DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions and Status of the Claims
2. Applicant’s election of Group II in the reply filed on 14 April 2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 48-49, 51, and 58-60 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 14 April 2026.
Claims 72-75, 77-81, 86-88, 91, and 94 are under prosecution.
Information Disclosure Statement
3. The Information Disclosure Statement filed 14 June 2024 is acknowledged and has been considered.
Specification
4. The use of trade names or marks used in commerce (including but not necessarily limited to Ion Torrent, Triton X-100, etc.), has been noted in this application. Any trade names or marks should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
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 Rejections - 35 USC § 112
5. 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.
6. Claims 72-75, 77-81, 86-88, 91, and 94 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.
A. Claim 72 (upon which claims 73-75, 77-81, 86-88, 91, and 94 depend) is indefinite in each of the following:
I. The recitation of a “single permeabilized cell or nucleus,” as it is unclear if the nucleus is required to be permeabilized.
It is noted that this limitation appears multiple times in claim 72, as well as in claims 77, 86 (upon which claims 87-88 , 91, and 94 depend) and 87.
II. The recitation “the permeabilized cell or nucleus,” which lacks antecedent basis in the previous recitation of “a single permeabilized cell or nucleus.”
B. Claims 77 and 87 are each indefinite as it is unclear how “the nascent RNA” (i.e., from the single permeabilized cell or nucleus of claim 72) can be from a plurality of permeabilized cells or nuclei (i.e., claim 77) or a population of permeabilized cells or nuclei (i.e., claim 87).
C. Claim 86 (upon which claims 87-88 91,and 94 depend) is indefinite in the recitation “the isolated nascent RNAs,” which lacks antecedent basis because there is no previous recitation of “isolated nascent RNAs.”
Claim Rejections - 35 USC § 103
7. 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.
8. 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.
9. Claims 72-75 and 77-78 are rejected under 35 U.S.C. 103 as being unpatentable over Cook et al. U.S. Patent Application Publication No. US 2004/0142339 A1, published 22 July 2004), Schildkraut et al. U.S. Patent Application Publication No US 2017/0253911 A1,published 7 September 2017), Kim (U.S. Patent Application Publication No. US 2015/0050697 A1, published 19 February 2015), and Liu et al. (Appl. Environmental Microbiol., vol. 73, pages 73-82, published 27 October 2006).
Regarding claim 72, Cook et al. teach methods comprising isolating a single cell (i.e., “a” cell, paragraphs 0067 and 0072 ), labeling nascent RNA (i.e., transcripts) in the cell via incorporation of a nucleotide analog (paragraphs 0027-0030). Cook et al. further teach reverse transcribing the nascent transcripts via RT-PCR (paragraph 0085) and sequencing the cDNA (paragraph 0042), and that the methods have the added advantage of providing a high-throughput technique which enables analysis of the primary transcripts produced in a cell (paragraph 0004). Thus, Cook et al. teach he known techniques discussed above.
Cook et al. do not each using alkyne or azide labeled NTPs.
However, Schildkraut et al. teach methods for sequencing of RNA (paragraph 0013), comprising labeling nascent RNA with labeled nucleotides (paragraph 0028), wherein the nucleotide comprises either an alkyne or an azide (paragraph 0161), Schildkraut et al. also teach the use of cell lysates (paragraph 0167), fragmenting the RNA transcripts (i.e., mRNA; paragraph 0016), and that the methods have the added advantage of using chemoselective reaction (paragraph 0087). Thus, Schildkraut et al. teach the known techniques discussed above.
While Schildkraut et al. discuss barcoding and RNA (paragraph 0110) and the use of copper-catalyzed azide-alkyne cycloaddition reactions (paragraph 0202), neither Cook et al. nor Schildkraut et al. teach the reaction is used to add a barcode.
However, Kim teaches methods utilizing incorporation of alkyne nucleotides into RNA for use in click chemistry (paragraph 0013), including for the addition of a barcode oligonucleotide (paragraph 0024). Kim also teaches the barcode identifies the source from which the nucleic acids is derived (paragraph 0128); thus, it would have been obvious for the barcode to identify the cell from which the nascent RNA was derive, and therefore is a cell-specific barcode. Kim further teaches the methods have the added advantage of achieving a desired level of accuracy of determining the identity of a nucleic acid (paragraph 0129). Thus, Kim teaches the known techniques discussed above.
