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 .
Election/Restrictions
Applicant’s species election without traverse of the biomolecule of “nucleic acid” in claim 4 is acknowledged.
Applicant’s response to the election requirement stated that claims 1-5, 9-11, 13-16, 18, 24-30 and 33 are encompassed by the election.
It is noted that claims 24-26 are canceled in the amended claims, thus claims 1-5, 9-11, 13-16, 18, 27-30 and 33 are pending and under examination on the merits.
Priority
This application 18/266,085 filed on 06/08/2023 is a 371 national phase of PCT/US21/63114 filed on 12/13/2021, and claims the benefit of provisional U.S. Patent Application No. 63/125,128, filed on 12/14/2020.
The priority date of claims 1-3 and their dependent claims is determined to be 12/14/2020, the filing date of provisional U.S. Patent Application No. 63/125,128.
Specification
The use of terms which are trade names or marks used in commerce (including IIlumina® and 10x Genomics®), 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 objected to because of the following informalities: Claim 29 is missing a period at the end of the claim. Appropriate correction is required.
Claim Interpretation
Claims 9 and 11 include the term “optionally” to describe “preparing the tissue sample” (claim 9) and “the detection agent” (claim 11). Claim scope is not limited by claim language that makes optional but does not require specific structural features. MPEP 2111.04.
Claims 1-3, 27 and 29-30 recite the limitation “sequence barcode”. The applicant fails to provide structural features for the term “sequence barcode” that would distinguish it from any other sequence known in the art. Thus, under the broadest reasonable interpretation “barcode” is interpreted to encompass any sequence.
Claim 1 recites the limitations “(c) incubating the labeling substrate of (b) with the gelated tissue sample of (a) under conditions that allow the first binding moiety to bind to the biomolecule or gel scaffold, thereby labeling the biomolecule or gel scaffold with a spatial barcode” and “(d) -- incubating said solution with a solution comprising a second binding moiety comprising a sequence barcode, under conditions that allow the second binding moiety to bind to a nucleic acid in the labeled biomolecule or labeled gel scaffold of (c), thereby further labeling the biomolecule or gel scaffold with the sequence barcode”. Claim 2 recites the limitations “(c) incubating the labeling substrate of (b) with the expanded tissue sample of (a) under conditions that allow the first binding moiety to bind to the biomolecule or gel scaffold, thereby labeling the biomolecule or gel scaffold with a spatial barcode” and “(d)-- incubating said solution with a solution comprising a second binding moiety comprising a sequence barcode, under conditions that allow the second binding moiety to bind to a nucleic acid in the labeled biomolecule or labeled gel scaffold of (c)”. Claim 3 recites the limitations “(c) incubating the labeling substrate of (b) with the gelated, expanded tissue sample of (a) under conditions that allow the first binding moiety to bind to the biomolecule or gel scaffold, thereby labeling the biomolecule or gel scaffold with a spatial barcode” and “(d) --- incubating said solution with a solution comprising a second binding moiety comprising a sequence barcode, under conditions that allow the second binding moiety to bind to a nucleic acid in the labeled biomolecule or labeled gel scaffold of (c), thereby further labeling the biomolecule or gel scaffold with the sequence barcode”.
Under the broadest reasonable interpretation, the incubating steps are interpreted to encompass any process that can allow the claimed binding events.
Claim Rejections - 35 USC § 112(b)
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 1-5, 9-11, 13-16, 18, 27-30 and 33 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, 2, and 3 recite the limitation "incubating said solution" in lines 17, 16, and 18 respectively. There is insufficient antecedent basis for the limitation “said solution” in the claim. It is assumed that the limitation is intended to reference the “suspension solution” within each claim and should recite “said suspension solution”.
Claims 4-5, 9-11, 13-16, 18, 27-30, and 33 are similarly indefinite because they directly or indirectly depend from claim 1.
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.
Claim(s) 1-5, 9-11, 13-16, 18, 27-30 and 33 is/are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by Frenz (US20200277664, published 09/03/2020).
Regarding claim 1, Frenz teaches methods for determining a location of a biological analyte in a biological sample, wherein the biological analyte is a nucleic acid (para 14).
Regarding step (a), the method comprises embedding a tissue sample in a hydrogel by infusing hydrogel subunits (i.e. using an embedding gel precursor solution) and polymerizing the hydrogel by an internal or external stimulus (para 233), which reads on “contacting the tissue sample with a lattice under conditions that allow gelation of the tissue sample “.
