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 1-2,4-10,12-17 and 43-47 are currently pending and under examination. Claims 3, 11, 34, and 35 are cancelled. Claims 18-33 and 36-42 were previously cancelled. Claims 2, 5-7, 9, 12-15, 17, and 43 have been amended. Claims 44-47 are new. Claims 1 and 43 are independent claims.
Response to Arguments
Objections Withdrawn
The objection to the description of Fig. 3 for improperly using a color reference is withdrawn following the applicants’ amendments.
The objection to the abstract of the disclosure for being fewer than 50 words is withdrawn following the applicants’ amendments.
The objection to the specification for improperly demarcated trademarks is withdrawn following the applicants’ amendments.
The objection to claim 34 is withdrawn following the applicants’ amendments and cancellation of the claim.
Rejections Withdrawn
The rejection of claim 5 under 35 U.S.C. 112(a) is withdrawn following the applicants’ amendments.
The rejection of claims 2-3, 11, 14-15, 17, 34, and 35 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point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention, is withdrawn following the applicants’ amendments and cancelation of claims 3, 11, 34, and 35.
The rejection of claim 1-17, 34-35 and 43 under 35 U.S.C. 103 as being unpatentable over Frisén et al. (WO 2016/162309 A1, cited on the IDS filed 10/30/2020) as evidenced by Chee et al. (US 6,355,431 B2) in view of Chen et al. (“ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing”, Nature Methods volume 13, pages 1013–1020 ,2016) is withdrawn.
New Rejections
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 text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1-2,4-10,12-17 and 43-47 are rejected under 35 U.S.C. 103 as being unpatentable over Frisén et al. (WO 2016/162309 A1, cited on the IDS filed 10/30/2020) as evidenced by Chee et al. (US 6,355,431 B2) in view of Chen et al. (“ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing”, Nature Methods volume 13, pages 1013–1020 ,2016) and further in view of Kim et al. (US 2004/0033503 A1, published Feb. 19, 2004).
Frisén teaches methods for obtaining spatially resolved nucleic acid information from tissue samples using capture probes associated with spatially indexed substrates. Regarding claim 1, Frisén teaches a method for spatially tagging nucleic acids of a biological specimen (Abstract). Frisén teaches obtaining a tissue sample from a subject (pg. 27, lines 23-25). The tissue sample can be sectioned using a cryostat (pg. 28, lines 3-15). Frisén teaches contacting the tissue sample with a permeabilizing agent (claim 42, pg. 27, line 33). Frisén teaches providing an array of beads on a solid support (pg. 3, lines 11-24). Frisén teaches a solid support can have wells, and attachment chemistries or adhesives are used to hold the beads in the wells (pg. 18, lines 3-12). Frisén incorporates Chee et al., US 6,355,431 B2, by reference (pg. 17, line 24). Chee teaches that an array comprises a plurality of discrete sites that can retain the beads through the use of chemically altered or active sites, such as spots of adhesive (par. 213), or the use of a uniform surface of adhesive or chemical functionalities (par. 214, 218). This would require contacting the solid support with a capture material and contacting the capture material-coated solid support with the beads. Frisén teaches the beads comprise an average diameter of 10 µm (claim 13, claim 88). Frisén teaches the probes on the beads comprise a barcode which is different from the barcode on other beads and a target capture sequence (Abstract; pg. 3, lines 11-24). Frisén teaches identifying the barcode sequence and the position on the solid support (pg. 3, lines 11-24; pg. 23, lines 5-16). Frisén teaches contacting the population of beads on the array with the tissue sample (Abstract; pg. 3, lines 11-24). Frisén teaches that the target nucleic acids that were hybridized to the probes can be sequenced (pg. 31, lines 32-35; pg. 32, lines 1-32).
Frisén does not teach that each bead comprises at least 1000 attached oligonucleotides. Frisén does teach that a solid support can include at least 1 x 109 different probes (pg. 18, lines 28-31). It would have been obvious to one of ordinary skill in the art to include at least 1000 attached oligonucleotides on each bead, as this would increase the number of available probes and would increase the efficiency of the array of beads, with no evidence of unexpected results.
Frisén does not teach contacting the section of the tissue sample with a DNA fragmenting agent, though Chen fills this knowledge gap. Chen is in the field of identifying spatial organization of DNA and teaches in situ methods for DNA detection comprising contacting a biological sample, immobilized on a slide with both a permeabilizing agent (Triton™ X-100 or NP-40, methods) and a DNA fragmenting agent, specifically, a Tn5 transposase complex (Abstract and throughout), which fragments genomic DNA in situ while adding adaptors (pg. 1013, left column, 2nd para. – right column, 2nd para.). Chen discloses that permeabilization allows enzymatic access to the DNA within the sample and that in situ tagmentation preserves spatial information about the DNA molecules.
