EP2831283A4 - Methods and composition for sequencing modified nucleic acids - Google Patents

Methods and composition for sequencing modified nucleic acids

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Withdrawn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)
French (fr)
Other versions
EP2831283A1 (en
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/en
Publication of EP2831283A4 publication Critical patent/EP2831283A4/en
Withdrawn legal-status Critical Current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 Methods and composition for sequencing modified nucleic acids Withdrawn EP2831283A4 (en)

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 (en) 2012-03-30 2013-03-18 Methods and composition for sequencing modified nucleic acids

Publications (2)

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

Family

ID=49261113

Family Applications (1)

Application Number Title Priority Date Filing Date
EP13769322.2A Withdrawn EP2831283A4 (en) 2012-03-30 2013-03-18 Methods and composition for sequencing modified nucleic acids

Country Status (4)

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

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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 (en) 2016-05-16 2017-11-23 Agilome, Inc. Graphene fet devices, systems, and methods of using the same for sequencing nucleic acids
MX2018014856A (en) * 2016-06-01 2019-03-07 Quantum Si Inc Pulse caller and base caller.
EP3366780B1 (en) * 2017-02-23 2020-05-06 Siemens Healthcare GmbH Single-molecule sequence and high sensitivity methylation analysis for tissue-specific analysis
CA3079252A1 (en) * 2017-11-03 2019-05-09 Guardant Health, Inc. Correcting for deamination-induced sequence errors
KR20200115590A (en) 2018-01-26 2020-10-07 퀀텀-에스아이 인코포레이티드 Machine-learnable pulse and base calls for sequencing devices
CN121472373A (en) 2018-05-22 2026-02-06 安序源有限公司 Methods, systems, and compositions for nucleic acid sequencing
WO2023055752A2 (en) 2021-09-28 2023-04-06 Axbio Inc. Methods for processing a nucleic acid sample and compositions thereof
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 (en) * 2024-08-20 2024-11-15 嘉应学院 A method and system for intelligent analysis of fish genetic data

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WO2009145818A1 (en) * 2008-03-31 2009-12-03 Pacific Biosciences Of California, Inc Single molecule loading methods and compositions
WO2010068289A2 (en) * 2008-12-11 2010-06-17 Pacific Biosciences Of California, Inc. Classification of nucleic acid templates
US20110183320A1 (en) * 2008-12-11 2011-07-28 Pacific Biosciences Of California, Inc. Classification of nucleic acid templates

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WO2008154317A1 (en) * 2007-06-06 2008-12-18 Pacific Biosciences Of California, Inc. Methods and processes for calling bases in sequence by incorporation methods
WO2009145818A1 (en) * 2008-03-31 2009-12-03 Pacific Biosciences Of California, Inc Single molecule loading methods and compositions
WO2010068289A2 (en) * 2008-12-11 2010-06-17 Pacific Biosciences Of California, Inc. Classification of nucleic acid templates
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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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 (en) 2015-02-04
WO2013148400A1 (en) 2013-10-03
CA2867489A1 (en) 2013-10-03

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