WO2014197805A3 - Molecular barcoding for multiplex sequencing - Google Patents

Molecular barcoding for multiplex sequencing Download PDF

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Publication number
WO2014197805A3
WO2014197805A3 PCT/US2014/041315 US2014041315W WO2014197805A3 WO 2014197805 A3 WO2014197805 A3 WO 2014197805A3 US 2014041315 W US2014041315 W US 2014041315W WO 2014197805 A3 WO2014197805 A3 WO 2014197805A3
Authority
WO
WIPO (PCT)
Prior art keywords
sequencing
multiplex sequencing
molecular barcoding
methods
multiplex
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.)
Ceased
Application number
PCT/US2014/041315
Other languages
French (fr)
Other versions
WO2014197805A2 (en
Inventor
Christopher D. ELZINGA
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.)
Athena Diagnostics Inc
Original Assignee
Athena Diagnostics 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 Athena Diagnostics Inc filed Critical Athena Diagnostics Inc
Priority to EP14808275.3A priority Critical patent/EP3004367A4/en
Priority to US14/896,152 priority patent/US20160115544A1/en
Priority to CA2914367A priority patent/CA2914367A1/en
Priority to JP2016518036A priority patent/JP2016520326A/en
Publication of WO2014197805A2 publication Critical patent/WO2014197805A2/en
Publication of WO2014197805A3 publication Critical patent/WO2014197805A3/en
Anticipated expiration legal-status Critical
Ceased 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/16—Primer sets for multiplex assays

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Zoology (AREA)
  • Engineering & Computer Science (AREA)
  • Wood Science & Technology (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Immunology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

Described herein are methods, compositions and kits for preparing samples for multiplex next generation nucleic acid sequencing. The methods entail the use of in-line barcodes that minimize barcode-confusing chimeras, purification procedures with low cost, and/or a quantitative amplification to generate a desired amount of polynucleotides for sequencing.
PCT/US2014/041315 2013-06-07 2014-06-06 Molecular barcoding for multiplex sequencing Ceased WO2014197805A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
EP14808275.3A EP3004367A4 (en) 2013-06-07 2014-06-06 Molecular barcoding for multiplex sequencing
US14/896,152 US20160115544A1 (en) 2013-06-07 2014-06-06 Molecular barcoding for multiplex sequencing
CA2914367A CA2914367A1 (en) 2013-06-07 2014-06-06 Molecular barcoding for multiplex sequencing
JP2016518036A JP2016520326A (en) 2013-06-07 2014-06-06 Molecular bar coding for multiplex sequencing

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201361956170P 2013-06-07 2013-06-07
US61/956,170 2013-06-07

Publications (2)

Publication Number Publication Date
WO2014197805A2 WO2014197805A2 (en) 2014-12-11
WO2014197805A3 true WO2014197805A3 (en) 2015-02-19

Family

ID=52008757

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2014/041315 Ceased WO2014197805A2 (en) 2013-06-07 2014-06-06 Molecular barcoding for multiplex sequencing

Country Status (5)

Country Link
US (1) US20160115544A1 (en)
EP (1) EP3004367A4 (en)
JP (1) JP2016520326A (en)
CA (1) CA2914367A1 (en)
WO (1) WO2014197805A2 (en)

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US11091810B2 (en) 2015-01-27 2021-08-17 BioSpyder Technologies, Inc. Focal gene expression profiling of stained FFPE tissues with spatial correlation to morphology
US9856521B2 (en) * 2015-01-27 2018-01-02 BioSpyder Technologies, Inc. Ligation assays in liquid phase
US10683534B2 (en) 2015-01-27 2020-06-16 BioSpyder Technologies, Inc. Ligation assays in liquid phase
WO2017044609A1 (en) 2015-09-08 2017-03-16 Cold Spring Harbor Laboratory Genetic copy number determination using high throughput multiplex sequencing of smashed nucleotides
US11708574B2 (en) 2016-06-10 2023-07-25 Myriad Women's Health, Inc. Nucleic acid sequencing adapters and uses thereof
WO2018064486A1 (en) 2016-09-29 2018-04-05 Counsyl, Inc. Noninvasive prenatal screening using dynamic iterative depth optimization
WO2018144216A1 (en) 2017-01-31 2018-08-09 Counsyl, Inc. Methods and compositions for enrichment of target polynucleotides
WO2018144217A1 (en) 2017-01-31 2018-08-09 Counsyl, Inc. Methods and compositions for enrichment of target polynucleotides
EP3602359A4 (en) 2017-03-24 2021-01-06 Myriad Women's Health, Inc. NUMBER OF COPIES VARIANT CALLER
US12391986B2 (en) 2021-09-30 2025-08-19 Microsoft Technology Licensing, Llc Anti-counterfeit tags using base ratios of polynucleotides

