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 1-19 are currently pending and under examination.
Information Disclosure Statement
The Information Disclosure Statements filed April 18, 2023; November 20, 2023; and October 31, 2025 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 2, Line 9, Page 3, Lines 30, Page 6, Line 5, Page 7, Line 11, Page 12, Line 32, Page 13, Lines 1-2, Page 14, Line 6, Page 15, Lines 9 and 20-22, Page 19, Line 22, Page 65, Lines 2-3, age 67, Line 1, Page 68, Line 33, Page 72, Lines 14 and 30, Page 74, Line 25, Page 76, Line 2, Page 82, Line 22 and References 2, 4, 12, 22-23, 30, 33-35, 40, 61, 64, 66, 74, Pages 88-91). 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.
Additionally, the use of the terms Triton® X-100 and Tween® 20 (see Page 14, Line 22, Page 32, Lines 2, Page 78, Lines 14-15, Page 80, Line 17, Page 85, Line 5, Page 88, Line 25, Page 87, Line 11, ), 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 Objections
Claim 18 is objected to because of the following informalities:
In claim 18, line 1, the term “preferably” should be deleted as RNA is required according to the last step of the claim.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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 13 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.
Regarding Claim 13, is considered vague and indefinite for the following reasons:
In line 3 of the claim, the term “substantially” is unclear and confusing. The term “substantially” is not defined in the specification, it is unclear as to the meaning of substantially all; Is there an amount of mRNA that is not hybridized? If so how much?
Claim Rejections - 35 USC § 102
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.
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.
Claims 1-17 and 19 are rejected under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by Imler et al. (U.S. Patent Application Publication US 2018/0237864 A1, published August 23, 2018), cited on the IDS filed April 18, 2023.
Regarding claim 1, Imler teaches a method of detecting a nucleic acid (Page 1, [0006], Pages 1-2, [0012] and Page 3, [0026]). Imler teaches providing a nucleic acid-containing compartment (e.g., paraffin-embedded tissue or section thereof, a fixed cell, Pages 2-3, [0025] and Page 11, [0116]). Imler teaches hybridizing a plurality of single-stranded DNA oligonucleotide probes to nucleic acid molecules within said compartment (Pages 1-2, [0012], Page 2, [0014], Pages 2-3, [0025] and Fig. 1). Imler teaches removing single-stranded DNA oligonucleotide probes from the compartment that have not specifically hybridized to any nucleic acid within the compartment (Page 2, [0015], Page 7, [0067]-[0068], Page 8, [0070], Page 9, [0087] and Page 11, [0114]). Imler teaches identifying single-stranded DNA-oligonucleotide probes specifically hybridized to nucleic acid molecules within said compartment by probe sequencing or probe amplification and thus determining nucleic acids corresponding to the probe present in said compartment (Pages 6-7, [0061]-[0062], Page 7, [0064], Pages 8-9, [0081]-[0082], Page 9, [0086]-[0087]). Imler teaches the method does not comprise sequential probe hybridization as a means to amplify nucleic acid detection (Page 6, [0057]-[0058] and Pages 8, [0081]).
Regarding claim 2, Imler teaches the method does not comprise an RNA isolation step (Examples 3, 5, 6 and 8).
Regarding claim 3, Imler teaches the method does not comprise a cDNA generation step (Example 1).
Regarding claim 4, Imler teaches the nucleic acid is RNA and/or mRNA (Page 3, [0026]).
Regarding claim 5, Imler teaches the nucleic acid is ssDNA or dsDNA, optionally, ssDNA (Page 8, [0080] and Figures 1-3).
Regarding claim 6, Imler teaches the nucleic acid-containing compartment is a eukaryotic cell, a nucleus of a eukaryotic cell, cytoplasm of a eukaryotic cell, a mitochondrion, a chloroplast, an exosome, a prokaryotic cell, a group of cells in a tissue, or a virus (Pages 2-3, [0025]-[0026]).
Regarding claim 7, Imler teaches the nucleic acid -containing compartment is sectioned before step (b) (Page 12, [0123]).
Regarding claim 8, Imler teaches the nucleic acid-containing compartment or cell are biochemically separated or dissociated before step (b) (Pages 11-12, [0120] and Figure 4).
Regarding claim 9, Imler teaches step (b) is preceded by fixation of the nucleic acid-containing compartment (Pages 2-3, [0025] and Figure 4).
Regarding claim 10, Imler teaches the nucleic acid-containing compartment is not fixated (Pages 2-3, [0025]).
Regarding claim 11, Imler teaches the single-stranded DNA oligonucleotide probes comprise a target region complementary to a nucleotide sequence of a target nucleic acid flanked by a pair of universal primer regions (Page 2, [0023], Page 5, [0050], Page 8, [0081] and Figures 1-2). Imler teaches the single-stranded DNA oligonucleotide probes further comprise a unique molecular identifier (Page 5, [0050] and Page 8, [0081]).
Regarding claim 12, Imler teaches the single-stranded DNA oligonucleotide probes specifically hybridize to a plurality of target nucleic acids present in the compartment (Pages 1-2, [0012], Page 2, [0014], Pages 2-3, [0025] and Fig. 1).
