CA2966442C - Sequencing from multiple primers to increase data rate and density - Google Patents

Sequencing from multiple primers to increase data rate and density Download PDF

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Publication number
CA2966442C
CA2966442C CA2966442A CA2966442A CA2966442C CA 2966442 C CA2966442 C CA 2966442C CA 2966442 A CA2966442 A CA 2966442A CA 2966442 A CA2966442 A CA 2966442A CA 2966442 C CA2966442 C CA 2966442C
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Prior art keywords
nucleic acid
primers
nucleotide
extension
sequencing
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CA2966442A
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English (en)
French (fr)
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CA2966442A1 (en
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Jonathan Mark Boutell
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Illumina Cambridge Ltd
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Illumina Cambridge Ltd
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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
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T7/00—Image analysis
    • G06T7/0002—Inspection of images, e.g. flaw detection
    • G06T7/0012—Biomedical image inspection
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T2207/00—Indexing scheme for image analysis or image enhancement
    • G06T2207/30—Subject of image; Context of image processing
    • G06T2207/30004—Biomedical image processing
    • G06T2207/30072—Microarray; Biochip, DNA array; Well plate

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  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Molecular Biology (AREA)
  • Biotechnology (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Genetics & Genomics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Biophysics (AREA)
  • Medical Informatics (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Radiology & Medical Imaging (AREA)
  • Quality & Reliability (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • General Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Chemical Kinetics & Catalysis (AREA)
CA2966442A 2014-11-05 2015-11-04 Sequencing from multiple primers to increase data rate and density Active CA2966442C (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
GBGB1419731.3A GB201419731D0 (en) 2014-11-05 2014-11-05 Sequencing from multiple primers to increase data rate and density
GB1419731.3 2014-11-05
PCT/GB2015/053324 WO2016071689A1 (en) 2014-11-05 2015-11-04 Sequencing from multiple primers to increase data rate and density

Publications (2)

Publication Number Publication Date
CA2966442A1 CA2966442A1 (en) 2016-05-12
CA2966442C true CA2966442C (en) 2024-03-12

Family

ID=52118764

Family Applications (1)

Application Number Title Priority Date Filing Date
CA2966442A Active CA2966442C (en) 2014-11-05 2015-11-04 Sequencing from multiple primers to increase data rate and density

Country Status (11)

Country Link
US (3) US20170298430A1 (enExample)
EP (2) EP3974538A1 (enExample)
JP (1) JP6789935B2 (enExample)
CN (2) CN107257862B (enExample)
AU (2) AU2015341568B2 (enExample)
CA (1) CA2966442C (enExample)
DK (1) DK3215638T3 (enExample)
ES (1) ES2889875T3 (enExample)
GB (1) GB201419731D0 (enExample)
SG (1) SG11201703629XA (enExample)
WO (1) WO2016071689A1 (enExample)

Families Citing this family (14)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2017190018A1 (en) 2016-04-29 2017-11-02 Omniome, Inc. Sequencing method employing ternary complex destabilization to identify cognate nucleotides
US10428378B2 (en) 2016-08-15 2019-10-01 Omniome, Inc. Sequencing method for rapid identification and processing of cognate nucleotide pairs
WO2018064311A2 (en) * 2016-09-28 2018-04-05 Life Technologies Corporation Methods and systems for reducing phasing errors when sequencing nucleic acids using termination chemistry
AU2017386515B2 (en) 2016-12-30 2021-08-19 Pacific Biosciences Of California, Inc. Method and system employing distinguishable polymerases for detecting ternary complexes and identifying cognate nucleotides
DE102017218849A1 (de) * 2017-10-23 2019-04-25 Robert Bosch Gmbh Reaktionsträger für eine mikrofluidische Vorrichtung und Verfahren zur Bestimmung einer Nukleotidsequenz
CN113249455A (zh) * 2020-02-12 2021-08-13 赛纳生物科技(北京)有限公司 一种基因测序中获得背景信号的方法
WO2023114392A1 (en) * 2021-12-16 2023-06-22 Ultima Genomics, Inc. Systems and methods for sequencing with multi-priming
JP2025509651A (ja) * 2022-03-15 2025-04-11 イルミナ インコーポレイテッド 並行サンプル及びインデックス配列決定
WO2023175040A2 (en) * 2022-03-15 2023-09-21 Illumina, Inc. Concurrent sequencing of forward and reverse complement strands on concatenated polynucleotides for methylation detection
CN115232867B (zh) * 2022-07-21 2024-01-30 深圳赛陆医疗科技有限公司 一种快速的二代基因测序方法
WO2024124379A1 (zh) * 2022-12-12 2024-06-20 深圳华大智造科技股份有限公司 一种多模板核酸同步测序的方法及其应用
US20240301464A1 (en) * 2023-01-17 2024-09-12 Illumina, Inc. Concurrent sequencing of forward and reverse complement strands on separate polynucleotides for methylation detection
CN117987521A (zh) * 2023-02-08 2024-05-07 深圳市真迈生物科技有限公司 测序方法
CN117721191B (zh) * 2024-02-07 2024-05-10 深圳赛陆医疗科技有限公司 基因测序方法、测序装置、可读存储介质和基因测序系统

