DETAILED ACTION
Status of the Claims
Claims 1-4, 6, 10, 18, 20, 28-29, 31-39, and 43 are currently pending and examined herein.
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 Objections
Claims 18, 20, and 32 are objected to because of the following informalities:
Claim 18 recites “wherein the introducing comprising” instead of “comprises”;
Claim 20 recites “to comprise” which should be “comprising”; and
Claim 32 recites "encapsulated singles" instead of "encapsulated single cells". Appropriate correction is required.
Claim Interpretation
Claim 36 recites the limitation “a sequence-able nucleic acid library”. The term “sequence-able” does not have an accepted meaning in the art and is not defined in the specification. Therefore, the broadest reasonable interpretation of “a sequence-able nucleic acid library” is a collection of nucleic acid molecules that is able to be sequenced using any method known in the art, such as Sanger sequencing, Next Generation Sequencing (NGS), or nanopore sequencing.
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 31 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 31 recites the limitation "encapsulated single cell droplets" in line 2. There is insufficient antecedent basis for this limitation in the claim as “droplets” is not recited in the instant claim nor in the claim on which it is dependent (claim 1). For the purposes of examination, this limitation will be interpreted as “encapsulated single cells” as recited in claim 1. This rejection can be overcome by omitting “droplets” in claim 31 or by making the claim dependent on a prior claim that recites the “droplets” limitation, such as claim 10. Other solutions are possible.
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.
McDermott et al.
Claims 1-4, 6, 10, 18, 20, 28-29, and 31-38 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by McDermott et al. (PGPub No: US 2022/0236258 A1).
Regarding claim 1, McDermott teaches a method of producing partitioned single cell/barcoded bead compositions (Fig. 11), comprising:
contacting a composition of encapsulated single cells (e.g., cell beads/microcapsules each encapsulating a single cell as per ¶ [0273]) with a plurality of microwells such that at least a portion of the plurality of microwells comprise a sole deposited encapsulated single cell (¶ [0273]); and
introducing barcoded beads (p. 38, ¶ [0270], lines 1-3) into microwells comprising deposited single cells to produce single cell/barcoded bead compositions (p. 38, ¶ [0270]).
Regarding claim 2, McDermott further teaches that the encapsulated single cells have a size that corresponds to the size of the microwells such that only one encapsulated single cell can fit into a microwell (p. 38, ¶ [0271], lines 14-19).
Regarding claim 3, McDermott further teaches that the size of the encapsulated single cell ranges from 10 to 100 μm (p. 14, ¶ [0119]).
Regarding claims 4 and 18, McDermott discloses that the contacting comprises flowing the composition of encapsulated single cells across openings of the plurality of microwells and/or flowing a composition of barcoded beads across openings of microwells comprising deposited single cells (p. 38, ¶ [0271]).
Regarding claim 6, McDermott further teaches that the contacting results in a majority of the plurality of microwells comprising a sole deposited encapsulated single cell (p. 38, ¶ [0271]).
Regarding claim 10, McDermott also discloses that the encapsulated single cells comprise gel encapsulated single cells or double emulsion single cell droplets (p. 9, ¶ [0090]).
Regarding claim 20, McDermott discloses that the introducing results in a majority of the microwells of the plurality of microwells comprising a single cell and a single bead (p. 38, ¶ [0271], lines 11-12)
Regarding claims 28 and 29, McDermott discloses that the method further comprises assessing the plurality of microwells following the contacting and/or introducing (p. 39, ¶ [0275])
Regarding claims 31-34, McDermott teaches producing the encapsulated single cells (p. 23, ¶ [0174], lines 15-18]). McDermott also teaches that the producing comprises preparing an initial composition of encapsulated single cells and selecting encapsulated single cells of interest from the initial composition to produce the composition of encapsulated single cells (p. 23, ¶ [0174], lines 39-41). Additionally, McDermott further teaches that the selecting comprises cell sorting (p. 23, ¶ [0174], line 9) and that the cell sorting optionally comprises fluorescence-activated cell sorting (FACS) (p. 23, ¶ [0174], lines 3-4).
Regarding claims 35-38, McDermott discloses lysing cells of partitioned single cell/barcoded bead compositions to release nucleic acids from the cells (p. 39, ¶ [0276], lines 7-9) and producing barcoded beads comprising hybridized released nucleic acids (p. 39, ¶ [0276], lines 17-20). McDermott further discloses preparing a sequence-able nucleic acid library from the barcoded beads comprising hybridized released nucleic acids ¶ p. 39, ¶ [0276], lines 20-23) and sequencing the nucleic acid library (p. 39, ¶ [0276], lines 23-24) via NGS (p. 8, ¶ [0083], lines 7-11).
