WO2014200926A3 - Analysis of polynucleotides - Google Patents

Analysis of polynucleotides Download PDF

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Publication number
WO2014200926A3
WO2014200926A3 PCT/US2014/041568 US2014041568W WO2014200926A3 WO 2014200926 A3 WO2014200926 A3 WO 2014200926A3 US 2014041568 W US2014041568 W US 2014041568W WO 2014200926 A3 WO2014200926 A3 WO 2014200926A3
Authority
WO
WIPO (PCT)
Prior art keywords
polynucleotides
analysis
labeling
kits
absence
Prior art date
Application number
PCT/US2014/041568
Other languages
French (fr)
Other versions
WO2014200926A2 (en
Inventor
Han Cao
Alex R. HASTIE
Ernest Tsz-tsun LAM
Original Assignee
Bionano Genomics, 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 Bionano Genomics, Inc. filed Critical Bionano Genomics, Inc.
Priority to US14/897,213 priority Critical patent/US20160201147A1/en
Priority to JP2016519575A priority patent/JP6556705B2/en
Priority to CN201480044219.XA priority patent/CN105683393B/en
Priority to EP14811715.3A priority patent/EP3008216A4/en
Publication of WO2014200926A2 publication Critical patent/WO2014200926A2/en
Publication of WO2014200926A3 publication Critical patent/WO2014200926A3/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
    • C12Q1/70—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
    • C12Q1/705—Specific hybridization probes for herpetoviridae, e.g. herpes simplex, varicella zoster
    • 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
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6858—Allele-specific amplification
    • 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
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • 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
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
    • G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
    • Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Immunology (AREA)
  • Genetics & Genomics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Pathology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Virology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

According to some embodiments herein, methods and kits for labeling and analyzing nucleic acids are provided, In some embodiments, sequence-specific labeling is performed on polynucleotide sequences associated with a host genome, and the presence or absence of patterns characteristic of extragenomic sequences are determined.
PCT/US2014/041568 2013-06-10 2014-06-09 Analysis of polynucleotides WO2014200926A2 (en)

Priority Applications (4)

Application Number Priority Date Filing Date Title
US14/897,213 US20160201147A1 (en) 2013-06-10 2014-06-09 Analysis of polynucleotides
JP2016519575A JP6556705B2 (en) 2013-06-10 2014-06-09 Polynucleotide analysis
CN201480044219.XA CN105683393B (en) 2013-06-10 2014-06-09 Polynucleotide analysis
EP14811715.3A EP3008216A4 (en) 2013-06-10 2014-06-09 Analysis of polynucleotides

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201361833378P 2013-06-10 2013-06-10
US61/833,378 2013-06-10

Publications (2)

Publication Number Publication Date
WO2014200926A2 WO2014200926A2 (en) 2014-12-18
WO2014200926A3 true WO2014200926A3 (en) 2015-03-12

Family

ID=52022911

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2014/041568 WO2014200926A2 (en) 2013-06-10 2014-06-09 Analysis of polynucleotides

Country Status (5)

Country Link
US (1) US20160201147A1 (en)
EP (1) EP3008216A4 (en)
JP (1) JP6556705B2 (en)
CN (1) CN105683393B (en)
WO (1) WO2014200926A2 (en)

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
FR3049090B1 (en) * 2016-03-21 2021-06-25 Sebastien Jean Serge Dupont ADAPTIVE BIOMETRIC AUTHENTICATION DEVICE BY ULTRASOUND, VISIBLE CONTRAST AND INFRARED LIGHT PHOTOGRAPHS, WITHOUT DISCLOSURE, THROUGH A DECENTRALIZED COMPUTER NETWORK
WO2018045141A1 (en) * 2016-09-02 2018-03-08 New England Biolabs, Inc. Analysis of chromatin using a nicking enzyme
CN108728430B (en) * 2017-04-21 2022-04-05 胤安国际（辽宁）基因科技股份有限公司 Method for preparing long DNA probe containing multiple repeating units
US11505826B2 (en) * 2017-07-12 2022-11-22 Agilent Technologies, Inc. Sequencing method for genomic rearrangement detection
WO2019178273A1 (en) * 2018-03-13 2019-09-19 Guardant Health, Inc. Methods for the non-invasive detection and monitoring of therapeutic nucleic acid constructs
CN111378647A (en) * 2018-12-27 2020-07-07 北京贝瑞和康生物技术有限公司 Method and kit for rapidly preparing monomolecular optical spectrum marker library
JP2023530751A (en) * 2020-06-25 2023-07-19 ペルセウス バイオミクス Kits and methods for characterizing viruses in samples

Family Cites Families (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2007097778A2 (en) * 2005-08-04 2007-08-30 New England Biolabs, Inc. Novel restriction endonucleases, dna encoding these endonucleases and methods for identifying new endonucleases with the same or varied specificity
US8221973B2 (en) * 2007-10-17 2012-07-17 Wisconsin Alumni Research Foundation Methods of whole genome analysis
US8524878B1 (en) * 2008-02-19 2013-09-03 Opgen, Inc. Methods of identifying an organism
JP5730762B2 (en) * 2008-06-30 2015-06-10 バイオナノ ジェノミックス、インク． Method and apparatus for single molecule whole genome analysis
WO2011050147A1 (en) * 2009-10-21 2011-04-28 Bionanomatrix, Inc . Methods and related devices for single molecule whole genome analysis
US20100330557A1 (en) * 2009-06-30 2010-12-30 Zohar Yakhini Genomic coordinate system
US20120283955A1 (en) * 2011-02-28 2012-11-08 Pathogenetix, Inc. Methods for data manipulation relating to polymer linear analysis

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
BADAY ET AL.: "Multicolor super-resolution DNA imaging for genetic analysis.", NANO LETT, vol. 12, no. 7, 11 June 2012 (2012-06-11), pages 3861 - 3866, XP055268597 *
BEN-DAVID ET AL.: "Identification and mapping of a common proviral integration site Fli-1 in erythroleukemia cells induced by Friend murine leukemia virus.", PROC NAT ACAD SCI, vol. 87, no. 4, February 1990 (1990-02-01), pages 1332 - 1336, XP055300966 *
DAS ET AL., SINGLE MOLECULE LINEAR ANALYSIS OF DNA IN NANO-CHANNEL LABELED WITH SEQUENCE SPECIFIC FLUORESCENT PROBES., vol. 38, no. 18, October 2012 (2012-10-01), pages E177 1 - 8, XP002670980 *
LAM ET AL.: "Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly.", NAT BIOTECHNOL, vol. 30, no. 8, August 2012 (2012-08-01), pages 771 - 776, XP002739644 *

Also Published As

Publication number Publication date
JP6556705B2 (en) 2019-08-07
JP2016523533A (en) 2016-08-12
WO2014200926A2 (en) 2014-12-18
EP3008216A2 (en) 2016-04-20
CN105683393A (en) 2016-06-15
EP3008216A4 (en) 2017-02-22
CN105683393B (en) 2020-08-07
US20160201147A1 (en) 2016-07-14

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