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
Claim(s) 77-95 are pending and under examination
Applicant’s election without traverse of Group I, which includes Claims 77-95 in the reply filed on 02/10/2026 is acknowledged.
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.
Claim(s) 77-92 and 95 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Lebofsky rt al. (US20200385791A1, EFD: June 14th 2019)
Regarding claims 77 and 88, Lebofsky discloses method for sample processing, comprising:
a) providing a partition comprising a support comprising: (i) a first set of nucleic acid barcode molecules, wherein first nucleic acid molecules of said first set of nucleic acid barcode molecules comprise a barcode sequence; (ii) a second set of nucleic acid barcode molecules, wherein second nucleic acid molecules of said second set of nucleic acid barcode molecules comprise said barcode sequence; (e.g. method comprising: a) providing a plurality of partitions wherein at least some partitions comprise multiple solid supports, where each solid support is linked to (i) a plurality of first solid support oligonucleotides and (ii) one or more second oligonucleotides; wherein both first and second oligonucleotides comprises the same support specific barcode sequence [¶0135, 0197, 0204])
b) using a first nucleic acid barcode molecule of said first nucleic acid barcode molecules and a second nucleic acid barcode molecule of said second nucleic acid barcode molecules to generate a barcoded nucleic acid molecule comprising: (i) a first region comprising said barcode sequence, or a complement thereof and (ii) a second region comprising said barcode sequence, or a complement thereof, wherein said first region and said second region are different. (e.g. b) releasing the first and second oligonucleotides from the solid supports; c) hybridizing of first solid support oligonucleotides to second oligonucleotides in the presence of a first polymerase to generate extended first solid support oligonucleotides that comprise a complement of the second oligonucleotide [¶0135])
Regarding claim 78, Lebofsky further discloses said partition further comprises an additional support comprising (i) a third set of nucleic acid barcode molecules and (ii) a fourth set of nucleic acid barcode molecules, wherein third nucleic acid molecules of said third set of nucleic acid barcode molecules comprise an additional barcode sequence and fourth nucleic acid molecules of said fourth set of barcode molecules comprise said additional barcode sequence. (e.g. partition comprising two or more solid supports, where each solid support comprises first and second oligonucleotide bearing support specific barcode [¶0204]. The first and second oligonucleotide populations on additional support(s) correspond to the claimed third and fourth oligonucleotide sets. )
Regarding claim 79, Lebofsky further discloses using said second nucleic acid molecules and said third nucleic acid molecules to generate a second barcoded nucleic acid molecule comprising said barcode sequence and said additional barcode sequence. (e.g. releasing oligonucleotides from each solid supports, extending first capture oligonucleotide using second oligonucleotide as template (both from same support), then the extended product from different supports pair with each other at complementary palindromic sequences. They are further extended, creating double strand DNA product contain barcodes from both supports [¶0135])
Regarding claims 80 and 81, Lebofsky further discloses sequencing said second barcoded nucleic acid molecule, generating a sequence read of said second barcoded nucleic acid molecule, thus identifying the two supports that were in the partition. (e.g. e) sequencing one or both strands of the double-stranded polynucleotides, wherein sequences comprising two different barcodes indicates the presence of two solid supports in the same partition. [¶0135])
Regarding claim 82, Lebofsky further discloses first nucleic acid barcode molecules further comprise a unique molecular index (e.g. particle specific barcode/ molecular barcode maybe included in primer during reverse transcription or incorporated into a solid or hydrogel support (e.g., a solid bead or particle or hydrogel bead or particle) [¶0079-0082])
Regarding claims 83-86, Lebofsky further discloses first set of nucleic acid barcode molecules comprise a multiplet identification sequence; wherein said multiplet identification sequence comprises a capture sequence. (e.g. the first oligonucleotide comprises a capture sequence that hybridize with the second oligonucleotides and initiate extension (steps a-c). The whole workflow (steps a-e) generates products that identify multiple supports within a partition. [¶0135]).