None of the previously cited references teach fragmentation with ZnCl2.
However, Liu et al. teach the fragmentation of RNA using ZnCl2 at 60oC (page 74, column 2), and that the fragmented RNAs have significantly improved hybridization efficiency (page 76, column 2). Thus, Liu et al. teach the known techniques discussed above.
It is noted that the courts have held that optimization through routine experimentation, and in particular, when related to differences in temperature, do not support patentability (In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955)).
It is also noted that the courts have stated where the claimed ranges “overlap or lie inside the ranges disclosed by the prior art” and even when the claimed ranges and prior art ranges do not overlap but are close enough that one skilled in the art would have expected them to have similar properties, a prima facie case of obviousness exists (see 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); Titanium Metals Corp. of America v. Banner, 778 F2d 775. 227 USPQ 773 (Fed. Cir. 1985) (see MPEP 2144.05.01).
Therefore, the claimed value merely represents an obvious variant and/or routine optimization of the values of the cited prior art.
Applicant is advised that MPEP 716.01(c) makes clear that “[t]he arguments of counsel cannot take the place of evidence in the record” (In re Schulze, 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965)). Thus, Applicant should not merely rely upon counsel’s arguments in place of evidence in the record.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of the cited prior art to arrive at the instantly claimed method with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in a method having the added advantages of:
A. Providing a high-throughput technique which enables analysis of the primary transcripts produced in a cell as explicitly taught by Cook et al. (paragraph 0004);
B. Utilizing a chemoselective reaction as explicitly taught by Schildkraut et al. (paragraph 0087);
C. Achieving a desired level of accuracy of determining the identity of
nucleic acid as explicitly taught by Kim (paragraph 0129); and
D. Providing fragmented RNAs have significantly improved hybridization efficiency as explicitly taught by Liu et al. (page 76, column 2).
In addition, it would have been obvious to the ordinary artisan that the known techniques of the cited prior art could have been combined with predictable results because the known techniques of the cited prior art predictably result in techniques useful for assaying RNA transcripts.
Regarding claim 73, the method of claim 72 is discussed above. Schildkraut et al. teach amplifying the cDNA via PCR to produce a PCR product (paragraphs 0012 and 0110).
Regarding claim 74, the method of claim 72 is discussed above. Cook et al. teach size selection of PCR products using gel electrophoresis (paragraph 0066), and Liu et al. teach the use of polyacrylamide gels (e.g., Fig. 2). Thus, it would have been obvious to size select the PCR products using polyacrylamide gel electrophoresis.
It is noted that there is no previous recitation of a PCR product in the instant claim or claim 72.
Regarding claim 75, the method of claim 72 is discussed above.
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 Kim that the analogs (i.e., bearing the click chemistry alkyne/azide) may be on a bead encompasses both embodiments wherein the barcode is or is not immobilized on a bead.
Applicant is again cautioned against merely relying upon counsel’s arguments in place of evidence in the record.
Regarding claim 77, the method of claim 72 is discussed above. Cook et al. teach using more than one cell (i.e., a population; paragraph 0026).
Regarding claim 78, the method of claim 72 is discussed above. Kim teaches the use of copper acetate (paragraph 0010).
10. Claims 79-81 are rejected under 35 U.S.C. 103 as being unpatentable over Cook et al. U.S. Patent Application Publication No. US 2004/0142339 A1, published 22 July 2004), Schildkraut et al. U.S. Patent Application Publication No US 2017/0253911 A1,published 7 September 2017), Kim (U.S. Patent Application Publication No. US 2015/0050697 A1, published 19 February 2015), and Liu et al. (Appl. Environmental Microbiol., vol. 73, pages 73-82, published 27 October 2006)as applied to claim 72 above, and further in view of Gee et al. (U.S. Patent Application Publication No. US 2015/0072396 A1, published 12 March 2015).
Regarding claims 79-81, the method of claim 72 is discussed above in Section 9.
None of the previously cited references teach the click reactions comprise the claimed reducing agents of accelerating ligands.
