CN113207299B - 用于管理下一代测序中的低样本输入的归一化对照 - Google Patents

用于管理下一代测序中的低样本输入的归一化对照 Download PDF

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CN113207299B
CN113207299B CN201980080514.3A CN201980080514A CN113207299B CN 113207299 B CN113207299 B CN 113207299B CN 201980080514 A CN201980080514 A CN 201980080514A CN 113207299 B CN113207299 B CN 113207299B
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sequence
polynucleotides
sequences
sample
control
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CN113207299A (zh
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E·哈尼斯
V·纳格什
L·G·本利
M·L·卡彭特
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ARC Bio LLC
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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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6865—Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • 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
    • C12Q2525/131—Modifications characterised by incorporating a restriction 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
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/143—Modifications characterised by incorporating a promoter sequence
    • 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
    • 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
    • C12Q2545/00—Reactions characterised by their quantitative nature
    • C12Q2545/10—Reactions characterised by their quantitative nature the purpose being quantitative analysis
    • C12Q2545/101—Reactions characterised by their quantitative nature the purpose being quantitative analysis with an internal standard/control
    • 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
    • C12Q2600/166—Oligonucleotides used as internal standards, controls or normalisation probes

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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)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (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)
CN201980080514.3A 2018-10-04 2019-10-04 用于管理下一代测序中的低样本输入的归一化对照 Active CN113207299B (zh)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201862741466P 2018-10-04 2018-10-04
US62/741,466 2018-10-04
US201962832560P 2019-04-11 2019-04-11
US62/832,560 2019-04-11
PCT/US2019/054843 WO2020072990A1 (en) 2018-10-04 2019-10-04 Normalization controls for managing low sample inputs in next generation sequencing

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CN113207299A CN113207299A (zh) 2021-08-03
CN113207299B true CN113207299B (zh) 2024-10-29

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US (1) US20220002781A1 (https=)
EP (2) EP3861135B1 (https=)
JP (1) JP7436493B2 (https=)
CN (1) CN113207299B (https=)
AU (1) AU2019356016B2 (https=)
CA (1) CA3115281A1 (https=)
DK (1) DK3861135T5 (https=)
IL (1) IL281982B2 (https=)
WO (1) WO2020072990A1 (https=)

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CA3136228A1 (en) 2019-04-09 2020-10-15 Arc Bio, Llc Compositions and methods for nucleotide modification-based depletion
FR3099182B1 (fr) * 2019-07-23 2022-11-25 Biomerieux Sa Procédé de détection et de quantification d'une espèce biologique d'intérêt par analyse métagénomique
FR3099181B1 (fr) * 2019-07-23 2022-11-18 Biomerieux Sa Procédé de détection et de quantification d'une espèce biologique d'intérêt par analyse métagénomique, avec prise en compte d'un calibrateur.
US20220017956A1 (en) * 2020-07-14 2022-01-20 Accugenomics, Inc. Endogenous complexity calibration ladder target
JP2024513187A (ja) * 2021-03-29 2024-03-22 イルミナ インコーポレイテッド ライブラリー中のｄｎａ損傷を評価し、アンプリコンサイズバイアスを正規化するための組成物及び方法
CN114891868A (zh) * 2022-05-31 2022-08-12 广州市金圻睿生物科技有限责任公司 一种基于ngs平台的微生物定量方法及试剂盒
US12430202B2 (en) 2022-12-05 2025-09-30 Western Digital Technologies, Inc. Nested error correction codes for DNA data storage
EP4713486A1 (en) * 2023-07-12 2026-03-25 The Regents of the University of California Biomarkers for identifying infectious and non-infectious causes of neurological illness
US12562755B2 (en) 2023-09-11 2026-02-24 Western Digital Technologies, Inc. Multi-tier error correction codes for DNA data storage

Citations (3)

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WO2015073080A1 (en) * 2013-11-12 2015-05-21 Life Technologies Corporation Reagents and methods for sequencing
WO2016001736A1 (en) * 2014-06-30 2016-01-07 Vela Operations Singapore Pte. Ltd. Compositions for quantitative and/or semi-quantitative mutation detection methods
WO2017165864A1 (en) * 2016-03-25 2017-09-28 Karius, Inc. Synthetic nucleic acid spike-ins

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WO2016100955A2 (en) 2014-12-20 2016-06-23 Identifygenomics, Llc Compositions and methods for targeted depletion, enrichment, and partitioning of nucleic acids using crispr/cas system proteins
EP3332034B1 (en) * 2015-08-06 2024-09-25 Arc Bio, LLC Systems and methods for genomic analysis
US10538758B2 (en) 2015-08-19 2020-01-21 Arc Bio, Llc Capture of nucleic acids using a nucleic acid-guided nuclease-based system
US10465232B1 (en) * 2015-10-08 2019-11-05 Trace Genomics, Inc. Methods for quantifying efficiency of nucleic acid extraction and detection
AU2016365720B2 (en) 2015-12-07 2020-11-26 Arc Bio, Llc Methods and compositions for the making and using of guide nucleic acids
AU2017223821B2 (en) 2016-02-23 2023-07-27 Arc Bio, Llc Methods and compositions for target detection
US20200190508A1 (en) 2017-06-07 2020-06-18 Arc Bio, Llc Creation and use of guide nucleic acids

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015073080A1 (en) * 2013-11-12 2015-05-21 Life Technologies Corporation Reagents and methods for sequencing
WO2016001736A1 (en) * 2014-06-30 2016-01-07 Vela Operations Singapore Pte. Ltd. Compositions for quantitative and/or semi-quantitative mutation detection methods
WO2017165864A1 (en) * 2016-03-25 2017-09-28 Karius, Inc. Synthetic nucleic acid spike-ins

Non-Patent Citations (2)

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Title
"Improving small RNA-seq by using a synthetic spike-in set for size-range quality control together with a set for data normalization";Mauro D. Locati等;《Nucleic Acids Research》;第43卷(第14期);第1-10页 *
"SASI-Seq_ sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing";Michael A Quail等;《BMC Genomics》;第15卷;第1-12页 *

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Publication number Publication date
WO2020072990A1 (en) 2020-04-09
EP4296373C0 (en) 2025-02-19
IL281982B2 (en) 2025-12-01
DK3861135T5 (da) 2024-09-09
DK3861135T3 (da) 2023-11-06
EP3861135A1 (en) 2021-08-11
CA3115281A1 (en) 2020-04-09
EP4296373A3 (en) 2024-01-24
AU2019356016B2 (en) 2026-01-08
IL281982A (en) 2021-05-31
US20220002781A1 (en) 2022-01-06
EP4296373A2 (en) 2023-12-27
EP3861135B1 (en) 2023-08-02
AU2019356016A1 (en) 2021-05-13
JP2022513343A (ja) 2022-02-07
JP7436493B2 (ja) 2024-02-21
EP4296373B1 (en) 2025-02-19
IL281982B1 (en) 2025-08-01
EP4296373B8 (en) 2025-03-26
CN113207299A (zh) 2021-08-03

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