It would have been prima facie obvious to one of ordinary skill in the art at the time of filing to modify Frisén tissue-section-based spatial mapping method by substituting or adding Chen’s in situ fragmentation and tagging step for the purpose of generating spatially resolved DNA abundance data, rather than (or in addition to) RNA abundance data, because Chen teaches that Tn5-mediated in situ tagmentation allows for efficient preparation of DNA libraries directly within intact biological samples, preserving spatial context. One of ordinary skill would recognize that applying Chen’s fragmentation and tagging approach to the nucleic acids released from Frisén permeabilized tissue sections would predictably yield spatially mapped DNA sequence data, using the same capture barcodes and positional decoding taught by Frisén. Such a combination would represent a predictable use of prior art elements according to their established functions to yield no more than the expected result.
While Frisén describes permeabilization occurring after placement of the tissue on the support, Frisén nonetheless teaches the step of permeabilizing tissue sections to render nucleic acids accessible for spatial capture (claim 42, pg. 27, line 33). Chen teaches treating tissues with a permeabilizing agent and a DNA fragmentation agent to expose genomic DNA for downstream spatial analysis (see Abstract, pg. 1013, left column, 2nd para. – right column, 2nd para., and throughout). The function of permeabilization and fragmentation in both references is to render DNA accessible for hybridization-based capture. Whether nucleic acid accessibility is induced immediately before or after contacting the capture-coated support does not alter the fundamental mechanism of spatial capture, which depends upon the diffusion of accessible DNA fragments and hybridization to surface-bound oligonucleotides. Rearranging known preparatory steps in a workflow absent evidence of criticality or unexpected results, constitutes a predictable variation within the skill of the ordinary artisan. See MPEP 2144.04; In re Burhans; Ex parte Rubin; In re Gibson. Applicants have not provided evidence demonstrating that performing permeabilization prior to contacting the support yields an unexpected technical effect or improved spatial resolution. Accordingly, the claimed sequence represents an obvious rearrangement of known process steps.
In regards to claims 2 and 4, Frisén teaches that the sample is permeabilized (Claims 42, 80, and 104) , while Chen teaches specifically using 0.5% Triton™ X-100 for 10 minutes, 0.1% NP-40 for 10 minutes, or 0.01% Igepal™ CA-630 for 10 minutes, to permeabilize the sample (methods section).
In regards to claim 5-7, Chen teaches using Tn5 transposase to fragment DNA and add adaptors. They teach applying the transposase mixture (containing Tn5 transposase, adapters, and mosaic oligonucleotides) to the sample for 30 minutes at 37 °C (see Chen, pg. 1023 left column 2nd paragraph).
In regards to claim 8, Frisén teaches that the tissue sample is a cryosection (pg. 28, lines 3-15).
In regards to claim 9 and 10, Chen demonstrates targeting genomic DNA molecules, and mitochondrial DNA molecules with their method (Fig. 2B, Fig. S3B, pg. 1014, right column, 3rd paragraph).
In regards to claim 12-15, Chen demonstrates contacting the sample with a nucleosome disrupting agent. The teach using 1% SDS on the slide for 5 minutes or using between 5 ng/mL and 50 µg/µL proteinase K (methods, pg. 1023).
It is well known in the art that nucleosome disruption can be accomplished by a variety of chemical or enzymatic agents that denature histones and loosen or degrade chromatin structure, including but not limited to detergents, proteases, acids, and high-salt buffers. See for example, “Molecular Cloning: A Laboratory Manual, 4th Ed.”, buffers”, which describes multiple alternative reagents for chromatin disruption depending on experimental needs (appendices 1 reagents and buffers). One of ordinary skill in the art at the time of filing would have recognized that these reagents are functional equivalents, all serving to remove or denature histone proteins to increase accessibility of nucleic acids. The specific choice of nucleosome-disrupting reagent is generally a matter of routine optimization and design choice, guided by factors such as downstream compatibility with enzymes, tissue fixation method, and sample type. As such, substituting HCl for SDS or proteinase K in the known tissue permeabilization/fragmentation workflows of the prior art would have been obvious to one of ordinary skill in the art, because it would represent a predictable substitution of one known equivalent for another to achieve the same goal of nucleosome disruption.
In regards to claim 16, Frisén teaches obtaining tissues samples from either brain, lung, liver, kidney, pancreas, heart, or gastrointestinal tract as well as many other sources (pg. 28 line 32 – pg. 29 line 14.)
