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 Claims
Claims 1-20 are currently pending. Claim 1 had been amended by Applicants’ amendment filed 04-28-2026. Claims 2-20 have been added by Applicants’ amendment filed 04-28-2026. No claims have been canceled by Applicants’ amendment filed 04-28-2026.
A complete reply to the final rejection must include cancellation of nonelected claims or other appropriate action (37 CFR 1.144) See MPEP § 821.01.
Therefore, claims 1-20 are under consideration to which the following grounds of rejection are applicable.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on April 28, 2026 has been considered. An initialed copy of the IDS accompanies this Office Action.
Priority
The present application filed March 20, 2023 is a CON of US Patent Application 15055407, filed February 26, 2016, which claims the benefit of US Provisional Patent Application 62/194,075, filed July 17, 2015; US Provisional Patent Application 62/173,899, filed June 10, 2015; US Provisional Patent Application 62/160,976, filed May 13, 2015; US Provisional Patent Application 62/128,849, filed March 5, 2015; and US Provisional Patent Application 62/126,397, filed February 27, 2015.
Withdrawn Objections/Rejections
Applicants’ amendment and arguments filed April 28, 2026 are acknowledged and have been fully considered. The Examiner has re-weighed all the evidence of record. Any rejection and/or objection not specifically addressed below are herein withdrawn.
Specification Objection
The objection to the disclosure is withdrawn for not including the current status of US Patent Application No. 15/055,407 (now abandoned), due to Applicant’s amendment of the Specification, in the reply filed 04-28-2026.
The objection to the disclosure is withdrawn because it contained an embedded hyperlink and/or other form of Browser-executable code, due to Applicant’s amendment of the Specification, in the reply filed 04-28-2026.
Maintained Objections/Rejections
Claim Interpretation: the term “specifically binds” such as in claims 5, 6 and 8 is interpreted to refer to a sequence that is capable of specific binding, such that the term does not refer to a sequence that is specifically bound to a region as recited in the claim.
The term “barcodes associated with the target” as recited in claim 16 is interpreted to refer to any type or amount of association (e.g., labeled by, in the same droplet, in different droplets, within the same sample, etc.).
Claim Rejections - 35 USC § 102
The rejection of claim 1 is maintained, and claims 2-20 are newly rejected, under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Harlan Robins (hereinafter “Robins”) (US Patent Application Publication No. 20140322716, published October 30, 2014; effective filing date June 15, 2012; of record) as evidenced by Illumina (Illumina, 2012, 1-3).
Regarding claims 1 and 2, Robins teaches compositions and methods are disclosed for uniquely tagging each rearranged gene segment that encodes a T cell receptor (TCR) and/or an immunoglobulin (Ig), in a DNA (or mRNA or cDNA reverse transcribed therefrom) sample from lymphoid cells, which permits accurate, high throughput quantification of distinct TCR and/or Ig encoding sequences; as well as, compositions and methods for quantitatively sequencing the genes that encode both chains of a TCR or Ig heterodimer in a single cell, for example, to characterize the degree of T or B cell clonality in a sample (corresponding to target molecule is mRNA that encodes TCR alpha chain or beta chain; the sample is a single cell; and a sample, claims 1-4) (Abstract). Robins teaches in Figure 1, a starting template population of genomic DNA or cDNA from a lymphoid cell-containing population (reading on a target in a sample), two or more cycles of PCR are performed using an oligonucleotide primer composition containing primers having the general formula U1-B1n-X (reading on extending a first oligo and extending a second oligo), where U1 comprises an oligonucleotide sequence comprising a first universal adaptor oligonucleotide sequence; B1 comprises an oligonucleotide that comprises either nothing or a first oligonucleotide barcode sequence of 6 to 20 contiguous nucleotides; and X comprises an oligonucleotide sequence comprising not more than 70 contiguous nucleotides of said adaptive immune receptor J region encoding gene sequence, or said complement thereof (reading on hybridizing target with first oligo and universal adaptor with target-specific sequence) (paragraphs [0017], lines 5-10; [0021], lines 11-13; [0074], lines 1-4; and Figure 1). Figure 1 is shown below:
