AU2021339819A1 - Base editing enzymes - Google Patents

Base editing enzymes Download PDF

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Publication number
AU2021339819A1
AU2021339819A1 AU2021339819A AU2021339819A AU2021339819A1 AU 2021339819 A1 AU2021339819 A1 AU 2021339819A1 AU 2021339819 A AU2021339819 A AU 2021339819A AU 2021339819 A AU2021339819 A AU 2021339819A AU 2021339819 A1 AU2021339819 A1 AU 2021339819A1
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AU
Australia
Prior art keywords
endonuclease
nucleic acid
sequence
seq
nos
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Pending
Application number
AU2021339819A
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English (en)
Inventor
Alan Brooks
Christopher Brown
Cristina Butterfield
Cindy CASTELLE
Jyun-Liang LIN
Brian C. Thomas
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Metagenomi Therapeutics Inc
Original Assignee
Metagenomi Inc
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Metagenomi Inc filed Critical Metagenomi Inc
Publication of AU2021339819A1 publication Critical patent/AU2021339819A1/en
Pending legal-status Critical Current

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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/102—Mutagenizing nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases [RNase]; Deoxyribonucleases [DNase]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/111—General methods applicable to biologically active non-coding nucleic acids
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1137—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against enzymes
    • C—CHEMISTRY; METALLURGY
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/70—Vectors or expression systems specially adapted for E. coli
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/85—Vectors or expression systems specially adapted for eukaryotic hosts for animal cells
    • C12N15/86—Viral vectors
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/87—Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
    • C12N15/90—Stable introduction of foreign DNA into chromosome
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/87—Introduction of foreign genetic material using processes not otherwise provided for, e.g. co-transformation
    • C12N15/90—Stable introduction of foreign DNA into chromosome
    • C12N15/902—Stable introduction of foreign DNA into chromosome using homologous recombination
    • C12N15/907—Stable introduction of foreign DNA into chromosome using homologous recombination in mammalian cells
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/24—Hydrolases (3) acting on glycosyl compounds (3.2)
    • C12N9/2497—Hydrolases (3) acting on glycosyl compounds (3.2) hydrolysing N- glycosyl compounds (3.2.2)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/78—Hydrolases (3) acting on carbon to nitrogen bonds other than peptide bonds (3.5)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y302/00—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2)
    • C12Y302/02—Hydrolases acting on glycosyl compounds, i.e. glycosylases (3.2) hydrolysing N-glycosyl compounds (3.2.2)
    • C12Y302/02027—Uracil-DNA glycosylase (3.2.2.27)
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Y—ENZYMES
    • C12Y305/00—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5)
    • C12Y305/04—Hydrolases acting on carbon-nitrogen bonds, other than peptide bonds (3.5) in cyclic amidines (3.5.4)
    • C12Y305/04004—Adenosine deaminase (3.5.4.4)
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K2319/00—Fusion polypeptide
    • C07K2319/01—Fusion polypeptide containing a localisation/targetting motif
    • C07K2319/09—Fusion polypeptide containing a localisation/targetting motif containing a nuclear localisation signal
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/20—Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPR]
    • C—CHEMISTRY; METALLURGY
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    • C12N2750/00—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA ssDNA viruses
    • C12N2750/00011—Details
    • C12N2750/14011—Parvoviridae
    • C12N2750/14111—Dependovirus, e.g. adenoassociated viruses
    • C12N2750/14141—Use of virus, viral particle or viral elements as a vector
    • C12N2750/14143—Use of virus, viral particle or viral elements as a vector viral genome or elements thereof as genetic vector
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2800/00—Nucleic acids vectors
    • C12N2800/10—Plasmid DNA
    • C12N2800/106—Plasmid DNA for vertebrates
    • C12N2800/107—Plasmid DNA for vertebrates for mammalian
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    • C12N2800/00—Nucleic acids vectors
    • C12N2800/80—Vectors containing sites for inducing double-stranded breaks, e.g. meganuclease restriction sites

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  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
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  • Bioinformatics & Cheminformatics (AREA)
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  • General Engineering & Computer Science (AREA)
  • Biotechnology (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Physics & Mathematics (AREA)
  • Plant Pathology (AREA)
  • Medicinal Chemistry (AREA)
  • Mycology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Virology (AREA)
  • Cell Biology (AREA)
  • Enzymes And Modification Thereof (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Graft Or Block Polymers (AREA)
  • Dental Preparations (AREA)
  • Paints Or Removers (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Peptides Or Proteins (AREA)
AU2021339819A 2020-09-11 2021-09-10 Base editing enzymes Pending AU2021339819A1 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US202063077057P 2020-09-11 2020-09-11
US63/077,057 2020-09-11
US202163222351P 2021-07-15 2021-07-15
US63/222,351 2021-07-15
PCT/US2021/049962 WO2022056324A1 (en) 2020-09-11 2021-09-10 Base editing enzymes

Publications (1)

Publication Number Publication Date
AU2021339819A1 true AU2021339819A1 (en) 2023-05-25

Family

ID=80629930

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Application Number Title Priority Date Filing Date
AU2021339819A Pending AU2021339819A1 (en) 2020-09-11 2021-09-10 Base editing enzymes

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Country Link
US (3) US12286654B2 (https=)
EP (1) EP4211234A4 (https=)
JP (1) JP2023540797A (https=)
KR (1) KR20230062873A (https=)
AU (1) AU2021339819A1 (https=)
CA (1) CA3192224A1 (https=)
GB (1) GB2605340B (https=)
MX (1) MX2023002913A (https=)
WO (1) WO2022056324A1 (https=)

