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 1-18 are currently pending. Claims 1-7 and 11-18 have been amended by Applicants’ amendment filed 08-26-2026. No claims have been added or canceled by Applicants’ amendment filed 08-26-2026.
Applicant's election of Group I without traverse, claims 1-18, directed to a method for identifying at least one critical quality attribute (CQA) of a protein of interest; and Applicant’s election of Species as follows:
Species (A): wherein two or more molecular barcodes are attached to each input fragment (claim 4),
Species (B): generating a pairing oligo to identify combinations of molecular barcodes attached to an input fragment to be used in pairing single-end reads (claim 5),
Species (C): wherein a pairing oligo shorter than the input fragment is generated by annealing two oligos (claim 6),
Species (D): wherein the splint oligonucleotide is a DNA oligonucleotide (claim 8),
Species (E): wherein the circularizing adapter is generated by annealing two oligo libraries containing designed molecular barcodes (claim 16),
Species (F): wherein the two molecular barcodes are randomized molecular barcodes (claim 15), and
Species (G): wherein the two orientations of the insert sequence are sequenced simultaneously (claim 17), in the reply filed May 29, 2026 was previously acknowledged.
Claims 2, 3, 7-16 and 18 were previously withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected species, there being no allowable generic or linking claim.
The restriction requirement is still deemed proper and is therefore made FINAL.
The claims will be examined insofar as they read on the elected species.
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, 4-6 and 17 are under consideration to which the following grounds of rejection are applicable.
Priority
The present application filed June 9, 2023 is a 35 U.S.C. 371 national stage filing of International Application PCT/US2020/064297, filed December 10, 2020.
Withdrawn Objections/Rejections
Applicants’ amendment and arguments filed August 26, 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.
Claim Rejections - 35 USC § 102
The rejection of claims 1, 4-6 and 17 is withdrawn under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Kennedy et al. (hereinafter “Kennedy”) (International Application WO2018175997, published March 23, 2018).
Kennedy does not specifically exemplify fragments comprising a first orientation and an inverted orientation.
In view of the withdrawn rejections, Applicant’s arguments are rendered moot.
Maintained Objections/Rejections
Claim Rejections - 35 USC § 112(b)
The rejection of claims 1, 4-6 and 17 is maintained 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.
Claims 1 and 6 are indefinite for the recitation of the term “at least a portion” such as recited in claim 1, lines 13, 14, 16 and 17 because a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) is considered indefinite, since the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). Note the explanation given by the Board of Patent Appeals and Interferences in Ex parte Wu, 10 USPQ2d 2031, 2033 (Bd. Pat. App. & Inter. 1989), as to where broad language is followed by "such as" and then narrow language. The Board stated that this can render a claim indefinite by raising a question or doubt as to whether the feature introduced by such language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. Note also, for example, the decisions of Ex parte Steigewald, 131 USPQ 74 (Bd. App. 1961); Ex parte Hall, 83 USPQ 38 (Bd. App. 1948); and Ex parte Hasche, 86 USPQ 481 (Bd. App. 1949). In the present instance, the claims recite the term “at least” is the broad recitation, while also reciting “a portion” which is a narrower statement of the range/limitation.
Claims 1 and 6 are indefinite for the recitation of the term “the first and second sequencing adaptor sequences” such as recited in claim 1, lines 18-19 and 21-23. There is insufficient antecedent basis for the term “the first and second sequencing adaptor sequences” in the claim because claim 1, lines 13-14 and 15 recite the terms “a first sequencing adaptor sequence” and “a second sequencing adaptor sequence”.
Claim 1 is indefinite for the recitation of the term “common input fragment” such as recited in claim 1, line 28 because claim 1 does not recite that the input fragments are derived from a common input fragment and, thus, the metes and bounds of the claim cannot be determined.
Claim 1 is indefinite for the recitation of the term “common” such as recited in claim 1, line 28 because the term “common” is relative term that renders the claim indefinite. The term “common” is not defined by the claim, and the Specification does not provide a standard for ascertaining the requisite amount of shared relationship and/or frequency as compared to some other value that qualifies as an “common input fragment”, such that one of ordinary skill in the art would not be reasonably appraised of the scope of the invention and, thus, the metes and bounds of the claim cannot be determined.
Claim 5 is indefinite for the recitation of the term “used to pair single-end reads obtained by sequencing the library of amplicons” such as recited in claim 5, lines 3-5 because claim 5 depends from claims 1 and 4, wherein claims 1 and 4 do not recite a “combination” of molecular barcodes and/or that sequencing produces single-end reads. Additionally, it is unclear how single-end reads are produced by sequencing in two different orientations. Moreover, the structure of the “pairing oligonucleotide” is unclear (e.g., single stranded, a duplex, etc.) and/or how a pairing oligonucleotide identifies the combination of the first molecular barcode and the second molecular barcode and, thus, the metes and bounds of the claim cannot be determined.
