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
Pursuant to a preliminary amendment filed May 29, 2026 claims 1-18 are currently pending in the instant application.
Response to Election/Restriction
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 is acknowledged.
Claims 2, 3, 7-16 and 18 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected species, there being no allowable generic or linking claim.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.
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.
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on June 9, 2023; September 4, 2024; and March 18, 2025 have been considered. Initialed copies of the IDSs accompany this Office Action.
Claim Objections/Rejections
Claim Objections
Claims 1, 4-6 and 17 are objected to because of the following informalities: Claims 1, 4-6 and 17 recite a mixture of pronouns including “the” and “said” within each claim, such that for consistency, a single pronoun reciting either “the” or “said” should be used.
Appropriate correction is required.
Claims 5 and 6 are objected to because of the following informalities: Claims 5 and 6 recite the term “oligo” and/or “oligos,” wherein the term “oligonucleotide” might be more appropriate.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(B) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 4-6 and 17 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.\
Claim 1 is indefinite for the recitation of the terms “the sequence tags” and “said sequence tags” such as recited in claim 1, lines 5, 7 and 10. There is insufficient antecedent basis for the term “the sequence tags” in the claim because claim 1, line 3 recites the term “one or more sequence tags.” The Examiner suggests that Applicant amend the claim to recite, for example, “primers complementary to the one or more sequence tags.”
Claim 1 is indefinite for the recitation of the term “in such a way” such as recited in claim 1, lines 10 and 13 because the term “in such a way” is unclear with regard to the method, manner and/or extent to which a step is performed; and it is unclear as to what “way” is meant by the term “in such a way” and, thus, the metes and bounds of the claim cannot be determined.
Claim 1 is indefinite for the recitation of the term “the sequencing adaptors” such as recited in claim 1, line 12. There is insufficient antecedent basis for the term “the sequencing adaptors” in the claim because claim 1, line 10 recites the term “sequencing adaptor sequences.”
Claim 1 is indefinite for the recitation of the terms “the insert” and “the insert sequences” such as recited in claim 1, lines 14-16. There is insufficient antecedent basis for the terms “the insert” and “the insert sequences” in the claim because claim 1, line 4 recites the term “an insert sequence.”
Claim 1 is indefinite for the recitation of the term “the molecular barcode sequences” such as recited in claim 1, line 14. There is insufficient antecedent basis for the term “the molecular barcode sequences” in the claim.
Claim 1 is indefinite for the recitation of the term “the molecular barcode reads” such as recited in claim 1, line 15. There is insufficient antecedent basis for the term “the molecular barcode reads” in the claim.
Claim 1 is indefinite for the recitation of the term “the same input fragment” such as recited in claim 1, line 16. There is insufficient antecedent basis for the term “the same input fragment” in the claim.
Claim 1 is indefinite for the recitation of the term “the different orientations” such as recited in claim 1, line 16. There is insufficient antecedent basis for the term “the different orientations” in the claim.
Claims 4 is indefinite for the recitation of the terms “two molecular barcodes are attached to each input fragment” such as recited in claim 4, lines 1-2 because claim 4 depends from instant claim 1, wherein claim 1 does not recite that the input fragments comprise molecular barcodes. Instead, claim 1 recites the production of ‘tagged fragments’, wherein the sequence tags comprise a molecular barcode and, thus, the metes and bounds of the claim cannot be determined.
Claim 5 is indefinite for the recitation of the terms “combinations of molecular barcodes”; “molecular barcodes attached to an input fragment” and/or “single-end reads” such as recited in claim 5, lines 1-3 because claim 5 depends from instant claims 1 and 4, wherein claims 1 and 4 do not recite the presence of combinations of molecular barcodes; that input fragments comprise molecular barcodes; and/or single-end reads. It is noted that claim 1 recites the production of ‘tagged fragments’, where the sequence tags comprise a molecular barcode and, thus, the metes and bounds of the claim cannot be determined.