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Robins teaches a method for labeling individual rearranged DNA sequences encoding a plurality of adaptive immune receptors in a biological sample that comprises lymphoid cells of a subject, the method comprising: (a) amplifying said rearranged DNA sequences using a first amplification primer set comprising an oligonucleotide primer composition described herein under conditions that promote amplification to obtain double-stranded DNA products, wherein each double-stranded DNA product comprises: (i) a sequence comprising at least two universal adaptor oligonucleotide sequences with one at each end of the product, at least one oligonucleotide barcode sequence, an X1 oligonucleotide sequence, an X2 oligonucleotide sequence, and (ii) a complementary sequence to the sequence in (i); (b) amplifying the double-stranded DNA products of (a) with a second amplification primer set comprising a plurality of first and second sequencing platform tag-containing oligonucleotides that each comprise either: (i) a first sequencing platform tag-containing oligonucleotide comprising an oligonucleotide sequence that is capable of specifically hybridizing to the first universal adaptor oligonucleotide and a first sequencing platform specific oligonucleotide sequence that is linked to and positioned 5' to the first universal adaptor oligonucleotide sequence, or (ii) a second sequencing platform tag-containing oligonucleotide comprising an oligonucleotide sequence that is capable of specifically hybridizing to the second universal adaptor oligonucleotide sequence and a second sequencing platform-specific oligonucleotide sequence that is linked to and positioned 5' to the second universal adaptor oligonucleotide sequence (corresponding to the ligated sequences comprising a first primer and a second primer, comprising the target and a stochastic barcode, claim 1) (paragraph [0018]). Robins teaches that the J-specific primer 110a contains a J primer sequence 100 that is complementary to a portion of the J segment, a barcode tag (BC1) 101 in Figure 1, or B1n in the generic formula) and also includes a first external universal adaptor sequence (U1) 102, while the V-specific primer 110b includes a V primer sequence 103 that is complementary to a portion of the V segment and a second external universal adaptor sequence (U2) 104, where the invention also contemplates related embodiments including where the barcode can instead or can in addition be present as part of the V-specific primer and is situated between the V-sequence and the second universal adaptor (corresponding to stochastic barcodes, claim 1) (paragraph [0074], lines 5-12; and Figure 1). Robins teaches sets of m and n barcode sequences are used in subsequent amplification steps, such as to individually label each rearranged TCR or IG sequence and then to uniformally label ("tailing") a set of sequences obtained from the same source, or sample, wherein the V and J primers 100 and 103 are capable of promoting the amplification of a TCR or lg encoding sequence that includes the CDR3 encoding sequence, which in Figure 1 includes the NDN region 111 corresponding to stochastic barcodes, claim 1) (paragraph [0075], lines 11-16; and Figure 1). Robins teaches that following no more than two amplification cycles, the first amplification primer set 110a, 110b is separated from the double-stranded product (corresponding to a first extension, a second extension; generating a complementary strand; and producing a double-stranded nucleotide sequence, claim 1) (paragraph [0075], lines 16-18; and Figure 1). Robins teaches that Figure 1 shows a starting template population of genomic DNA or cDNA from a lymphoid cell-containing population, two or more cycles of PCR are performed using an oligonucleotide primer composition that contains primers having the general formula U1-B1-X as described herein, wherein the J-specific primer 110a contains a J primer sequence 100 that is complementary to a portion of the J segment, a barcode tag (BC1) 101, and also includes a first external universal adaptor sequence (U1) 102, while the V-specific primer 110b includes a V primer sequence 103 that is complementary to a portion of the V segment and a second external universal adaptor sequence (U2) 104 (interpreting oligonucleotide primers as a first agent and a second oligonucleotide comprising a target-specific region; and a stochastic region, claim 1) (paragraph [0076]). Robins teaches that the second amplification primer set 120a, 120b can introduce sequencing platform-specific oligonucleotide sequences (Adap1, 105 and Adap2, 106 in Figure 1); however these are not necessary in certain other related embodiments, wherein the second amplification primer set 120a, 120b can also optionally introduce a second oligonucleotide barcode identifier tag (BC2, 107 in Figure 1), such as a single barcode sequence that can desirably identify all products of the amplification from a particular sample (e.g., as a source subject-identifying code) and ease multiplexing