KR20220098183A - 세포-유리 medip 시퀀싱을 위한 합성 스파이크-인 대조군 및 이의 사용 방법 - Google Patents

세포-유리 medip 시퀀싱을 위한 합성 스파이크-인 대조군 및 이의 사용 방법 Download PDF

Info

Publication number
KR20220098183A
KR20220098183A KR1020227018998A KR20227018998A KR20220098183A KR 20220098183 A KR20220098183 A KR 20220098183A KR 1020227018998 A KR1020227018998 A KR 1020227018998A KR 20227018998 A KR20227018998 A KR 20227018998A KR 20220098183 A KR20220098183 A KR 20220098183A
Authority
KR
South Korea
Prior art keywords
dna
fragment
methylated
control
cell
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
KR1020227018998A
Other languages
English (en)
Korean (ko)
Inventor
사만다 엘 윌슨
슈 이 션
데 카르발로 다니엘 디니즈
마이클 엠 호프만
티모시 제이 트리체
Original Assignee
유니버시티 헬스 네트워크
반 안델 리서치 인스티튜트
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 유니버시티 헬스 네트워크, 반 안델 리서치 인스티튜트 filed Critical 유니버시티 헬스 네트워크
Publication of KR20220098183A publication Critical patent/KR20220098183A/ko
Pending legal-status Critical Current

Links

Images

Classifications

    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6804Nucleic acid analysis using immunogens
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844Nucleic acid amplification reactions
    • C12Q1/6858Allele-specific amplification
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1003Extracting or separating nucleic acids from biological samples, e.g. pure separation or isolation methods; Conditions, buffers or apparatuses therefor
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12NMICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09Recombinant DNA-technology
    • C12N15/10Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034Isolating an individual clone by screening libraries
    • C12N15/1082Preparation or screening gene libraries by chromosomal integration of polynucleotide sequences, HR-, site-specific-recombination, transposons, viral vectors
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6806Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q1/00Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869Methods for sequencing
    • C12Q1/6874Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2522/00Reaction characterised by the use of non-enzymatic proteins
    • C12Q2522/10Nucleic acid binding proteins
    • C12Q2522/101Single or double stranded nucleic acid binding proteins
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2535/00Reactions characterised by the assay type for determining the identity of a nucleotide base or a sequence of oligonucleotides
    • C12Q2535/122Massive parallel sequencing
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2537/00Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/164Methylation detection other then bisulfite or methylation sensitive restriction endonucleases
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2545/00Reactions characterised by their quantitative nature
    • C12Q2545/10Reactions characterised by their quantitative nature the purpose being quantitative analysis
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2545/00Reactions characterised by their quantitative nature
    • C12Q2545/10Reactions characterised by their quantitative nature the purpose being quantitative analysis
    • C12Q2545/101Reactions characterised by their quantitative nature the purpose being quantitative analysis with an internal standard/control
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/154Methylation markers
    • CCHEMISTRY; METALLURGY
    • C12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12QMEASURING 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
    • C12Q2600/00Oligonucleotides characterized by their use
    • C12Q2600/166Oligonucleotides used as internal standards, controls or normalisation probes

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Biomedical Technology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Plant Pathology (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Pathology (AREA)
  • Virology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
KR1020227018998A 2019-11-06 2020-11-06 세포-유리 medip 시퀀싱을 위한 합성 스파이크-인 대조군 및 이의 사용 방법 Pending KR20220098183A (ko)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201962931411P 2019-11-06 2019-11-06
US62/931,411 2019-11-06
PCT/CA2020/051507 WO2021087615A1 (en) 2019-11-06 2020-11-06 Synthetic spike-in controls for cell-free medip sequencing and methods of using same

Publications (1)

Publication Number Publication Date
KR20220098183A true KR20220098183A (ko) 2022-07-11

Family

ID=75849048

Family Applications (1)

Application Number Title Priority Date Filing Date
KR1020227018998A Pending KR20220098183A (ko) 2019-11-06 2020-11-06 세포-유리 medip 시퀀싱을 위한 합성 스파이크-인 대조군 및 이의 사용 방법

Country Status (9)

Country Link
US (1) US20230024827A1 (https=)
EP (2) EP4435118A3 (https=)
JP (1) JP2023502018A (https=)
KR (1) KR20220098183A (https=)
CN (1) CN115087744A (https=)
BR (1) BR112022008714A2 (https=)
CA (1) CA3157323A1 (https=)
GB (1) GB2609715B (https=)
WO (1) WO2021087615A1 (https=)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN111154846A (zh) * 2020-01-13 2020-05-15 四川大学华西医院 一种甲基化核酸的检测方法
US12592321B2 (en) 2020-06-19 2026-03-31 University Health Network Cancer detection and classification using methylome analysis
CN114045342A (zh) * 2021-12-01 2022-02-15 大连晶泰生物技术有限公司 一种游离DNA(cfDNA)甲基化突变的检测方法及试剂盒
KR20250019610A (ko) * 2022-03-21 2025-02-10 빌리언투원, 인크. 치료 모니터링을 위한 메틸화된 세포 유리 dna의 분자 계수

