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 .
Claims 1-11 are currently pending and under examination.
Information Disclosure Statement
The Information Disclosure Statements filed May 01, 2023; and June 10, 2024 have been considered.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see Page 6, Last Line). 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 GEXSCOPE® (see Page 3, Last Paragraph, Page 4, x2, First Paragraph and Page 5, First Paragraph), 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.
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
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 8 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(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.
The instant specification does not provide support for the invention as claimed. Instant claim 8 recites the limitation, wherein the enzyme is a terminal transferase, to add specific nucleotide sequence to the 3’ of RNA. While the specification does disclose that a tag can be added to the 3’ end of the non-coding RNA by enzymatic approaches, the specification does not disclose using a terminal transferase to add specific nucleotide sequence to the 3’ of RNA.
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 and 10 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 RNA" in line 1. There is insufficient antecedent basis for this limitation in the claim.
Claim 10 recites the limitation “the analysis method” in line 1. There is insufficient antecedent basis for this limitation in the claim.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 2 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claim 2 recites the limitation “the RNA is non-coding RNA”. Independent claim 1 requires the RNA to be non-coding RNA, therefore dependent claim 2 fails to further limit the type of RNA used. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-7 and 9-11 are rejected under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by Van Oudenaarden et al. (U.S. Patent Application Publication US 2022/0195515 A1, published June 23, 2022, effectively filed October 29, 2019).
Regarding claim 1, Van Oudenaarden teaches a method for analyzing whole transcriptome comprising coding and non-coding RNA, at single cell level (Abstract and Page 3, [0043]). Van Oudenaarden teaches adding a specific tag sequence on the 3' of RNA (Abstract, Page 3, [0058] and Page 4, [0061]). Van Oudenaarden capture the tagged RNA with a primer that recognize the tag sequence (Abstract, Page 1, [0011], and Page 3, [0043]-[0044]). Van Oudenaarden teaches reverse transcribe the tagged RNA to cDNA (Page 3, [0046]-[0050], Page 3, [0052]-[0057] and Page 5, [0083]-[0084]). Van Oudenaarden teaches amplifying cDNA (Page 1, [0024]). Van Oudenaarden teaches analyzing amplified cDNA (Page 1, [0024]-[0029].
Regarding claim 2, Van Oudenaarden teaches the RNA is non-coding RNA (Page 4, [0063]).
Regarding claim 3, Van Oudenaarden teaches the primer sequence comprises a sequence that acts as cell barcode that identifies each single cells (Page 3, [0051] and [0057], Pages 3-4, [0060]-[0061] and Page 6, [0120]). Van Oudenaarden a specific sequence that can be used to prime the reverse transcription of the tagged RNA (Page 1, [0005], Page 3, [0056], and page 5, [0083]-[0084]). Van Oudenaarden teaches a sequence that can be used for amplification of the cDNA (Page 5, [0081]-[0083]).
Regarding claim 4, Van Oudenaarden teaches the primer sequence comprise a unique molecular index (UMI) sequence that can be used to quantify cDNA (Page 1, [0028], Page 3, [0052] and Page 4, [0061]).
Regarding claim 5, Van Oudenaarden teaches the tag sequence is added by using an enzyme (Page 3, [0058]).
Regarding claim 6, Van Oudenaarden teaches the tag sequence is added chemically (Page 3, [0058]).
Regarding claim 7, Van Oudenaarden teaches the enzyme is a Poly(A) Polymerase, to add a stretch of A to the 3' of RNA (Page 3, [0058]).
Regarding claim 9, Van Oudenaarden teaches the enzyme is a ligase, to add specific sequence to the 3' of RNA (Page 3, [0058]).
Regarding claim 10, Van Oudenaarden teaches the analysis method is sequencing (Abstract, Page 4, [0061] and Page 6, [0118]).
Regarding claim 11, A product or kit that includes reagents needed to enable the process as described in Claim 1 (Page 2, [0039] and Pages 7-9, Tables 1-13 in Materials and Methods).
Van Oudenaarden teaches each and every limitation of claims 1-7 and 9-11, therefore Van Oudenaarden anticipates claims 1-7 and 9-11.
Claim Rejections - 35 USC § 103
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.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Van Oudenaarden et al. (U.S. Patent Application Publication US 2022/0195515 A1, published June 23, 2022, effectively filed October 29, 2019).
Regarding claim 8, Van Oudenaarden teaches polyadenylation at the 3’ terminus of the RNA and that the adenylation (A specific nucleotide sequence) may be performed using any convenient approach, as well as using any other enzyme suitable for catalyzing the incorporation of adenine residues at the 3′ terminus of the precursor RNA (Page 3, [0058]).
Van Oudenaarden does not explicitly teach the enzyme is a terminal transferase, to add specific nucleotide sequence to the 3' of RNA.
However, it would have been prima facie obvious to one having ordinary skill in the art before the effective filing date of the claimed invention to modify the method of Van Oudenaarden by using a terminal transferase to add specific nucleotide sequences to the 3’ end of RNA because Van Oudenaarden teaches polyadenylation at the 3’ terminus of the RNA and that the adenylation may be performed using any convenient approach, as well as using any other enzyme suitable for catalyzing the incorporation of adenine residues at the 3′ terminus of the precursor RNA and the combination of using specifically a terminal transferase would have yielded predictable outcome of adding a sequence (polyadenylation) to the 3’ end of the RNA.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA DANIELLE PARISI whose telephone number is (571)272-8025. The examiner can normally be reached Mon - Friday 7:30-5:00 Eastern with alternate Fridays off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached at 571-272-2876. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JESSICA D PARISI/Examiner, Art Unit 1684
/HEATHER CALAMITA/Supervisory Patent Examiner, Art Unit 1684