Claim 6 is indefinite for the recitation of the term “a first oligonucleotide and a second oligonucleotide” such as recited in claim 6, lines 2-3 because claim 6 depends from claims 1, 4 and 5, wherein claims 1, 4, and 5 do not recite the presence of a first oligonucleotide and a second oligonucleotide, such that it is unclear how the pairing oligonucleotide is produced and, thus, the metes and bounds of the claim cannot be determined.
Claims 4 and 17 are indefinite insofar as they ultimately depend from instant claim 1.
Claim Rejections - 35 USC § 112(d)
The rejection of claims 5 and 6 is maintained 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.
Claim 5 recites (in part): “further comprising generating a pairing oligo to identify combinations… sequencing the library of amplicons” such as recited in claim 5, lines 1-5 because claim 5 depends from claim 1 and 4, wherein claims 1 and 4 do not recite single-end reads, a combination of first molecular barcodes and second molecular barcodes, and/or using the combination to pair to single-end reads. Thus, claim 5 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 6 recites (in part): “where a pairing oligonucleotide has a length less than a length of the input fragment…the extended second oligonucleotide” in lines 1-8 because claim 6 depends from claims 1, 4 and 5, wherein claims 1, 4 and 5 do not recite the presence of a first oligonucleotide and a second oligonucleotide. Thus, claim 6 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.
New Objections/Rejections
Claim Interpretation
The “thereby” clause recited in claim 1 is not given patentable weight because it is interpreted to express the intended result of a process step positively recited [See, MPEP § 2111.04(I)].
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 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.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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.
Claims 1, 4-6 and 17 are rejected under 35 U.S.C. 103 as being unpatentable over Peter et al. (hereinafter “Peter”) (US Patent No. 10711269, issued July 14, 2020; filed January 18, 2017) in view of Kurihara et. al. (hereinafter “Kurihara”) (US Patent No. 10155942, issued December 18, 2018; effective filing date November 5, 2012). This is a new rejection necessitated by amendment of the claims in the response filed 08-26-2026.
Regarding claims 1, 6 (in part) and 17, Peter teaches making an asymmetrically-tagged sequencing library is provided including obtaining a symmetrically-tagged library of cDNA or genomic DNA fragments, hybridizing a tailed first primer to the 3' sequence tag of the library and extending the same to produce primer extension products, and amplifying the primer extension products using a pair of tailed primers to produce asymmetrically-tagged library (Abstract). Peter teaches that Figure 1, Panel A shows the method, which can comprise: (a) obtaining a symmetrically-tagged library of cDNA or genomic DNA fragments, wherein at least some of the members of the library comprise a top strand or insert sequence 2 comprising a 5' sequence tag 4 and a 3' sequence tag 6, wherein the 5' and 3' sequence tags have complementary sequences referred to as A2 and A2'; (b) hybridizing a first primer 8 to the 3' sequence tag 6 of the library, wherein the first primer 8 comprises a 3' region 10 (of at least 10, at least 12 or at least 15 nucleotides in length) which is complementary to the 3' sequence tag 6 of the library, and a 5' noncomplementary tail 12, i.e., a tail that that is not complementary to either of the 3' or 5' tag sequences (or other sequences in the library); (c) extending the first primer 8 to produce primer extension products 14 that comprises, from 5' to 3', the sequence of the first primer 8, a sequence of a fragment 16, and the complement of a 5' sequence tag of step (a) 18, such that the amplification of primer extension products 14 is shown in panel B of Figure 1; (d) panel B, amplifying the primer extension products of (c) using: (i) a forward primer of formula A4-A3 20, wherein sequence A4 is a 5' tail and sequence A3 is contained in the sequence of the first primer 8; and (ii) a reverse primer of formula A5-A2 22, wherein sequence A5 is a 5' tail and sequence A2 is contained in the 5' sequence tag of (a) 4, wherein this amplification step comprises an asymmetrically-tagged library in which at least some of the members comprise a top strand 24 comprising (i) a first end 26 comprising sequence A5, (ii) the sequence of a fragment, and (ii) a second end 28 comprising the complement of sequence A4 (interpreted as performing a first-stage amplification; tagging each end of the fragments with an adapter tag; a first-stage amplification; a second-stage amplification; using primers complementary to the first sequence tag and the second sequence tag; and thereby generating amplicons having two orientations, claims 1 and 6) (col 12, 23-30, 34-35, 39-46). Figure 1, Panel A and Panel B are shown below:
