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
This Non-Final Office Action is responsive to the communication received 05/08/2026.
Election/Restrictions
Applicant’s election without traverse in the Reply filed on 05/08/2026 of Group I, Claim(s) 1, 4 and 62-78 is acknowledged.
Applicant has elected without traverse in the Reply filed on 05/08/2026 the following species:
A. analyzing the amplified barcoded cDNAs comprises: determining an expression profile of each of one or more of the RNA targets using a number of UMIs with different sequences associated with the RNA target in the sequencing information; and determining an expression profile of the second RNA target using a number of UMIs with different sequences associated with the second RNA target in the sequencing information (claim 78)
The Restriction/Election Requirements are deemed proper and are made FINAL.
Claims 1, 4, 6 and 62-78 are pending.
Claim 6 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the Reply filed on 05/08/2026.
Claim 4 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species, there being no allowable generic or linking claim. Election was made without traverse in the Reply filed on 05/08/2026.
Claims 1 and 62-78 are under examination in this Office Action.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1 and 62-78 are rejected under 35 U.S.C. 101 because the claimed invention is directed to nonstatutory subject matter. The claim(s) does/do not fall within at least one of the four categories of patent eligible subject matter because the claimed invention is directed to a judicial exception, an abstract idea (mental processes), without significantly more. Claims 62-78 depend directly or indirectly from claim 1.
The claim 1 limitation directed to an abstract idea (mental processes) is amplifying the barcoded cDNAs; and analyzing the amplified barcoded cDNAs, or products thereof.
The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claim recites additional elements that consist of well understood, routine, conventional activity already engaged in by the scientific community.
The claim 1 limitations directed to well understood, routine, conventional activity already engaged in by the scientific community are a method for single cell analysis comprising: partitioning a cell and a bead attached with a plurality of barcode oligonucleotides into a partition, wherein each barcode oligonucleotide of the plurality of barcode oligonucleotides comprises a cell barcode and a unique molecular identifier (UMI), wherein first barcode oligonucleotides of the plurality of barcode oligonucleotides each comprises a poly-dT sequence capable of binding to a poly-A tail of a first messenger ribonucleic acid (mRNA) target, wherein second barcode oligonucleotides of the plurality of barcode oligonucleotides each comprises a probe sequence and optionally a poly-dT sequence, and wherein the probe sequence is a non-poly-dT sequence and is capable of binding to a second RNA target at a sequence that is not a poly-A sequence; hybridizing the first barcode oligonucleotides and the second barcode oligonucleotides attached to the bead in the partition with RNA targets associated with the cell in the partition; reverse transcribing the RNA targets hybridized to the first barcode oligonucleotides and the second barcode oligonucleotides to generate barcoded complementary deoxyribonucleic acids (cDNAs). Belhocine et al. (08/15/2019) PCT International Patent Application Publication WO 2019/157529 A1 cited in the 6/11/2024 IDS (hereinafter referred to as "Belhocine") teaches a method for single cell analysis comprising: partitioning a cell and a bead attached with a plurality of barcode oligonucleotides into a partition, wherein each barcode oligonucleotide of the plurality of barcode oligonucleotides comprises a cell barcode and a unique molecular identifier (UMI), wherein first barcode oligonucleotides of the plurality of barcode oligonucleotides each comprises a poly-dT sequence capable of binding to a poly-A tail of a first messenger ribonucleic acid (mRNA) target, wherein second barcode oligonucleotides of the plurality of barcode oligonucleotides each comprises a probe sequence and optionally a poly-dT sequence, and wherein the probe sequence is a non-poly-dT sequence and is capable of binding to a second RNA target at a sequence that is not a poly-A sequence; hybridizing the first barcode oligonucleotides and the second barcode oligonucleotides attached to the bead in the partition with RNA targets associated with the cell in the partition; reverse transcribing the RNA targets hybridized to the first barcode oligonucleotides and the second barcode oligonucleotides to generate barcoded complementary deoxyribonucleic acids (cDNAs) (see Figure 10D, [0005] to [0021] and [00322] to [00406]).
Claim Rejections - 35 USC § 102
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 and 62-78 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Belhocine et al. (08/15/2019) PCT International Patent Application Publication WO 2019/157529 A1 cited in the 6/11/2024 IDS (hereinafter referred to as "Belhocine").
