WO2009097626A3 - Paired-end reads in sequencing by synthesis - Google Patents

Paired-end reads in sequencing by synthesis Download PDF

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Publication number
WO2009097626A3
WO2009097626A3 PCT/US2009/032970 US2009032970W WO2009097626A3 WO 2009097626 A3 WO2009097626 A3 WO 2009097626A3 US 2009032970 W US2009032970 W US 2009032970W WO 2009097626 A3 WO2009097626 A3 WO 2009097626A3
Authority
WO
WIPO (PCT)
Prior art keywords
sequencing
synthesis
methods
paired
end reads
Prior art date
Application number
PCT/US2009/032970
Other languages
French (fr)
Other versions
WO2009097626A2 (en
Inventor
Timothy Harris
Original Assignee
Helicos Biosciences Corporation
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
Priority claimed from US12/025,033 external-priority patent/US7767400B2/en
Application filed by Helicos Biosciences Corporation filed Critical Helicos Biosciences Corporation
Priority to EP09706204A priority Critical patent/EP2247741A4/en
Publication of WO2009097626A2 publication Critical patent/WO2009097626A2/en
Publication of WO2009097626A3 publication Critical patent/WO2009097626A3/en

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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

Abstract

The disclosure provides methods of generating paired reads in sequencing-by-synthesis process, particularly, in systems with relatively short read lengths (e.g., 15-35 bases), such as for example, in single molecule sequencing by synthesis. Several implementations of the methods are provided. Of particular advantage are the methods that permit re-sequencing of the template, which yields lower error rates. The invention further provides methods of using paired reads, for example, for positioning them over repeats or for assembly into large sequences, including whole genome assembly.
PCT/US2009/032970 2008-02-03 2009-02-03 Paired-end reads in sequencing by synthesis WO2009097626A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
EP09706204A EP2247741A4 (en) 2008-02-03 2009-02-03 Paired-end reads in sequencing by synthesis

Applications Claiming Priority (6)

Application Number Priority Date Filing Date Title
US12/025,033 2008-02-03
US12/025,033 US7767400B2 (en) 2008-02-03 2008-02-03 Paired-end reads in sequencing by synthesis
US4739708P 2008-04-23 2008-04-23
US61/047,397 2008-04-23
US9891008P 2008-09-22 2008-09-22
US61/098,910 2008-09-22

Publications (2)

Publication Number Publication Date
WO2009097626A2 WO2009097626A2 (en) 2009-08-06
WO2009097626A3 true WO2009097626A3 (en) 2009-09-24

Family

ID=40913521

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2009/032970 WO2009097626A2 (en) 2008-02-03 2009-02-03 Paired-end reads in sequencing by synthesis

Country Status (2)

Country Link
EP (1) EP2247741A4 (en)
WO (1) WO2009097626A2 (en)

Families Citing this family (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2002044425A2 (en) 2000-12-01 2002-06-06 Visigen Biotechnologies, Inc. Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity
GB0514935D0 (en) 2005-07-20 2005-08-24 Solexa Ltd Methods for sequencing a polynucleotide template
EP2427572B1 (en) * 2009-05-01 2013-08-28 Illumina, Inc. Sequencing methods
US10036063B2 (en) 2009-07-24 2018-07-31 Illumina, Inc. Method for sequencing a polynucleotide template
US10174368B2 (en) 2009-09-10 2019-01-08 Centrillion Technology Holdings Corporation Methods and systems for sequencing long nucleic acids
WO2011032040A1 (en) 2009-09-10 2011-03-17 Centrillion Technology Holding Corporation Methods of targeted sequencing
EP2633069B1 (en) * 2010-10-26 2015-07-01 Illumina, Inc. Sequencing methods
US20120252682A1 (en) * 2011-04-01 2012-10-04 Maples Corporate Services Limited Methods and systems for sequencing nucleic acids
US10829816B2 (en) 2012-11-19 2020-11-10 Apton Biosystems, Inc. Methods of analyte detection
US10378053B2 (en) * 2017-03-17 2019-08-13 Apton Biosystems, Inc. Sequencing and high resolution imaging
ES2905265T3 (en) 2012-11-19 2022-04-07 Apton Biosystems Inc Digital analysis of molecular analytes using single molecule detection
CN105112516A (en) * 2015-08-14 2015-12-02 深圳市瀚海基因生物科技有限公司 Single-molecule targeted sequencing method, device and system and application
JP2022501026A (en) * 2018-09-19 2022-01-06 アプトン バイオシステムズ インコーポレイテッド Highly packed layers of analytes and detection methods
CA3165571C (en) 2019-12-23 2023-02-07 Singular Genomics Systems, Inc. Methods for long read sequencing

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030044796A1 (en) * 1996-11-29 2003-03-06 Neri Bruce P. Reactions on dendrimers
US20030073081A1 (en) * 1999-03-19 2003-04-17 Takara Shuzo Co., Ltd Method for amplifying nucleic acid sequence
US20030143535A1 (en) * 2000-06-17 2003-07-31 Third Wave Technologies, Inc. Nucleic acid accessible hybridization sites
US20030182068A1 (en) * 2001-10-30 2003-09-25 Battersby Bronwyn J. Device and methods for directed synthesis of chemical libraries
US20060040297A1 (en) * 2003-01-29 2006-02-23 Leamon John H Methods of amplifying and sequencing nucleic acids
US20070099212A1 (en) * 2005-07-28 2007-05-03 Timothy Harris Consecutive base single molecule sequencing

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030044796A1 (en) * 1996-11-29 2003-03-06 Neri Bruce P. Reactions on dendrimers
US20030073081A1 (en) * 1999-03-19 2003-04-17 Takara Shuzo Co., Ltd Method for amplifying nucleic acid sequence
US20030143535A1 (en) * 2000-06-17 2003-07-31 Third Wave Technologies, Inc. Nucleic acid accessible hybridization sites
US20030182068A1 (en) * 2001-10-30 2003-09-25 Battersby Bronwyn J. Device and methods for directed synthesis of chemical libraries
US20060040297A1 (en) * 2003-01-29 2006-02-23 Leamon John H Methods of amplifying and sequencing nucleic acids
US20070099212A1 (en) * 2005-07-28 2007-05-03 Timothy Harris Consecutive base single molecule sequencing

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
See also references of EP2247741A4 *

Also Published As

Publication number Publication date
EP2247741A2 (en) 2010-11-10
EP2247741A4 (en) 2011-02-23
WO2009097626A2 (en) 2009-08-06

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