Family Cites Families (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
PT2850211T (pt) * 2012-05-14 2021-11-29 Irepertoire Inc Método para aumentar a precisão na deteção quantitativa de polinucleótidos
EP3022321B1 (en) * 2013-07-16 2021-01-13 Zymo Research Corporation Mirror bisulfite analysis
EP3978627A1 (en) * 2016-03-25 2022-04-06 Karius, Inc. Methods using synthetic nucleic acid spike-ins
KR102522067B1 (ko) * 2016-05-03 2023-04-13 유니버시티 헬스 네트워크 무-세포 메틸화된 dna의 포획 방법 및 이의 이용
WO2018017710A1 (en) * 2016-07-19 2018-01-25 Exact Sciences Development Company, Llc Nucleic acid control molecules from non-human organisms
BR112020000681A2 (pt) * 2017-07-12 2020-07-14 University Health Network detecção e classificação de cancro utilizando análise de metilome
CN111094583A (zh) * 2017-08-04 2020-05-01 十亿至一公司 与生物靶相关的定量中利用靶相关分子的测序输出确定和分析
US20210156863A1 (en) * 2017-11-03 2021-05-27 University Health Network Cancer detection, classification, prognostication, therapy prediction and therapy monitoring using methylome analysis
NZ765943A (en) * 2018-01-08 2022-10-28 Ludwig Inst For Cancer Res Ltd Bisulfite-free, base-resolution identification of cytosine modifications

Also Published As

Publication number Publication date
GB2609715A (en) 2023-02-15
GB202207732D0 (en) 2022-07-13
US20230024827A1 (en) 2023-01-26
EP4055183A1 (en) 2022-09-14
BR112022008714A2 (pt) 2022-07-19
WO2021087615A1 (en) 2021-05-14
JP2023502018A (ja) 2023-01-20
CN115087744A (zh) 2022-09-20
EP4055183A4 (en) 2023-12-06
EP4435118A3 (en) 2025-01-15
EP4435118A2 (en) 2024-09-25
CA3157323A1 (en) 2021-05-14
GB2609715B (en) 2025-07-30

Similar Documents

Publication Publication Date Title
Cheetham et al. Overcoming challenges and dogmas to understand the functions of pseudogenes
Huang et al. Genome-wide identification of mRNA 5-methylcytosine in mammals
Salk et al. Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations
Cheng et al. Consistent global structures of complex RNA states through multidimensional chemical mapping
KR20220098183A (ko) 세포-유리 medip 시퀀싱을 위한 합성 스파이크-인 대조군 및 이의 사용 방법
CN108603228B (zh) 通过分析无细胞dna确定肿瘤基因拷贝数的方法
Smola et al. Selective 2′-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) for direct, versatile and accurate RNA structure analysis
Li et al. Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study
Chan et al. Detecting m6A at single-molecular resolution via direct RNA sequencing and realistic training data
Orton et al. Distinguishing low frequency mutations from RT-PCR and sequence errors in viral deep sequencing data
JP6612220B2 (ja) 核酸における化学修飾の検出
US20240076720A1 (en) Methods for analyzing nucleic acids
Heidegger et al. Development and inter-laboratory validation of the VISAGE enhanced tool for age estimation from semen using quantitative DNA methylation analysis
JP2017537646A (ja) シーケンシングコントロール
JP2019517774A (ja) 核酸を濃縮及びキャプチャーするためのプローブと設計方法
Mittempergher et al. MammaPrint and BluePrint molecular diagnostics using targeted RNA next-generation sequencing technology
Wang et al. LEAD‐m6A‐seq for Locus‐Specific Detection of N6‐Methyladenosine and Quantification of Differential Methylation
JP7044270B2 (ja) 配列データの正規化のための新規のspike inオリゴヌクレオチド
Fu et al. Computational analysis of DNA methylation from long-read sequencing
JP2020530270A (ja) ゲノム再編成検出のための配列決定方法
Ji et al. Male-specific age prediction based on Y-chromosome DNA methylation with blood using pyrosequencing
Wang et al. Detection of genetic variation and base modifications at base-pair resolution on both DNA and RNA
Cradic et al. A simple method for gene phasing using mate pair sequencing
Cheng et al. Whole genome error-corrected sequencing for sensitive circulating tumor DNA cancer monitoring
Thapliyal et al. Next Generation Sequencing: Latent applications in clinical diagnostics with the advent of bioinformatic frameworks

Legal Events

Date Code Title Description
PA0105 International application

St.27 status event code: A-0-1-A10-A15-nap-PA0105

P11-X000 Amendment of application requested

St.27 status event code: A-2-2-P10-P11-nap-X000

P13-X000 Application amended

St.27 status event code: A-2-2-P10-P13-nap-X000

PG1501 Laying open of application

St.27 status event code: A-1-1-Q10-Q12-nap-PG1501

A201 Request for examination
E13-X000 Pre-grant limitation requested

St.27 status event code: A-2-3-E10-E13-lim-X000

P11-X000 Amendment of application requested

St.27 status event code: A-2-2-P10-P11-nap-X000

P13-X000 Application amended

St.27 status event code: A-2-2-P10-P13-nap-X000

PA0201 Request for examination

St.27 status event code: A-1-2-D10-D11-exm-PA0201

D13-X000 Search requested

St.27 status event code: A-1-2-D10-D13-srh-X000

D21 Rejection of application intended

Free format text: ST27 STATUS EVENT CODE: A-1-2-D10-D21-EXM-PE0902 (AS PROVIDED BY THE NATIONAL OFFICE)

PE0902 Notice of grounds for rejection

St.27 status event code: A-1-2-D10-D21-exm-PE0902

T11 Administrative time limit extension requested

Free format text: ST27 STATUS EVENT CODE: U-3-3-T10-T11-OTH-X000 (AS PROVIDED BY THE NATIONAL OFFICE)

T11-X000 Administrative time limit extension requested

St.27 status event code: U-3-3-T10-T11-oth-X000

P11 Amendment of application requested

Free format text: ST27 STATUS EVENT CODE: A-2-2-P10-P11-NAP-X000 (AS PROVIDED BY THE NATIONAL OFFICE)

P11-X000 Amendment of application requested

St.27 status event code: A-2-2-P10-P11-nap-X000