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 September 17, 2025 is acknowledged.
Status of the Application
2. Claims 9-36 and 39-40 are pending under examination. Claims 1-8, 37-38 were canceled. The Applicant’s arguments have been fully considered and found persuasive in-part for the reasons that follow.
Maintained Claim Rejections - 35 USC § 102
3. 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 9-36 and 39-40 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Abate et al. (US 2017/0009274).
Abate et al. teach method of claim 9, comprising: (a) providing a plurality of different nucleic acid analytes (nucleic acid target sequences) derived from one or more cells; (b) ligating different combination of nucleic acid analytes to generate a plurality of different nucleic acid analyte together to generate a plurality of templates; (c) partitioning, into a partition (discrete entity or droplet) among a plurality of partitions: (i) a template of the plurality of templates or a product thereof, wherein the template comprises a combination of nucleic acid analytes of different nucleic acid analytes and (ii) a plurality of barcode molecules comprising a partition-specific barcode sequence; and (d) generating a plurality of amplicons within the partition using the template and the plurality of barcode molecules, wherein amplicons of the plurality of amplicons comprise (i) the partition-specific barcode sequence, and (ii) an overlapping sequence of the template or complement thereof (para 0267-0272, 0122-0134, 0137-0140, 0278, 0217, 1420, 0026-0033, 0140, 0197-0201, 1344-1445).
With reference to claim 10, Abate et al. teach that the method further comprises sequencing the plurality of amplicons or derivatives thereof to obtain a plurality of sequence reads, wherein sequence reads of the plurality of sequence reads comprise the partition-specific barcode sequence or complement thereof and the overlapping sequence of the template or complement thereof. (para 0026-0029, 0122, 0140, 0131-0135, 0197-0201, 1344-1450).
With reference to claim 11, Abate et al. teach that the method further comprises assembling the sequence reads of the plurality of sequence reads based on the overlapping sequence of the template or complement thereof to generate an assembled template sequence (para 0026-0031, 0122).
With reference to claim 12, Abate et al. teach that the ligating the plurality of different nucleic acid analytes comprises random ligation (para 0096-0097).
With reference to claim 13, Abate et al. teach that the assembled template sequence comprises sequences of combination of nucleic acid analytes comprised by the template (para 0026-0031, 0122, 1448, 0217-0220).
With reference to claim 14-16, 25, Abate et al. teach that the assembled template sequence comprises a contiguous sequence of the combination of nucleic acid analytes comprised by the template, the combination of the nucleic acid analytes comprised by the template, identifies the template from other templates of the plurality of templates by a combination and an arrangement of the nucleic acid (para 0217-0218, 0122).
With reference to claim 17-18, 21, Abate et al. teach that the plurality of different nucleic acid analytes comprises single-stranded, double-stranded nucleic acids or cDNA (para 0051, 0071, 0031).
With reference to claim 19-20, 22, Abate et al. teach that the assembled template sequence comprises a full-length sequence of a nucleic acid analyte of combination of nucleic acid analytes comprised by the template, said full-length sequence is a cDNA (para 0031).
With reference to claim 23, Abate et al. teach that the cDNA molecules are generated from RNA molecules from one or more cells, and wherein the cDNA molecules comprise cell-specific barcode sequences associated with cells from which the cDNAs are derived (para 0091, 0031-0032).
With reference to claim 24, Abate et al. teach that the combination of nucleic acid analytes comprised by the template is a combination of cDNA molecules and cDNA molecules do not comprise a unique molecular identifier (para 0033).
With reference to claim 26-28, Abate et al. teach that the plurality of different nucleic acid analytes derived from one or more cells, analytes comprise cell-free DNA or circulating cell-free DNA (para 0305-0306, 0031, 1155).
With reference to claim 29-30, Abate et al. teach that the plurality of barcode molecules is a plurality of barcoded amplification primers, the barcoded amplification primers comprise random N-mer priming sequences (para 0090-0097).
With reference to claim 31, Abate et al. teach that step c) comprises co-partitioning into the partition: i) the template, and ii) a particle coupled to the plurality of barcoded amplification primers; and wherein the method further comprises releasing the barcoded amplification primers from the particle in the partition (para 0120, 0133, 0136-0138, 0096-0099).
With reference to claim 32, Abate et al. teach that the partition is a droplet or a well (para 0080).
With reference to claim 33, Abate et al. teach that the template is a circular template (para 0051, 0071).
With reference to claim 34, Abate et al. teach that the combination of nucleic acid analytes of the template is a ligation product of at least 5 different nucleic acid analyte molecules (para 0217).
With reference to claim 35-36, Abate et al. teach that wherein the template is a circular template, wherein the method comprises performing rolling circle amplification of the circular template to generate a rolling circle amplification product (RCP), and wherein the partition comprises the RCP or a fragment of the RCP, wherein the method comprises fragmenting the RCP, and wherein the partition comprises a fragment of the RCP (para 0109-0111, 0187-0189, 1160).
With reference to claim 39, Abate et al. teach that the method further comprising generating the plurality of partitions (discrete entities) (para 0089).
With reference to claim 40, Abate et al. teach that the method further comprising: (e) obtaining sequence reads of the amplicons or derivatives thereof, wherein the sequence reads comprise the partition-specific barcode sequence or complement thereof and the overlapping sequence of the template or complement thereof; and (f) assembling the sequence reads based on the overlapping sequence of the template or complement thereof to generate an assembled sequence (para 0026, 0031, 0117-0124, 0197-0201). For all the above the claims are anticipated.
Response to Arguments:
With reference to the rejection of claims 9-36 and 39-40 under 35 USC 102(a)(1) as being anticipated by Abate et al., the Applicant’s arguments and the amendment have been fully considered and found unpersuasive. The amendment did no change the scope of the claims because Abate et al. teach said limitations. Abate et al. teach plurality of different nucleic acid analytes (target nucleic acids) from one or more cells and ligating, fusing, linking or connecting together by overlap extension said different nucleic acid analytes to generate plurality of templates (para 0267-0272, 0278, 0122-0132, 0137-0140, 01160-1204, 1344, 1461, 0217, 0110-0113, 0026). With reference to the Applicant’s arguments drawn to examiner cited paragraphs 0134 and 01384, the arguments were found unpersuasive because said paragraphs teach one of the alternative steps to ligate nucleic acids, that is by ligation through adaptors and the broader scope of the limitation ‘ligating’ in claim 9 is within the scope of the ligating, fusing, linking or connecting by overlap extension of target nucleic acids as taught by Abate et al. For all the above the rejection has been maintained and restated to address the amendment.
Double Patenting-Withdrawn
4. The rejection of claims under obviousness type of double patenting has been withdrawn in view of the terminal disclaimer.
Conclusion
No claims are allowable.
THIS ACTION IS MADE FINAL. 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