Claim 6 is indefinite for the recitation of the term “shorter” such as recited in claim 6, line 1 because the term “shorter” is a relative term that renders the claim indefinite. The term “shorter” is not defined by the claim, and the Specification does not provide a standard for ascertaining the requisite length of a pairing oligo as compared to some other value for an input fragment that qualifies as generating a shorter pairing oligo, such that one of ordinary skill in the art would not be reasonably appraised of the scope of the invention.
Claim 6 is indefinite for the recitation of the terms “a pairing oligo shorter than the input fragment”; “two oligos”; and/or “first stage amplification products” such as recited in claim 6, lines 1-3, wherein claim 6 depends from instant claims 1, 4 and 5, such that claims 1, 4 and 5 do not recite the length of input fragments; the presence of two oligos; and/or first stage amplification products and, thus, the metes and bounds of the claim cannot be determined.
Claim 17 is indefinite for the recitation of the term “the two orientations” such as recited in claim 17, line 1. There is insufficient antecedent basis for the term “the two orientations” in the claim because claim 1, lines 11-12 recites the term “at least two different orientations.” Moreover, claim 17, depends from instant claim 1, wherein claim 1 does not recite sequencing insert sequences. Instead, claim 1 recites ‘sequencing said library”. Additionally, it is noted that the insert sequence is a portion of the tagged fragment, such that it is unclear whether only the insert sequences are sequenced (e.g., where the sequencing the tags are not sequenced). Furthermore, instant claim 1 recites that the input sequences are sequenced from the different orientations and, thus, the metes and bounds of the claim cannot be determined.
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 4-6 and 17 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.
Claim 4 recites (in part): “wherein the two molecular barcodes are attached to each input fragment” such as recited in claim 4, lines 1-2 because claim 4 depends from instant claim 1, wherein claim 1 does not recite that the input fragments comprise molecular barcodes, combinations of molecular barcodes and/or pairing single-end reads. Thus, claim 4 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 5 recites (in part): “further comprising generating a pairing oligo to identify combinations of molecular barcodes attached to an input fragment to be used in pairing single end reads” such as recited in claim 5, lines 1-3 because claim 5 depends from claim 1 and 4, wherein claims 1 and 4 do not recite that the input fragments comprise molecular barcodes, combinations of molecular barcodes; single-end reads, and/or pairing 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 oligo shorter than the input fragment is generated by annealing two oligos, wherein one of the oligos has regions complementary to both ends of the first-stage amplification products, followed by extension and ligation” in lines 1-3 because claim 6 depends from claim 1, 4 and 5, wherein claims 1, 4 and 5 do not recite a pairing oligo shorter than the input fragment; two oligos and/or first stage amplification products. 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.
Claim 17 recites (in part): “where the two orientations of the insert sequence are sequenced simultaneously” in lines 1-2 because claim 17 depends from instant claim 1, such that claim 1 does not recite that there are two orientations for the insert sequence; and claim 1 does not recite sequencing the insert sequences. Thus, claim 17 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 § 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 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.
Claims 1, 4-6 and 17 are rejected 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).