Regarding steps (b) and (c), Frenz further teaches contacting the biological sample with a substrate including a plurality of capture probes immobilized on the substrate, wherein a capture probe (first binding moiety) comprises a spatial barcode and a capture domain, and permeabilizing the sample under conditions sufficient to allow a biological analyte within the biological sample to bind to a capture probe (para 6), which reads on the embodiment of a substrate with a first binding moiety capable of binding to a biomolecule released from the gelated tissue sample.
Regarding step (d), Frenz teaches dissociating a spatially-barcoded sample for analysis via droplet or flow cell analysis methods (i.e. in a suspension solution) (paras 21, 451). Frenz further teaches selectively enriching one or more analytes of interest (e.g., target analytes) after analyte capture. For example, one or more analytes of interest can be enriched by addition of one or more oligonucleotides to the pool of captured analytes that have been released (e.g. are in a suspension solution) (para 927). Frenz teaches the use of barcoded oligonucleotides (sequence barcodes) on beads (a second binding moiety), with oligonucleotides that can hybridize and capture an mRNA (nucleic acid) (para 995). Frenz teaches the use of such beads with oligonucleotides in a partition, which satisfies the requirement of “incubating -- with a solution comprising a second binding moiety comprising a sequence barcode, under conditions that allow the second binding moiety to bind to a nucleic acid in the labeled biomolecule—".
Regarding step (e), Frenz teaches determining the identity of the analytes and the spatial location of each analyte within the biological sample (para 316).
Regarding claim 2, Frenz teaches methods for determining a location of a biological analyte in a biological sample, wherein the biological analyte is a nucleic acid (para 14).
Regarding step (a), the method comprises embedding a tissue sample in a hydrogel by infusing hydrogel subunits (expansion gel precursor solution) and polymerizing the hydrogel (para 233). Frenz teaches the hydrogel can be expanded (e.g., isometric expansion) (para 247) which increases the volume of the sample (paras 254, 255), which reads on “expanding the tissue sample with an expansion gel precursor solution and thereby forming an expanded tissue sample “.
Regarding steps (b) and (c), Frenz further teaches contacting the biological sample with a substrate including a plurality of capture probes immobilized on the substrate, wherein a capture probe (first binding moiety) comprises a spatial barcode and a capture domain, and permeabilizing the sample under conditions sufficient to allow a biological analyte within the biological sample to bind to a capture probe (para 6), which reads on the embodiment of a substrate with a first binding moiety capable of binding to a biomolecule released from the expanded tissue sample.
Regarding step (d), Frenz teaches dissociating a spatially-barcoded sample for analysis via droplet or flow cell analysis methods (i.e. in a suspension solution) (paras 21, 451). Frenz further teaches selectively enriching one or more analytes of interest (e.g., target analytes) after analyte capture. For example, one or more analytes of interest can be enriched by addition of one or more oligonucleotides to the pool of captured analytes that have been released (e.g. are in a suspension solution) (para 927). Frenz teaches the use of barcoded oligonucleotides (sequence barcodes) on beads (a second binding moiety), with oligonucleotides that can hybridize and capture an mRNA (nucleic acid) (para 995). Frenz teaches the use of such beads with oligonucleotides in a partition, which satisfies the requirement of “incubating -- with a solution comprising a second binding moiety comprising a sequence barcode, under conditions that allow the second binding moiety to bind to a nucleic acid in the labeled biomolecule—".
Regarding step (e), Frenz teaches determining the identity of the analytes and the spatial location of each analyte within the biological sample (para 316).
Regarding claim 3, Frenz teaches methods for determining a location of a biological analyte in a biological sample, wherein the biological analyte is a nucleic acid (para 14).
Regarding step (a), the method comprises embedding a tissue sample in a hydrogel by infusing hydrogel subunits (embedding gel precursor solution) and polymerizing the hydrogel by an internal or external stimulus (para 233), which reads on “contacting the tissue sample with a lattice under conditions that allow gelation of the tissue sample and thereby forming a gelated tissue sample”. Frenz also teaches the hydrogel can be expanded (e.g., isometric expansion) (para 247) which increases the volume of the sample (paras 254, 255), which reads on “expanding the tissue sample to form a gelated, expanded tissue sample “.
Regarding steps (b) and (c), Frenz further teaches contacting the biological sample with a substrate including a plurality of capture probes immobilized on the substrate, wherein a capture probe (first binding moiety) comprises a spatial barcode and a capture domain, and permeabilizing the sample under conditions sufficient to allow a biological analyte within the biological sample to bind to a capture probe (para 6), which reads on the embodiment of a substrate with a first binding moiety capable of binding to a biomolecule released from the gelated, expanded tissue sample.