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Peter teaches that one feature of the invention is that it creates an asymmetrically tagged library from target fragments, but the adaptor sequence directly adjacent to the insert sequence (for example, A2 and A2' in Figure 1, or A1 in Figure 2) remains symmetrical (col 13, lines 7-11; and Figure 1 and 2). Peter teaches that the insert sequence 2 itself will not be symmetrical, meaning that it will have different sequence information at the 5' and 3' ends, wherein the sequence information at both ends of the target fragment 2 can be determined by annealing a sequencing primer (which can be homologous to the sequence denoted region 10 in Figure 1) to the symmetrical adapter sequence (interpreted as first, second, and annealing a sequencing adapter to the sequence tag, claim 1) (col 13, lines 11-17). Peter teaches that after a single round of primer extension with a primer 5' A3-A1, a pair of duplex molecules is produced with one duplex end and one unpaired, Y-shaped end and, although these two duplex molecules are similar in structure, they differ in the orientation of the insert sequence (interpreted as a first-stage amplification; double-stranded amplicons; comprising a barcode; different orientations; and that are obtained simultaneously, claims 1 and 17) (col 13, line 67; and col 14, lines 1-5). Peter teaches that the method can be implemented using sequence tags that contain a molecular barcode (as illustrated by the "NNNNNN" and "ZZZZZZ" sequence in Figures 3 and 5), wherein the 5' and 3' sequence tags of (a) each comprise a molecular barcode that varies in sequence in the library (interpreted as comprising molecular barcodes at each end, claim 1) (col 14, lines 56-61). Peter teaches that unless otherwise indicated or implicit from the context, a polynucleotide defined by a formula can have additional sequence, a primer binding site, a molecular barcode, a promoter, or a spacer, etc., at its 3' end, its 5' end or both the 3' and 5' ends (interpreted as comprising molecular barcodes at both ends, claim 1) (col 10, lines 48-52). Peter teaches that a tagged sample can be combined with tagged samples from other sources, e.g., 2 or more sources, 3 or more sources, 5 or more sources, 5000 or more sources, up to and including about 10,000 or more sources, where the molecular barcode of the tags allows the sequences from different sources to be distinguished after they are analyzed (col 17, lines 9-17). Peter teaches that after the primer extension step, the library can be amplified using a pair of primers comprising sequences A2 and A3, wherein the primers only contain the A2 and A3 sequences, and/or as illustrated in Figure 2, the A2 and A3 sequences can be joined to other primer or adapter sequences A4 and A5 (interpreted as second-stage amplification; third and fourth primer pairs annealing to the sequence tags; and including primer adaptors, claim 1) (col 14, lines 26-31). Figure 2 is shown below:
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Peter teaches that at the end of the PCR amplification in Figure 2, two sequenceable molecules are formed: one with adapter A5 on the 5' end of the top strand (black), and adapter A4' on the 3' end of the top strand (black), and a second one with adapter A5 on the 5' end of the bottom strand (grey), and adapter A4' on the 3' end of the bottom strand (grey) (interpreted as generating amplicons that comprise an insert sequence at a first orientation and an insert sequences in a second, inverted orientation; and obtained simultaneously, claims 1 and 17) (col 14, lines 49-55; and Figure 2). Peter teaches the A4 and A5 sequences can be compatible with the next generation sequencing platform being used to sequence the library; and/or the library can be amplified using primers that have tail sequences that are compatible with the next generation sequencing platform being used to sequence the library, wherein the products can be sequenced using any suitable method including, but not limited to Illumina's reversible terminator method (interpreted as sequencing by next generation sequencing, claim 1) (col 16, lines 59-67).
Regarding claim 4, Peter teaches that unless otherwise indicated or implicit from the context, a polynucleotide defined by a formula can have additional sequence, a primer binding site, a molecular barcode, a promoter, or a spacer, etc., at its 3' end, its 5' end or both the 3' and 5' ends (interpreted as comprising molecular barcodes at both ends, claims 1 and 4) (col 10, lines 48-52). Peter teaches that the method can be implemented using sequence tags that contain a molecular barcode (as illustrated by the "NNNNNN" and "ZZZZZZ" sequence in Figures 3 and 5), wherein the 5' and 3' sequence tags of (a) each comprise a molecular barcode that varies in sequence in the library (interpreted as comprising molecular barcodes at each end, claim 1) (col 14, lines 56-61).
Regarding claim 5, Peter illustrates an exemplary ligation-based library preparation method that uses a molecular barcode, wherein the 5' tail of the first primer of (b) can also comprise a molecular barcode or a sample index that varies in sequence (as illustrated by the "XXXXXX" sequence in Figures 3 and 5 (col 2, lines 22-24; col 15, lines 12-16; and Figure 5). Figure 5 (in part) is shown below:
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(interpreted as oligonucleotide pairing, claim 5) (Figure 5, in part).