Family Cites Families (57)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA1323293C (en) 1987-12-11 1993-10-19 Keith C. Backman Assay using template-dependent nucleic acid probe reorganization
CA1341584C (en) 1988-04-06 2008-11-18 Bruce Wallace Method of amplifying and detecting nucleic acid sequences
AU3539089A (en) 1988-04-08 1989-11-03 Salk Institute For Biological Studies, The Ligase-based amplification method
US5130238A (en) 1988-06-24 1992-07-14 Cangene Corporation Enhanced nucleic acid amplification process
ATE144556T1 (de) 1988-06-24 1996-11-15 Amgen Inc Verfahren und mittel zum nachweis von nukleinsäuresequenzen
ATE138106T1 (de) 1988-07-20 1996-06-15 David Segev Verfahren zur amplifizierung und zum nachweis von nukleinsäuresequenzen
US5185243A (en) 1988-08-25 1993-02-09 Syntex (U.S.A.) Inc. Method for detection of specific nucleic acid sequences
WO1991006678A1 (en) 1989-10-26 1991-05-16 Sri International Dna sequencing
US5573907A (en) 1990-01-26 1996-11-12 Abbott Laboratories Detecting and amplifying target nucleic acids using exonucleolytic activity
KR950013953B1 (ko) 1990-01-26 1995-11-18 애보트 래보라토리즈 리가제 연쇄 반응에 적용가능한 표적 핵산의 증폭 방법
US5455166A (en) 1991-01-31 1995-10-03 Becton, Dickinson And Company Strand displacement amplification
WO1995021271A1 (en) 1994-02-07 1995-08-10 Molecular Tool, Inc. Ligase/polymerase-mediated genetic bit analysistm of single nucleotide polymorphisms and its use in genetic analysis
CA2185239C (en) 1994-03-16 2002-12-17 Nanibhushan Dattagupta Isothermal strand displacement nucleic acid amplification
US5846719A (en) 1994-10-13 1998-12-08 Lynx Therapeutics, Inc. Oligonucleotide tags for sorting and identification
US5750341A (en) 1995-04-17 1998-05-12 Lynx Therapeutics, Inc. DNA sequencing by parallel oligonucleotide extensions
DE19515552A1 (de) * 1995-04-27 1996-10-31 Europ Lab Molekularbiolog Simultane Sequenzierung von Nukleinsäuren
GB9620209D0 (en) 1996-09-27 1996-11-13 Cemu Bioteknik Ab Method of sequencing DNA
GB9626815D0 (en) 1996-12-23 1997-02-12 Cemu Bioteknik Ab Method of sequencing DNA
EP2327797B1 (en) 1997-04-01 2015-11-25 Illumina Cambridge Limited Method of nucleic acid sequencing
US6969488B2 (en) 1998-05-22 2005-11-29 Solexa, Inc. System and apparatus for sequential processing of analytes
AR021833A1 (es) 1998-09-30 2002-08-07 Applied Research Systems Metodos de amplificacion y secuenciacion de acido nucleico
US6274320B1 (en) 1999-09-16 2001-08-14 Curagen Corporation Method of sequencing a nucleic acid
AU1075701A (en) * 1999-10-08 2001-04-23 Protogene Laboratories, Inc. Method and apparatus for performing large numbers of reactions using array assembly
US7611869B2 (en) 2000-02-07 2009-11-03 Illumina, Inc. Multiplexed methylation detection methods
US7582420B2 (en) 2001-07-12 2009-09-01 Illumina, Inc. Multiplex nucleic acid reactions
US7955794B2 (en) 2000-09-21 2011-06-07 Illumina, Inc. Multiplex nucleic acid reactions
US7001792B2 (en) 2000-04-24 2006-02-21 Eagle Research & Development, Llc Ultra-fast nucleic acid sequencing device and a method for making and using the same
EP2100971A3 (en) 2000-07-07 2009-11-25 Visigen Biotechnologies, Inc. Real-time sequence determination
US7211414B2 (en) 2000-12-01 2007-05-01 Visigen Biotechnologies, Inc. Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity
EP1472335A4 (en) * 2001-11-08 2005-12-28 Univ Johns Hopkins METHODS AND SYSTEMS FOR SEQUENCING NUCLEIC ACIDS
US7057026B2 (en) 2001-12-04 2006-06-06 Solexa Limited Labelled nucleotides
AU2003259350A1 (en) 2002-08-23 2004-03-11 Solexa Limited Modified nucleotides for polynucleotide sequencing
AU2004253882B2 (en) 2003-06-20 2010-06-10 Illumina, Inc. Methods and compositions for whole genome amplification and genotyping
GB0321306D0 (en) 2003-09-11 2003-10-15 Solexa Ltd Modified polymerases for improved incorporation of nucleotide analogues
