DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
Applicant’s election without traverse of Group I, (i) Plurality of cells; (ii) A prokaryotic hyperactive transposase; (iii) Tn5 mutants; (iv) Triple Tn5 mutants in the reply filed on 8/6/2026 is acknowledged.
Claims 18-19, 21, 33-39, 41-44, 46-49, 51-55, 57-64 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention/species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 8/6/2026.
Claims 1, 2, 6-17, 22-31 and 98 are being examined.
Priority
The instant application was filed 03/11/2024 and claims priority from provisional application 63489335 , filed 03/09/2023.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 8/26/2026 are being considered by the examiner.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - Sequences appearing in the specification are not identified by sequence identifiers (i.e., “SEQ ID NO:X” or the like) in accordance with 37 CFR 1.831(c). for example pages 51-53 specification filed 3/11/2024 or pages 52-55 of specification filed 6/27/2024
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Claim Rejections - 35 USC § 112
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, 2, 6-17, 22-31 and 98 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites, “isolating DNA sequences, obtaining one or more cells or nuclei from a sample.” The metes and bounds are unclear if the isolating DNA sequences relates to obtaining one or more cells or nuclei. The claim should be amended to clarify.
Claim 1 recites, “conducting a tagmentation reaction with a hyperactive transposase on the isolated DNA sequences cells or nuclei to produce a plurality of nucleic acid libraries.” The recitation of hyperactive suggest there is less than hyperactive. However the specification does not provide a standard to differentiate hyperactive from less than hyperactive. Further the metes and bounds are vague and unclear what is required of “hyperactive transposase on the isolated DNA sequences cells or nuclei.” It is confusing if they are in the alternative, all required, etc.
Claim 10 recites, “wherein the hyperactive transposase controls fragment size based on concentration of the isolated DNA sequences.” The metes and bounds are unclear how a hyperactive transposase by itself controls fragment size, as enzyme amount, magnesium concentration, pH, length of input DNA, time of incubation, etc. play a role in the length. Thus it is unclear how a hyperactive transposase controls fragment size.
Claim 11 recites, “the hyperactive transposase comprises hairpin oligonucleotides to generate long fragments.” The metes and bounds are confusing and unclear how a protein (hyperactive transposase) comprises hairpin oligonucleotides. Further the recitation of long fragments suggests there are short and normal fragments. The specification does not provide a standard to differentiate long fragments from short fragments and normal fragments
Claim 12 recites, “wherein long fragments generated.” The metes and bound are unclear what fragments are generated as claim 1 from which the recitation depends does not provide any steps of generating fragments. This may be addressed by amending claim 12 to depend from claim 11.
Claims 24 and 25 recite, “ratio of transposase:DNA “ The metes and bounds are unclear if the DNA is the adapters or hairpin oligonucleotides or the DNA from cells or nuclei.
Claim 30 recites, “wherein the sample is a biological sample.” The claim is confusing and unclear as the independent claim requires, “obtaining one or more cells or nuclei.” Thus the metes and bounds are unclear how samples comprising nucleic or cells can be from a sample other than a biological sample. Thus it is unclear how claim 30 limits claim 1.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 1-2, 6-17, 22, 26-31 is/are rejected under 35 U.S.C. 103 as being unpatentable over Belhocine (US 20200248176), Picelli (Genome Research (2014) volume 24, pages 2033-2040), Addey (Genome Research (2021) volume 31, pages 1693-1705) .
As noted in the MPEP 2111.02, “If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.” Further, 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). Accordingly, the claim language of "a method of genome and epigenome sequencing” merely sets forth the intended use or purpose of the claimed methods, but does not limit the scope of the claims as claim provide no steps with epigenomics.
Belhocine teaches, “Methods and systems for sample preparation techniques that allow amplification (e.g., whole genome amplification) and sequencing of chromatin accessible regions of single cells are provided. The methods and systems generally operate by forming or providing partitions (e.g., droplets) including a single biological particle and a single bead comprising a barcoded oligonucleotide. The preparation of barcoded next-generation sequencing libraries prepared from a single cell is facilitated by the transposon-mediated transposition and fragmentation of a target nucleic acid sequence. The methods and systems may be configured to allow the implementation of single-operation or multi-operation chemical and/or biochemical processing within the partitions.” (abstract)
With regards to claim 1, Belhocine teaches, “[0035] In some embodiments, the method further comprises (a) lysing a plurality of cells in the presence of a cell lysis agent and a blocking agent; and (b) separating a plurality of nuclei from the plurality of lysed cells to generate the plurality of biological particles, wherein the blocking agent reduces the fraction of sequencing reads corresponding to a mitochondrial genome compared to sequencing reads obtained in the absence of the blocking agent. In some embodiments, the blocking agent is bovine serum albumin (BSA).” Thus Belhocine teaches isolate DNA sequences from one or more cells.
