EP2831283A4 - Procédés et composition permettant le séquençage d'acides nucléiques modifiés - Google Patents

Procédés et composition permettant le séquençage d'acides nucléiques modifiés

Info

Publication number
EP2831283A4
EP2831283A4 EP13769322.2A EP13769322A EP2831283A4 EP 2831283 A4 EP2831283 A4 EP 2831283A4 EP 13769322 A EP13769322 A EP 13769322A EP 2831283 A4 EP2831283 A4 EP 2831283A4
Authority
EP
European Patent Office
Prior art keywords
composition
methods
nucleic acids
modified nucleic
sequencing modified
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.)
Withdrawn
Application number
EP13769322.2A
Other languages
German (de)
English (en)
Other versions
EP2831283A1 (fr
Inventor
Jonas Korlach
Stephen Turner
Tyson A Clark
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Pacific Biosciences of California Inc
Original Assignee
Pacific Biosciences of California Inc
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 Pacific Biosciences of California Inc filed Critical Pacific Biosciences of California Inc
Publication of EP2831283A1 publication Critical patent/EP2831283A1/fr
Publication of EP2831283A4 publication Critical patent/EP2831283A4/fr
Withdrawn legal-status Critical Current

Links

Classifications

    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A90/00—Technologies having an indirect contribution to adaptation to climate change
    • Y02A90/10—Information and communication technologies [ICT] supporting adaptation to climate change, e.g. for weather forecasting or climate simulation

Landscapes

  • 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)
  • Microbiology (AREA)
  • Immunology (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Analytical Chemistry (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
EP13769322.2A 2012-03-30 2013-03-18 Procédés et composition permettant le séquençage d'acides nucléiques modifiés Withdrawn EP2831283A4 (fr)

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US201261617999P 2012-03-30 2012-03-30
US201261721206P 2012-11-01 2012-11-01
US201261721339P 2012-11-01 2012-11-01
US201361799237P 2013-03-15 2013-03-15
US201361789354P 2013-03-15 2013-03-15
PCT/US2013/032816 WO2013148400A1 (fr) 2012-03-30 2013-03-18 Procédés et composition permettant le séquençage d'acides nucléiques modifiés

Publications (2)

Publication Number Publication Date
EP2831283A1 EP2831283A1 (fr) 2015-02-04
EP2831283A4 true EP2831283A4 (fr) 2015-11-04

Family

ID=49261113

Family Applications (1)

Application Number Title Priority Date Filing Date
EP13769322.2A Withdrawn EP2831283A4 (fr) 2012-03-30 2013-03-18 Procédés et composition permettant le séquençage d'acides nucléiques modifiés

Country Status (4)

Country Link
EP (1) EP2831283A4 (fr)
AU (1) AU2013240166A1 (fr)
CA (1) CA2867489A1 (fr)
WO (1) WO2013148400A1 (fr)