Regarding step (d), Frenz teaches dissociating a spatially-barcoded sample for analysis via droplet or flow cell analysis methods (i.e. in a suspension solution) (paras 21, 451). Frenz further teaches selectively enriching one or more analytes of interest (e.g., target analytes) after analyte capture. For example, one or more analytes of interest can be enriched by addition of one or more oligonucleotides to the pool of captured analytes that have been released (e.g. are in a suspension solution) (para 927). Frenz teaches the use of barcoded oligonucleotides (sequence barcodes) on beads (a second binding moiety), with oligonucleotides that can hybridize and capture an mRNA (nucleic acid) (para 995). Frenz teaches the use of such beads with oligonucleotides in a partition, which satisfies the requirement of “incubating -- with a solution comprising a second binding moiety comprising a sequence barcode, under conditions that allow the second binding moiety to bind to a nucleic acid in the labeled biomolecule—".
Regarding step (e), Frenz teaches determining the identity of the analytes and the spatial location of each analyte within the biological sample (para 316).
Regarding claim 4, Frenz teaches the biological analyte is a nucleic acid (para 14).
Regarding claim 5, Frenz teaches the thickness of a tissue can be at least 0.1 micrometers, 0.1, 0.2, 0.3, 0.4, 0.5, 0.7, 1.0, 1.5, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15,
20, 30, 40, or 50 micrometers. Thicker sections can also be used if desired or convenient, e.g., at least 70, 80, 90, or 100 micrometers or more. Frenz further teaches sections with thicknesses larger or smaller than these ranges can also be analyzed (para 216).
Regarding claim 9, Frenz teaches providing contacting the sample with a cell tagging agent comprising a dye (para 63). The cell tagging agent can be added to the hydrogel contemporaneously with polymerization, i.e. while preparing the sample (para 240).
Regarding claim 10, Frenz teaches placing the sample on a slide and imaging the sample as part of the sample preparation, which reads on imaging the sample prior to preparing by embedding (para 319).
Regarding claim 11, Frenz teaches the cell tagging agent can comprise a barcode (para 63), which reads on comprising a spatial barcode.
Regarding claim 13, Frenz teaches substrates including can be a slide or a hydrogel (para 466), or a bead (para 475).
Regarding claim 14, Frenz teaches a substrate can include tens to hundreds of thousands or millions of individual oligonucleotide (i.e. capture probes or first binding moieties) molecules (e.g., at least about 10,000, 50,000, 100,000, 500,000, 1,000,000, 10,000,000, 100,000,000, 1,000,000,000, or 10,000,000,000 oligonucleotide molecules) (para 475).
Regarding claim 15, Frenz teaches capture probes (first binding moieties) can be cleavable (paras 76, 362, Fig. 7). Frenz teaches using photo-masks such that only specific regions of the array are exposed to cleavable stimuli, which reads on first binding moieties that are releasable from the substrate in designated locations (para 365). .
Regarding claim 16, Frenz teaches a plurality of capture probes (first binding moieties) immobilized on a substrate (para 6). Frenz further teaches a plurality of capture probes comprising spatial barcodes can be placed on an array (substrate) with a pre-determined pattern, which reads on in designated locations (para 552) and a spatial barcode is associated with a particular location in an array or on a substrate (para 390).
Regarding claim 18, Frenz teaches a spatial barcode is a contiguous nucleic acid segment (i.e. oligonucleotide) (para 390).
Regarding claim 27, Frenz teaches barcoded oligonucleotides on beads (para 995).
Regarding claim 28, Frenz teaches the bead can be a gel bead such as a hydrogel bead (para 639).
Regarding claim 29, Frenz teaches that individual beads can be coupled to any number of individual nucleic acid molecules (i.e. second binding moieties comprising sequence barcodes), for example, from one to tens to hundreds of thousands or even millions of individual nucleic acid molecules (para 956). The nucleic acid molecule can
include a barcode sequence that can be bead-specific such that the barcode sequence is common to all nucleic acid molecules coupled to the same bead (para 957), which satisfies the requirement of a unique sequence barcode associated with from about 1 to about 1 x 106 primer sequences.
Regarding claim 30, Frenz teaches barcoded oligonucleotides (sequence barcodes) may include poly-T primer segments that allow priming and replication in a reverse transcription reaction (para 322).
Regarding claim 33, Frenz teaches a biological sample contacted with the array is embedded in a hydrogel matrix to locally cross-link analytes of interest (para 1362), which reads on biomolecules captured in a hydrogel sample.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA GRAY whose telephone number is (571)272-0116. The examiner can normally be reached Monday-Friday 8-5 with second Fridays off.
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/JESSICA GRAY/Examiner, Art Unit 1682
/WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682