multiple samples to allow for higher throughput, such that the barcode (BC2, 107 in Figure 1) is a modification that increases the throughput of the assay, such that it allows samples to be multiplexed on the sequencer, but is not required (adap1 and adap2 corresponding to adaptor oligonucleotides comprising a binding site, claim 1) (paragraph [0079], lines 1-14). Robins teaches that sequencing adapters can be put onto each end of all reverse transcribed/amplified TCR and/or IG encoding segments including by synthesizing universal adaptor sequences onto each end of each cDNA molecule outside of the well-specific barcode, then adapters can be synthesized onto each molecule in a tailing PCR reaction, where in such embodiments fusion RT primers can be synthesized and used for the first cDNA strand synthesis, such that these primers will all contain the same unique DNA barcode, as well as universal (e.g., pGEX) priming sites (corresponding to ligating adapters comprising a binding site for an amplification primer to the ds nucleotide sequence; and amplifying, claim 1) (paragraph [0133], lines 2-8). Robins teaches that upon completion of the first cDNA strand synthesis by reverse transcription, the contents of all plate wells will be recovered in a quantitative manner and pooled, purified, and split into a multiplicity of wells for PCR with universal adapter primers (pGEX) containing "tail" sequences designed to incorporate sequences to be used for amplification and sequencing using a next-generation sequence analysis system (e.g., Illumina); alternatively, the sequencing platform specific adapters can be ligated onto the ends of tagged molecules (e.g., Illumina TrueSeq sample preparation method), the molecules from all the wells are pooled thus generating a high-complexity sequencing library of uniquely tagged BCR or TCR ds-cDNA products; and then the molecules are all sequenced using high-throughput sequencing (Illumina TruSeq adaptors correspond to double-stranded adaptors; corresponding to ligating double-stranded adapters comprising a binding site for an amplification primer to the ds nucleotide sequence; and amplifying, claim 1) (paragraph [0133], lines 8-18), wherein it is known that Illumina TruSeq adaptors are double-stranded Y-shaped adaptors including
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as evidenced by Illumina (pg. 2, Figure 2).
Regarding claims 3 and 4, Robins teaches compositions and methods are disclosed for uniquely tagging each rearranged gene segment that encodes a T cell receptor (TCR) and/or an immunoglobulin (Ig), in a DNA (or mRNA or cDNA reverse transcribed therefrom) sample from lymphoid cells, which permits accurate, high throughput quantification of distinct TCR and/or Ig encoding sequences; as well as, compositions and methods for quantitatively sequencing the genes that encode both chains of a TCR or Ig heterodimer in a single cell, for example, to characterize the degree of Tor B cell clonality in a sample (corresponding to target molecule is mRNA that encodes TCR alpha chain or beta chain; and a sample, claims 1, 3 and 4) (Abstract).
Regarding claim 5, Robins teaches that oligonucleotide RT primers include oligonucleotide sequences that specifically hybridize to target adaptive immune receptor encoding regions such as V, J or C region sequences, and also include oligonucleotide barcode sequences as molecular labels, along with universal adaptor oligonucleotide sequences as described herein (corresponding to target-specific sequence specifically binding to the C region of the TCR alpha chain or beta chain, claim 5) (paragraph [0115], lines 1-5).
Regarding claim 6, Robins teaches that V represents an adaptive immune receptor variable (V) region gene and Vpr represents a region of such a gene to which a V-specific oligonucleotide primer specifically anneals; and NDN represents the diversity (D) region found in some adaptive immune receptor encoding genes, flanked on either side by junctional nucleotides (N) which can include non-templated nucleotides, wherein Adap1 and Adap2 represent sequencing platform-specific adapters (corresponding to binding a V region and/or a D region of the TCR alpha chain or beta chain, claim 6) (paragraph [0062], lines 5-9; and Figure 1). Robins teaches that the J-specific primer 110a contains a J primer sequence 100 that is complementary to a portion of the J segment, a barcode tag (BC1) 101 in Figure 1, or B1n in the generic formula) and also includes a first external universal adaptor sequence (U1) 102, while the V-specific primer 110b includes a V primer sequence 103 that is complementary to a portion of the V segment and a second external universal adaptor sequence (U2) 104 (corresponding to binding a V region of the TCR alpha chain or beta chain, claim 6) (paragraph [0074], lines 5-9; and Figure 1).