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20110257031A1 (en) * 2010-02-12 2011-10-20 Life Technologies Corporation Nucleic acid, biomolecule and polymer identifier codes

Family Cites Families (10)

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Publication number Priority date Publication date Assignee Title
ATE483822T1 (en) * 2002-10-11 2010-10-15 Univ Erasmus PRIMERS FOR NUCLEIC ACID AMPLIFICATION IN PCR-BASED CLONALITY STUDIES
WO2004087916A1 (en) * 2003-03-28 2004-10-14 Japan As Represented By Director General Of National Rehabilitation Center For Persons With Disabilities METHOD OF SYNTHESIZING cDNA
US20060223122A1 (en) * 2005-03-08 2006-10-05 Agnes Fogo Classifying and predicting glomerulosclerosis using a proteomics approach
GB2424946A (en) * 2005-04-05 2006-10-11 Stratec Biomedical Systems Ag A detection system for substance binding using up-converting fluorescent probes
EP2529026B1 (en) * 2010-01-25 2013-11-13 Rd Biosciences Inc. Self-folding amplification of target nucleic acid
EP2531608B1 (en) * 2010-02-05 2020-08-19 Siemens Healthcare Diagnostics Inc. Methods for increasing multiplex level by externalization of passive reference in polymerase chain reactions
ES2623859T3 (en) * 2010-03-04 2017-07-12 Miacom Diagnostics Gmbh Enhanced Multiple FISH
US20110319290A1 (en) * 2010-06-08 2011-12-29 Nugen Technologies, Inc. Methods and Compositions for Multiplex Sequencing
WO2012162161A1 (en) * 2011-05-20 2012-11-29 Phthisis Diagnostics Microsporidia detection system and method
AU2012304328B2 (en) * 2011-09-09 2017-07-20 The Board Of Trustees Of The Leland Stanford Junior University Methods for obtaining a sequence

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20110257031A1 (en) * 2010-02-12 2011-10-20 Life Technologies Corporation Nucleic acid, biomolecule and polymer identifier codes

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
"NEXTflex DNA Barcodes - 48", BIOO SCIENTIFIC, pages 2, XP055327413, Retrieved from the Internet <URL:HTTP://WWW.GOOGLE.COM/URL?SA=T&RCT=J&Q=&ESRC=S&SOURCE=WEB&CD=3&VED=0CDQQFJAC&URL=HTTP%3A%2F%2FWWW.ZOOLOGY.UBC.CA%2F-RIESEBERG%2FRIESEBERGRESOURCES%2FWP-CONTENT%2FUPLOADS%2F2012%2F03%2F514104-NEXTFLEX-DNA-BARCODES-48.PDF&EI=_JWHVLRZC4GNYASC6IK4BW&USG=AFQJCNHNQ8TPTJSD-QUWWDUJVV> [retrieved on 20140922] *
HAAG CHRISTINE: "Parallel Copy Number Variation and Sequence Variation Detection Using Amplicon based Sequencing on the GS Junior System", ROCHE, 1 April 2012 (2012-04-01), pages 1 - 4, XP055301387, Retrieved from the Internet <URL:HTTP://WWW.GOOGLE.COM/URL?SA=T&RCT=J&Q=&ESRC=S&SOURCE=WEB&CD=1&VED=0CB4QFJAA&URL=HTTP%3A%2F%2F454.COM%2FDOWNLOADS%2FGSJUNIORCNVDETECTIONAPPLICATIONNOTE.PDF&EI=BZV_VJ7DBQWQIGKSI4DGDA&USG=AFQJCNEGHN-9WQYVIMSVFTRTKDZSHEPYNW&SIG2=L_QJ4XAWE5DSDJJ_IXKVGG&BBVM> [retrieved on 20141201] *
ROHLAND ET AL., COST-EFFECTIVE, HIGH-THROUGHPUT DNA SEQUENCING LIBRARIES FOR MULTIPLEXED TARGET CAPTURE., vol. 22, no. 5, 1 May 2012 (2012-05-01), pages 939 - 946, XP002760943 *

Also Published As

Publication number Publication date
JP2016520326A (en) 2016-07-14
US20160115544A1 (en) 2016-04-28
CA2914367A1 (en) 2014-12-11
EP3004367A2 (en) 2016-04-13
EP3004367A4 (en) 2017-02-22
WO2014197805A2 (en) 2014-12-11

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