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 .
Status of the Application
The Reply to Office Action filed October 15, 2025 is acknowledged.
Claims 1-7, 9-20, 22-23, 27-28 and 30-41 were pending. Claims 1, 3-7, 9-10, 16-19, 22, 27-28, 30, 32-33, 35-37 and 40-41 are being examined on the merits. Claims 2, 11-15, 20, 23, 31, 34 and 38-39 are canceled.
Response to Arguments
Applicant’s arguments filed October 15, 2025 have been fully considered.
All of the previously made objections and rejections are WITHDRAWN in view of Applicant’s arguments and claim amendments.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 36 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 36 recites that the unenriched sequencing library is a transcriptome sequencing
library. Claim 36 indirectly depends from claim 1, which has been amended to recite that the unenriched sequence library is generated by “amplifying barcoded nucleic acid molecules of the first plurality of barcoded nucleic acid molecules” and that the “first plurality of barcoded nucleic acid molecules” is in turn generated by reverse transcribing RNA molecules using a primer region comprising a “poly-T sequence”. The ordinary artisan would understand that using such a primer would generate a transcriptome library by hybridizing to the polyA tails of the mRNA molecules present in the reaction volume. This is also discussed in the instant specification (e.g., para. 237). Thus, regarding claim 36, it is not clear that the unenriched sequence library can comprise anything other than a transcriptome sequencing library. Consequently, claim 36 does not further limit claim 1 (or intervening claims 3, 4, 9, and 35), and is in improper dependent form.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Allowable Subject Matter
Claims 1, 3-7, 9-10, 16-19, 22, 27-28, 30, 32-33, 35, 37 and 40-41 are allowed.
The closest prior art is Vigneault1 (US Patent App. Pub. No. 2016/0032282), Agresti2 (US Patent App. Pub. No. 2016/0060621) and Brown3 (Profiling tissue-resident T cell repertoires by RNA sequencing, Genome Medicine, 7:125, 1-8, 2015), the teachings of each of which are discussed, at least, in the Non-Final Office Action mailed June 18, 2025. However, the references do not teach or suggest the instant claim 1 limitations requiring that the particle in each partition comprise first and second subsets of nucleic acid barcode molecules, wherein the nucleic acid barcode molecules in each of the first and second subsets comprise the same partition-specific barcode sequence, and further wherein each barcode molecule in the first subset additionally comprises a primer region comprising a poly-T sequence, while each barcode molecule in the second subset additionally comprises a primer region specific for a TCR or BCR constant region. Vigneault teaches embodiments where the particles comprise nucleic acid barcode molecules with primer regions comprising a poly-T sequence (e.g., para. 347) and different embodiments where the particles comprise nucleic acid barcode molecules with primer regions specific for a TCR or BCR constant region (e.g., para. 348). Vigneault additionally teaches that the nucleic acid barcode molecules can comprise primer regions with more than one target-specific sequence, e.g., an IgH mRNA and an IgL mRNA (para. 261). However, Vigneault does not teach an embodiment where the primer regions comprise a first subset with a poly-T sequence and a second subset with a target-specific sequence. Thus, Vigneault teaches multiplexing two target-specific reverse transcription reactions in the same partition and on the same particle, but neither Vigneault nor the other references teach or suggest multiplexing whole transcriptome reverse transcription (with the poly-T sequence) with target-specific reverse transcription in the same partition and on the same particle. Further, there would not appear to be any reason to modify the Vigneault method in such a manner, nor is it clear that there would be an expectation of success in the ordinary artisan made such a modification. Thus, independent claim 1 and its dependent claims are free of the art.
Conclusion
Claims 1, 3-7, 9-10, 16-19, 22, 27-28, 30, 32-33, 35-37 and 40-41 are being examined. Claims 1, 3-7, 9-10, 16-19, 22, 27-28, 30, 32-33, 35, 37 and 40-41 are allowed. Claim 36 is rejected.
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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/CAROLYN L GREENE/Examiner, Art Unit 1681
/GARY BENZION/Supervisory Patent Examiner, Art Unit 1681
1 Vigneault was cited in the Information Disclosure Statement submitted September 20, 2022.
2 Agresti was cited in the Information Disclosure Statement submitted September 20, 2022.
3 Brown was cited in the PTO-892 Notice of References Cited mailed February 29, 2024.