With regards to claims 1 and 62-78, Belhocine teaches:
a) as in claims 1 and 62-78, a method for single cell analysis comprising: partitioning a cell and a bead attached with a plurality of barcode oligonucleotides into a partition, wherein each barcode oligonucleotide of the plurality of barcode oligonucleotides comprises a cell barcode and a unique molecular identifier (UMI), wherein first barcode oligonucleotides of the plurality of barcode oligonucleotides each comprises a poly-dT sequence capable of binding to a poly-A tail of a first messenger ribonucleic acid (mRNA) target, wherein second barcode oligonucleotides of the plurality of barcode oligonucleotides each comprises a probe sequence and optionally a poly-dT sequence, and wherein the probe sequence is a non-poly-dT sequence and is capable of binding to a second RNA target at a sequence that is not a poly-A sequence; hybridizing the first barcode oligonucleotides and the second barcode oligonucleotides attached to the bead in the partition with RNA targets associated with the cell in the partition; reverse transcribing the RNA targets hybridized to the first barcode oligonucleotides and the second barcode oligonucleotides to generate barcoded complementary deoxyribonucleic acids (cDNAs); amplifying the barcoded cDNAs; and analyzing the amplified barcoded cDNAs, or products thereof; wherein barcoding the nucleic acids associated with the cell comprises: hybridizing the first barcode oligonucleotides and the second barcode oligonucleotides attached to the bead in each partition of the partitions with nucleic acid targets associated with the cell in the partition; extending the first barcode oligonucleotides and the second barcode oligonucleotides attached to the bead and hybridized to the nucleic acid targets using the nucleic acids as templates to generate single-stranded barcoded nucleic acids; and generating double-stranded barcoded nucleic acids from the single-stranded barcoded nucleic acids; wherein extending the single-stranded barcoded nucleic acids comprises further extending the single-stranded barcoded nucleic acids using a template switching oligonucleotide; comprising pooling the beads prior to or subsequent to extending the first barcode oligonucleotides and the second barcode oligonucleotides attached to the bead to generate the single-stranded barcoded nucleic acids or prior to or subsequent to generating the double-stranded barcoded nucleic acids; wherein extending the first barcode oligonucleotides and the second barcode oligonucleotides attached to the bead and hybridized to the nucleic acid targets comprises extending the first barcode oligonucleotides and the second barcode oligonucleotides attached to the bead and hybridized to the nucleic acid targets in bulk or in the partition, and wherein generating the double-stranded barcoded nucleic acids comprises generating the double-stranded barcoded nucleic acids from the single-stranded barcoded nucleic acids in bulk or in the partition; comprising: amplifying the barcoded nucleic acid to generate amplified barcoded nucleic acids; processing the amplified barcoded nucleic acids to generate processed barcoded nucleic sequencing the processed barcoded nucleic acids; wherein processing the amplified barcoded nucleic acids comprises: fragmenting the amplified barcoded nucleic acids to generate fragmented barcoded nucleic acids; adding a second polymerase chain reaction (PCR) primer-binding sequence; and generating processed barcoded nucleic acids comprising sequencing primer sequences from the fragmented barcoded nucleic acids; wherein at least 50% of partitions of the plurality of partitions comprise a single cell of the plurality of cells and a single bead of the plurality of beads; wherein the probe sequences of barcode oligonucleotides of the plurality of barcode oligonucleotides comprise a degenerate sequence, wherein the degenerate sequence spans, or corresponds to, a mutation; wherein the cell barcodes of two barcode oligonucleotides of the plurality of barcode oligonucleotides attached to a bead of the beads comprise an identical sequence, wherein the cell barcodes of two barcode oligonucleotides attached to two beads of the beads comprise different sequences, and/or wherein the cell barcode of each barcode oligonucleotide is at least 6 nucleotides in length; wherein the UMIs of two barcode oligonucleotides attached to a bead of the beads comprise different sequences; wherein each barcode oligonucleotide of the plurality of barcode oligonucleotides comprises a first polymerase chain reaction (PCR) primer-binding sequence; wherein the RNA targets comprise at least 10 different second nucleic acid targets; wherein the second nucleic acid target comprises a T-cell receptor (TCR), or an mRNA product thereof, wherein the probe sequence is capable of binding to a constant region, or a portion thereof, of the TCR; wherein the cell is infected with a virus, wherein the second nucleic acid target is a gene of the virus, or a nucleic acid product thereof; comprising enriching the one or more second nucleic acid targets using one or more enrichment primers of a panel, wherein the panel is customizable; comprising sequencing the amplified barcoded cDNAs to obtain sequencing information; wherein analyzing the amplified barcoded cDNAs comprises: determining an expression profile of each of one or more of the RNA targets using a number of UMIs with different sequences associated with the RNA target in the sequencing information; and determining an expression profile of the second RNA target using a number of UMIs with different sequences associated with the second RNA target in the sequencing information (see Figure 10D, [0005] to [0021] and [00322] to [00406]).
Thus, Belhocine anticipates the present claims.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to Christian Boesen whose telephone number is 571-270-1321. The Examiner can normally be reached on Monday-Friday 9:00 AM to 5:00 PM.
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/CHRISTIAN C BOESEN/Primary Examiner, Art Unit 1684
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