WO2024254224A3 - Procédés analytiques pour génomes de vecteurs de virus adéno-associés et leurs utilisations - Google Patents

Procédés analytiques pour génomes de vecteurs de virus adéno-associés et leurs utilisations Download PDF

Info

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
Authority
WO
WIPO (PCT)
Prior art keywords
methods
aav
genomes
analyzing
associated virus
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
PCT/US2024/032678
Other languages
English (en)
Other versions
WO2024254224A2 (fr
Inventor
Michael Xavier Doss JESUDOSS
Erno Pungor
Salvatore J. ORLANDO
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.)
Biomarin Pharmaceutical Inc
Original Assignee
Biomarin Pharmaceutical 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 Biomarin Pharmaceutical Inc filed Critical Biomarin Pharmaceutical Inc
Publication of WO2024254224A2 publication Critical patent/WO2024254224A2/fr
Publication of WO2024254224A3 publication Critical patent/WO2024254224A3/fr
Anticipated expiration legal-status Critical
Pending legal-status Critical Current

Links

Classifications

    • 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

Landscapes

  • 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

L'invention concerne des procédés d'analyse de génomes de virus adéno-associés (AAV) et leur utilisation. Les procédés et les utilisations comprennent les procédés de préparation de génomes d'AAV pour le séquençage, et des procédés d'analyse et de caractérisation de génomes d'AAV. Par exemple, les procédés d'analyse d'AAV comprennent des étapes consistant à aligner des séquences nucléotidiques de référence sur des lectures de séquence de génomes d'AAV ; à déterminer des scores d'alignement de chaque séquence nucléotidique de référence aux lectures de séquence et à identifier des types de brin des génomes d'AAV sur la base des scores d'alignement ; à déterminer des première et seconde coordonnées dans les lectures de séquence sur la base d'alignements avec les séquences nucléotidiques de référence utilisées pour identifier un type de brin ; et à analyser des séquences adjacentes aux première et seconde coordonnées pour identifier des configurations ITR des génomes d'AAV.
PCT/US2024/032678 2023-06-08 2024-06-06 Procédés analytiques pour génomes de vecteurs de virus adéno-associés et leurs utilisations Pending WO2024254224A2 (fr)

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 (fr) 2024-12-12
WO2024254224A3 true WO2024254224A3 (fr) 2025-04-03

Family

ID=93794714

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2024/032678 Pending WO2024254224A2 (fr) 2023-06-08 2024-06-06 Procédés analytiques pour génomes de vecteurs de virus adéno-associés et leurs utilisations

Country Status (1)

Country Link
WO (1) WO2024254224A2 (fr)

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 *

Also Published As

Publication number Publication date
WO2024254224A2 (fr) 2024-12-12

Similar Documents

Publication Publication Date Title
Depledge et al. Direct RNA sequencing on nanopore arrays redefines the transcriptional complexity of a viral pathogen
Gouveia et al. Shortlisting SARS‐CoV‐2 peptides for targeted studies from experimental data‐dependent acquisition tandem mass spectrometry data
Kilianski et al. Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer
Alnaji et al. Sequencing framework for the sensitive detection and precise mapping of defective interfering particle-associated deletions across influenza A and B viruses
Salovska et al. Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation
Keßler et al. The intracellular proteome of African swine fever virus
Papillon-Cavanagh et al. Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas
Chang et al. Multiple nucleic acid binding sites and intrinsic disorder of severe acute respiratory syndrome coronavirus nucleocapsid protein: implications for ribonucleocapsid protein packaging
Assarsson et al. Kinetic analysis of a complete poxvirus transcriptome reveals an immediate-early class of genes
Strong et al. Comprehensive high-throughput RNA sequencing analysis reveals contamination of multiple nasopharyngeal carcinoma cell lines with HeLa cell genomes
Zook et al. Synthetic spike-in standards improve run-specific systematic error analysis for DNA and RNA sequencing
Bezstarosti et al. Targeted proteomics as a tool to detect SARS-CoV-2 proteins in clinical specimens
Kovalenko et al. Complete genome sequence of a virulent African swine fever virus from a domestic pig in Ukraine
Forni et al. An APOBEC3 mutational signature in the genomes of human-infecting orthopoxviruses
Ejegod et al. The BD Onclarity HPV assay on samples collected in SurePath medium meets the international guidelines for human papillomavirus test requirements for cervical screening
Labisch et al. Infectious titer determination of lentiviral vectors using a temporal immunological real-time imaging approach
Sun et al. Comprehensive evaluation of RNA and DNA viromic methods based on species richness and abundance analyses using marmot rectal samples
Bowen et al. Comparison of herpes simplex virus 1 strains circulating in Finland demonstrates the uncoupling of whole-genome relatedness and phenotypic outcomes of viral infection
Boldogkői et al. Transcriptomic study of Herpes simplex virus type-1 using full-length sequencing techniques
Chorlton Reanalysis of Alzheimer’s brain sequencing data reveals absence of purported HHV6A and HHV7
Dueck et al. Mutational analysis of vaccinia virus E3 protein: the biological functions do not correlate with its biochemical capacity to bind double-stranded RNA
Wu et al. Deep RNA sequencing reveals complex transcriptional landscape of a bat adenovirus
WO2024254224A3 (fr) Procédés analytiques pour génomes de vecteurs de virus adéno-associés et leurs utilisations
Lecomte et al. The SSV‐Seq 2.0 PCR‐Free method improves the sequencing of adeno‐associated viral vector genomes containing GC‐Rich regions and homopolymers
Liu et al. Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications

Legal Events

Date Code Title Description
NENP Non-entry into the national phase

Ref country code: DE