Status of the Claims
Claims 1-14 and 17-22 are pending and examined herein.
Claims 15 and 16 are canceled.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Interpretation
Claim 1 recites steps labeled (a), (b), and (c). However, there is no language in the claim indicating a specific order in which these steps must be carried out. Therefore, the broadest reasonable interpretation of the claim encompasses methods in which the recited steps are carried out in an order other than how they are recited.
Additionally, claim 1 recites the limitation of “preparing” nuclei from a sample. The specification does not disclose a specific definition of “preparing”, and so the broadest reasonable interpretation is taken to mean anything done to make the nuclei ready for a subsequent step.
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.
Claim 20 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.
Claim 20 contains the trademark/trade name TWEENTM. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe polysorbate 20 and, accordingly, the identification/description is indefinite.
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.
Giresi
Claims 1-5, 7-9, 12-14, 17-20, and 22 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Giresi (US PGPub No: 2021/0269849).
Regarding claim 1, Giresi discloses a method for determining the presence of a biomolecule and the sequence of a nucleic acid from a single nuclei (p. 4, ¶[0041]) comprising:
preparing single nuclei from a sample comprising multiple cells (p. 5, ¶[0044]; p. 12, ¶[0070]);
contacting the nuclei with an affinity reagent that is capable of binding to the biomolecule and has a first barcode under conditions that allow binding of the reagent to the biomolecule (p. 6, ¶[0049]; Fig. 11);
sequencing nucleic acids from the nuclei under conditions that allow determining the presence of the biomolecule and sequencing the nucleic acids (p. 7, ¶[0058]; claim 36).
Regarding claim 2, Giresi further discloses detection of the affinity reagent binding to the biomolecule (p. 5, ¶[0042]; p. 7, ¶[0058]) and a sequencing reaction comprising fragmenting genomic DNA at accessible regions of chromatin, which is the technique of ATAC-seq (p. 5, ¶[0043]; p. 7, ¶[0058]).
Regarding claims 3 and 19-20, Giresi further discloses permeabilizing cells under conditions that allow isolation of intact nuclei with a buffer comprising TWEENTM-20 (p. 5, ¶[0044]).
Regarding claims 4-5 and 7-9, Giresi further discloses that the sample is a tissue sample or a cell line, and that if it is a tissue sample it can be an animal biopsy from a solid tumor (p. 3, ¶[0032-3].
Regarding claims 12-14, Giresi further discloses that the biomolecule is a transcription factor (p. 8, ¶[0064]) or a protein involved in epigenetic regulation (p. 11, ¶[0068]).
Regarding claims 17 and 18, Giresi further discloses that the presence of more than 2 biomolecules and more than 2 nucleic acids are determined (p. 4, [0041]: “ the methods described herein may be used to analyze a plurality of different protein-nucleic acid interactions simultaneously”, emphasis added).
Regarding claim 22, Giresi further discloses encapsulating nuclei into droplets that also contain beads with barcoded oligonucleotides (p. 7, ¶[0055]; [0057]) and releasing barcoded oligos from the beads and allowing them to hybridize (p. 17, ¶[0112]; Fig. 8 – “releasable linkage 806”).
Regev et al.
Claims 1-4, 6, 10-13, and 17-22 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Regev et al. (US PGPub No: 2021/0171938).
Regarding claim 1, Regev discloses a method of determining the presence of a biomolecule and the sequence of nucleic acids from a single nuclei (p. 2, ¶[0016-7]) comprising:
preparing single nuclei from a sample comprising multiple cells (Fig. 12A – #1 or #3);
contacting the nuclei with an affinity reagent (p. 15, ¶ [0134]: “binding agent”) that is capable of binding to the biomolecule and has a first barcode under conditions that allow binding of the reagent to the biomolecule (Fig. 12A – #2);
sequencing nucleic acids from the nuclei under conditions that allow determining the presence of the biomolecule and sequencing the nucleic acids (Fig. 12A – #4 and 5).
Regarding claim 2, Regev further discloses detection of the barcoded affinity reagent binding to the biomolecule (p. 9, ¶[0083]) and a sequencing reaction comprising scRNA-seq (p. 5, ¶[0064]).
Regarding claims 3 and 19-20, Regev further discloses step (a) (Fig. 12A - #1) comprises permeabilizing cells under conditions that allow isolation of intact nuclei (p. 37, ¶[0325] and [0330] – ST buffer) with a buffer comprising BSA, sodium chloride, calcium chloride, and magnesium chloride (p. 37, ¶[0323]).
Regarding claims 3, 19, and 21, Regev also further discloses fixing nuclei by contacting the cells with a buffer comprising methanol or paraformaldehyde (p. 10, ¶[0097]).
Regarding claims 4, 6, and 10, Regev further discloses that the sample is a frozen tissue sample (p. 32-33, ¶[0306] and [0308]).
Regarding claim 11, Regev further discloses imaging the tissue sample (p. 33, ¶[0309] – “nuclei were counted”; p. 37, ¶[0335]) prior to step (a) (Fig. 12A - #3; p. 33, ¶[0309] – “pooled”).
Regarding claims 12 and 13, Regev further discloses that the biomolecule is a protein (p. 5, ¶[0064] – nuclear pore complex).
Regarding claims 17 and 18, Regev further discloses that the presence of more than 2 biomolecules and more than 2 nucleic acids are determined (p. 9, ¶[0083] – “[the sample barcoded oligonucleotides] can be captured and sequenced together with mRNAs”, emphasis added).
Regarding claim 22, Regev further discloses encapsulating nuclei into droplets that also contain beads with barcoded oligonucleotides (Fig. 12A - #4).
Conclusion
No claims are allowed.
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/ALEXANDRA OLSON/Examiner, Art Unit 1684
/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684
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