Regarding claim 1, Kennedy teaches methods and compositions for targeted nucleic acid sequence enrichment, as well as uses of such enrichment for error-corrected nucleic acid sequencing applications (Abstract, lines 1-2). Kennedy teaches methods including the steps of providing double-stranded nucleic acid material wherein the nucleic acid material comprises a single molecule identifier sequence on each strand of the nucleic acid material and an adapter sequence on at least one of the 5' and 3' ends of each strand of the nucleic acid material (corresponding to an adapter sequence on one end on input fragment; and comprising a barcode), wherein a first adapter sequence is located on one of the 5' end or 3' end of a first strand of the nucleic acid material, and a second adapter sequence is located on an opposite end of a second strand of the nucleic acid material (corresponding to an adapter sequence on the other end of the input fragment; and comprising a barcode), and wherein the first strand and the second strand originated from the same double-stranded nucleic acid molecule (corresponding to identifying read pairs of sequences derived from the same input fragment); amplifying the nucleic acid material (corresponding to a first-stage amplification); separating the amplified nucleic acid material into a first sample and a second sample, amplifying the first strand in the first sample through use of a primer specific to the first adapter sequence to provide a first nucleic acid product, amplifying the second strand in the second sample through use of a primer specific to the second adapter sequence to provide a second nucleic acid product sequencing each of the first nucleic acid product and second nucleic acid product (corresponding to a second-stage amplification); and comparing the sequence of the first nucleic acid product to the sequence of the second nucleic acid product (corresponding to sequencing to obtain reads), such that a nucleic acid material comprises an adapter sequence on each of the 5' and 3' ends of each strand of the nucleic acid material (corresponding to as ligating one or more tags to produce a tagged fragment; performing first-stage amplification; primers complementary to sequence tags; and performing second-stage amplification, claim 1) (paragraph [0013]). Kennedy teaches that a single molecule identifier sequence comprises an endogenous shear point or an endogenous sequence that can be positionally related to the shear point, wherein a single molecule identifier sequence is at least of one of a degenerate or semi-degenerate barcode sequence, one or more nucleic acid fragment ends of the nucleic acid material, or a combination thereof that uniquely labels the double-stranded nucleic acid molecule (corresponding to at least one sequence tag comprises a barcode, claim 1) (paragraph [0018]). Kennedy teaches ligating a double-stranded nucleic acid material to at least one double-stranded degenerate barcode sequence to form a double-stranded nucleic acid molecule barcode complex, wherein the double-stranded degenerate barcode sequence comprises the single molecule identifier sequence in each strand (corresponding to at least one sequence tag comprises a barcode, claim 1) (paragraph [0019]). Kennedy teaches that before the providing step, the method can comprise the steps of cutting the nucleic acid material to form a target nucleic acid fragment of substantially known length; and ligating an adapter (e.g., an adapter sequence) to a target nucleic acid (e.g., a target nucleic acid fragment) (corresponding to ligating adapters to input fragments, claim 1) (paragraph [0025]). Kennedy teaches that multiplexed loci-specific PCRs are performed such that the resulting PCR products in each tube are derived from only one of the two original strands of a given DNA molecule sample (corresponding to identifying read pairs of sequences derived from the same input fragment); according to the following procedure, using a sample that is split into two tubes (a first tube and a second tube) as described herein, comprising: in the first tube, PCR is performed using a primer specific for hybridizing to the "Read 1" (i.e. Illumina P5) adapter sequence (Figure 4, Step 3; grey arrow), as well as primers specific to the genetic loci of interest, tailed with the sequence for the Read 2 (i.e. Illumina P7) adapter sequences (Figure 4, Step 3; black arrow w/grey tail), wherein it is proposed that this step provides that amplification products with one P5 and one P7 sequence at each termini only occurs from DNA derived from one strand of the original parental DNA molecule (i.e. initial sample DNA), such that sequentially or simultaneously, a similar reaction is repeated in the second tube: amplification occurs from the amplification product derived from the opposite strand of the same genomic location as compared to the amplification of the sample in the first tube, wherein this is achieved by using a loci-specific primer that anneals to the opposite strand orientation as in tube 1 (i.e., anti-reference versus reference sequence) and is tailed with the opposite universal primer sequence (i.e. P5 instead of P7) and an adapter primer to the opposite universal primer sequence (i.e. P7 instead of P5) (corresponding to being sequenced from different orientations, claim 1) (paragraph [0208]). Figure 4 is shown below:
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Kennedy teaches that since cfDNA is already fragmented, no cutting (e.g. CRISPR/Cas9) is required, such that SPLiT-DS is performed as described in previous examples, with the addition of a nested PCR; and the resultant fragments will be sequenced with a MiSeq v3 150 cycles approximately 10 samples will be multiplexed in a cartridge for a total of 2.5 million reads each (nested PCR corresponding to a first-stage and second-stage amplification; and MiSeq corresponding to as sequencing to obtain sequence reads for the insert and molecular barcode; and identifying read pairs derived from the same input fragment, claim 1) (paragraph [00263]).
