%. MPEP 2144.05 makes it clear that: In the case where the claimed ranges "overlap or lie inside ranges disclosed by the prior art" a prima facie case of obviousness exists. In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976); In re Woodruff, 919 F.2d 1575, 16 USPQ2d 1934 (Fed. Cir. 1990) and a prima facie case of obviousness exists where the claimed ranges or amounts do not overlap with the prior art but are merely close. Titanium Metals Corp. of America v. Banner, 778 F.2d 775, 783, 227 USPQ 773, 779 (Fed. Cir. 1985) (Court held as proper a rejection of a claim directed to an alloy of "having 0.8% nickel, 0.3% molybdenum, up to 0.1% iron, balance titanium" as obvious over a reference disclosing alloys of 0.75% nickel, 0.25% molybdenum, balance titanium and 0.94% nickel, 0.31% molybdenum, balance titanium." The proportions are so close that prima facie one skilled in the art would have expected them to have the same properties."). See also Warner-Jenkinson Co., Inc. v. Hilton Davis Chemical Co., 520 U.S. 17, 41 USPQ2d 1865 (1997).
Regarding claim 9, Sather teaches a method wherein the analysis and steps of modification can be repeated until heterogeneity of modified transcript is reduced (e.g., Sather para 0355). It is noted that a reference may be relied upon for all that it would have reasonably suggested to one having ordinary skill the art, including nonpreferred embodiments (see MPEP § 2123). Thus, the teaching of Sather that analysis and modification steps can be repeated to reduce RNA heterogeneity that will impact expression or function of CAR, encompasses the alternative embodiment wherein the analysis and modification steps are not repeated, where RNA heterogeneity has no impact on the expression or function of the CAR.
Regarding claim 10, Sather teaches a method comprising removing variants (i.e., above 5% of the variants) in order to achieve >95% RNA homogeneity (e.g., Sather para 0314), and analyzing variants to determine whether they should be removed or replaced based on impact on protein expression, expression on cell surface or reduced function (e.g., Sather para 0313).
Claims 11-13 and 16-20 are rejected under 35 U.S.C. 103 as being unpatentable over Sather (US PG PUB 2019/0161553, published 05/30/2019, US PAT DOC AA on IDS dated 12/15/2022) in view of Hong et al (2018, published 02/07/2018).
Regarding claim 11, Sather teaches a method of performing an in silico analysis (e.g., Sather para 0346) comprising detecting splice sites, including cryptic splice sites (e.g., Sather para 0343), removing and replacing undesired variants with synonymous codons (e.g., Sather para 0337, 0354) reading on the limitation “performing an in-silico analysis of the gene construct to encoding said gene product to identify and alter a sequence that may cause the undesired variant; replacing the detected sequence which may cause the undesired variant with an alternative sequence, wherein the alternative sequence is derived comprising synonymous codon substitution” of the instantly rejected claim 11. Sather teaches that the in silico analysis and steps of modification can be repeated until heterogeneity of modified transcript is reduced compared to the heterogeneity of the initial transcript, and where the frequency percentage of expression is determined through in vivo methods (e.g., Sather paras 0355, 0314, 0316) reading on the limitation “repeating the in-silico and replacing steps to create a new gene construct, if the frequency percentage of the undesired variant in the gene product from the in-vivo analysis is greater than a predetermined value of acceptable frequency percentage of the undesired variant” of the instantly rejected claim 11. Sather teaches repeating the in silico analysis, steps of modification and in vivo analysis where frequency percentage is determined until a desired metric is reached, such as heterogeneity of transcript is reduced (e.g., Sather paras 0355, 0314, 0316), reading on the limitation “measuring a frequency percentage of the undesired variant expressed by the new gene construct comprising performing an in-vivo analysis of one or more genes expressed by the new gene construct comprising performing a RNA-sequencing analysis of an RNA product transcribed from the new gene construct, wherein the frequency percentage of the undesired variant is determined”
Sather does not teach an in vivo analysis where the frequency percentage is determined by using RNA sequencing and at least two splice aware aligners, but these were known in the art and were taught by Hong et al.
Hong et al teaches a method of in vivo analysis of RNA variant analysis via RNA sequencing (e.g., Hong abstract; page 2, last para; page 3, first para), where frequency of RNA variants are determined by spice-aware aligners (i.e., HISAT2, STAR, STAR2, Subread and Subjunc) (e.g., Hong et al., Fig 4b; abstract) reading on the limitation “performing a RNA-sequencing analysis of an RNA product transcribed from the gene construct, wherein the frequency percentage of the undesired variant is determined at least in part by using a splice-aware aligner from the RNA- sequencing analysis” of the instantly rejected claim 11.
It would have been prima facie obvious before the effective filing date of the claimed invention for a person having ordinary skill in the art to have performed the method of in vivo RNA sequencing and splice-aware aligner analysis of Hong et al with the in silico detection and replacement of undesired variants of Sather. The skilled artisan would have been motivated to use the in vivo RNA sequencing and splice-aware aligner analysis of Hong et al based on the teachings Hong et al, that they followed the multi-step analysis method for identifying RNA variants, and found that selection of alignment tool was the most important factor (e.g., Hong et al., page 3, last para; page 4, first para) and that identification of RNA variants is highly dependent on alignment algorithm, highlighting the importance of alignment tool selection (e.g., Hong et al., page 5, para 3). Thus, the addition of the in vivo RNA sequencing and splice-aware aligner of Hong et al to the in silico undesired variant detection and replacement of Sather would have been a simple combination of known methods to yield predicable results.
Regarding claim 12, Hong et al teaches a method of using five separate splice-aware aligners (i.e., HISAT2, STAR, STAR2, Subread and Subjunc) (e.g., Hong et al., Fig 4).