Regarding claim 7, Robins teaches amplifying the double-stranded DNA products of (a) with a second amplification primer set comprising a plurality of first and second sequencing platform tag-containing oligonucleotides that each comprise either: (i) a first sequencing platform tag-containing oligonucleotide comprising an oligonucleotide sequence that is capable of specifically hybridizing to the first universal adaptor oligonucleotide and a first sequencing platform specific oligonucleotide sequence that is linked to and positioned 5' to the first universal adaptor oligonucleotide sequence, or (ii) a second sequencing platform tag-containing oligonucleotide comprising an oligonucleotide sequence that is capable of specifically hybridizing to the second universal adaptor oligonucleotide sequence and a second sequencing platform-specific oligonucleotide sequence that is linked to and positioned 5' to the second universal adaptor oligonucleotide sequence (corresponding to a second oligonucleotide comprising a binding site for a second amplification primer, claim 7) (paragraph [0018], lines 10-16).
Regarding claim 8, Robins teaches that V represents an adaptive immune receptor variable (V) region gene and Vpr represents a region of such a gene to which a V-specific oligonucleotide primer specifically anneals; and NDN represents the diversity (D) region found in some adaptive immune receptor encoding genes, flanked on either side by junctional nucleotides (N) which can include non-templated nucleotides, wherein Adap1 and Adap2 represent sequencing platform-specific adapters (corresponding to a second primer that specifically binds to V region or the V-D junction of a TCR alpha chain or beta chain, claim 8) (paragraph [0062], lines 5-9; and Figure 1).
Regarding claim 9, Robins teaches that oligonucleotide RT primers include oligonucleotide sequences that to target adaptive immune receptor encoding regions such as V, J or C region sequences, and also include specifically hybridize oligonucleotide barcode sequences as molecular labels, along with universal adaptor oligonucleotide sequences as described (interpreted as barcodes comprising a molecular label, claim 9) (paragraph [00115], lines 1-5). Robins teaches that one way to do this is to convert cellular mRNA to cDNA by reverse transcription, and to add to the cDNA products a molecular label in the form of an oligonucleotide barcode during the reverse transcription step (interpreted as barcodes comprising a molecular label, claim 9) (paragraph [00124], lines 3-5).
Regarding claim 10, Robins teaches sets of m and n barcode sequences are used in subsequent amplification steps (e.g., to individually label each rearranged TCR or IG sequence and then to uniformally label ("tailing") a set of sequences obtained from the same source, or sample (uniformally labeling of sequences from the same source corresponds to a universal label, claim 10) (paragraph [0075], lines 11-13).
Regarding claim 11, Robins teaches that the sequencing platform specific adapters can be ligated onto the ends of tagged molecules (e.g., Illumina TrueSeq sample preparation method), the molecules from all the wells are pooled thus generating a high-complexity sequencing library of uniquely tagged BCR or TCR ds-cDNA products; and then the molecules are all sequenced using high-throughput sequencing (Illumina TruSeq adaptors correspond to double-stranded adaptors; corresponding to ligating double-stranded adapters comprising a binding site for an amplification primer to the ds nucleotide sequence; and amplifying, claim 1) (paragraph [0133], lines 13-18), wherein it is known that Illumina TruSeq adaptors are double-stranded Y-shaped adaptors having the structure:
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; and comprising a T-overhang one strand and a free phosphate on the other strand as evidenced by Illumina (pg. 2, Figure 2; and col 2, third full paragraph).
Regarding claim 12, Robins teaches that the methods include identifying as originating from the same cell sequences that are members of an X1 and an X2 sequence cluster set that belong to the same one or more barcode sequence sets (the barcode sets correspond to cellular labels, claim 12) (paragraph [0048], lines 9-11). Robins teaches matching particular pairs of adaptive immune receptor heterodimer subunit encoding sequences to identify them as having originated from the same lymphoid cell (encoding to identify sequences originating from the same cells as corresponding to cellular labels, claim 12) (paragraph [00119], lines 6-7).
Regarding claim 13, Robins teaches that the sequencing platform specific adapters can be ligated onto the ends of tagged molecules such as in the Illumina TrueSeq sample preparation method (corresponding to ligating to both the 5’ end and the 3’ end of the sequence, claim 13) (paragraph [0133], lines 13-15). Robins teaches that adaptor sequences of the invention are located at the 5' and 3' ends of template sequences SEQ ID NOS: 1-1630 (corresponding to ligating to both the 5’ end and the 3’ end of the sequence, claim 13) (paragraph [0179], lines 1-3).