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US9290800B2 (en) 2013-03-15 2016-03-22 Pacific Biosciences Of California, Inc. Targeted rolling circle amplification
CN105917003A (zh) 2013-11-17 2016-08-31 宽腾矽公司 用于生物和化学试样的快速分析的有源像素集成装置
US20170356028A1 (en) * 2014-10-22 2017-12-14 bis Biosciences, Inc. Bacterial epigenomic analysis
US10020300B2 (en) 2014-12-18 2018-07-10 Agilome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US9618474B2 (en) 2014-12-18 2017-04-11 Edico Genome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US9859394B2 (en) 2014-12-18 2018-01-02 Agilome, Inc. Graphene FET devices, systems, and methods of using the same for sequencing nucleic acids
US9857328B2 (en) 2014-12-18 2018-01-02 Agilome, Inc. Chemically-sensitive field effect transistors, systems and methods for manufacturing and using the same
US10006910B2 (en) 2014-12-18 2018-06-26 Agilome, Inc. Chemically-sensitive field effect transistors, systems, and methods for manufacturing and using the same
US10429342B2 (en) 2014-12-18 2019-10-01 Edico Genome Corporation Chemically-sensitive field effect transistor
WO2017201081A1 (fr) 2016-05-16 2017-11-23 Agilome, Inc. Dispositifs à fet au graphène, systèmes et leurs méthodes d'utilisation pour le séquençage d'acides nucléiques
MX2018014856A (es) * 2016-06-01 2019-03-07 Quantum Si Inc Llamador de pulso y llamador de base.
EP3366780B1 (fr) * 2017-02-23 2020-05-06 Siemens Healthcare GmbH Analyse de séquence de molécules individuelles et de méthylation à très haute sensibilité pour analyse spécifique de tissus
CA3079252A1 (fr) * 2017-11-03 2019-05-09 Guardant Health, Inc. Correction d'erreurs de sequence induites par desamination
KR20200115590A (ko) 2018-01-26 2020-10-07 퀀텀-에스아이 인코포레이티드 서열화 디바이스들을 위한 머신 학습 가능형 펄스 및 염기 호출
CN121472373A (zh) 2018-05-22 2026-02-06 安序源有限公司 用于核酸测序的方法、系统和组合物
WO2023055752A2 (fr) 2021-09-28 2023-04-06 Axbio Inc. Procédés de traitement d'un échantillon d'acide nucléique et compositions associées
US20230295608A1 (en) * 2022-03-17 2023-09-21 Regeneron Pharmaceuticals, Inc. Methods for Characterization of Viral Genome Using Base Modifications
AU2024207414A1 (en) * 2023-01-13 2025-06-12 F. Hoffmann-La Roche Ag Detection of modified nucleobases in dna samples
CN118658521B (zh) * 2024-08-20 2024-11-15 嘉应学院 一种用于鱼类的基因数据智能分析方法及系统

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WO2008154317A1 (fr) * 2007-06-06 2008-12-18 Pacific Biosciences Of California, Inc. Méthodes et procédés pour identifier des bases dans des procédés d'incorporation en fonction de la séquence
WO2009145818A1 (fr) * 2008-03-31 2009-12-03 Pacific Biosciences Of California, Inc Procédés et compositions de charge de molécule individuelle
WO2010068289A2 (fr) * 2008-12-11 2010-06-17 Pacific Biosciences Of California, Inc. Classification de matrices d'acides nucléiques
US20110183320A1 (en) * 2008-12-11 2011-07-28 Pacific Biosciences Of California, Inc. Classification of nucleic acid templates

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US5795782A (en) 1995-03-17 1998-08-18 President & Fellows Of Harvard College Characterization of individual polymer molecules based on monomer-interface interactions
WO2000006770A1 (fr) 1998-07-30 2000-02-10 Solexa Ltd. Biomolecules en rangees et leur utilisation dans une procedure de sequençage
US7056661B2 (en) 1999-05-19 2006-06-06 Cornell Research Foundation, Inc. Method for sequencing nucleic acid molecules
US6917726B2 (en) 2001-09-27 2005-07-12 Cornell Research Foundation, Inc. Zero-mode clad waveguides for performing spectroscopy with confined effective observation volumes
WO2005014506A2 (fr) 2003-08-06 2005-02-17 Department Of Science & Technology (Dst) Procede de fabrication d'un engrais a liberation biologique d'un micro-element nutritif anionique sous forme de molybdene
US20060046258A1 (en) * 2004-02-27 2006-03-02 Lapidus Stanley N Applications of single molecule sequencing
US7399614B2 (en) 2004-06-30 2008-07-15 Applera Corporation 5-methylcytosine detection, compositions and methods therefor
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US7170050B2 (en) 2004-09-17 2007-01-30 Pacific Biosciences Of California, Inc. Apparatus and methods for optical analysis of molecules
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CA2622872A1 (fr) 2005-09-30 2007-04-12 Pacific Biosciences Of California, Inc. Surfaces reactives, substrats et procedes de production et d'utilisation correspondants
US7998717B2 (en) 2005-12-02 2011-08-16 Pacific Biosciences Of California, Inc. Mitigation of photodamage in analytical reactions
US8921086B2 (en) 2005-12-22 2014-12-30 Pacific Biosciences Of California, Inc. Polymerases for nucleotide analogue incorporation
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US20080277595A1 (en) 2007-05-10 2008-11-13 Pacific Biosciences Of California, Inc. Highly multiplexed confocal detection systems and methods of using same
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WO2009120374A2 (fr) 2008-03-28 2009-10-01 Pacific Biosciences Of California, Inc. Procédés et compositions pour la préparation d’échantillon d’acide nucléique
MX2010010600A (es) 2008-03-28 2011-03-30 Pacific Biosciences California Inc Composiciones y metodos para secuenciacion de acidos nucleicos.
WO2009145820A2 (fr) 2008-03-31 2009-12-03 Pacific Biosciences Of California, Inc. Génération de polymérases modifiées pour une précision améliorée dans le séquençage d'une seule molécule
CA2737505C (fr) 2008-09-16 2017-08-29 Pacific Biosciences Of California, Inc. Substrats et systemes optiques et leurs procedes d'utilisation
US8481264B2 (en) 2008-09-19 2013-07-09 Pacific Biosciences Of California, Inc. Immobilized nucleic acid complexes for sequence analysis
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US20130138358A1 (en) 2010-02-24 2013-05-30 Pacific Biosciences Of California, Inc. Algorithms for sequence determination