Belhocine teaches, “[0251] In some cases, whole cells may be used as the input material for an ATAC-seq analysis (e.g., as described herein). In some cases, nuclei may be used as the input material for an ATAC-seq analysis. For example, nuclei may be used as the input material where mitochondrial DNA is removed prior to tagmentation of genomic DNA. In this approach, whole cells may be gently lysed to remove their cytoplasmic membrane whilst leaving the nuclear membrane and nucleoprotein packaging of the genome intact. In some cases, a lysis buffer used to lyse whole cells may comprise one or more of Tris-HCl, NaCl, magnesium ions (e.g., MgCl.sub.2), and a lysis agent. A lysis agent may be, for example, NP40, Tween-20, Digitonin, Nonident P40, or DBDM. Mitochondria may be washed away along with other cellular debris during subsequent centrifugation steps to yield a suspension of nuclei.” Belhocine teaches, “0109] In some embodiments, the transposase is a Tn5 transposase. In some embodiments, the transposase is a mutated, hyperactive Tn5 transposase.” Belhocine teaches tagmentation using hyperactive transposase on DNA sequences isolated from cells to produce libraries..
Belhocine teaches filling in gaps from transposition reaction (0295).
Belhocine teaches partitioning (fractionating) the library after tagmentation (0371).
Belhocine teaches, “[0006] Certain applications may benefit from the amplification or sequencing of species obtained from single cells obtained from a much larger population. In some cases, the single cells of interest may be quite rare.”
Thus it would have been prima facie obvious to one of skill in the art prior to the effective filing date of the claims to isolate DNA sequences from cells, conduct tagmentation with a hyperactive transposase to produce nucleic acid libraries, repair gaps in the DNA libraries resulting from the tagmentation reaction, partitioning the nucleic acid library’s and sequencing the libraries.
While claims 2, 6-7, provide concentration of DNA sequences. Review of the specification did not reveal an unexpected result based on DNA concentration,
Belhocine does not specifically teach concentration of DNA.
However, Picelli provides an article on Tn5 transposase and tagmentation procedures. (title abstract). Picelli teaches , “The protocol is slightly different according to the input DNA used in the tagmentation reaction.” (2039, column 1, top) Picelli teaches starting the tagementation reaction with 5 ng or more of DNA (2039, column 1, top)
MPEP 2144.05 II A States:
II. ROUTINE OPTIMIZATION
A. Optimization Within Prior Art Conditions or Through Routine Experimentation
Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In reAller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955)
Therefore it would have been prima facie obvious to one of ordinary skill in the art to optimize the amount of isolated DNA in the tagmentation reaction. The artisan would be motivated to optimize DNA concentration in the tagmentation reaction to conserve samples for other assays and to minimize artifacts from too much or too little DNA in the tagmentation. The artisan would have a reasonable expectation of success as the artisan is merely using known reagents.
With regards to claim 8-9, Belhocine teaches, “[0035] In some embodiments, the method further comprises (a) lysing a plurality of cells in the presence of a cell lysis” Belhocine teaches the use of lysed cells in tagementation assay (title, abstract, throughout).
Behlocine does not specifically teach the length of the fragments or use of hairpin olignculetodies.
With regards to claims 10-13, Picelli teaches in figure 2c teaches of 100 to 500 bp in length,
Addey teaches the use of hairpin oligonucleotides (figure 3).
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to use a hyperactive TN5 transposase with hairpin oligonucleotides to produce fragments of 100 base pairs or longer. The artisan would be motivated to use hairpin oligonucleotides and TN5 transposase to provide longer sequence reads. The artisan would have a reasonable expectation of success as the artisan is using known reagents and concentrations.
With regards to claims 14-17, Picelli teaches, “Transposition is a very infrequent event in vivo, and hyperactive mutants were historically derived by introducing three missense mutations in the 476 residues of the Tn5 protein (E54K, M56A, L372P).” (page 2033, bottom 1st column, top of 2nd column).
With regards to claim 22, Behlocine teaches next generation high throughout sequencing (0283)
With regards to claim 26-27, Picelli teaches tagmentation 25oC to 55oC. (2034, 2nd column top).