Regarding claim 13, Imler teaches the single-stranded DNA oligonucleotide probes form a library that specifically hybridizes to substantially all mRNAs, optionally, substantially all RNAs present in the compartment (Page 8, [0081]).
Regarding claim 14, Imler teaches between step (c) and (d), an amplification of bound single-stranded DNA oligonucleotide probes is carried out (Page 2, [0015], Page 7, [0067]-[0068] and Page 11, [0114]).
Regarding claim 15, Imler teaches the bound single-stranded DNA oligonucleotide probes are identified by sequencing, preferably next generation sequencing (Example 3 and Figures 4 and 6).
Regarding claim 16, Imler teaches the bound single-stranded DNA oligonucleotide probes are identified by amplification, preferably by quantitative PCR (Page 6, [0061] and Page 7, [0064]).
Regarding claim 17, Imler teaches spatially mapping detected nucleic acids in said compartment (Page 1, [0008] and Example 8). Imler teaches sectioning the compartment prior to step (b) to obtain a collection of fractions and thus separating nucleic acid molecules from each other depending on their localization (Page 1, [0008]). Imler teaches identifying the single-stranded DNA-oligonucleotide probes specifically hybridized to nucleic acid molecules within each fraction in step (d) and thus determining the presence or absence of RNA corresponding to the probe in each fraction as well as mapping nucleic acids within the compartment (Page 1, [0008], Page 9, [0086]-[0087] and Figures 5 and 7).
Regarding claim 19, Imler teaches determining gene expression in single cells, groups of cells or intracellular compartments (Page 1, [0008]). Imler teaches identifying isoforms and allele-specific variants of RNAs within a compartment (Page ,[0026],[0033]-[0034], [0040]). Imler teaches quantifying transcription of genes (Page , [0023], Page , [0111] and Example 3). Imler teaches identifying cell types of complex heterogenous tissue (Page, [0058] and Page , [0028]). Imler teaches identifying endogenous and exogenous dsDNA and ssDNA within a compartment (Pages 2-3, [0025]-[0026]). Imler teaches mapping RNA location in the compartment, mapping RNA and nucleic acid loci location in the compartment, mapping RNA and protein location in the compartment as well as, mapping RNA, protein and nucleic acid loci location in the compartment (Page 1, [0008], Page 8, [0074], Page 9, [0086]-[0087] and [0089]-[0090] and Figures 5).
Imler teaches each and every limitation of claims 1-17 and 19 and therefore Imler anticipated claims 1-17 and 19.
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 18 is rejected under 35 U.S.C. 103 as being unpatentable over Imler et al. (U.S. Patent Application Publication US 2018/0237864 A1, published August 23, 2018), as applied to claims 1-17 and 19 above, in view of Pombo et al. (WIPO International Application Publication WO 2016/156469 A1, published October 06, 2016), cited on the IDS filed November 20, 2023.
Regarding claim 18, Imler teaches detection of nucleic acid, preferably RNA, is combined with the detection of at least one DNA locus within said compartment (Pages 2-3, [0025]-[0026] and Pages 8, [0075]-[0076]). Imler teaches determining the presence or absence of at least one DNA locus in each fraction (Pages 1-2, [0012], Page 9, [0087] and Pages 2-3, [0025]-[0026]). Imler teaches at least one DNA locus and the single-stranded DNA oligonucleotide probe(s) specifically hybridized to RNA. (Pages 1-2, [0012], Page 2, [0014], Pages 2-3, [0025], Page 8, [0074] and Fig. 1).
Imler does not teach or suggest determining co-segregation of said at least one DNA locus.
Pombo teaches determining interaction of a plurality of nucleic acid loci in a compartment comprising nucleic acids, using probes (Abstract and Page 3, First Paragraph). Pombo teaches the nucleic acids may be RNA, DNA, protein or fragment thereof (Page 10, First Paragraph). Pombo teaches probes hybridized to RNA (Page 3, First Paragraph and Page 6, Last Paragraph). Pombo teaches determining co-segregation of DNA loci (Abstract and Page 6, First paragraph). Pombo teaches analyzing the co-segregation allows for identifying the frequency of molecular interactions across a cell population as well as mapping (Abstract). Pombo teaches Pombo teaches the present methods provides for improved determination of nucleic acids by avoiding bias based on ligation of fragmented nucleic acids which allows for simultaneous analysis of all nucleic acid interactions in the genome (Pages 4, Last Paragraph—Page 5, First Paragraph).
It would have been obvious to one having ordinary skill in the art before the effective filing date of the invention to modify the teachings of Imler with the teachings of Pombo, to determining co-segregation of at least one DNA loci. This allows for identifying the frequency of molecular interactions across a cell population as well as mapping of analytes, as well as providing for improved determination of nucleic acids by avoiding bias based on ligation of fragmented nucleic acids which allows for simultaneous analysis of all nucleic acid interactions in the genome as taught by Pombo (Abstract and (Pages 4, Last Paragraph—Page 5, First Paragraph).
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