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EP3063301A4 - Next generation genomic sequencing methods - Google Patents

Next generation genomic sequencing methods Download PDF

Info

Publication number
EP3063301A4
EP3063301A4 EP14856946.0A EP14856946A EP3063301A4 EP 3063301 A4 EP3063301 A4 EP 3063301A4 EP 14856946 A EP14856946 A EP 14856946A EP 3063301 A4 EP3063301 A4 EP 3063301A4
Authority
EP
European Patent Office
Prior art keywords
next generation
sequencing methods
genomic sequencing
generation genomic
methods
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Withdrawn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
EP14856946.0A
Other languages
German (de)
French (fr)
Other versions
EP3063301A1 (en
Inventor
Luke T. Daum
Gerald W. Fischer
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.)
Longhorn Vaccines and Diagnostics LLC
Original Assignee
Longhorn Vaccines and Diagnostics LLC
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 Longhorn Vaccines and Diagnostics LLC filed Critical Longhorn Vaccines and Diagnostics LLC
Publication of EP3063301A1 publication Critical patent/EP3063301A1/en
Publication of EP3063301A4 publication Critical patent/EP3063301A4/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Withdrawn legal-status Critical Current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
    • C12Q1/70—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving virus or bacteriophage
    • C12Q1/701—Specific hybridization probes
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6893—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for protozoa

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Zoology (AREA)
  • Analytical Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Physics & Mathematics (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Virology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
EP14856946.0A 2013-10-29 2014-10-29 Next generation genomic sequencing methods Withdrawn EP3063301A4 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201361897015P 2013-10-29 2013-10-29
PCT/US2014/062889 WO2015066174A1 (en) 2013-10-29 2014-10-29 Next generation genomic sequencing methods

Publications (2)

Publication Number Publication Date
EP3063301A1 EP3063301A1 (en) 2016-09-07
EP3063301A4 true EP3063301A4 (en) 2017-07-19

Family

ID=53005068

Family Applications (1)

Application Number Title Priority Date Filing Date
EP14856946.0A Withdrawn EP3063301A4 (en) 2013-10-29 2014-10-29 Next generation genomic sequencing methods

Country Status (5)

Country Link
EP (1) EP3063301A4 (en)
CN (1) CN106170560A (en)
AU (1) AU2014342414B2 (en)
CA (1) CA2929108A1 (en)
WO (1) WO2015066174A1 (en)

