DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Priority
This application is a CON of 16/845,664 (04/10/2020 ABN)
16/845,664 is a CON of 15/525,876 (05/10/2017 ABN)
15/525,876 is a 371 of PCT/US15/67147 (12/21/2015)
PCT/US15/67147 has PRO 62/094,919 (12/19/2014)
PCT/US15/67147 has PRO 62/094,917 (12/19/2014)
PCT/US15/67147 has PRO 62/094,924 (12/19/2014).
Status
Claims 21-28 are currently pending.
Claim rejections not reiterated in this action are withdrawn.
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.
Claims 21-28 are rejected under 35 U.S.C. 103 as being unpatentable over Nolan (WO2012/106385) in view of Fu et al. (US20130116130).
Nolan discloses ([00125], [00191], [00230], [00240], [00244], [00246]; claims 261-307; figures 1-11) the labelling principle similar to the instant claims, i.e. (i) labelling one or more target molecules in a population of mixed cells with unique binding moieties ("UBA") that are linked to a nucleic acid forming an epitope specific barcode ("ESB"), (ii) and attaching to the ESB in several rounds of a split pool synthesis complex cell origination barcodes ("COB") built up from several assayable polymers subunits ("APS"), i.e. short nucleic acid sequences respectively - as depicted in Nolan Fig. 2:
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Target molecules or target molecule expressing subsets of cells are identified by decoding the barcodes via amplification and sequencing.
Regarding claim 21 (in italics) Nolan teaches a method for generating barcoded cDNA, comprising:
(a) creating a mixture of cells that are fixed and permeabilized; ([00116]: “Cells may be fixed prior to the addition of UBAs, ESBs or prior to COB assembly. Suitable cell permeabilization methods are known in the art and can be used to deliver components of the assay into cells and cellular components.”; [00300]: “The cells are immediately fixed and permeabilized by adding 50 mL cold methanol.”; [00164]: “cells in one tube will have a mixture of cells”)
(c) reverse transcribing the mRNA in the cells to produce cDNA; and (claim 6; [0059]: “non limiting examples of polynucleotides: … complementary DNA (cDNA), which is a DNA representation of mRNA, usually obtained by reverse transcription of messenger RNA (mRNA) or by amplification”)
(d) adding a barcode to the cDNA by a method that comprises stepwise ligation of at least two assayable polymer subunits to the 5' end of the cDNA via successive rounds of split pool synthesis, ([00110], [00164]-[00170]; claims 17, 113, 203; Figs. 3-4)
wherein each round comprises:
(i) splitting the cells into a plurality of aliquots (claim 196 step c: “performing n rounds of split pool synthesis, each round comprising; i) splitting the population of particles into m reaction volumes; ii) contacting one or more reaction volumes with an APS from the APS set specific for the round; iii) pooling two or more reaction volumes;”),
(ii) incubating each aliquot with a different assayable polymer subunit,
(iii) ligating the assayable polymer subunit onto the cDNA, ([00170]: “The APSs can be linked via ligase.”)
(iv) optionally rinsing the cells, and
(v) pooling of the aliquots;
wherein the barcode is made up of distinct combinations of the different assayable polymer subunits ([0075]; [0096]-[00102]; claim 16).
Although Nolan teaches generating cDNA from cell mRNA, Nolan does not specifically teach claim 21’s step of (b) hybridizing a poly-dT oligonucleotide to mRNA in the cells.
Fu teaches methods of analyzing nucleic acids by attachment of label-tags/barcodes and specifically teaches the well-known technique of reverse transcription of mRNA from into cDNA using oligo dT primers ([0174]-[0179]). The prior art are in the same field of endeavor of nucleic acid analysis via barcoding and one of ordinary skill in the art would have readily considered combining the teaching of Nolan and Fu to perform reverse transcription to generate barcoded cDNA and arrive at the claimed invention with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to utilize the well-known techniques in the art to generate the barcoded cDNA as taught by Nolan for the identification and analysis of cellular nucleic acids.
Regarding claim 22, Fu also teaches attaching the label-tag/barcode utilizing a splint adaptor/oligonucleotide which one of ordinary skill in the art would consider and arrive at the claimed invention.
Regarding claim 23, Nolan teaches utilizing a random sequence in the APS ([00115]: “one or more APSs may further comprise a random tag region allowing for subsequent normalization of the detected COBs (Figures 6-11). Variations of suitable methods making use of such random tag regions are known in the art”) which one of ordinary skill in the art would have considered utilizing and arrive at the claimed invention.