However, Gee et al. teach methods wherein click chemistry reactions are performed (Abstract), and include the use of THPTA (i.e., claim 81; paragraph 0111) as well as a copper reducing agent (i.e., claim 79); in the form of any of TCEP, 2-mercaptoethanol, or dithiothreitol (i.e., claim 80; paragraph 0315). Gee et al. also teach the methods have the added advantage of reducing the amount of copper so as to reduce deleterious effects on biomolecules, including polynucleotides (paragraph 0003). Thus, Gee et al. teach the known techniques discussed above.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of Gee et al. with the previously cited prior art to arrive at the instantly claimed methods with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in methods having the added advantage of reducing the amount of copper so as to reduce deleterious effects on the polynucleotides as explicitly taught by Gee et al. (paragraph 0003). In addition, it would have been obvious to the ordinary artisan that the known techniques of Gee et al. could have been combined with the cited prior art with predictable results because the known techniques of Gee et al. predictably result in reagents useful for performing click chemistry
11. Claims 86-88, 91, and 94 are rejected under 35 U.S.C. 103 as being unpatentable over Cook et al. U.S. Patent Application Publication No. US 2004/0142339 A1, published 22 July 2004), Schildkraut et al. U.S. Patent Application Publication No US 2017/0253911 A1,published 7 September 2017), Kim (U.S. Patent Application Publication No. US 2015/0050697 A1, published 19 February 2015), and Liu et al. (Appl. Environmental Microbiol., vol. 73, pages 73-82, published 27 October 2006) as applied to claim 72 above, and further in view of van Haastert et al. (U..S. Patent Application Publication No. US 2015/0297626 A1, published 22 October 2015).
Regarding claim 86, the method of claim 72 is discussed above in Section 9.
Schildkraut et al. teach sequencing RNA (paragraph 0013), as well as comparison to controls (e.g., paragraph 0283). Kim also teaches sequencing RNA (paragraph 0047),and Cook et al each monitoring changes that occur when cells differentiate (paragraph 000)
None of the previously cited references discuss activation states or qPCR.
However, van Haastert et al. teach methods that include assessment of activation states in tumor cells (paragraph 0284), or differentiation in tumor cells (paragraph 0307). Van Haastert et al. further teach use of qPCR for monitoring transcript (i.e., mRNA) levels (paragraph 0513). Van Haastert et al. also teach RNA molecules are detected from a given subject and healthy control and the differences (i.e., increase or decrease) is detected, as well as differentiation as compared to a control (paragraph 0307), and that the methods have the added advantage of aiding in the prevention, treatment, regression, curing and/or delaying of disease (paragraph 0006). Thus, van Haastert et al teach the known techniques discussed above.
It would therefore have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to have combined the teachings of van Haastert et al. with the previously cited prior art to arrive at the instantly claimed methods with a reasonable expectation of success. The ordinary artisan would have been motivated to make the combination because said combination would have resulted in methods having the added advantage of aiding in the preventions, treatment, regression, curing, and or/ delaying of disease as explicitly taught by van Haastert et al. (paragraph 0006). In addition, it would have been obvious to the ordinary artisan that the known techniques of van Haastert et al. could have been combined with the cited prior art with predictable results because the known techniques of van Haastert et al. predictably result in reagents useful for assessing diseases in a subject.
Regarding claim 87, the method of claim 86 is discussed above. Cook et al. teach using more than one cell (i.e., a population; paragraph 0026).
Regarding claim 88, the method of claim 86 is discussed above. Van Haastert et al. teach the controls are healthy controls (paragraph 0268), and that the controls are a specific cell type, in the form of melanocytes (paragraph 0268-0269)
Regarding claim 91, the method of claim 86 is discussed above. Van Haastert et al. teach the controls are healthy controls (paragraph 0268), as well as using a specific differentiation marker (paragraph 0320).
Regarding claim 94, the method of claim 86 is discussed above. Van Haastert et al. teach the controls are healthy controls (paragraph 0268), as well as looking at a specific activation state (paragraph 0237).
Conclusion
13. No claim is allowed.
14. Any inquiry concerning this communication or earlier communications from the examiner should be directed to Robert T. Crow whose telephone number is (571)272-1113. The examiner can normally be reached M-F 8:00-4:30.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Anne Gussow can be reached at 571-272-6047. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Robert T. Crow
Primary Examiner
Art Unit 1683
/Robert T. Crow/Primary Examiner, Art Unit 1683
Prosecution Insights