Peter does not specifically exemplify that the pairing oligonucleotide has a length less than the length of the input fragment (claim 6, in part).
Regarding claim 6 (in part), Kurihara teaches that making dual barcoded nucleic acid molecule for sequencing including having a first and a second barcode on the same end of a nucleic acid molecule can permit a sequencing read to begin with the second barcode, continue through the first barcode and then into the nucleic acid molecule, such that identification of the second barcode, first barcode, and sequence of the nucleic acid molecule can therefore be obtained in a single read as opposed to having to provide a sequencing read from each end of the nucleic acid molecule in order to read the sequence of a single barcode back from a distal end of the nucleic acid molecule (interpreted as a single-end read, claim 5) (col 1, lines 56-67; and col 2, line 1). Kurihara teaches a method of making a dual barcoded nucleic acid molecule comprising: coupling one strand of a stem-loop oligonucleotide to a nucleic acid molecule to form a first barcode coupled nucleic acid molecule, wherein the stem-loop oligonucleotide including an intramolecular inverted repeat and a loop, the inverted repeat including a first barcode displacing one strand of the stem-loop oligonucleotide from the first barcode coupled nucleic acid molecule to form a first barcoded nucleic acid molecule; annealing a primer to the first barcoded nucleic acid molecule, the primer including a first portion complementary to the first barcoded nucleic acid molecule and a second portion including a second barcode; and extending the annealed primer to form a dual barcoded nucleic acid molecule, the dual barcoded nucleic acid molecule including the second barcode, the first barcode, and at least a portion of the nucleic acid molecule, wherein the first portion of the primer anneals to the first barcode or to a portion of the first barcode (interpreted as an insert comprising a first barcode and a second barcode, claim 6) (col 1, lines 57-67; and col 2, lines 4-23). Kurihara teaches that the ligated adaptors and gDNA fragments having the first set of barcodes can then be subjected to a primer extension reaction or PCR using a primer having a second set of barcodes, such that the resulting nucleic acid molecules each have one barcode from the first set of barcodes adjacent to one barcode from the second set of barcodes on at least one end of the nucleic acid molecule (col 6, lines 16-23). Kurihara teaches that having a first and a second barcode on the same end of a nucleic acid molecule can permit a sequencing read to begin with the second barcode, continue through the first barcode and then into the nucleic acid molecule, such that identification of the second barcode, first barcode, and sequence of the nucleic acid molecule can therefore be obtained in a single read as opposed to having to provide a sequencing read from each end of the nucleic acid molecule in order to read the sequence of a single barcode back from a distal end of the nucleic acid molecule, as is the case in traditional methods of using dual sequencing barcodes (interpreted as pairing a first barcode and second barcode, claim 6) (col 7, lines 56-67). Kurihara teaches that another advantage is that the first and second barcodes can be added in two separate steps (col 8, lines 1-3). Kurihara teaches that at a fixed size of a flanking terminal inverted repeat, the shorter the insert, the stronger the suppression effect and vice versa (interpreted as the length is shorter than the length of the input fragment, claim 6) (col 8, lines 35-37). Kurihara teaches that efficiency in attaching the first barcode via adaptor ligation can be utilized for preventing bias and preserving the representation of nucleic acid molecules in a sample, conversely, coupling the second barcode via primer extension can efficiently employ a long primer including the second barcode (col 8, lines 47-53).
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 dual barcoded nucleic acid molecules for sequencing as exemplified by Kurihara, 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 producing an asymmetrically-tagged sequencing library including dual-tagged insert fragments comprising adapter-barcodes on each end, wherein the duplex molecules differ in the orientation of the insert sequence as disclosed by Peter, to include the method of dual barcoding nucleic acid molecules including forming a first barcode coupled nucleic acid molecule, a stem-loop oligonucleotide including an intramolecular inverted repeat and a loop, wherein the inverted repeat includes a first barcode as taught by Kurihara with a reasonable expectation of success in producing libraries of asymmetrically-tagged nucleic acid fragments that can be sequenced on NGS platforms; and/or in obtaining the identity of the second barcode, first barcode, and sequence of the nucleic acid molecule in a single read.
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.
The Examiner suggests that Applicant amend claim 1 to add steps describing the synthesis of the oligonucleotide pairs (as shown in instant Figures 2A and 2B) to instant claim 1.
Conclusion
Claims 1, 4-6 and 17 are rejected.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AMY M BUNKER whose telephone number is (313) 446-4833. The examiner can normally be reached on Monday-Friday (6am-2:30pm).
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/AMY M BUNKER/Primary Examiner, Art Unit 1684