Families Citing this family (25)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11041216B2 (en) 2007-10-01 2021-06-22 Longhorn Vaccines And Diagnostics, Llc Compositions and methods for detecting and quantifying nucleic acid sequences in blood samples
SG11201600853UA (en) 2013-08-05 2016-03-30 Twist Bioscience Corp De novo synthesized gene libraries
WO2016172377A1 (en) 2015-04-21 2016-10-27 Twist Bioscience Corporation Devices and methods for oligonucleic acid library synthesis
KR20180050411A (en) 2015-09-18 2018-05-14 트위스트 바이오사이언스 코포레이션 Oligonucleotide mutant library and its synthesis
KR20180058772A (en) 2015-09-22 2018-06-01 트위스트 바이오사이언스 코포레이션 Flexible substrate for nucleic acid synthesis
WO2017091809A1 (en) * 2015-11-25 2017-06-01 Longhorn Vaccines And Diagnostics, Llc Compositions and methods for detecting and quantifying nucleic acid sequences in blood samples
CN105950726A (en) * 2016-05-16 2016-09-21 杭州市疾病预防控制中心 Mycobacterium tuberculosis pyrazinamide molecule drug sensitivity detection method
GB2568444A (en) 2016-08-22 2019-05-15 Twist Bioscience Corp De novo synthesized nucleic acid libraries
EP3516528A4 (en) 2016-09-21 2020-06-24 Twist Bioscience Corporation Nucleic acid based data storage
EP3541973B1 (en) * 2016-11-18 2024-03-27 Twist Bioscience Corporation Polynucleotide libraries having controlled stoichiometry and synthesis thereof
JP2020508661A (en) 2017-02-22 2020-03-26 ツイスト バイオサイエンス コーポレーション Nucleic acid based data storage
WO2018170169A1 (en) 2017-03-15 2018-09-20 Twist Bioscience Corporation Variant libraries of the immunological synapse and synthesis thereof
IL271205B1 (en) 2017-06-12 2024-10-01 Twist Bioscience Corp Methods for seamless nucleic acid assembly
WO2018231864A1 (en) 2017-06-12 2018-12-20 Twist Bioscience Corporation Methods for seamless nucleic acid assembly
JP2020536504A (en) 2017-09-11 2020-12-17 ツイスト バイオサイエンス コーポレーション GPCR-coupled protein and its synthesis
US10368502B2 (en) 2017-09-25 2019-08-06 Multiple Energy Technologies Llc Bioceramic and carbon-based hydroponic systems, methods and devices
US10894242B2 (en) 2017-10-20 2021-01-19 Twist Bioscience Corporation Heated nanowells for polynucleotide synthesis
SG11202006460SA (en) 2018-01-04 2020-08-28 Twist Bioscience Corp Dna-based digital information storage
WO2019204703A1 (en) * 2018-04-20 2019-10-24 Longhorn Vaccines And Diagnostics, Llc Rapid methods for the detection of microbial resistance
SG11202011467RA (en) 2018-05-18 2020-12-30 Twist Bioscience Corp Polynucleotides, reagents, and methods for nucleic acid hybridization
US11492728B2 (en) 2019-02-26 2022-11-08 Twist Bioscience Corporation Variant nucleic acid libraries for antibody optimization
CA3144644A1 (en) 2019-06-21 2020-12-24 Twist Bioscience Corporation Barcode-based nucleic acid sequence assembly
EP4034566A4 (en) 2019-09-23 2024-01-24 Twist Bioscience Corporation Variant nucleic acid libraries for crth2
CN112779343A (en) * 2019-11-07 2021-05-11 杭州迪安医学检验中心有限公司 Pathogenic microorganism drug sensitivity detection method
CN112410406A (en) * 2020-11-23 2021-02-26 深圳基因家科技有限公司 Method for determining amplification cycle number of library

Citations (10)

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Publication number Priority date Publication date Assignee Title
US5550040A (en) * 1993-06-23 1996-08-27 Hoffman-La Roche Inc. Method, reagents and kits for the detection of Neisseria gonorrhoeae
WO2003080870A1 (en) * 2002-03-20 2003-10-02 Handylab Polynucleotide primers and probes for rapid detection of group b streptococcus (gbs)
WO2005001128A2 (en) * 2003-04-11 2005-01-06 University Of Florida Research Foundation, Inc. Materials and methods for producing dna libraries and detecting and identifying microorganisms
US20090233292A1 (en) * 2007-11-30 2009-09-17 Daniele Podini Method and kit for identification of genetic polymorphisms
US20110281754A1 (en) * 2006-09-12 2011-11-17 Longhorn Vaccines & Diagnostics, Llc Compositions and methods for detecting, identifying and quantitating mycobacterial-specific nucleic acids
CN102250924A (en) * 2010-05-17 2011-11-23 中国疾病预防控制中心病毒病预防控制所 Getah virus complete genome sequence, amplification method and primers
US20120034685A1 (en) * 2010-08-06 2012-02-09 Tandem Diagnostics, Inc. Assay systems for determination of source contribution in a sample
WO2012037531A1 (en) * 2010-09-16 2012-03-22 Gen-Probe Incorporated Capture probes immobilizable via l-nucleotide tail
WO2013022961A1 (en) * 2011-08-08 2013-02-14 3The Broad Institute Compositions and methods for co-amplifying subsequences of a nucleic acid fragment sequence
WO2013169998A1 (en) * 2012-05-09 2013-11-14 Longhorn Vaccines And Diagnostics, Llc Ion torrent genomic sequencing

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* Cited by examiner, † Cited by third party
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US20090215050A1 (en) * 2008-02-22 2009-08-27 Robert Delmar Jenison Systems and methods for point-of-care amplification and detection of polynucleotides

