WO2023175037A3 - Concurrent sequencing of forward and reverse complement strands on separate polynucleotides for methylation detection - Google Patents

Concurrent sequencing of forward and reverse complement strands on separate polynucleotides for methylation detection Download PDF

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Publication number
WO2023175037A3
WO2023175037A3 PCT/EP2023/056665 EP2023056665W WO2023175037A3 WO 2023175037 A3 WO2023175037 A3 WO 2023175037A3 EP 2023056665 W EP2023056665 W EP 2023056665W WO 2023175037 A3 WO2023175037 A3 WO 2023175037A3
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WO
WIPO (PCT)
Prior art keywords
reverse complement
methylation detection
thymine
uracil
sequencing
Prior art date
Application number
PCT/EP2023/056665
Other languages
French (fr)
Other versions
WO2023175037A2 (en
Inventor
Aathavan KARUNAKARAN
Shagesh SRIDHARAN
Jonathan Boutell
Gery VESSERE
Original Assignee
Illumina, Inc.
Illumina Cambridge Limited
Illumina Software, Inc.
Illumina Singapore Pte. Ltd.
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 Illumina, Inc., Illumina Cambridge Limited, Illumina Software, Inc., Illumina Singapore Pte. Ltd. filed Critical Illumina, Inc.
Priority to AU2023234670A priority Critical patent/AU2023234670A1/en
Priority to EP23715419.0A priority patent/EP4341426A2/en
Priority to CA3223653A priority patent/CA3223653A1/en
Publication of WO2023175037A2 publication Critical patent/WO2023175037A2/en
Publication of WO2023175037A3 publication Critical patent/WO2023175037A3/en

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    • 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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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

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

Abstract

The invention relates to methods and associated products for preparing polynucleotide sequences for detection of modified cytosines and sequencing said polynucleotides to detect modified cytosines. The methods comprise treatment of the target polynucleotide with a conversion reagent that is configured to convert a modified cytosine to thymine or a nucleobase which is read as thymine/uracil, and/or configured to convert an unmodified cytosine to uracil or a nucleobase which is read as thymine/uracil. In particular embodiments, portions of both strands of the treated target are sequenced concurrently.
PCT/EP2023/056665 2022-03-15 2023-03-15 Concurrent sequencing of forward and reverse complement strands on separate polynucleotides for methylation detection WO2023175037A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
AU2023234670A AU2023234670A1 (en) 2022-03-15 2023-03-15 Concurrent sequencing of forward and reverse complement strands on separate polynucleotides for methylation detection
EP23715419.0A EP4341426A2 (en) 2022-03-15 2023-03-15 Concurrent sequencing of forward and reverse complement strands on separate polynucleotides for methylation detection
CA3223653A CA3223653A1 (en) 2022-03-15 2023-03-15 Concurrent sequencing of forward and reverse complement strands on separate polynucleotides for methylation detection

Applications Claiming Priority (22)

Application Number Priority Date Filing Date Title
US202263269383P 2022-03-15 2022-03-15
US63/269,383 2022-03-15
US202263328444P 2022-04-07 2022-04-07
US63/328,444 2022-04-07
US202363439501P 2023-01-17 2023-01-17
US202363439417P 2023-01-17 2023-01-17
US202363439438P 2023-01-17 2023-01-17
US202363439522P 2023-01-17 2023-01-17
US202363439466P 2023-01-17 2023-01-17
US202363439491P 2023-01-17 2023-01-17
US202363439519P 2023-01-17 2023-01-17
US202363439415P 2023-01-17 2023-01-17
US202363439443P 2023-01-17 2023-01-17
US63/439,491 2023-01-17
US63/439,438 2023-01-17
US63/439,417 2023-01-17
US63/439,522 2023-01-17
US63/439,519 2023-01-17
US63/439,415 2023-01-17
US63/439,501 2023-01-17
US63/439,466 2023-01-17
US63/439,443 2023-01-17

Publications (2)

Publication Number Publication Date
WO2023175037A2 WO2023175037A2 (en) 2023-09-21
WO2023175037A3 true WO2023175037A3 (en) 2023-11-23

Family

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Family Applications (2)

Application Number Title Priority Date Filing Date
PCT/EP2023/056668 WO2023175040A2 (en) 2022-03-15 2023-03-15 Concurrent sequencing of forward and reverse complement strands on concatenated polynucleotides for methylation detection
PCT/EP2023/056665 WO2023175037A2 (en) 2022-03-15 2023-03-15 Concurrent sequencing of forward and reverse complement strands on separate polynucleotides for methylation detection

Family Applications Before (1)

Application Number Title Priority Date Filing Date
PCT/EP2023/056668 WO2023175040A2 (en) 2022-03-15 2023-03-15 Concurrent sequencing of forward and reverse complement strands on concatenated polynucleotides for methylation detection

Country Status (4)

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EP (2) EP4341425A2 (en)
AU (2) AU2023233839A1 (en)
CA (2) CA3223669A1 (en)
WO (2) WO2023175040A2 (en)

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Also Published As

Publication number Publication date
CA3223669A1 (en) 2023-09-21
WO2023175040A2 (en) 2023-09-21
WO2023175037A2 (en) 2023-09-21
CA3223653A1 (en) 2023-09-21
EP4341426A2 (en) 2024-03-27
AU2023233839A1 (en) 2024-01-18
EP4341425A2 (en) 2024-03-27
AU2023234670A1 (en) 2024-01-18
WO2023175040A3 (en) 2023-11-02

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