With regards to claim 28, Addey teaches multiplexed analysis (1701, 1st full paragraph)
With regards to claim 29, Behlocine teaches unique barcodes (0095).
With regards to claim 30, Behlocine teaches cells which are biological samples.
With regard to claim 31, Behlocine teaches, “ [0006] Certain applications may benefit from the amplification or sequencing of species obtained from single cells obtained from a much larger population.”
Thus it would have been prima facie obvious to one of ordinary skill in the art prior to the effective prior to the effective filing date of the claims amplification is not required for the method of Behlocine. The artisan would be motivated as Behlocine teaches, “ [0006] Certain applications may benefit from the amplification or sequencing of species obtained from single cells obtained from a much larger population.” Thus the artisan recognize Behlocine teaches amplification is not required for all applications. The artisan would have a reasonable expectation of success as the artisan is merely using known methods.
Claim(s) 24-25 is/are rejected under 35 U.S.C. 103 as being unpatentable over Belhocine (US 20200248176), Picelli (Genome Research (2014) volume 24, pages 2033-2040), Addey (Genome Research (2021) volume 31, pages 1693-1705) as applied to claims 1-2, 6-17, 22, 26-31 above, and further in view of Crofts (mysystems (2021( volume 6 e00524-21).
The teachings of Behlocine, Picelli and Addey are set forth above.
While Behlocine, Picelli and Addey teach a method of isolating NA from on or more cells, performing a tagmentation assay with hyperactive transposase, filling gaps , fractionating and sequencing. Behlocine, Picelli and Addey do not specifically teach ratio of transposase to DNA.
However, Crofts teaches “DNA fragments for sequencing on the Illumina platform, we were able to alter this by adjusting the ratio of transposome to input. Using 0.5 ng of transposome per ng of target DNA yielded a fragmentation pattern centered around 2.5 kb.” (page 4, last full paragraph).
MPEP 2144.05 II A States:
II. ROUTINE OPTIMIZATION
A. Optimization Within Prior Art Conditions or Through Routine Experimentation
Generally, differences in concentration or temperature will not support the patentability of subject matter encompassed by the prior art unless there is evidence indicating such concentration or temperature is critical. “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In reAller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955)
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to optimize the transposase to DNA ratio. The artisan would be motivated to optimize the transposase to DNA ratio to provide longer tagmentation products as suggested by Croft. The artisan would have a reasonable expectation of success as the artisan is merely following the teachings of the art.
Claim(s) 98 is/are rejected under 35 U.S.C. 103 as being unpatentable over Belhocine (US 20200248176), Picelli (Genome Research (2014) volume 24, pages 2033-2040), Addey (Genome Research (2021) volume 31, pages 1693-1705) as applied to claims 1-2, 6-17, 22, 26-31 above, and further in view of Henning (G3 genes genome genetics (2018) .
The teachings of Behlocine, Picelli and Addey are set forth above.
While Behlocine, Picelli and Addey teach a method of isolating NA from on or more cells, performing a tagmentation assay with hyperactive transposase, filling gaps , fractionating and sequencing. Behlocine, Picelli and Addey do not specifically teach a Tn5 with R27S, E54K, and L372P.
However, Henning teaches, “this initial experiment demonstrated that both purified Tn5 constructs are active and produce libraries suitable for sequencing from small amounts of input material. Interestingly, the hyperactive Tn5 version carrying the additional R27S mutation showed higher sensitivity toward the ratio of Tn5-to-cDNA molecules than the regular hyperactive Tn5E54K,L372P enzyme.(page 82, 2nd column, 2nd full paragraph)
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to use the Tn5 with R27S, E54K, and L372P. The artisan would be motivated to use Tn5 with R27S, E54K, and L372P as Henning teaches, “the hyperactive Tn5 version carrying the additional R27S mutation showed higher sensitivity toward the ratio of Tn5-to-cDNA molecules than the regular hyperactive Tn5E54K,L372P enzyme” . The artisan would have a reasonable expectation of success as the artisan is merely following the teachings of the art.
Claim(s) 23 is/are rejected under 35 U.S.C. 103 as being unpatentable over Belhocine (US 20200248176), Picelli (Genome Research (2014) volume 24, pages 2033-2040), Addey (Genome Research (2021) volume 31, pages 1693-1705) as applied to claims 1-2, 6-17, 22, 26-31 above, and further in view Gong (Jove Journal of visualized experiments (2019) volume 145, e58954, pages 1-10) .
The teachings of Behlocine, Picelli and Addey are set forth above.