Regarding claim 14, Robins teaches compositions and methods are disclosed for uniquely tagging each rearranged gene segment that encodes a T cell receptor (TCR) and/or an immunoglobulin (Ig), in a DNA (or mRNA or cDNA reverse transcribed therefrom) sample from lymphoid cells (corresponding to a plurality of the target, claim 14) (Abstract, lines 1-2).
Regarding claim 15, Robins teaches that the invention provides a method for labeling individual rearranged DNA sequences encoding a plurality of adaptive immune receptors in a biological sample that comprises lymphoid cells of a subject, the method comprising: amplifying said rearranged DNA sequences using a first amplification primer set to promote amplification to obtain double-stranded DNA products, wherein each double-stranded DNA product comprises at least one oligonucleotide barcode sequence; and that each of the plurality of oligonucleotide sequences of general formula
U3-B3-V2, V2 comprises a unique oligonucleotide sequence; and in each of the plurality of oligonucleotide sequences of general formula U4-B4-J2, J2 comprises a unique oligonucleotide sequence (corresponding to a plurality of each target; and each target comprising a unique stochastic barcode, claims 14 and 15) (paragraphs [0017], lines 37-40; and [0018], lines 1-8).
Regarding claim 16, Robins teaches that the compositions and methods described herein permit quantitative sequencing of DNA sequences encoding both chains of an adaptive immune receptor heterodimer in a single cell (corresponding to counting the targets by counting barcodes associated with the target, claim 16) (paragraph [0003]). Robins teaches that DNA encoding sequences (e.g., CDR3 encoding DNA) of first and second adaptive immune receptor polypeptide encoding genes from the same cell, after which the individual microdroplets are disrupted (e.g., by chemical, physical and/or mechanical dissolution, dissociation, breakage, etc.) and the released barcoded dsDNAs are amplified with universal oligonucleotide primers and sequencing platform-specific adapters to permit large-scale multiplexed quantitative sequencing (corresponding to counting the targets by counting barcodes associated with the target, claim 16) (paragraph [0064]).
Regarding claim 17, Robins teaches that as shown in Figure 1, the J-specific primer 110a contains a J primer sequence 100 that is complementary to a portion of the J segment, a barcode tag (BC1) 101 in Figure 1, or B1n in the generic formula; and also includes a first external universal adaptor sequence (U1) 102, while the V-specific primer 110b includes a V primer sequence 103 that is complementary to a portion of the V segment and a second external universal adaptor sequence (U2) 104 (corresponding to a universal label comprising a primer binding site, claim 17) (paragraph [0074], lines 4-8; and Figure 1).
Regarding claim 18, Robins teaches that the third amplification primer set comprises:
(i) a plurality of first sequencing platform tag containing oligonucleotides that each comprise an oligonucleotide sequence that is capable of specifically hybridizing to the first universal adaptor oligonucleotide and a first sequencing platform-specific oligonucleotide sequence, and (ii) a plurality of second sequencing platform tag-containing oligonucleotides that each comprise an oligonucleotide sequence that is capable of specifically hybridizing to the second universal adaptor oligonucleotide sequence and a second sequencing platform-specific oligonucleotide sequence (corresponding to a primer binding site capable of hybridizing to a PCR primer or a sequencing primer, claim 18) (paragraph [0106], lines 5-12).
Regarding claim 19, Robins teaches a plurality of oligonucleotides in the second amplification primer set each further comprises either or both of: (i) a sample-identifying barcode oligonucleotide which comprises a third barcode oligonucleotide B5 comprising an oligonucleotide barcode sequence of 6 to 20 contiguous nucleotides; or a spacer oligonucleotide of any sequence of 1 to 20 contiguous nucleotides (corresponding to 5 to 30 nucleotides in length, claim 19) (paragraph [0019]).
Regarding claim 20, Robins teaches that universal sequencing primers, complementary to the sequencing platform-specific adapters can desirably be used in order to allow sample indexing of multiple samples, where a sample specific index will be used for each pool of uniquely tagged IGH / TCR products, originating from 96, 384, 1536 etc. original RT reaction wells (interpreted as amplification using sequencing primers, claim 20) (paragraph [00134], lines 1-4).
Robins meets all the limitations of the claims and, therefore, anticipates the claimed invention.
