AU2021341688B2 - Compositions and methods for amplifying polynucleotides - Google Patents

Compositions and methods for amplifying polynucleotides

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Publication number
AU2021341688B2
AU2021341688B2 AU2021341688A AU2021341688A AU2021341688B2 AU 2021341688 B2 AU2021341688 B2 AU 2021341688B2 AU 2021341688 A AU2021341688 A AU 2021341688A AU 2021341688 A AU2021341688 A AU 2021341688A AU 2021341688 B2 AU2021341688 B2 AU 2021341688B2
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Prior art keywords
primers
capture
orthogonal
capture primers
substrate
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AU2021341688A
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AU2021341688A1 (en
Inventor
Jason Betley
Jeffrey Fisher
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Illumina Cambridge Ltd
Illumina Inc
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Illumina Cambridge Ltd
Illumina Inc
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    • 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
    • C12Q1/6834—Enzymatic or biochemical coupling of nucleic acids to a solid phase
    • C12Q1/6837—Enzymatic or biochemical coupling of nucleic acids to a solid phase using probe arrays or probe chips
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
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    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C12Q1/6855—Ligating adaptors
    • 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
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    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/186—Modifications characterised by incorporating a non-extendable or blocking moiety
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • 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
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/204—Modifications characterised by specific length of the oligonucleotides
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2527/00—Reactions demanding special reaction conditions
    • C12Q2527/107—Temperature of melting, i.e. Tm
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50—Detection characterised by immobilisation to a surface
    • C12Q2565/513—Detection characterised by immobilisation to a surface characterised by the pattern of the arrayed oligonucleotides
    • 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
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/50—Detection characterised by immobilisation to a surface
    • C12Q2565/543—Detection characterised by immobilisation to a surface characterised by the use of two or more capture oligonucleotide primers in concert, e.g. bridge amplification

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Wood Science & Technology (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Analytical Chemistry (AREA)
  • Immunology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Microbiology (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)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Saccharide Compounds (AREA)
AU2021341688A 2020-09-14 2021-08-27 Compositions and methods for amplifying polynucleotides Active AU2021341688B2 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202063077857P 2020-09-14 2020-09-14
US63/077,857 2020-09-14
PCT/US2021/048064 WO2022055729A1 (en) 2020-09-14 2021-08-27 Compositions and methods for amplifying polynucleotides

Publications (2)

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AU2021341688A1 AU2021341688A1 (en) 2023-01-05
AU2021341688B2 true AU2021341688B2 (en) 2025-09-18

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US (2) US11913067B2 (enExample)
EP (1) EP4211269B1 (enExample)
JP (1) JP2023540422A (enExample)
KR (1) KR20230069047A (enExample)
CN (1) CN115777024A (enExample)
AU (1) AU2021341688B2 (enExample)
BR (1) BR112022026860A2 (enExample)
CA (1) CA3182296A1 (enExample)
ES (1) ES3007341T3 (enExample)
IL (1) IL299327A (enExample)
MX (1) MX2022014724A (enExample)
TW (1) TW202225412A (enExample)
WO (1) WO2022055729A1 (enExample)
ZA (1) ZA202213367B (enExample)

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EP4305193B1 (en) * 2021-03-09 2025-09-17 Illumina, Inc. Polymers, methods of making polymers, and methods of coupling oligonucleotides to polymers
WO2023069927A1 (en) * 2021-10-20 2023-04-27 Illumina, Inc. Methods for capturing library dna for sequencing
US20240052406A1 (en) * 2022-08-04 2024-02-15 Singular Genomics Systems, Inc. Competitive methods and compositions for amplifying polynucleotides
US20240167088A1 (en) * 2022-11-02 2024-05-23 Esbiolab Llc Methods and devices of generating clusters of amplicons
CN117987522A (zh) * 2023-02-08 2024-05-07 深圳市真迈生物科技有限公司 测序方法
EP4695420A1 (en) * 2023-04-14 2026-02-18 Illumina, Inc. Capturing and amplifying polynucleotides

Citations (1)

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WO2012025250A1 (en) * 2010-08-27 2012-03-01 Illumina Cambridge Ltd. Methods for paired - end sequencing of polynucleotides

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GB0514909D0 (en) 2005-07-20 2005-08-24 Solexa Ltd Methods of nucleic acid amplification and sequencing
US8999642B2 (en) * 2008-03-10 2015-04-07 Illumina, Inc. Methods for selecting and amplifying polynucleotides
CN102597256B (zh) * 2009-08-25 2014-12-03 伊鲁米那股份有限公司 选择和扩增多核苷酸的方法
US8895249B2 (en) 2012-06-15 2014-11-25 Illumina, Inc. Kinetic exclusion amplification of nucleic acid libraries
EP2840148B1 (en) * 2013-08-23 2019-04-03 F. Hoffmann-La Roche AG Methods for nucleic acid amplification
GB201410646D0 (en) 2014-06-14 2014-07-30 Illumina Cambridge Ltd Methods of increasing sequencing accuracy
PL3218511T3 (pl) 2014-11-11 2020-10-19 Illumina Cambridge Limited Sposoby i macierze do wytwarzania i sekwencjonowania monoklonalnych klastrów kwasu nukleinowego
PT3234187T (pt) * 2014-12-15 2021-05-26 Illumina Inc Método para colocação de moleculas de alvo unico num substrato
ITUA20162640A1 (it) * 2016-04-15 2017-10-15 Menarini Silicon Biosystems Spa Metodo e kit per la generazione di librerie di dna per sequenziamento massivo parallelo
WO2018071522A1 (en) * 2016-10-11 2018-04-19 Life Technologies Corporation Rapid amplification of nucleic acids
GB201704754D0 (en) 2017-01-05 2017-05-10 Illumina Inc Kinetic exclusion amplification of nucleic acid libraries
CA3113808A1 (en) * 2018-10-24 2020-04-30 University Of Washington Methods and kits for depletion and enrichment of nucleic acid sequences
BR112020026667A2 (pt) * 2018-12-19 2021-07-27 Illumina, Inc. métodos para melhorar a prioridade de clonalidade do agrupamento de polinucleotídeo
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US20240240243A1 (en) 2024-07-18
BR112022026860A2 (pt) 2023-04-11
EP4211269A1 (en) 2023-07-19
CN115777024A (zh) 2023-03-10
MX2022014724A (es) 2023-03-06
EP4211269B1 (en) 2024-11-06
AU2021341688A1 (en) 2023-01-05
ES3007341T3 (en) 2025-03-19
JP2023540422A (ja) 2023-09-25
IL299327A (en) 2023-02-01
WO2022055729A1 (en) 2022-03-17
US11913067B2 (en) 2024-02-27
ZA202213367B (en) 2025-03-26
TW202225412A (zh) 2022-07-01
CA3182296A1 (en) 2022-03-17
KR20230069047A (ko) 2023-05-18
US20220090187A1 (en) 2022-03-24

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