Regarding claim 4, Kennedy teaches ligating a double-stranded nucleic acid material to at least one double-stranded degenerate barcode sequence to form a double-stranded nucleic acid molecule barcode complex, wherein the double-stranded degenerate barcode sequence comprises the single molecule identifier sequence in each strand (corresponding two molecular barcodes attached to each input fragment, claim 4) (paragraph [0019]). Kennedy teaches in Figure 4, Step 1, that the input fragment comprises four molecular barcodes as shown below (corresponding two molecular barcodes attached to each input fragment, claim 4) (Figure 4, Step 1):
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Regarding claim 5, Kennedy teaches that after generating the double-stranded target nucleic acid complex comprising at least one single molecule identifier (SMl) and at least one strand-defining element (SDE), or where one or both of these elements will be subsequently introduced, the complex can be subjected to DNA amplification, such as with PCR, or any other biochemical method of DNA amplification (e.g., rolling circle amplification, multiple displacement amplification, isothermal amplification, bridge amplification or surface-bound amplification, such that one or more copies of the first strand target nucleic acid sequence and one or more copies of the second strand target nucleic acid sequence are produced; and then subjected to DNA sequencing such as by using a Next Generation massively parallel DNA sequencing platform (e.g., Figure 1B) (corresponding to generating a pairing oligo to identify combinations of barcodes attached to input fragments to be used in pairing single-end reads, claim 5) (paragraph [0092]; and Figure 1B). Kennedy also teaches in Figure 4, step 1 (supra), the presence of complementary barcode sequences, such that the ends form a pair of oligonucleotides (Figure 4).
Regarding claim 6, Kennedy teaches that MIPSTR uses targeted capture of STR loci by single-molecule Molecular Inversion Probes (smMIPs) to specifically anneal to the sequences flanking the STR loci, such that after polymerase extension of the 3’-end of the smMIP, the ends are ligated and subjected to PCR amplification and sequencing (corresponding to pairing oligo shorter than the input fragment is generated by annealing two oligos complementary to both end of the first-stage amplification products, followed by extension and ligation, claim 6) (paragraph [0010]). Kennedy teaches that the nucleic acid material has been cut to provide strands of nucleic acid material having similar lengths between about 1 and 1,000,000 bases (corresponding to smMIPs that are shorter than the input fragment (paragraph [0015], lines 1-2)
Regarding claim 17, DNA sequencing using a Next Generation massively parallel DNA sequencing platform (e.g., Figure 1B) (corresponding to sequencing, claim 17) (paragraph [0092]; and Figure 1B). Kennedy teaches that massively parallel sequencing (MPS), and also known as next generation DNA sequencing (NGS) systems has the potential to address several challenging issues in forensics analysis, wherein the platforms offer previously unparalleled capacity to allow for the simultaneous analysis of STRs and single nucleotide polymorphisms (SNPs) in nuclear and mitochondrial DNA (mtDNA), which will dramatically increase the power of discrimination between individuals and offers the possibility to determine ethnicity and even physical attributes (phenotypes) (corresponding to sequencing simultaneous sequencing of inserts, claim 17) (paragraph [0005]).
Kennedy meets all the limitations of the claims and, therefore, anticipates the claimed invention.
Conclusion
Claims 1, 4-6 and 17 are rejected.
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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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Heather Calamita can be reached on (571) 272-2876. The fax phone number for the organization where this application or proceeding is assigned is (571) 273-8300.
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/AMY M BUNKER/Primary Examiner, Art Unit 1684
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