Response to Arguments
Applicant’s arguments filed April 28, 2026 have been fully considered but they are not persuasive. Applicants essentially assert that: (a) Robins neither expressly nor inherently teaches ligating a double-stranded adaptor oligonucleotide to a double-stranded nucleotide sequence before the claimed barcoded amplification (Applicant Remarks, pg.11, first partial paragraph).
Regarding (a), although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26USPQ2d 1057 (Fed. Cir. 1993). As noted in MPEP § 2112.01(I):
where the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). "When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not." In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990).
Applicant’s assertion that Robins neither expressly nor inherently teaches ligating a double-stranded adaptor oligonucleotide to a double-stranded nucleotide sequence before the claimed barcoded amplification, is not found persuasive. The Examiner contends that Robins teaches all of the limitations of the instant claims. For example -
Robins teaches:
The sequencing platform specific adapters can be ligated onto the ends of tagged molecules (e.g., Illumina TrueSeq sample preparation method), the molecules from all the wells are pooled thus generating a high-complexity sequencing library of uniquely tagged BCR or TCR ds-cDNA products; and then the molecules are all sequenced using high-throughput sequencing (paragraph [0133], lines 13-18);
wherein it is known that Illumina TruSeq adaptors are double-stranded Y-shaped adaptors as evidenced by Illumina (pg. 2, Figure 2; and col 2, third full paragraph) (the Illumina TruSeq adaptors correspond to double-stranded adaptors as recited in claim 1, and are no longer Y-shaped after amplification).
Figure 2 (in part) is shown below:
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Robins teaches all of the limitations of the claim and, thus, anticipates the claimed invention. The claims remains rejected.
New Objections/Rejections
Claim Objections
Claims 1-20 are objected to because of the following informalities: Claims 1-20 recite a mixture of pronouns including “the” and “said” within each claim (e.g., said target (line 3) and the first nucleotide sequence (lines 8-9)), such that for consistency, a single pronoun reciting either “the” or “said” should be used.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
Claims 2, 5-8, 11, 13, 14, 16 and 19 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention. This is a new rejection necessitated by amendment of the claims in the response filed 04-28-2026.
Claims 2 and 14 are indefinite for the recitation of the term “the sample” such as recited in claim 2, line 1 because claims 2 and 14 depend from instant claim 1, wherein claim 1 only recites the term “sample” in the preamble of the claim. A preamble is generally not accorded any patentable weight where it merely recites the purpose of a process or the intended use of a structure, and where the body of the claim does not depend on the preamble for completeness but, instead, the process steps or structural limitations are able to stand alone. See; In re Hirao, 535 F.2d 67, 190 USPQ 15 (CCPA 1976); and Kropa v. Robie, 187 F.2d 150, 152, 88 USPQ 478, 481 (CCPA 1951) and, thus, the metes and bounds of the claim cannot be determined.
Claim 5 is indefinite for the recitation of the term “the C region” such as recited in claim 5, line 2. There is insufficient antecedent basis for the term “the C region” in the claim. The Examiner suggests that Applicant amend the claim to recite, for example, “specifically binds to a C region of the TCR alpha chain.”
Claim 5, 6 and 8 are indefinite for the recitation of the term “specifically binds to” such as recited in claim 5, line 1-2 because the binding status of the sequence referred to is unclear. For example, it is unclear whether the term is referring to a sequence that is specifically bound to a region, OR whether the term is referring to a sequence that is capable of specifically binding to a region (e.g., the target-specific sequence is specifically bound to the C region; or the target-specific sequence can specifically bind the C region) and, thus, the metes and bounds of the claim cannot be determined.
Claim 7 is indefinite for the recitation of the term “the second oligonucleotide comprises a binding site for the second amplification primer” such as recited in claim 7, lines 1-2 because claim 7 depends from instant claim 1, wherein claim 1 already recites that the “second oligonucleotide comprises a second target-specific sequence” in lines 6-7, such that the second oligonucleotide cannot comprise something entirely different within a dependent claim and, thus, the metes and bounds of the claim cannot be determined.
Claim 11 is indefinite for the recitation of the term “the double-stranded adaptor oligonucleotide has a T overhang…on the other strand” such as recited in claim 11, lines 1-2 because claim 11 depends from instant claim 1, wherein claim 1 already recites that the “double-stranded adaptor oligonucleotide comprising a binding site for a first amplification primer” in line 10, such that the double-stranded adaptor oligonucleotide cannot comprise something entirely different within a dependent claim and, thus, the metes and bounds of the claim cannot be determined.