In regards to claim 17, this claim depends on claim depends on claim 1 and further recite that the tissue sample is obtained from a tumor, and the capture material is a liquid electrical tape. Frisén teaches that samples may be obtained from cancer patients and specifically formulates cancer cell identification in tumors as the problem to be solved by their methods (see pg. 2, lines 5-29, pg. 30, 2nd para.). In regards to the “liquid electrical tape” of claim 17, the specification does specifically describe the chemistry of the liquid electrical tape, though it does state “An exemplary liquid electrical tape of the instant disclosure is Permatex™ liquid electrical tape, which is a weatherproof protectant for wiring and electrical connections.” Permatex product description states “this electrical tape goes on as a liquid and dries to a vinyl polymer”. For purposes of examining this claim, this is the limitation will be interpreted to mean the capture material is “a liquid dried to form a vinyl polymer” which consistent with the wording of claim 43 as well (see Permatex product page). While the combination of Frisen, Chee, and Chen teach the limitations of claim 1, and that the sample is derived from a tumor, the combination does not teach that the capture material for the beads is a liquid dried to form a vinyl polymer.
Kim fills that knowledge gap and teaches forming an attachment layer on a support for oligonucleotide arrays by applying a liquid composition that solidifies to form a polymer coating. Kim teaches that the attachment layer can be formed by dissolving monomers or polymer materials in a solvent to create a fluid composition that is applied to a support and subsequently solidified (see Kim [0034]-[0036]). Kim explicitly teaches that PVC resins may be used as the attachment layer material (see [0035]). Polyvinyl chloride (PVC) is a well-known vinyl polymer. Thus Kim teaches applying a liquid composition that, upon drying or solidification, forms a vinyl polymer coating on a substrate, therefore, Kim teaches a liquid that dries to form a vinyl polymer as recited in the claims.
It would have been prima facie obvious to one of ordinary skill in the art at the time of filing to utilize the polymer coating techniques taught by Kim for forming polymer layers on array substrates in the spatial capture systems of Frisén and Chee because polymer coatings were commonly used in array fabrication to provide surface attachment layers, protective coatings, or functional surfaces capable of supporting immobilized oligonucleotides. Substituting one known polymer coating material (e.g. PVC or other vinyl polymers) for another polymer coating used in array fabrication would have been an obvious design choice within the ordinary skill in the art.
In regards to claim 44, Frisén teaches using their methods to identify any of a variety of conditions “including but not limited to, an autoimmune disease, cancer, cystic fibrosis, aneuploidy, pathogenic infection, psychological condition, hepatitis, diabetes, sexually transmitted disease, heart disease, stroke, cardiovascular disease, multiple sclerosis or muscular dystrophy” (see pg. 29 2nd para.), thus reading on the limitation of claim 44, wherein the spatially-resolvable DNA abundance data identifies regions of copy number variation (CNV), regions of aneuploidy, or regions of related cellular lineage in the section of the tissue sample.
In regards to claim 45, Frisén teaches using samples that have been fixed (see pg. 27 last para. – pg. 28 3rd para.).
In regards to claim 46, Frisén teaches using glass surfaces such as slides as a solid support (see pg. 13 2nd para.) and teaches using materials that can be either non-porous or porous, and “include, but are not limited to, glass and modified or functionalized glass, plastics (including acrylics, polystyrene and copolymers of styrene and other materials, polypropylene, polyethylene, polybutylene, polyurethanes, Teflon™, cyclic olefins, polyimides etc.), nylon, ceramics, resins, Zeonor, silica or silica-based materials including silicon and modified silicon, carbon, metals, inorganic glasses, optical fiber bundles, and polymers” (see pg. 13, 2nd para.).
In regards to claim 47, Frisén teaches using sequencing-by-ligation techniques to identify nucleic acids (see pg. 24 last para.)
In regards to claim 43, it would have been prima facie obvious to one of ordinary skill in the art at the time of filing to generate a kit including the materials and instructions needed to perform the methods outlined above, including “a permeabilizing agent (see Frisén claim 42, pg. 27, line 33; Chen methods); a fragmentation agent (see Chen Abstract, and throughout; Tn5 transposase); a capture material-coated solid support with a population of 1-100 µm diameter beads (see Frisén pg. 42 para. 3, claim 13), wherein the capture material is a liquid electrical tape or a liquid dried to form a vinyl polymer (see Kim [0035]), and wherein each bead has at least 1000 attached oligonucleotides (see Frisén pg. 18, lines 28-31) and wherein at least 1000 attached oligonucleotides of each bead each comprises: (a) a bead identification sequence that is common to all at least 1000 oligonucleotides on each bead (see Frisén pg. 3 2nd para.) and (b) a target DNA-specific capture sequence (see Frisén pg. 2, 2nd para. and throughout), thereby forming a subpopulation of beads attached to the solid support (see Frisén pg. 20 3rd para.).” One of ordinary skill in the art would understand that a kit would come with instructions for use.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Matthew H Raymonda whose telephone number is (703)756-5807. The examiner can normally be reached Monday - Friday 10:00 am - 4:00 pm.
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/MATTHEW HAROLD RAYMONDA/Examiner, Art Unit 1684
/AARON A PRIEST/Primary Examiner, Art Unit 1681
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