US7169560B2 (en) * 2003-11-12 2007-01-30 Helicos Biosciences Corporation Short cycle methods for sequencing polynucleotides
EP2789383B1 (en) 2004-01-07 2023-05-03 Illumina Cambridge Limited Molecular arrays
US7315019B2 (en) 2004-09-17 2008-01-01 Pacific Biosciences Of California, Inc. Arrays of optical confinements and uses thereof
WO2006064199A1 (en) 2004-12-13 2006-06-22 Solexa Limited Improved method of nucleotide detection
JP4990886B2 (ja) 2005-05-10 2012-08-01 ソレックサ リミテッド 改良ポリメラーゼ
GB0514936D0 (en) 2005-07-20 2005-08-24 Solexa Ltd Preparation of templates for nucleic acid sequencing
US7405281B2 (en) 2005-09-29 2008-07-29 Pacific Biosciences Of California, Inc. Fluorescent nucleotide analogs and uses therefor
SG170802A1 (en) 2006-03-31 2011-05-30 Solexa Inc Systems and devices for sequence by synthesis analysis
US7754429B2 (en) * 2006-10-06 2010-07-13 Illumina Cambridge Limited Method for pair-wise sequencing a plurity of target polynucleotides
EP2089517A4 (en) 2006-10-23 2010-10-20 Pacific Biosciences California POLYMERASEENZYME AND REAGENTS FOR ADVANCED NUCKIC ACID SEQUENCING
EP2677309B9 (en) 2006-12-14 2014-11-19 Life Technologies Corporation Methods for sequencing a nucleic acid using large scale FET arrays, configured to measure a limited pH range
US8349167B2 (en) 2006-12-14 2013-01-08 Life Technologies Corporation Methods and apparatus for detecting molecular interactions using FET arrays
US8262900B2 (en) 2006-12-14 2012-09-11 Life Technologies Corporation Methods and apparatus for measuring analytes using large scale FET arrays
EP2121983A2 (en) * 2007-02-02 2009-11-25 Illumina Cambridge Limited Methods for indexing samples and sequencing multiple nucleotide templates
EP2209911B1 (en) * 2007-10-19 2013-10-16 The Trustees of Columbia University in the City of New York Dna sequencing with non-fluorescent nucleotide reversible terminators and cleavable label modified nucleotide terminators and a deoxyinosine analogue with a reversible terminator group
US20100137143A1 (en) 2008-10-22 2010-06-03 Ion Torrent Systems Incorporated Methods and apparatus for measuring analytes
US20110195410A1 (en) * 2009-12-07 2011-08-11 Gene Check, Inc. Compositions and methods related to solid phase sequence detection and genotyping
CN102140534A (zh) * 2010-12-15 2011-08-03 深圳华大基因科技有限公司 一种hbv基因的核苷酸突变位点的检测方法
US8951781B2 (en) 2011-01-10 2015-02-10 Illumina, Inc. Systems, methods, and apparatuses to image a sample for biological or chemical analysis
EP3333269B1 (en) * 2011-03-31 2021-05-05 Dana-Farber Cancer Institute, Inc. Methods to enable multiplex cold-pcr
US20120252682A1 (en) * 2011-04-01 2012-10-04 Maples Corporate Services Limited Methods and systems for sequencing nucleic acids
US9453258B2 (en) 2011-09-23 2016-09-27 Illumina, Inc. Methods and compositions for nucleic acid sequencing
JP6159391B2 (ja) 2012-04-03 2017-07-05 イラミーナ インコーポレーテッド 核酸シークエンシングに有用な統合化した読取りヘッド及び流体カートリッジ

Also Published As

Publication number Publication date
US20230160006A1 (en) 2023-05-25
AU2015341568A1 (en) 2017-05-25
GB201419731D0 (en) 2014-12-17
ES2889875T3 (es) 2022-01-14
JP6789935B2 (ja) 2020-11-25
HK1243465A1 (en) 2018-07-13
CA2966442A1 (en) 2016-05-12
SG11201703629XA (en) 2017-06-29
CN107257862B (zh) 2021-08-03
AU2021286342A1 (en) 2022-01-20
US11555218B2 (en) 2023-01-17
DK3215638T3 (da) 2021-10-18
JP2017533709A (ja) 2017-11-16
CN113564238A (zh) 2021-10-29
EP3215638B1 (en) 2021-08-11
US20200392573A1 (en) 2020-12-17
EP3974538A1 (en) 2022-03-30
AU2021286342B2 (en) 2024-05-30
AU2015341568B2 (en) 2021-09-16
CN113564238B (zh) 2025-08-05
WO2016071689A1 (en) 2016-05-12
CN107257862A (zh) 2017-10-17
EP3215638A1 (en) 2017-09-13
US20170298430A1 (en) 2017-10-19

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