Claim 11 is indefinite for the recitation of the term “the other strand” such as recited in claim 11, line 2. There is insufficient antecedent basis for the term “the other strand” in the claim.
Claim 13 is indefinite for the recitation of the terms “the 5’ end” and “the 3’ end” such as recited in claim 13, line 2. There is insufficient antecedent basis for the terms “the 5’ end” and “the 3’ end” in the claim.
Claim 16 is indefinite for the recitation of the term “the number” such as recited in claim 16, line 1. There is insufficient antecedent basis for the term “the number” in the claim.
Claim 19 is indefinite for the recitation of the terms “at least about” and “at most about” such as recited in claim 19, lines 1-2 because each of the terms comprises two ranges. For example, the limitation of “at least” starts at 5 nucleotides, and limitation of “about” may start at the point that is slightly less than 5 nucleotides or slightly greater than 5 nucleotides. The term “at most” starts at 30 nucleotides; while the limitation of “about” may start at the point that is slightly less than 30 nucleotides or slightly greater than 30 nucleotides. Therefore the recitation of “at least about” is a recitation of two ranges making the claims indefinite. The Examiner suggest amending the claim to “at least” or “about” for clarity.
Claim Rejections - 35 USC § 112(d)
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.
Claims 2, 7, 11 and 14 are rejected under 35 U.S.C. 112(d) 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. This is a new rejection necessitated by amendment of the claims in the response filed 04-28-2026.
Claims 2 and 14 recite (in part): “wherein the sample” such as recited in claim 2, line 1 because claims 2 and 14 depend from instant claim 1, wherein instant claim 1 does not recite the presence of a sample in the body of the claim. Thus, claims 2 and 14 are improper dependent claims 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 7 recites (in part): “wherein the second oligonucleotide comprises a binding site for the second amplification primer” such as recited in claim 7, lines 1-2 because claim 7 depends from instant claim 1, wherein claim 1 already recites that the “second oligonucleotide comprises a second target-specific sequence” in lines 6-7, such that the second oligonucleotide cannot comprise something entirely different within a dependent claim. Thus, claim 7 is an improper dependent claim 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 11 recites (in part): “wherein the double-stranded adaptor oligonucleotide has a T overhang on one strand and a free phosphate on the other strand ” such as recited in claim 11, lines 1-2 because claim 11 depends from instant claim 1, wherein claim 1 already recites that the “double-stranded adaptor oligonucleotide comprising a binding site for a first amplification primer” in line 10, such that the double-stranded adaptor oligonucleotide cannot comprise something entirely different within a dependent claim. Thus, claim 11 is an improper dependent claim 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.
Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
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 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 may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
Claims 1-20 are rejected under 35 U.S.C. 103 as being unpatentable over Robins (International Application Publication WO2013188831A1, published December 19, 2013; effectively filed June 15, 2012; of record) in view of Fu et. al. (hereinafter “Fu”) (US Patent No. 10941396, issued March 9, 2021; effective filing date February 27, 2012) as evidenced by Illumina (Illumina, 2012, 1-3). This is a new rejection necessitated by amendment of the claims in the response filed 04-28-2026.
The teachings of Robins as applied to claims 1-20 are described supra.
Robins does not specifically exemplify counting distinct stochastic barcodes (claim 16, in part).
