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 .
Election/Restrictions
Applicant’s election of the particular species the is H3K27me3 (relevant to claim 5) in the reply filed on 03/10/2026 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)).
Claim Rejections - 35 USC § 112 - Indefiniteness
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 1-19 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.
Claims 1-19 are unclear over recitation of the phrase “a region of the second barcode” (as recited in line 7 of claim 1), because there does not appear to be a proper antecedent basis for a “second barcode”. Claim 1 recites “a second unique region for spatial barcoding”, but it is not clear if this second region which is recited with an intended use is the required “second barcode”, or if it is something other than a barcode that is then used to perform a barcoding step or procedure.
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.
Claim(s) 1-9, 11, 12 and 15-19 are is/are rejected under 35 U.S.C. 103 as being unpatentable over Liu et al (2019) in view of Chen et al (2016).
Regarding claim 1, Liu et al teaches methods for spatial detection of biological targets in tissues samples. Liu et al teaches delivering a first and a second set of barcoded polynucleotides to a region of interest in a tissue sample, where the polynucleotides are delivered through microfluidic microchannels of a two devices clamped to the region of interest which are oriented perpendicular to each other, and teaches polynucleotides including ligation linkers (relevant to claim 6), barcode regions, and a sequence for recognition of a primer for DNA amplification (e.g.: Figure 1), relevant to steps (a)-(d) of claim 1. Liu et al further teaches ligation of the nucleic acids and imagining the region of interest (e.g.: Figs 1 and 2) relevant to steps (e)-(f) of claim 1, and lysing the tissue sample with a lysis buffer and extracting DNA from the lysed sample (e.g.: METHOD DETAILS - cDNA collection and purification) relevant to steps (g)-(h) of claim 1.
Regarding claim 3, Liu et al teaches permeabilization of the tissue sample prior to delivery of polynucleotides (e.g.: METHOD DETAILS - Adding the first set of barcodes and reverse transcription).
Relevant to claims 3 and 4, Liu et al teaches delivery of a primary antibody specific for a protein of interest to the tissue (e.g.: Figure 1).
Relevant to claims 7-9, Liu et al teaches sequencing barcodes (e.g.: QUANTIFICATION AND STATISTICAL ANALYSIS - Sequence alignment and generation of gene expression matrix) and constructing a spatial map of the tissue sample (e.g.: QUANTIFICATION AND STATISTICAL ANALYSIS - Clustering and spatial differential expression analysis; Figs. 1-5) including the identification of anatomical features from the tissue sample.
Relevant to claims 11 and 12, Liu et al teaches microfluidic devices fabricated from PDMS with 50 parallel channels (e.g.: Figure 2).
Relevant to claim 15, Liu et al teaches using a vacuum (i.e.: negative pressure) to deliver reagents through the microfluidic devices (e.g.: Fig 2).
Relevant to claim 16, Liu et al teaches microfluidic devices that deliver reagents to the tissue through holes positioned above the region of interest (e.g.: RESULTS - Microfluidic device for the DBiT process; Fig. 2).
Relevant to claim 17, Liu et al teaches barcodes that include barcode A (1-50) and barcode B (1-50) (e.g.: Figure 1).
Relevant to claim 18 and 19, Liu et al teaches fluorescence and optical imagining (e.g.: Fig. 2) of glass slides (e.g.: METHOD DETAILS - Microfluidic device fabrication and assembly).
Liu et al does not exemplify methods that include delivering reagents that include a transposase and a linker adapter sequence (relevant to step (a) of claim 1) and first polynucleotide that include a region for ligation to the linker adapter sequence (relevant to step (b) of claim 1). Liu et al does not teach delivering to the tissue sample an antibody directed to an epigenomic marker and secondary antibody (relevant to claim 3) where the epigenomic marker is H3K27me3 (relevant to claim 5, as consonant with the election). However, Liu et al does suggest that the methods of spatial tissue analysis using microfluidic devices could be applied to epigenomic analysis using Assay for Transposase-Accessible Chromatin (ATAC) based methods (e.g.: p.14-15 – Discussion). And the steps of ATAC including the use of transposases and linker adapters, as well antibodies directed to H3K27me3, were known in the prior art and art taught by Chen et al.