Patent Citations (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5550040A (en) * 1993-06-23 1996-08-27 Hoffman-La Roche Inc. Method, reagents and kits for the detection of Neisseria gonorrhoeae
WO2003080870A1 (en) * 2002-03-20 2003-10-02 Handylab Polynucleotide primers and probes for rapid detection of group b streptococcus (gbs)
WO2005001128A2 (en) * 2003-04-11 2005-01-06 University Of Florida Research Foundation, Inc. Materials and methods for producing dna libraries and detecting and identifying microorganisms
US20110281754A1 (en) * 2006-09-12 2011-11-17 Longhorn Vaccines & Diagnostics, Llc Compositions and methods for detecting, identifying and quantitating mycobacterial-specific nucleic acids
US20090233292A1 (en) * 2007-11-30 2009-09-17 Daniele Podini Method and kit for identification of genetic polymorphisms
CN102250924A (en) * 2010-05-17 2011-11-23 中国疾病预防控制中心病毒病预防控制所 Getah virus complete genome sequence, amplification method and primers
US20120034685A1 (en) * 2010-08-06 2012-02-09 Tandem Diagnostics, Inc. Assay systems for determination of source contribution in a sample
WO2012037531A1 (en) * 2010-09-16 2012-03-22 Gen-Probe Incorporated Capture probes immobilizable via l-nucleotide tail
WO2013022961A1 (en) * 2011-08-08 2013-02-14 3The Broad Institute Compositions and methods for co-amplifying subsequences of a nucleic acid fragment sequence
WO2013169998A1 (en) * 2012-05-09 2013-11-14 Longhorn Vaccines And Diagnostics, Llc Ion torrent genomic sequencing

Non-Patent Citations (6)

* Cited by examiner, † Cited by third party
Title
DAUM L T ET AL: "Genetic analysis of Mycobacterium tuberculosis drug-resistance genes from samples shipped in PrimeStore MTM and sequenced using the next-generation Ion Torrent", INTERNET CITATION, 4 May 2012 (2012-05-04), pages 1, XP002741633, Retrieved from the Internet <URL:http://www.lhnvd.com/000_vig_user_files/site_uploaded/54713/ESPIDMTBIonTorrentPoster2012.pdf> [retrieved on 20150701] *
GRABENSTEINER ET AL: "Development of a multiplex RT-PCR for the simultaneous detection of three viruses of the honeybee (Apis mellifera L.): Acute bee paralysis virus, Black queen cell virus and Sacbrood virus", JOURNAL OF INVERTEBRATE PATHO, SAN DIEGO, CA, US, vol. 94, no. 3, 14 February 2007 (2007-02-14), pages 222 - 225, XP005887833, ISSN: 0022-2011, DOI: 10.1016/J.JIP.2006.11.006 *
HOWDEN B P ET AL: "Evolution of Multidrug Resistance during Staphylococcus aureus Infection Involves Mutation of the Essential Two Component Regulator WalKR", PLOS PATHOGENS, vol. 7, no. 11, 10 November 2011 (2011-11-10), pages 1 - 15, XP055169475, DOI: 10.1371/journal.ppat.1002359 *
JUN-ICHIRO SEKIGUCHI ET AL: "Detection of Multidrug Resistance in Mycobacterium tuberculosis", JOURNAL OF CLINICAL MICROBIO, AMERICAN SOCIETY FOR MICROBIOLOGY, US, vol. 45, no. 1, 1 January 2007 (2007-01-01), pages 179 - 192, XP008139017, ISSN: 0095-1137, [retrieved on 20061115], DOI: 10.1128/JCM.00750-06 *
MELLMANN A ET AL: "Prospective Genomic Characterization of the German Enterohemorrhagic Escherichia coli O104:H4 Outbreak by Rapid Next Generation Sequencing Technology", PLOS ONE, vol. 6, no. 7, 20 July 2011 (2011-07-20), pages e22751, XP055199494, DOI: 10.1371/journal.pone.0022751 *
See also references of WO2015066174A1 *

Also Published As

Publication number Publication date
AU2014342414A1 (en) 2016-05-19
AU2014342414B2 (en) 2017-06-29
EP3063301A1 (en) 2016-09-07
CN106170560A (en) 2016-11-30
WO2015066174A1 (en) 2015-05-07
CA2929108A1 (en) 2015-05-07

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