Behlocine teaches, “0100] The term “sequencing,” as used herein, generally refers to methods and technologies for determining the sequence of nucleotide bases in one or more polynucleotides. The polynucleotides can be, for example, nucleic acid molecules such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), including variants or derivatives thereof (e.g., single stranded DNA). Sequencing can be performed by various systems currently available, such as, without limitation, a sequencing system by Illumina®, Pacific Biosciences (PacBio®), Oxford Nanopore®, or Life Technologies (Ion Torrent®). Alternatively or in addition, sequencing may be performed using nucleic acid amplification, polymerase chain reaction (PCR) (e.g., digital PCR, quantitative PCR, or real time PCR), or isothermal amplification. Such systems may provide a plurality of raw genetic data corresponding to the genetic information of a subject (e.g., human), as generated by the systems from a sample provided by the subject. In some examples, such systems provide sequencing reads (also “reads” herein). A read may include a string of nucleic acid bases corresponding to a sequence of a nucleic acid molecule that has been sequenced. In some situations, systems and methods provided herein may be used with proteomic information.”
While Behlocine, Picelli and Addey teach a method of isolating NA from on or more cells, performing a tagmentation assay with hyperactive transposase, filling gaps , fractionating and sequencing. Behlocine, Picelli and Addey do not specifically teach a single molecule sequencing.
However, Gong teaches, “Recent progress in single-molecule sequencing offers significantly longer read length, which can facilitate the detection of the full spectrum of SVs7,8,9, and offers accurate and complete assembly of complex microbial and mammalian genomes6,10. The nanopore platform performs single molecule sequencing by directly measuring the current changes mediated by DNA passage through the pores11,12,13. Unlike any existing DNA sequencing chemistry, nanopore sequencing can generate long (tens to thousands of kilobases) reads in real-time without relying on polymerase kinetics or artificial amplification of the DNA sample. Therefore, nanopore long-read sequencing (NLR-seq) holds great promise for generating ultra-long read lengths well beyond 100 kb, which would greatly advance genomic and biomedical analyses14, particularly in the low-complexity or repeat-rich regions of the genomes1”.(page 1, 2nd full paragraph of introduction)
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to nanopore single molecule sequencing. The artisan would be motivated to use nanopore single molecule sequencings as Gong teaches it allows for ultralong reads. The artisan would have a reasonable expectation of success as the artisan is merely following the teachings of the art.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1, 2, 6-17, 22-31 and 98 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-29 of U.S. Patent No. 10,619,207. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
As noted in the MPEP 2111.02, “If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.” Further, 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). Accordingly, the claim language of "a method of genome and epigenome sequencing” merely sets forth the intended use or purpose of the claimed methods, but does not limit the scope of the claims as claim provide no steps with epigenomics.
The instant claims are drawn to A method of genome and epigenome sequencing, comprising: isolating DNA sequences, obtaining one or more cells or nuclei from a sample; conducting a tagmentation reaction with a hyperactive transposase on the isolated DNA sequences cells or nuclei to produce a plurality of nucleic acid libraries; repairing gaps in nucleic libraries ;fractionating the nucleic acid libraries; and, sequencing the nucleic acid libraries.
The claims of 207 are drawn to a method for generating a sequencing library from a plurality of cells, comprising: a) lysing a plurality of cells to provide a plurality of cell nuclei, wherein the plurality of cell nuclei comprises chromatin; b) contacting a cell nucleus of the plurality of cell nuclei with a transposase complex such that polynucleotides of the cell nucleus are tagmented at regions of open chromatin to produce a plurality of tagged fragments; and c) performing one or more nucleic acid reactions on the tagged fragment to produce a sequencing library. Dependent claim draw the invention to wherein said Tn5 transposase is a hyperactive Tn5 transposase.
Therefore it would have been prima facie obvious to one ordinary skill in the art prior to the effective filing date of the claims the claims of the patent encompass the instant claims.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 2, 6-17, 22-31 and 98 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 10,889,859. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
As noted in the MPEP 2111.02, “If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.” Further, 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). Accordingly, the claim language of "a method of genome and epigenome sequencing” merely sets forth the intended use or purpose of the claimed methods, but does not limit the scope of the claims as claim provide no steps with epigenomics.
The instant claims are drawn to A method of genome and epigenome sequencing, comprising: isolating DNA sequences, obtaining one or more cells or nuclei from a sample; conducting a tagmentation reaction with a hyperactive transposase on the isolated DNA sequences cells or nuclei to produce a plurality of nucleic acid libraries; repairing gaps in nucleic libraries ;fractionating the nucleic acid libraries; and, sequencing the nucleic acid libraries.