Chen et al teaches ATAC-see, which allows imaging of the accessible genome in situ as well as and deep sequencing to reveal the identity of the imaged elements. Relevant to the instantly rejected claims, Chen et al teaches contacting a sample of fixed and permeabilized cells (e.g.: p.1014; Online Methods - Slide preparation and fixation) with reagents including a bifunctional transposome comprising a transposase and linker adapters (e.g.: Fig 1), relevant to claim 1. Chen et al also teaches visualization of proteins using mouse anti-H3K27me3 primary antibodies and goat anti-mouse-Atto647N secondary antibodies (e.g.: Online Methods - Immunostaining), relevant to claims 3-5.
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have incorporated the ATAC-see methods of genome analysis taught by Chen et al, into the spatial analysis methods of Liu et al. The skilled artisan would have been motivated to perform the spatial analysis methods of Liu et al using the epigenomic analysis of Chen et al based on the expressed suggestion of Liu et al that the methods can be applied to barcoding DNA sequences for high-spatial-resolution Assay for Transposase-Accessible Chromatin (e.g.: p.15) and the methods may be used to spatially barcode a range of molecular information including epigenetic states (e.g.: p.4; p.16).
Claim(s) 10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Liu et al (2019) in view of Chen et al (2016) as applied to claims 1-9, 11, 12 and 15-19 above, and further in view of Powell et al (EP 2183282; 2015).
Liu et al in view of Chen et al renders obvious the methods of claim 1, from which instantly rejected claim 10 depends, including the delivery of reagent to a tissue sample mounted on a substrate. Further relevant to the rejection of claim 10, Liu et al teaches methods of tissue sample handling including fixing slides of frozen tissue in formaldehyde and permeabilizing the tissue (METHOD DETAILS – Tissue Handling; Adding the first set of barcodes and reverse transcription) prior to barcoding.
Liu et al in view of Chen et al does not specifically teach FFPE tissue, washing to deparaffinize, rehydration, or enzymatic permeabilization. But such steps in the analysis of tissue samples with reagents to detect biomolecules in the samples were known in the prior art and are taught by Powell et al.
Powell et al teaches (p.24-25) examples of methods to detect targets in FFPE tissue samples using antibodies. Powell teaches et al methods including using xylene to deparaffinize tissue sections, rehydrate through graded alcohols to distilled water, and treating slides using trypsin.
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have used the known methods of processing tissue samples taught by Powell et al to prepare samples for the methods rendered obvious by Liu et al in view of Chen et al. Where Powell et al teaches that such methods are well-known method, and that variations on such methods are readily determined with routine experimentation by those of ordinary skill in the art, the use of such know methods would be the simple substitution of know steps with predictable results.
Claim(s) 13 and 14 is/are rejected under 35 U.S.C. 103 as being unpatentable over Liu et al (2019) in view of Chen et al (2016) as applied to claims 1-9, 11, 12 and 15-19 above, and further in view of Fan et al (US PG Pub 2019/0324028).
Liu et al in view of Chen et al renders obvious the methods of claim 1, from which instantly rejected claims 13 and 14 depend, including the delivery of reagent to a tissue sample mounted on a substrate using microchannels.
Liu et al in view of Chen et al does not specifically teach microchannels that are serpentine (claim 13), or the use of a third set of barcoded reagents. But such steps in the spatial analysis of biomolecules in tissue samples were suggested in the prior art.
Fan et al teaches devices and methods for the analysis of biomolecules at discrete locations in a microchamber (e.g.: Fig. 6) and teaches that such device may include individual serpentine microchannels (e.g.: para 0254), relevant to claim 13. Fan et al further teaches that analysis of a sample may include a plurality of reagents for the detection of different targets of interest (e.g.: para 0183-186).
It would have been prima facie obvious to someone with ordinary skill in the relevant art before the effective filing date of the rejected claims to have performed the methods rendered obvious by Liu et al in view of Chen et al using the devices and methods taught by Fan et al. The skilled artisan would have been motivated to incorporate the teachings of Fan et al into the methods of Liu et al in view of Chen et al because the skilled artisan would recognize that having additional channels at additional locations related to the tissue sample would allow for a more comprehensive detection of biomolecules throughout the tissue sample.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-19 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of copending Application No. 18/740,662 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the conflicting claims are directed to the analysis of biomolecules in a tissue sample on a substrate using microchannels to deliver reagents including a transposase with adaptor sequences and barcoded nucleic acids.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claim is allowed.
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Stephen Kapushoc
Primary Examiner
Art Unit 1683
/STEPHEN T KAPUSHOC/Primary Examiner, Art Unit 1683
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