CA2999902A1 - Methods and compositions for enrichment of amplification products - Google Patents

Methods and compositions for enrichment of amplification products Download PDF

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Publication number
CA2999902A1
CA2999902A1 CA2999902A CA2999902A CA2999902A1 CA 2999902 A1 CA2999902 A1 CA 2999902A1 CA 2999902 A CA2999902 A CA 2999902A CA 2999902 A CA2999902 A CA 2999902A CA 2999902 A1 CA2999902 A1 CA 2999902A1
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CA
Canada
Prior art keywords
sequence
target polynucleotide
primer
copies
polynucleotide
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Pending
Application number
CA2999902A
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English (en)
French (fr)
Inventor
Li Weng
Shengrong LIN
Ling Fung Tang
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Accuragen Holdings Ltd
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Accuragen Holdings Ltd
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Publication of CA2999902A1 publication Critical patent/CA2999902A1/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
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6858—Allele-specific amplification
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/20—Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
    • 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
    • C12Q2525/155—Modifications characterised by incorporating/generating a new priming site
    • 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
    • C12Q2525/30—Oligonucleotides characterised by their secondary structure
    • C12Q2525/301—Hairpin 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
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/30—Oligonucleotides characterised by their secondary structure
    • C12Q2525/307—Circular 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
    • C12Q2531/00—Reactions of nucleic acids characterised by
    • C12Q2531/10—Reactions of nucleic acids characterised by the purpose being amplify/increase the copy number of target nucleic acid
    • C12Q2531/125—Rolling circle
    • 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
    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/16—Assays for determining copy number or wherein the copy number is of special importance
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Biophysics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Analytical Chemistry (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Macromonomer-Based Addition Polymer (AREA)
  • Enzymes And Modification Thereof (AREA)
CA2999902A 2015-10-09 2016-10-07 Methods and compositions for enrichment of amplification products Pending CA2999902A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201562239690P 2015-10-09 2015-10-09
US62/239,690 2015-10-09
PCT/US2016/056126 WO2017062863A1 (en) 2015-10-09 2016-10-07 Methods and compositions for enrichment of amplification products

Publications (1)

Publication Number Publication Date
CA2999902A1 true CA2999902A1 (en) 2017-04-13

Family

ID=58488563

Family Applications (1)

Application Number Title Priority Date Filing Date
CA2999902A Pending CA2999902A1 (en) 2015-10-09 2016-10-07 Methods and compositions for enrichment of amplification products

Country Status (12)

Country Link
US (3) US10752942B2 (enExample)
EP (1) EP3359693B1 (enExample)
JP (3) JP7008016B2 (enExample)
KR (1) KR20180055905A (enExample)
CN (2) CN114807323A (enExample)
AU (2) AU2016334233B2 (enExample)
CA (1) CA2999902A1 (enExample)
HK (1) HK1259101A1 (enExample)
IL (2) IL258236B (enExample)
MX (2) MX2018004284A (enExample)
SG (1) SG11201802864RA (enExample)
WO (1) WO2017062863A1 (enExample)

Cited By (1)

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CN107177693A (zh) * 2017-07-19 2017-09-19 中山大学 一种多倍pcr扩增方法

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US11286519B2 (en) 2013-12-11 2022-03-29 Accuragen Holdings Limited Methods and compositions for enrichment of amplification products
ES2707744T3 (es) 2013-12-11 2019-04-04 Accuragen Holdings Ltd Métodos para detectar variantes de secuencia raras
US11859246B2 (en) 2013-12-11 2024-01-02 Accuragen Holdings Limited Methods and compositions for enrichment of amplification products
EP3359693B1 (en) 2015-10-09 2025-03-19 Accuragen Holdings Limited Methods for enrichment of amplification products
CN108699505A (zh) * 2015-12-03 2018-10-23 安可济控股有限公司 用于形成连接产物的方法和组合物
CA3024630A1 (en) 2016-05-16 2017-11-23 Accuragen Holdings Limited Method of improved sequencing by strand identification
AU2017290237B2 (en) 2016-06-30 2020-10-22 GRAIL, Inc Differential tagging of RNA for preparation of a cell-free DNA/RNA sequencing library
SG11201901296TA (en) 2016-08-15 2019-03-28 Accuragen Holdings Ltd Compositions and methods for detecting rare sequence variants
CN107760763B (zh) * 2017-11-20 2021-05-11 东南大学 一种用于茎环引物-滚环扩增反应的茎环引物以及茎环引物-滚环扩增的应用
CN109971825B (zh) * 2017-12-28 2020-11-10 南京金斯瑞生物科技有限公司 快速制备桑格测序模板的方法
US11203782B2 (en) 2018-03-29 2021-12-21 Accuragen Holdings Limited Compositions and methods comprising asymmetric barcoding
US12049665B2 (en) 2018-06-12 2024-07-30 Accuragen Holdings Limited Methods and compositions for forming ligation products
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CN110820051B (zh) * 2018-12-28 2023-04-28 广州表观生物科技有限公司 一种高灵敏度融合基因检测方法及其应用
KR102102107B1 (ko) * 2019-05-30 2020-04-20 단국대학교 천안캠퍼스 산학협력단 이동성 유전인자 SINE 선택적 발굴을 위한 HiSeq 시퀀서 기반의 DNA 라이브러리 제작 방법
WO2020263978A1 (en) * 2019-06-25 2020-12-30 Accuragen Holdings Limited Methods and systems for disease detection
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WO2021101835A1 (en) * 2019-11-19 2021-05-27 Xiao Bing Wang Method for identifying gene fusions by circle cdna amplification
CN115151657A (zh) * 2019-12-20 2022-10-04 安可济控股有限公司 用于疾病检测的方法和系统
KR102468839B1 (ko) 2020-06-03 2022-11-18 주식회사 제노헬릭스 Rna 검출 방법
KR20230028450A (ko) * 2020-06-26 2023-02-28 윌리엄 마쉬 라이스 유니버시티 앰플리콘 포괄적 풍부화
JP2023547366A (ja) * 2020-10-21 2023-11-10 イルミナ インコーポレイテッド 複数のインサートを含む配列決定鋳型、並びに配列決定スループットを改善するための組成物及び方法
WO2022103750A1 (en) * 2020-11-11 2022-05-19 Accuragen Holdings Limited Methods and systems for sample normalization
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CN113832147B (zh) * 2021-09-08 2024-06-14 华南农业大学 一种高效的大片段dna合成与扩增的pcr引物、方法及应用

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CN107177693B (zh) * 2017-07-19 2020-11-06 中山大学 一种多倍pcr扩增方法

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