AU2016305103C1 - Single-molecule sequencing of plasma DNA - Google Patents

Single-molecule sequencing of plasma DNA Download PDF

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Publication number
AU2016305103C1
AU2016305103C1 AU2016305103A AU2016305103A AU2016305103C1 AU 2016305103 C1 AU2016305103 C1 AU 2016305103C1 AU 2016305103 A AU2016305103 A AU 2016305103A AU 2016305103 A AU2016305103 A AU 2016305103A AU 2016305103 C1 AU2016305103 C1 AU 2016305103C1
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dna fragments
concatemer
dna
sequence
cell
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AU2016305103A1 (en
AU2016305103B2 (en
Inventor
Suk Hang Cheng
Rossa Wai Kwun Chiu
Yuk-Ming Dennis Lo
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Chinese University of Hong Kong CUHK
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Chinese University of Hong Kong CUHK
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Priority to AU2020202153A priority Critical patent/AU2020202153B2/en
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Publication of AU2016305103C1 publication Critical patent/AU2016305103C1/en
Priority to AU2023202572A priority patent/AU2023202572B2/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
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • 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
    • 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
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/483—Physical analysis of biological material
    • G01N33/487—Physical analysis of biological material of liquid biological material
    • G01N33/48707—Physical analysis of biological material of liquid biological material by electrical means
    • G01N33/48721—Investigating individual macromolecules, e.g. by translocation through nanopores
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • 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
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • C12Q2521/00—Reaction characterised by the enzymatic activity
    • C12Q2521/50—Other enzymatic activities
    • C12Q2521/501—Ligase
    • 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
    • C12Q2525/151—Modifications characterised by repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
    • 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
    • C12Q2525/191—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
    • C12Q2525/197—Modifications characterised by incorporating a spacer/coupling moiety
    • 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
    • C12Q2527/00—Reactions demanding special reaction conditions
    • C12Q2527/146—Concentration of target or template
    • 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
    • C12Q2565/60—Detection means characterised by use of a special device
    • C12Q2565/631—Detection means characterised by use of a special device being a biochannel or pore

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Immunology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Microbiology (AREA)
  • Genetics & Genomics (AREA)
  • Biomedical Technology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Food Science & Technology (AREA)
  • General Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Medicinal Chemistry (AREA)
  • Nanotechnology (AREA)
  • Urology & Nephrology (AREA)
  • Hematology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Investigating Or Analyzing Materials By The Use Of Electric Means (AREA)
AU2016305103A 2015-08-12 2016-08-12 Single-molecule sequencing of plasma DNA Active AU2016305103C1 (en)

Priority Applications (2)

Application Number Priority Date Filing Date Title
AU2020202153A AU2020202153B2 (en) 2015-08-12 2020-03-26 Single-molecule sequencing of plasma DNA
AU2023202572A AU2023202572B2 (en) 2015-08-12 2023-04-27 Single-molecule sequencing of plasma DNA

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201562204396P 2015-08-12 2015-08-12
US62/204,396 2015-08-12
PCT/CN2016/094802 WO2017025059A1 (en) 2015-08-12 2016-08-12 Single-molecule sequencing of plasma dna

Related Child Applications (1)

Application Number Title Priority Date Filing Date
AU2020202153A Division AU2020202153B2 (en) 2015-08-12 2020-03-26 Single-molecule sequencing of plasma DNA

Publications (3)

Publication Number Publication Date
AU2016305103A1 AU2016305103A1 (en) 2018-03-22
AU2016305103B2 AU2016305103B2 (en) 2020-01-02
AU2016305103C1 true AU2016305103C1 (en) 2020-06-04

Family

ID=57983895

Family Applications (3)

Application Number Title Priority Date Filing Date
AU2016305103A Active AU2016305103C1 (en) 2015-08-12 2016-08-12 Single-molecule sequencing of plasma DNA
AU2020202153A Active AU2020202153B2 (en) 2015-08-12 2020-03-26 Single-molecule sequencing of plasma DNA
AU2023202572A Active AU2023202572B2 (en) 2015-08-12 2023-04-27 Single-molecule sequencing of plasma DNA

Family Applications After (2)

Application Number Title Priority Date Filing Date
AU2020202153A Active AU2020202153B2 (en) 2015-08-12 2020-03-26 Single-molecule sequencing of plasma DNA
AU2023202572A Active AU2023202572B2 (en) 2015-08-12 2023-04-27 Single-molecule sequencing of plasma DNA

Country Status (12)

Country Link
US (2) US11319586B2 (https=)
EP (1) EP3334843A4 (https=)
JP (3) JP6867045B2 (https=)
CN (2) CN107849607B (https=)
AU (3) AU2016305103C1 (https=)
CA (1) CA2995422A1 (https=)
HK (1) HK1248286A1 (https=)
IL (3) IL285795B (https=)
MY (1) MY188348A (https=)
SA (1) SA518390907B1 (https=)
TW (2) TWI728994B (https=)
WO (1) WO2017025059A1 (https=)