The claims of 859 are drawn to a method for analyzing chromatin, comprising: (a) isolating a plurality of cell nuclei from a cell sample; (b) contacting chromatin from a nucleus of said plurality of cell nuclei with an insertional enzyme complex to produce a plurality of tagged fragments of genomic deoxyribonucleic acid (DNA) in said nucleus; (c) providing said nucleus into a nucleic acid reaction mixture, wherein said nucleic acid reaction mixture comprises at most a single nucleus; and (d) performing one or more nucleic acid reactions on a tagged fragment of said plurality of tagged fragments. Dependent claim draw the invention to wherein said Tn5 transposase is a hyperactive Tn5 transposase.
Therefore it would have been prima facie obvious to one ordinary skill in the art prior to the effective filing date of the claims the claims of the patent encompass the instant claims.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 2, 6-17, 22-31 and 98 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 11,519,032. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
As noted in the MPEP 2111.02, “If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.” Further, 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). Accordingly, the claim language of "a method of genome and epigenome sequencing” merely sets forth the intended use or purpose of the claimed methods, but does not limit the scope of the claims as claim provide no steps with epigenomics.
The instant claims are drawn to A method of genome and epigenome sequencing, comprising: isolating DNA sequences, obtaining one or more cells or nuclei from a sample; conducting a tagmentation reaction with a hyperactive transposase on the isolated DNA sequences cells or nuclei to produce a plurality of nucleic acid libraries; repairing gaps in nucleic libraries ;fractionating the nucleic acid libraries; and, sequencing the nucleic acid libraries.
The claims of 032 are drawn to a method for analyzing chromatin, comprising: (a) contacting chromatin of a cell with an insertional enzyme complex such that polynucleotides of said chromatin are cleaved and tagged at regions of open chromatin to produce a plurality of tagged nucleic acid fragments, wherein said insertional enzyme complex does not comprise an antibody specific to a protein that is part of said chromatin, and wherein the plurality of tagged nucleic acid fragments comprise molecular tags comprising sequencing adaptors; (b) performing one or more nucleic acid reactions on the tagged nucleic acid fragments to produce a plurality of sequence reads; and (c) making an epigenetic map of a region of the cell genome by mapping information obtained from the sequence reads to the region of the genome.. Dependent claim draw the invention to the insertional enzyme being a hyperactive Tn5 transposase.
Therefore it would have been prima facie obvious to one ordinary skill in the art prior to the effective filing date of the claims the claims of the patent encompass the instant claims.
Dependent claims are obvious as they are coextensive in scope.
Claims 1, 2, 6-17, 22-31 and 98 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-30 of U.S. Patent No. 11,597,974. Although the claims at issue are not identical, they are not patentably distinct from each other because they are coextensive in scope.
As noted in the MPEP 2111.02, “If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.” Further, 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). Accordingly, the claim language of "a method of genome and epigenome sequencing” merely sets forth the intended use or purpose of the claimed methods, but does not limit the scope of the claims as claim provide no steps with epigenomics.
The instant claims are drawn to A method of genome and epigenome sequencing, comprising: isolating DNA sequences, obtaining one or more cells or nuclei from a sample; conducting a tagmentation reaction with a hyperactive transposase on the isolated DNA sequences cells or nuclei to produce a plurality of nucleic acid libraries; repairing gaps in nucleic libraries ;fractionating the nucleic acid libraries; and, sequencing the nucleic acid libraries.
The claims of 974 are drawn to a method for analyzing chromatin, comprising: (a) contacting chromatin in a permeabilized cell nucleus of a mammalian cell with an insertional enzyme complex such that polynucleotides of said permeabilized cell nucleus are cleaved and tagged at regions of open chromatin to produce a plurality of tagged nucleic acid fragments, wherein a tagged nucleic acid fragment comprises molecular tags comprising sequencing adaptors; (b) performing one or more nucleic acid reactions on the tagged nucleic acid fragments to produce a plurality of sequence reads; and (c) making an epigenetic map of a region of the permeabilized cell nucleus genome by mapping information obtained from the sequence reads to the region of the genome.. Dependent claim draw the invention to the insertional enzyme being a hyperactive Tn5 transposase.
Therefore it would have been prima facie obvious to one ordinary skill in the art prior to the effective filing date of the claims the claims of the patent encompass the instant claims.
Dependent claims are obvious as they are coextensive in scope.
Summary
No claims are allowed.
Conclusion
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/Steven Pohnert/ Primary Examiner, Art Unit 1683
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