Regarding claim 13, Sather teaches a method that includes repeating the steps of identifying splice sites (e.g., Sather paras 0340, 0355), including identical sites (e.g., Sather para 1313) and replacing them with synonymous codons (e.g., Sather para 0354-0355).
Regarding claim 16, Sather teaches a method wherein the gene construct comprises a sequence encoding a chimeric antigen receptor (e.g., Sather abstract; para 0005).
Regarding claim 17, Sather teaches a method of eliminating undesired splice sites to improve or optimize expression of a particular product, such as a chimeric antigen receptor (CAR), at a specific degree of RNA heterogeneity (i.e., or RNA homogeneity) (e.g., Sather para 0313), and that the undesired splice sites negatively impacts expression on cell surfaces or reduces protein expression or function in CAR (e.g., Sather para 0313).
Regarding claim 18, Sather teaches a method wherein the predetermined value of desired RNA homogeneity for CAR expression on cell surfaces and the antigen binding domain is 95-100%(e.g., Sather para 0313, 0100), meaning expression of undesired splice sites for the above expressed functions is between 0-5%. MPEP 2144.05 makes it clear that: In the case where the claimed ranges "overlap or lie inside ranges disclosed by the prior art" a prima facie case of obviousness exists. In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976); In re Woodruff, 919 F.2d 1575, 16 USPQ2d 1934 (Fed. Cir. 1990) and a prima facie case of obviousness exists where the claimed ranges or amounts do not overlap with the prior art but are merely close. Titanium Metals Corp. of America v. Banner, 778 F.2d 775, 783, 227 USPQ 773, 779 (Fed. Cir. 1985) (Court held as proper a rejection of a claim directed to an alloy of "having 0.8% nickel, 0.3% molybdenum, up to 0.1% iron, balance titanium" as obvious over a reference disclosing alloys of 0.75% nickel, 0.25% molybdenum, balance titanium and 0.94% nickel, 0.31% molybdenum, balance titanium." The proportions are so close that prima facie one skilled in the art would have expected them to have the same properties."). See also Warner-Jenkinson Co., Inc. v. Hilton Davis Chemical Co., 520 U.S. 17, 41 USPQ2d 1865 (1997).
Regarding claim 19, Sather teaches a method wherein the analysis and steps of modification can be repeated until heterogeneity of modified transcript is reduced (e.g., Sather para 0355). It is noted that a reference may be relied upon for all that it would have reasonably suggested to one having ordinary skill the art, including nonpreferred embodiments (see MPEP § 2123). Thus, the teaching of Sather that analysis and modification steps can be repeated to reduce RNA heterogeneity that will impact expression or function of CAR, encompasses the alternative embodiment wherein the analysis and modification steps are not repeated, where RNA heterogeneity has no impact on the expression or function of the CAR.
Regarding claim 20, Sather teaches a method comprising removing variants (i.e., above 5% of the variants) in order to achieve >95% RNA homogeneity (e.g., Sather para 0314), and analyzing variants to determine whether they should be removed or replaced based on impact on protein expression, expression on cell surface or reduced function (e.g., Sather para 0313).
Claims 4, 5, 14 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Sather (US PG PUB 2019/0161553, published 05/30/2019, US PAT DOC AA on IDS dated 12/15/2022) in view of Hong et al (2018, published 02/07/2018) as applied to claims 1 and 11 above, and further in view of Tuller (WO 2017/056094, published 04/06/2017)
Sather in view of Hong et al renders obvious the method of detecting a replacing an undesired variant in a gene construct of claims 1 and 11, upon which the instantly rejected claims 4, 5, 14 and 15 depend.
Sather in view of Hong et al does not teach a matrix of subsection combinations and acquiring a Hamming distance from them, but this was known in the art and was taught by Tuller.
Regarding claim 4, Tuller teaches building an alignment matrix of synonymous codon substitutions (e.g., Tuller page 35, lines 27-31) and that the diversity of alignments can be measured by Hamming distance (e.g., Tuller page 35, line 6).
Regarding claim 5, Tuller teaches a method of substituting randomized codons based on codon frequency, but where other relevant biological constraints may be substituted, such as Hamming distance (e.g., Tuller page 35 lines 6 and 27-32; page 36, lines 1-2 and 7-8).
Regarding claim 14, Tuller teaches building an alignment matrix of synonymous codon substitutions (e.g., Tuller page 35, lines 27-31) and that the diversity of alignments can be measured by Hamming distance (e.g., Tuller page 35, line 6).
Regarding claim 15, Tuller teaches a method of substituting randomized codons based on codon frequency, but where other relevant biological constraints may be substituted, such as Hamming distance (e.g., Tuller page 35 lines 6 and 27-32; page 36, lines 1-2 and 7-8).
It would have been prima facie obvious before the effective filing date of the claimed invention for a person having ordinary skill in the art to have performed the method of generating an alignment matrix and used Hamming distance to determine sequence diversity of Tuller with the in vivo RNA sequencing and splice-aware aligner analysis and in silico detection and replacement of undesired variants of Sather in view of Hong et al. The skilled artisan would have been motivated to use the matrix and Hamming distance of Tuller, as Hamming distance is a commonly used metric in determining diversity in silico when sequence diversity is a desired trait, and by the teachings of Tuller that their matrix model may improve the robustness and computational efficiency of the subsequent stages of their method (e.g., Tuller page 35, lines 1-4). Thus, the addition of the generation of an alignment matrix and use of Hamming distance to determine sequence diversity of Tuller to the in vivo RNA sequencing and splice-aware aligner analysis and in silico detection and replacement of undesired variants of Sather in view of Hong et al would have been a simple combination of known methods to yield predicable results.
Conclusion
No claims allowed.
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/G.Y./Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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