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EP3700856A4 (en) 2017-10-26 2021-12-15 Ultima Genomics, Inc. METHODS AND SYSTEMS FOR SEQUENCE CALL
EP3731959B1 (en) 2017-12-29 2025-10-08 Clear Labs, Inc. Automated priming and library loading device
WO2019204720A1 (en) * 2018-04-20 2019-10-24 The Regents Of The University Of California Nucleic acid sequencing methods and computer-readable media for practicing same
WO2020185790A1 (en) 2019-03-10 2020-09-17 Ultima Genomics, Inc. Methods and systems for sequence calling
US12205674B2 (en) 2019-06-21 2025-01-21 Coopersurgical, Inc. System and method for determining genetic relationships between a sperm provider, oocyte provider, and the respective conceptus
WO2021108532A2 (en) * 2019-11-25 2021-06-03 William Marsh Rice University Linear dna assembly for nanopore sequencing
WO2022008641A1 (en) 2020-07-08 2022-01-13 Roche Sequencing Solutions, Inc. Split-pool synthesis apparatus and methods of performing split-pool synthesis
CN116710571A (zh) 2020-10-15 2023-09-05 卡帕生物系统公司 用于下一代测序文库制备的电泳装置和方法
CN114507708A (zh) * 2020-11-16 2022-05-17 唐纳德·李 一种制备长分子测序dna的方法
EP4308723B1 (en) 2021-03-15 2025-04-23 F. Hoffmann-La Roche AG Targeted next-generation sequencing via anchored primer extension
CN117098854A (zh) 2021-03-26 2023-11-21 豪夫迈·罗氏有限公司 杂交缓冲液配制品
WO2022207682A1 (en) 2021-04-01 2022-10-06 F. Hoffmann-La Roche Ag Immune cell counting of sars-cov-2 patients based on immune repertoire sequencing
US20220328135A1 (en) * 2021-04-12 2022-10-13 The Chinese University Of Hong Kong Base modification analysis using electrical signals
WO2023023561A1 (en) * 2021-08-17 2023-02-23 Quantapore, Inc. Multiplex binding assays with optical nanopore readout
US20250243536A1 (en) * 2021-10-18 2025-07-31 Belgian Volition Srl Use of nanopore sequencing for determining the origin of circulating dna
EP4547839A1 (en) 2022-06-30 2025-05-07 Kapa Biosystems, Inc. Controlling for tagmentation sequencing library insert size using archaeal histone-like proteins
CN114898802B (zh) * 2022-07-14 2022-09-30 臻和(北京)生物科技有限公司 基于血浆游离dna甲基化测序数据的末端序列频率分布特征确定方法、评价方法及装置
EP4581153A1 (en) 2022-09-02 2025-07-09 F. Hoffmann-La Roche AG Improvements to next-generation target enrichment performance
WO2024215528A1 (en) 2023-04-13 2024-10-17 Ventana Medical Systems, Inc. Proliferation assay for fixed solid tumors
CN121605113A (zh) 2023-06-14 2026-03-03 豪夫迈·罗氏有限公司 5-甲酰基胞嘧啶的加速标记及在核酸甲基化测序中的应用
WO2025193604A1 (en) 2024-03-11 2025-09-18 Ventana Medical Systems, Inc. Non-enzymatic dissociation of ffpe tissue and generation of single cells with intact cell surface markers
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US20130040827A1 (en) * 2011-08-14 2013-02-14 Stephen C. Macevicz Method and compositions for detecting and sequencing nucleic acids
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EP1225234A2 (en) * 2001-01-20 2002-07-24 Agilent Technologies, Inc. (a Delaware corporation) Synthesis of nucleic acid
WO2006095169A1 (en) * 2005-03-08 2006-09-14 Lingvitae As Method for preparing polynucleotides for analysis
US20120045771A1 (en) * 2008-12-11 2012-02-23 Febit Holding Gmbh Method for analysis of nucleic acid populations
US20130040827A1 (en) * 2011-08-14 2013-02-14 Stephen C. Macevicz Method and compositions for detecting and sequencing nucleic acids
WO2016077313A1 (en) * 2014-11-11 2016-05-19 Bgi Shenzhen Multi-pass sequencing

Also Published As

Publication number Publication date
JP7506408B2 (ja) 2024-06-26
TWI728994B (zh) 2021-06-01
IL285795A (en) 2021-09-30
CN107849607A (zh) 2018-03-27
TW202130815A (zh) 2021-08-16
AU2016305103A1 (en) 2018-03-22
MY188348A (en) 2021-12-02
US11319586B2 (en) 2022-05-03
TWI793586B (zh) 2023-02-21
IL257074B (en) 2021-09-30
AU2020202153A1 (en) 2020-04-16
JP2021118691A (ja) 2021-08-12
EP3334843A1 (en) 2018-06-20
TW201718874A (zh) 2017-06-01
AU2016305103B2 (en) 2020-01-02
JP2024113130A (ja) 2024-08-21
AU2023202572B2 (en) 2025-04-10
JP7810455B2 (ja) 2026-02-03
IL294192B1 (en) 2023-04-01
US20220205038A1 (en) 2022-06-30
IL294192B2 (en) 2023-08-01
WO2017025059A1 (en) 2017-02-16
SA518390907B1 (ar) 2021-09-08
EP3334843A4 (en) 2019-01-02
HK1245850A1 (zh) 2018-08-31
AU2023202572A1 (en) 2023-05-18
IL294192A (en) 2022-08-01
AU2020202153B2 (en) 2023-02-02
JP2018531583A (ja) 2018-11-01
IL285795B (en) 2022-07-01
US20170044606A1 (en) 2017-02-16
JP6867045B2 (ja) 2021-04-28
CA2995422A1 (en) 2017-02-16
CN115433769A (zh) 2022-12-06
CN107849607B (zh) 2022-10-11
IL257074A (en) 2018-03-29
HK1248286A1 (zh) 2018-10-12

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