Regarding claim 87, Lebofsky further discloses capture sequence comprises a poly-T sequence and said sequence complementary to said capture sequence comprises a poly-A sequence (In some embodiments, the capture sequence comprises poly dT [¶0037, 0113, 0122, 0129, 0196])
Regarding claim 89, Lebofsky further discloses partition is a droplet or microwell. [¶0012, 0038, 0047, 0078]
Regarding claims 90 and 91, Lebofsky further discloses amount of said first nucleic acid barcode molecules on said support is higher than said amount of said second nucleic acid barcode molecules on said support. (e.g. the ratio of first solid support oligonucleotides to second oligonucleotides is at least at least 5:1, 10:1, 100:1, 1000:1, 5000:1, 10000:1, 20000:1; 30000:1. 40000:1, 50000:1; 60000:1, 70000:1; 80000:1, 90000:1, or 100000:1 [¶0135])
Regarding claim 92, Lebofsky discloses method for sample processing, comprising: partitioning a plurality of supports in a plurality of partitions, wherein a support of said plurality of supports comprises (i) a first set of nucleic acid barcode molecules, wherein first nucleic acid molecules of said first set of nucleic barcode molecules are configured to capture a target nucleic acid and (ii) a second set of nucleic acid barcode molecules, wherein second nucleic acid molecules of said second set of nucleic acid barcode molecules are configured to interact with said first nucleic acid barcode molecules, and wherein said first nucleic acid barcode molecules comprise a barcode sequence and said second nucleic acid barcode molecules comprises said barcode sequence. (e.g. method comprising: a) providing a plurality of partitions wherein at least some partitions comprise multiple solid supports, where each solid support is linked to (i) a plurality of first solid support oligonucleotides and (ii) one or more second oligonucleotides; wherein both first and second oligonucleotides comprises the same support specific barcode sequence [¶0135, 0197, 0204]. Capture sequence maybe a a gene-specific sequence [¶0037, 0122, 0129, 0196]. The second oligonucleotides comprise sequence complementary to the first oligonucleotide’s capture sequence, thus allow interaction with first oligo nucleotide [¶0135])
Regarding claim 95, Lebofsky discloses partitioning generates a plurality of partitions and wherein a partition of said plurality of partitions comprises at least one support of said plurality of supports. (e.g. a) providing a plurality of partitions wherein at least some partitions comprise multiple solid supports [¶0135])
Claim Rejections - 35 USC § 103
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 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Lebofsky et al. and Habib et al.
Claim(s) 93 is/are rejected under 35 U.S.C. 103 as being unpatentable over by Lebofsky rt al. (US20200385791A1, EFD: June 14th 2019) in view of Habib et al. (Nat Methods. 2017;14(10):955-958).
Regarding claim 93, Lebofsky does not disclose partitioning is performed by Poisson loading.
Habib discloses Poisson loading of nucleis and/or beads [“Coencapsulation of nuclei and barcode beads” section]
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to use Poisson loading as partitioning method in Lebofsky’s detection method because Poisson loading is a well-known method in the art of microfluidics and is used in high-throughput sequencing methods such as DroNc-seq and Drop-seq [“Coencapsulation of nuclei and barcode beads” section]. This modification would constitute combining known elements according to known methods to yield predictable results. See KSR International Co. v. Teleflex Inc., 550 U.S. 398, 415-421, USPQ2d 1385, 1395 — 97 (2007) (MPEP § 2143, A, D).
Lebofsky et al. and Love et al.
Claim(s) 94 is/are rejected under 35 U.S.C. 103 as being unpatentable over by Lebofsky rt al. (US20200385791A1, EFD: June 14th 2019) in view of Love et al. (US20190218607A1, EFD: December 7th , 2017).
Regarding claim 94, Lebofsky does not disclose partitioning is performed by super-Poisson loading.
Love discloses super-Poisson loading the array of wells with cells and/or beads [¶0240].
As of the application’ s effective filing date, it would have been prima facie obvious to a person of ordinary skill in the art to use super-Poisson loading as partitioning method in Lebofsky’s detection method because super-Poisson loading results in a high number of usable wells (e.g., those having a single cell and/or a single bead) [0348-0352].
Conclusion
No claims are allowed
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Khai Quynh Tien Pham whose telephone number is (571)272-6998. The examiner can normally be reached M-T, 9-4 ET.
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/KHAI QUYNH TIEN PHAM/Examiner, Art Unit 1684
/JEREMY C FLINDERS/Primary Examiner, Art Unit 1684
