WO2024254224A3 - Analytical methods for adeno-associated virus vector genomes and uses thereof - Google Patents

Analytical methods for adeno-associated virus vector genomes and uses thereof Download PDF

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Publication number
WO2024254224A3
WO2024254224A3 PCT/US2024/032678 US2024032678W WO2024254224A3 WO 2024254224 A3 WO2024254224 A3 WO 2024254224A3 US 2024032678 W US2024032678 W US 2024032678W WO 2024254224 A3 WO2024254224 A3 WO 2024254224A3
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Prior art keywords
methods
aav
genomes
analyzing
associated virus
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Ceased
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PCT/US2024/032678
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French (fr)
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WO2024254224A2 (en
Inventor
Michael Xavier Doss JESUDOSS
Erno Pungor
Salvatore J. ORLANDO
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Biomarin Pharmaceutical Inc
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Biomarin Pharmaceutical Inc
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Publication of WO2024254224A3 publication Critical patent/WO2024254224A3/en
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • 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
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • 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
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • 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
    • C12N2750/14151—Methods of production or purification of viral material
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/191—Modifications characterised by incorporating an adaptor
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2535/00—Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/122—Massive parallel sequencing

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biochemistry (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Microbiology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Biomedical Technology (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Virology (AREA)
  • Plant Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)

Abstract

Methods of analyzing adeno associated virus (AAV) genomes and use thereof are provided herein. The methods and uses include the methods of preparing an AAV genomes for sequenc-ing, and methods of analyzing and characterizing AAV genomes. For example, the AAV analy-sis methods include steps of aligning reference nucleotide sequences to sequence reads of AAV genomes; determining alignment scores of each reference nucleotide sequence to the sequence reads and identifying strand types of the AAV genomes based on the alignment scores; determin-ing first and second coordinates within the sequence reads based on alignments with the refer-ence nucleotide sequences used to identify strand type; and analyzing sequences adjacent to the first and second coordinates to identify ITR configurations of the AAV genomes.
PCT/US2024/032678 2023-06-08 2024-06-06 Analytical methods for adeno-associated virus vector genomes and uses thereof Ceased WO2024254224A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202363506879P 2023-06-08 2023-06-08
US63/506,879 2023-06-08

Publications (2)

Publication Number Publication Date
WO2024254224A2 WO2024254224A2 (en) 2024-12-12
WO2024254224A3 true WO2024254224A3 (en) 2025-04-03

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PCT/US2024/032678 Ceased WO2024254224A2 (en) 2023-06-08 2024-06-06 Analytical methods for adeno-associated virus vector genomes and uses thereof

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Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20130303407A1 (en) * 2005-08-02 2013-11-14 Rubicon Genomics Compositions and methods for processing and amplification of dna, including using multiple enzymes in a single reaction
US20200123574A1 (en) * 2017-05-05 2020-04-23 Voyager Therapeutics, Inc. Compositions and methods of treating amyotrophic lateral sclerosis (als)
US20230002786A1 (en) * 2020-01-07 2023-01-05 The University Of North Carolina At Chapel Hill Synthetic adeno-associated virus inverted terminal repeats and methods of their use as promoters

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20130303407A1 (en) * 2005-08-02 2013-11-14 Rubicon Genomics Compositions and methods for processing and amplification of dna, including using multiple enzymes in a single reaction
US20200123574A1 (en) * 2017-05-05 2020-04-23 Voyager Therapeutics, Inc. Compositions and methods of treating amyotrophic lateral sclerosis (als)
US20230002786A1 (en) * 2020-01-07 2023-01-05 The University Of North Carolina At Chapel Hill Synthetic adeno-associated virus inverted terminal repeats and methods of their use as promoters

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
P. WARD, P. ELIAS, R. M. LINDEN: "Rescue of the Adeno-Associated Virus Genome from a Plasmid Vector: Evidence for Rescue by Replication", JOURNAL OF VIROLOGY, vol. 77, no. 21, 1 November 2003 (2003-11-01), US , pages 11480 - 11490, XP055595908, ISSN: 0022-538X, DOI: 10.1128/JVI.77.21.11480-11490.2003 *
TRAN NGOC TAM, HEINER CHERYL, WEBER KRISTINA, WEIAND MICHAEL, WILMOT DANIELLA, XIE JUN, WANG DAN, BROWN ALEXANDER, MANOKARAN SANGE: "AAV-Genome Population Sequencing of Vectors Packaging CRISPR Components Reveals Design-Influenced Heterogeneity", MOLECULAR THERAPY- METHODS & CLINICAL DEVELOPMENT, vol. 18, 1 September 2020 (2020-09-01), GB , pages 639 - 651, XP093083949, ISSN: 2329-0501, DOI: 10.1016/j.omtm.2020.07.007 *

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