Regarding claim 16 (in part), Fu teaches methods, kits and systems are disclosed for analyzing one or more molecules in a sample comprising quantitation of the one or more molecules, wherein individual molecules can quantitated by PCR, arrays, beads, emulsions, droplets, or sequencing, such that the method can further comprise stochastic labeling of the one or more molecules with a plurality of oligonucleotide tags to produce one or more stochastically labeled molecules including comprising amplifying, sequencing, detecting, and/or quantifying the stochastically labeled molecules (corresponding to quantifying/counting, claim 16) (Abstract). Fu teaches that the label and/or oligonucleotide tag can further comprise a unique identifier region; as well as, a universal primer binding site (col 4, lines 10-18). Fu teaches that the primer is a universal primer that binds to the oligonucleotide tag including the primer binding site of the oligonucleotide tag (col 5, lines 4-8). Fu teaches that the method comprises conducting polymerase chain reaction (PCR) on the labeled-molecule or any product thereof to produce a double-stranded labeled molecule (col 6, lines 8-11). Fu teaches that methods for ligating adaptors to fragments of nucleic acid are well known, wherein adaptors can be double-stranded, single-stranded, or partially single-stranded; and adaptors are formed from two oligonucleotides that have a region of complementarity, for example, about 10 to 30 bases, or about 15 to 40 bases of perfect complementarity, wherein the two oligonucleotides are hybridized together to form a double-stranded region (corresponding to double-stranded adaptors; and ligating a first oligo and a second oligo, claim 1) (col 11, lines 44-51). Fu teaches that all of the positive spots are summed to provide a total count of unique stochastic labels (corresponding to counting the number of targets by counting distinct stochastic barcodes associated with the target, claim 16) (col 21, lines 34-36). Fu teaches that Figure 27 depicts a schematic for analyzing one or more molecules, wherein the method can comprise: (a) reverse transcribing an mRNA molecule (2710) with an oligonucleotide tag (2720) comprising an oligo-dU sequence (2730), unique identifier region (2740), and a universal primer binding site (2750) to produce a cDNA copy (2760) of the mRNA molecule, wherein the cDNA copy (2760) comprises the unique identifier region (2740) and the universal primer binding site (2750); and (b) amplifying the cDNA copy with a first primer (2790) comprising an oligo-dU sequence and a second primer (2780) comprising the universal primer sequence to produce stochastically labeled amplicons, such that the method can include treating the molecules with one or more restriction enzymes; and conducting an emulsion PCR reaction on the stochastically labeled molecules (including a first and second extension, claim 1) (col 52, lines 63-67; and col 53, lines 1-11). Figure 27 is shown below:
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Fu teaches that the method can comprise ligating one or more primers to the digested stochastically labeled amplicon to produce a primer-stochastically labeled amplicon, wherein the primer can be a sequencing primer; and sequencing the primer-stochastically labeled amplicon (interpreted as ligating; and sequencing, claim 1) (col 53, lines 39-44). Fu teaches that the unique identifier sequence can comprise a predetermined sequence or a random sequence, and wherein the target-specific sequence of the oligonucleotide tag can be specific for a plurality of targets (interpreted as a plurality of targets, claim 14) (col 63, lines 26-31). Fu teaches that as shown in Figure 17, detecting the unique identifier regions comprises hybridizing the stochastically labeled amplicons to a solid support (e.g., array), wherein the stochastically labeled amplicons can hybridize to discrete locations on the solid support and the number of different unique identifier regions can be determined by counting the number of discrete locations as detected by fluorescence (corresponding to counting the number of targets by counting distinct stochastic barcodes associated with the target, claim 16) (col 49, lines 17-23). Fu teaches that absolute quantitation of mRNA molecules can occur by the detection and counting of different unique identifier regions (col 49, lines 45-47).
It is prima facie obvious to combine prior art elements according to known methods to yield predictable results; the court held that, "…a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. KSR International Co. v. Teleflex Inc., 550 U.S. ___, ___, 82 USPQ2d 1385, 1395 (2007); Sakraida v. AG Pro, Inc., 425 U.S. 273, 282, 189 USPQ 449, 453 (1976); Anderson’s-Black Rock, Inc. v. Pavement Salvage Co., 396 U.S. 57, 62-63, 163 USPQ 673, 675 (1969); Great Atlantic & P. Tea Co. v. Supermarket Equipment Corp., 340 U.S. 147, 152, 87 USPQ 303, 306 (1950)”. Therefore, in view of the benefits of the absolute quantitation of mRNA molecules as disclosed by Fu, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of uniquely tagging each gene segment that encodes a T cell receptor and/or immunoglobulin in a sample including via amplification and sequencing as disclosed by Robins to include methods of counting and/or quantitating stochastically labeled molecules (e.g., mRNA molecules) in a sample as taught by Fu with a reasonable expectation of success in accurately determining the quantity of one or more specific species of nucleic acids in a sample including for clinical and research investigation and/or analysis; and/or in determining the original number of molecules of each species within a sample including within a single cell.
Thus, in view of the foregoing, the claimed invention, as a whole, would have been obvious to one of ordinary skill in the art at the time the invention was made. Therefore, the claims are properly rejected under 35 USC §103(a) as obvious over the art.
Conclusion
Claims 1-20 are 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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/AMY M BUNKER/Primary Examiner, Art Unit 1684
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