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 .
DETAILED ACTION
1. The applicant’s response to the office action filed on March 09, 2026 is acknowledged.
Status of the Application
2. Claims 1, 8, 10, 11, 13, 16, 18, 20, 25, 40-41, 52, 58, 61, 70 are pending under examination. New claims 115-119 are added. Claims 66-67 are previously withdrawn from further consideration as being drawn to non-elected group. Claims 6, 11, 14 and 16-56 were canceled. The Applicant’s arguments and the amendment have been fully considered and found persuasive in-part for the following reasons.
Objection to the specification-Withdrawn
3. The objection to the specification has been withdrawn in view of the amendment.
Claim Rejections - 35 USC § 102-Maintained
4. 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.
Claims 1, 8, 10-11, 13, 16, 18, 20, 25, 40-41, 52, 58, 61 and 115-119 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Agresti et al. (US 2016/0060621).
Agresti et al. teach a method of claim 1, for analyzing a target nucleic acid from a cell comprising: linking an oligonucleotide tag (barcode oligonucleotide) in a discrete partition to a target nucleic acid attached, thereby producing a barcoded target nucleic acid (para 0115, 0020-0032: indicating ligating or linking barcode oligonucleotide to a target nucleic acid of a cell in a partition or droplet), wherein the discrete partition comprises: (i) a target nucleic acid derived from a single cell, at least a part of which
target nucleic acids being added with oligonucleotide adapter sequences to become the target nucleic acids attached (para 0020-0022, 0036-0039, 0067-0068): and (ii) a solid support comprising an oligonucleotide tag attached, the oligonucleotide tag (hairpin barcode oligonucleotide) comprising a first chain and a second chain, the first chain comprising a barcode sequence and a hybridization sequence located at the 3' end of the barcode sequence, the second chain comprising a first portion complementary to the hybridization sequence of the first chain and a second portion complementary to the oligonucleotide adapter sequence attached to the target nucleic acid, and the first chain and the second chain forming a partially double- stranded structure, or the second chain and the target nucleic acid attached form a partially double-stranded structure (hairpin structure) (para 0068-0069, 0180-0181, 0115-0118); wherein the oligonucleotide tag is releasably attached to the solid support (para 0069-0070); and the method comprises releasing the oligonucleotide tag from the solid support and linking the released oligonucleotide tag to the target nucleic acid attached in step ii), thereby producing a barcoded target nucleic acid (para 0070), wherein a ligase in the discrete partition links the oligonucleotide tag to the target nucleic acid attached (para 0115, 0070); and wherein ii) comprises hybridizing the second portion of the second chain in the oligonucleotide tag with the oligonucleotide adapter attached to the target nucleic acid, and linking the hybridization sequence of the first chain in the oligonucleotide tag to the oligonucleotide adapter attached to the target nucleic acid, thereby producing the barcoded target nucleic acid (para 0068-0069, 0180-0182, 0115-0118).
With reference to claim 8, 10, Agresti et al. teach that the solid support is a bead and the discrete partition is a hole or droplet (para 0058, 0007).
With reference to claim 11, Agresti et al. teach that the barcode sequence comprises a cell barcode sequence, and each oligonucleotide tag attached to the same solid support comprises the same cell barcode sequence (para 0058-0061, 0118).
With reference to claim 13, Agresti et al. teach that the method further comprising, before the linking: co-distributing the target nucleic acid derived from the single cell and the solid support attached with at least one oligonucleotide tag into the discrete partition (para 0176).
With reference to claim 16, Agresti et al. teach that the target nucleic acid attached comprises a unique molecular identification region (para 0005, 0008).
With reference to claim 18, Agresti et al. teach that the oligonucleotide tag further comprises an amplification primer recognition region (para 0014, 0023).
With reference to claim 20, Agresti et al. teach that the method further comprising: obtaining a characterization result of the barcoded target nucleic acid; and identifying the sequence of the target nucleic acid as deriving from the single cell based at least in part on the presence of the same cell barcode sequence in the characterization result obtained in the obtaining (para 0096).
With reference to claim 25, Agresti et al. teach that each of the discrete partitions comprises at most the target nucleic acids derived from the single cell (para 0020-0021).
With reference to claim 40, Agresti et al. teach that the method further comprising: releasing at least a part of the target nucleic acids from the single cell in the discrete partition to the outside of the cell, as released target nucleic acids; and linking the released target nucleic acids to the oligonucleotide tags in the linking, thereby producing the barcoded target nucleic acid (para 0020-0021).
With reference to claim 41, Agresti et al. teach that the method further comprising: introducing at least a part of the oligonucleotide tags released from the solid support into the single cell, as released oligonucleotide tags; and linking them-the released oligonucleotide tags to the target nucleic acids the linking, thereby producing barcoded target nucleic acids (para 0115-0118).
With reference to claim 52, 58, Agresti et al. teach that the method further comprising: reverse transcribing the RNA before the linking; and generating the target nucleic acid attached and fragmenting DNA derived from the single cell before the linking wherein the target nucleic acid attached is generated after or during the fragmentation (para 0065, 0027, 0038-0039).
With reference to claim 61, Agresti et al. teach that the method further comprising: fragmenting DNA derived from the single cell before the linking wherein the fragmenting comprises integrating the sequence comprising the oligonucleotide adapter into the DNA with a transposase-nucleic acid complex, and releasing the transposase to obtain the target nucleic acid attached (para 0022, 0065).
With reference to claim 115, 117-119, Agresti et al. teach that the ligase includes T4 ligase and the target nucleic acid comprises DNA, RNA or cDNA or genomic DNA (para 0076-0078, 0068-0069, 0007).
With reference to claim 116, Agresti et al. teach that the target nucleic acid comprises an exogenous nucleic acid comprise that linked to protein, which can bind to target molecules in the cell (para 0049-0051, 0064, 0175). For all the above the claims are anticipated.
Response to Arguments:
With reference to the rejection of claims under 35 USC102(a)(1) as being anticipated by Agresti et al. the Applicant’s arguments and the amendment have been fully considered and found persuasive in-part. The rejection of claim 70 is withdrawn in view of the amendment. With reference to the rejection of claims 1, 8, 10-11, 13, 16, 18, 20, 25, 40-41, 52, 58, 61, the amendment incorporating the limitations of canceled claims did not change the scope of the claims because as discussed in the previous office action Agresti et al. teach the limitations of the canceled claims. The rejection has been maintained restated to address the amendment and include new claim limitations.
New Rejections Necessitated by the Amendment
Claim Rejections - 35 USC § 112
5. 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.
A. Claims 1, 8, 10, 11, 13, 16, 18, 20, 25, 40-41, 52, 58, 61 and 70 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. The claim 1 and 70 recites step ‘b)’. It is unclear and indefinite because it is not clear if the b) is referring to step ii) or does it refer to any additional method step.
B. Claim 70 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 70 recites the limitation "the single nucleic acid sequence in the barcoded target nucleic acid" in wherein clause of b). There is insufficient antecedent basis for this limitation in the claim. The limitation is unclear and indefinite because the limitation lacks support in the preceding lines of the claim and it is not clear what the limitation is referring to in the claim.
Conclusion
Claim 70 is free of prior art.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
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Suryaprabha Chunduru
Primary Examiner
Art Unit 1681
/SURYAPRABHA CHUNDURU/Primary Examiner, Art Unit 1681
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