Regarding claim 24, Nolan teaches the barcode (COB) comprises biotin ([00105]: “In some embodiments, a biotin anchor is attached to the COB”; [00149]: “[00149] The COBs of the present invention can be labeled with any of a variety of label monomers, such as a radioisotope, fluorochrome, dye, enzyme, nanoparticle, chemiluminescent marker, biotin, or other monomer known in the art that can be detected directly”) which one of ordinary skill in the art would have considered utilizing and arrive at the claimed invention.
Regarding claim 25, Nolan teaches immobilization/isolating via use of a bead ([00105]: “In some embodiments, a biotin anchor is attached to the COB, ESB and/or UBA, allowing immobilization of the COBs, COB-ESB complexes, or COB/ESB/UBA complexes on a streptavidin surface (e.g. coated slide or bead).”) which one of ordinary skill in the art would have considered utilizing and arrive at the claimed invention.
Regarding claim 26, Nolan teaches detection via sequencing ([00131]: “In any of the embodiments, the detection or quantification analysis of the COBs can be accomplished by sequencing. The APS subunits or entire COBs can be detected via full sequencing of all DNA tags by any suitable methods known in the art, e.g., Illumina HiSeq 2000, including the sequencing methods described herein.”) which one of ordinary skill in the art would have considered utilizing and arrive at the claimed invention.
Regarding claim 27, Nolan teaches the barcode/COB identifies an individual cell ([0096]: “Each COB provides a unique code that can be associated to a specific cell of origin.”) which one of ordinary skill in the art would have considered utilizing and arrive at the claimed invention.
Regarding claim 28, Nolan teaches rinsing cells in the course of split-pool synthesis ([00300]-[00301]) which one of ordinary skill in the art would have considered utilizing the same routine steps and arrive at the claimed invention.
With each of the above claims, the level of skill in the art is very high such that one of ordinary skill in the art would consider routine the combination of elements from the teaching of the art in the same field of endeavor. One of ordinary skill in the art would have recognized that the results of the combination would be predictable due to the well-known nature and optimizations routinely performed in the art. Thus, one of ordinary skill in the art would have arrived at the invention as claimed with a reasonable expectation of success.
Response to Remarks – 35 USC 103
Applicant argues that Fu hybridizes primers in solution and not in cells and thus does not render the claimed invention obvious with the teaching of Nolan which is in cells.
The argument is not persuasive because Nolan teaches reverse transcription in cells (claim 6; [0059]: “non limiting examples of polynucleotides: … complementary DNA (cDNA), which is a DNA representation of mRNA, usually obtained by reverse transcription of messenger RNA (mRNA) or by amplification”; [00163], [00169]: “the invention provides methods for tagging target molecules within cells”), including the use of primers ([0065]) which one of ordinary skill in the art would find the selection and use of as routine. Fu establishes factually what was well-known to one of ordinary skill in the art, specifically the technique of reverse transcription of mRNA from into cDNA using oligo dT primers ([0174]-[0179]). Thus, one of ordinary skill in the art would have considered using the same primer as Fu and arrive at the claimed invention with a reasonable expectation of success.
Double Patenting
Claims 21-28 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-22 of U.S. Patent No. 10626442 in view of Nolan (WO2012/106385) and Fu et al. (US20130116130) as detailed in the 35 USC 103 rejection above and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because the patent claims are to overlapping subject matter and shares the same disclosure of Nolan described in the 35 USC 103 rejections supra and the patent claims with the supporting disclosure would render obvious the instant claims as detailed above.
Claims 21-28 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 12378596 in view of Nolan (WO2012/106385) and Fu et al. (US20130116130) as detailed in the 35 USC 103 rejection above and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because the patent claims are to a method of overlapping subject matter and shares the same disclosure of Nolan described in the 35 USC 103 rejections supra and the patent claims with the supporting disclosure would render obvious the instant claims as detailed above.
Claims 21-28 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13, 15-21 of copending Application No. 18202674 in view of Nolan (WO2012/106385) and Fu et al. (US20130116130) as detailed in the 35 USC 103 rejection above and incorporated herein. Although the claims at issue are not identical, they are not patentably distinct from each other because the copending application claims are to a method of overlapping subject matter and the copending application claims with the supporting disclosure would render obvious the instant claims as detailed above.
This is a provisional nonstatutory double patenting rejection.
Response to Remarks – Double Patenting
Applicant requested the argument be held in abeyance and does not make substantive arguments. Thus, the rejections are maintained.
Conclusion
The claims are not in condition for allowance.
THIS ACTION IS MADE FINAL. 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 ROBERT H HAVLIN whose telephone number is (571)272-9066. The examiner can normally be reached on 9am - 6pm.
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/ROBERT H HAVLIN/Primary Patent Examiner, Art Unit 1626