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Publication number Priority date Publication date Assignee Title
WO2008154317A1 (fr) * 2007-06-06 2008-12-18 Pacific Biosciences Of California, Inc. Méthodes et procédés pour identifier des bases dans des procédés d'incorporation en fonction de la séquence
WO2009145818A1 (fr) * 2008-03-31 2009-12-03 Pacific Biosciences Of California, Inc Procédés et compositions de charge de molécule individuelle
WO2010068289A2 (fr) * 2008-12-11 2010-06-17 Pacific Biosciences Of California, Inc. Classification de matrices d'acides nucléiques
US20110183320A1 (en) * 2008-12-11 2011-07-28 Pacific Biosciences Of California, Inc. Classification of nucleic acid templates

Non-Patent Citations (6)

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Title
BENJAMIN FLUSBERG: "Direct detection of DNA methylation and mutagenic damage through single-molecule, real-time (SMRT (TM)) DNA sequencing", 101ST ANNUAL MEETING OF THE AMERICAN-ASSOCIATION-FOR-CANCER-RESEARCH; WASHINGTON, DC, USA; APRIL 17 -21, 2010, 1 April 2010 (2010-04-01), XP055215735, Retrieved from the Internet <URL:http://www.abstractsonline.com/Plan/ViewAbstract.aspx?mID=2521&sKey=ad61b071-5ab9-4f64-bf00-14f780960c07&cKey=68c67e8a-73b3-4b54-8a51-7bc1e5ae1748&mKey=0591fa3b-afef-49d2-8e65-55f41ee8117e> [retrieved on 20150923] *
ELIZABETH A. MANRAO ET AL: "Nucleotide Discrimination with DNA Immobilized in the MspA Nanopore", PLOS ONE, vol. 6, no. 10, 1 January 2011 (2011-01-01), pages e25723 - e25723, XP055028552, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0025723 *
FLUSBERG BENJAMIN A ET AL: "Direct detection of DNA methylation during single-molecule, real-time sequencing", NATURE METHODS, NATURE PUBLISHING GROUP, GB, vol. 7, no. 6, 1 July 2010 (2010-07-01), pages 461 - 465, XP009142171, ISSN: 1548-7105, [retrieved on 20100509], DOI: 10.1038/NMETH.1459 *
JAMES CLARKE ET AL: "Continuous base identification for single-molecule nanopore DNA sequencing", NATURE NANOTECHNOLOGY, vol. 4, no. 4, 1 April 2009 (2009-04-01), pages 265 - 270, XP055028415, ISSN: 1748-3387, DOI: 10.1038/nnano.2009.12 *
See also references of WO2013148400A1 *
THOMPSON JOHN F ET AL: "The properties and applications of single-molecule DNA sequencing", GENOME BIOLOGY, BIOMED CENTRAL LTD., LONDON, GB, vol. 12, no. 2, 24 February 2011 (2011-02-24), pages 217, XP021091788, ISSN: 1465-6906 *

Also Published As

Publication number Publication date
AU2013240166A1 (en) 2014-10-30
EP2831283A1 (fr) 2015-02-04
WO2013148400A1 (fr) 2013-10-03
CA2867489A1 (fr) 2013-10-03

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