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EP3204496A1 (en) 2014-10-10 2017-08-16 Editas Medicine, Inc. Compositions and methods for promoting homology directed repair
CN121555430A (zh) 2018-05-11 2026-02-24 比姆医疗股份有限公司 使用可编程碱基编辑器系统取代病原性氨基酸的方法
KR20210055733A (ko) 2018-09-07 2021-05-17 빔 테라퓨틱스, 인크. 핵염기 편집 시스템을 전달하기 위한 조성물 및 방법
EP3850088A4 (en) 2018-09-07 2023-07-19 Beam Therapeutics, Inc. Compositions and methods for improving base editing
WO2020168122A1 (en) 2019-02-13 2020-08-20 Beam Therapeutics Inc. Modified immune cells having adenosine deaminase base editors for modifying a nucleobase in a target sequence
EP4034138A4 (en) 2019-09-27 2024-07-31 Beam Therapeutics, Inc. COMPOSITIONS AND METHODS FOR THE TREATMENT OF LIQUID CANCERS
GB2617658B (en) 2020-03-06 2024-04-17 Metagenomi Inc Class II, type V CRISPR systems
GB2608292B (en) * 2020-03-31 2024-02-14 Metagenomi Inc Class II, type II CRISPR systems
CA3192224A1 (en) 2020-09-11 2022-03-17 Jyun-Liang LIN Base editing enzymes
AU2021347359A1 (en) 2020-09-25 2023-05-18 Beam Therapeutics Inc. Fratricide resistant modified immune cells and methods of using the same
BR112023014719A2 (pt) * 2021-01-22 2023-12-05 Metagenomi Inc Novas nucleases quiméricas e manipuladas
CA3225082A1 (en) 2021-08-27 2023-03-02 Brian C. Thomas Enzymes with ruvc domains
AU2022380842A1 (en) * 2021-11-05 2024-05-23 Metagenomi Therapeutics, Inc. Base editing enzymes
MX2024006257A (es) 2021-11-24 2024-07-29 Metagenomi Inc Sistemas de endonucleasas.
CN121241133A (zh) * 2023-03-31 2025-12-30 阿伯生物技术公司 Crispr核酸酶多肽和包含此类crispr核酸酶多肽的基因编辑系统
WO2025003344A1 (en) * 2023-06-28 2025-01-02 Alia Therapeutics Srl Type ii cas proteins and applications thereof
WO2025106894A1 (en) * 2023-11-15 2025-05-22 Profluent Bio Inc. Adenine deaminases and compositions, systems, and methods thereof
WO2025240372A1 (en) * 2024-05-13 2025-11-20 Metagenomi, Inc. Compositions and methods for editing t cells

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KR102547316B1 (ko) * 2016-08-03 2023-06-23 프레지던트 앤드 펠로우즈 오브 하바드 칼리지 아데노신 핵염기 편집제 및 그의 용도
US11192929B2 (en) 2016-12-08 2021-12-07 Regents Of The University Of Minnesota Site-specific DNA base editing using modified APOBEC enzymes
EP3572525A4 (en) 2017-01-17 2020-09-30 Institute for Basic Science PROCEDURE FOR IDENTIFYING AN OFF-TARGET BASIC EDITING SITE BY BREAKING A SINGLE DNA STRAND
CA3057192A1 (en) 2017-03-23 2018-09-27 President And Fellows Of Harvard College Nucleobase editors comprising nucleic acid programmable dna binding proteins
KR102758434B1 (ko) * 2017-03-30 2025-01-21 고쿠리츠 다이가쿠 호진 교토 다이가쿠 게놈 편집에 의한 엑손 스키핑 유도 방법
US9982279B1 (en) * 2017-06-23 2018-05-29 Inscripta, Inc. Nucleic acid-guided nucleases
AU2018290843B2 (en) * 2017-06-26 2025-04-24 Massachusetts Institute Of Technology CRISPR/Cas-adenine deaminase based compositions, systems, and methods for targeted nucleic acid editing
JP2021506251A (ja) * 2017-12-14 2021-02-22 クリスパー セラピューティクス アーゲー 新規ｒｎａプログラム可能エンドヌクレアーゼ系、ならびにゲノム編集および他の適用におけるその使用
US11946040B2 (en) * 2019-02-04 2024-04-02 The General Hospital Corporation Adenine DNA base editor variants with reduced off-target RNA editing
US20220298494A1 (en) 2019-02-14 2022-09-22 Metagenomi Ip Technologies, Llc Enzymes with ruvc domains
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GB2608292B (en) * 2020-03-31 2024-02-14 Metagenomi Inc Class II, type II CRISPR systems
GB2700205B (en) 2020-09-11 2026-04-15 Metagenomi Therapeutics Inc Base editing enzymes
CA3192224A1 (en) 2020-09-11 2022-03-17 Jyun-Liang LIN Base editing enzymes
AU2022380842A1 (en) * 2021-11-05 2024-05-23 Metagenomi Therapeutics, Inc. Base editing enzymes

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EP4211234A1 (en) 2023-07-19
GB2605340A8 (en) 2024-02-21
US20230374482A1 (en) 2023-11-23
GB2605340A (en) 2022-09-28
CA3192224A1 (en) 2022-03-17
WO2022056324A1 (en) 2022-03-17
US20220364067A1 (en) 2022-11-17
GB2605340B (en) 2024-12-18
JP2023540797A (ja) 2023-09-26
MX2023002913A (es) 2023-06-01
EP4211234A4 (en) 2025-04-30
KR20230062873A (ko) 2023-05-09
US20230348876A1 (en) 2023-11-02
GB202209534D0 (en) 2022-08-10
US12286654B2 (en) 2025-04-29

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