Fu et al.
Claims 39 and 43 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by Fu et al. (PGPub No: US 2016/0289740 A1).
Regarding claim 39, Fu teaches a microwell array wherein a majority (p. 22, ¶ [0165]; p. 24, ¶ [0179], lines 5-6) of the microwells of the microwell array comprises both a single cell (p. 16, ¶ [ 0117], lines 9-12) and a barcoded bead (p. 12, ¶ [0082]).
Regarding claim 43, Fu further teaches that the microwell array is present on a bottom surface of a flow cell (p. 37, ¶ [0298]).
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.
U.S. 11,408,812
Claims 1 and 31-33 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4-5, and 13-14 of U.S. Patent No. 11408812. Although the claims at issue are not identical, they are not patentably distinct from each other because:
Regarding claim 1, the reference application discloses a method comprising contacting a composition of encapsulated cells with a plurality of microwells such that at least a portion of the plurality of microwells comprise a sole deposited encapsulated single cell (claim 1) and introducing (claim 4) barcoded beads (claim 5) into microwells comprising deposited single cells to produce partitioned single cell/barcoded bead compositions.
Regarding claims 31-33, the reference application additionally discloses producing the encapsulated single cells (claim 1 and 13), that the producing comprises selecting encapsulated single cells of interest (claim 1 and 14), and that the selecting comprises cell sorting (claim 14).
U.S. 17/174,249
Claims 1 and 35-37 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 4, 7, 14, and 19 of copending Application No. 17174249 in view of McDermott et al.
Regarding claim 1, the reference application discloses a method comprising contacting a composition of single cells with a plurality of partitions such that at least a portion of the plurality of partitions comprise a sole deposited single cell (claim 4) and introducing barcoded beads (claim 19) into partitions comprising deposited single cells (claim 4). The differences between the instant and reference applications are that the reference application does not claim microwells, nor does it claim encapsulated single cells.
While the reference application discloses depositing single cells into partitions, it does not claim that the partitions are microwells. However, one of ordinary skill in the art would recognize that microwells are an obvious variant of a partition. Indeed, this is evidenced by the specification of the reference application which discloses that, “In some embodiments, the partition is a well or a droplet” (p. 10, ¶ [0019]). The use of the disclosure to determine the scope of “partition” is appropriate in this case because, while the disclosure of a reference application cannot be used as prior art in a double patenting rejection, MPEP § 804(II)(B)(1) states that:
Further, those portions of the specification which provide support for the reference claims may also be examined and considered when addressing the issue of whether a claim in the application defines an obvious variation of an invention claimed in the reference patent or application.
The reference application also does not disclose encapsulation of the single cells. As discussed in paragraph 8a of this action, McDermott discloses partitioning of encapsulated single cells. Furthermore, McDermott states that “encapsulated biological particles can provide certain potential advantages” such as withstanding longer storage time, allowing for longer incubation times, and their ability to be deposited into other partitions. Furthermore, based on the methods of McDermott, it is clear that applying the encapsulated single cells to the method disclosed in the reference application would have a reasonable expectation of success. Therefore, the method of claim 1 of the instant application are rendered obvious over the reference application in view of McDermott.
Regarding claims 35-37, the reference application further discloses lysing cells of partitioned single cell/barcoded bead compositions (claim 14) to release nucleic acids form the cells and produce barcoded beads comprising hybridized released nucleic acids (claim 7). It further discloses preparing and sequencing a sequence-able nucleic acid library from the barcoded beads comprising hybridized released nucleic acids (claim 7).
This is a provisional nonstatutory double patenting rejection.
U.S. 17/531,555
Claim 1 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 5 of copending Application No. 17531555 in view of McDermott.
Regarding claim 1, the reference application discloses a method comprising contacting a composition of single cells with a plurality of microwells such that at least a portion of the plurality of microwells comprise a sole deposited single cell (claim 5) and introducing barcodes into microwells comprising deposited single cells (claim 5). The reference application does not teach encapsulation of the single cells, nor that the barcodes comprise barcoded beads.
McDermott discloses encapsulation of single cells and motivation for applying this method to the reference application as discussed in paragraph 12a above. Additionally, McDermott teaches barcoded beads as discussed herein in paragraph 8a. McDermott also discloses that barcodes can be attached to a bead in order to aid in their delivery to a particular partition, allowing for accurate assignment downstream information. Based on the disclosure and teachings of McDermott, it would have been obvious to one of ordinary skill in the art to apply the barcoded beads of McDermott to the barcodes of the reference application with a reasonable expectation of success.
This is a provisional nonstatutory double patenting rejection.
Conclusion
No claims are allowed.
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/ALEXANDRA OLSON/Examiner, Art Unit 1684
/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684