EP3976828A4 - Séquençage par émergence - Google Patents

Séquençage par émergence Download PDF

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Publication number
EP3976828A4
EP3976828A4 EP20812953.6A EP20812953A EP3976828A4 EP 3976828 A4 EP3976828 A4 EP 3976828A4 EP 20812953 A EP20812953 A EP 20812953A EP 3976828 A4 EP3976828 A4 EP 3976828A4
Authority
EP
European Patent Office
Prior art keywords
emergence
sequencing
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.)
Pending
Application number
EP20812953.6A
Other languages
German (de)
English (en)
Other versions
EP3976828A1 (fr
Inventor
Kalim Mir
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.)
Xgenomes Corp
Original Assignee
Xgenomes Corp
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 US16/425,929 external-priority patent/US11427867B2/en
Application filed by Xgenomes Corp filed Critical Xgenomes Corp
Publication of EP3976828A1 publication Critical patent/EP3976828A1/fr
Publication of EP3976828A4 publication Critical patent/EP3976828A4/fr
Pending 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
    • C12Q1/6869—Methods for sequencing
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/20—Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6816—Hybridisation assays characterised by the detection means
    • C12Q1/6818—Hybridisation assays characterised by the detection means involving interaction of two or more labels, e.g. resonant energy transfer
    • 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
    • G—PHYSICS
    • G11—INFORMATION STORAGE
    • G11C—STATIC STORES
    • G11C13/00—Digital stores characterised by the use of storage elements not covered by groups G11C11/00, G11C23/00, or G11C25/00
    • G11C13/0002—Digital stores characterised by the use of storage elements not covered by groups G11C11/00, G11C23/00, or G11C25/00 using resistive RAM [RRAM] elements
    • G11C13/0009—RRAM elements whose operation depends upon chemical change
    • G11C13/0014—RRAM elements whose operation depends upon chemical change comprising cells based on organic memory material
    • G11C13/0019—RRAM elements whose operation depends upon chemical change comprising cells based on organic memory material comprising bio-molecules
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/30—Detection of binding sites or motifs
    • 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
    • C12Q2563/00—Nucleic acid detection characterized by the use of physical, structural and functional properties
    • C12Q2563/113—Nucleic acid detection characterized by the use of physical, structural and functional properties the label being electroactive, e.g. redox labels
    • 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
    • C12Q2600/156—Polymorphic or mutational markers

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Physics & Mathematics (AREA)
  • Organic Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Genetics & Genomics (AREA)
  • Molecular Biology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • General Health & Medical Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Medical Informatics (AREA)
  • Immunology (AREA)
  • Theoretical Computer Science (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
EP20812953.6A 2019-05-29 2020-05-27 Séquençage par émergence Pending EP3976828A4 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US16/425,929 US11427867B2 (en) 2017-11-29 2019-05-29 Sequencing by emergence
PCT/US2020/034726 WO2020243187A1 (fr) 2019-05-29 2020-05-27 Séquençage par émergence

Publications (2)

Publication Number Publication Date
EP3976828A1 EP3976828A1 (fr) 2022-04-06
EP3976828A4 true EP3976828A4 (fr) 2023-06-28

Family

ID=73553066

Family Applications (1)

Application Number Title Priority Date Filing Date
EP20812953.6A Pending EP3976828A4 (fr) 2019-05-29 2020-05-27 Séquençage par émergence

Country Status (7)

Country Link
EP (1) EP3976828A4 (fr)
JP (1) JP2022534920A (fr)
KR (1) KR20220034054A (fr)
CN (1) CN114207149A (fr)
AU (1) AU2020282704A1 (fr)
CA (1) CA3140900A1 (fr)
WO (1) WO2020243187A1 (fr)

Families Citing this family (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2022232709A2 (fr) * 2021-04-06 2022-11-03 Xgenomes Corp. Systèmes, procédés et compositions pour détecter des modifications épigénétiques d'acides nucléiques
EP4216105A1 (fr) * 2022-01-25 2023-07-26 Leica Microsystems CMS GmbH Marqueur et procédé d'analyse d'échantillons biologiques
WO2023250364A1 (fr) * 2022-06-21 2023-12-28 Nautilus Subsidiary, Inc. Procédé pour la détection d'analytes sur des sites dont la distance n'est pas optiquement résolvable
CN116596933B (zh) * 2023-07-18 2023-09-29 深圳赛陆医疗科技有限公司 碱基簇检测方法及装置、基因测序仪及存储介质

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20040033510A1 (en) * 1996-10-30 2004-02-19 Institut Pasteur And Centre National De La Recherche Scientifique (Cnrs). Method for the diagnosis of genetic diseases by molecular combing and diagnostic kit
WO2019108853A1 (fr) * 2017-11-29 2019-06-06 Xgenomes Corp. Séquençage d'acides nucléiques par émergence

Family Cites Families (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US7071324B2 (en) * 1998-10-13 2006-07-04 Brown University Research Foundation Systems and methods for sequencing by hybridization
MXPA04000432A (es) * 2001-07-15 2004-10-27 Keck Graduate Inst Amplificacion de fragmentos de acido nucleico empleando agentes de mella.
US7276338B2 (en) * 2003-11-17 2007-10-02 Jacobson Joseph M Nucleotide sequencing via repetitive single molecule hybridization
CN108603227A (zh) * 2015-11-18 2018-09-28 卡利姆·U·米尔 超分辨率测序

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20040033510A1 (en) * 1996-10-30 2004-02-19 Institut Pasteur And Centre National De La Recherche Scientifique (Cnrs). Method for the diagnosis of genetic diseases by molecular combing and diagnostic kit
WO2019108853A1 (fr) * 2017-11-29 2019-06-06 Xgenomes Corp. Séquençage d'acides nucléiques par émergence

Non-Patent Citations (7)

* Cited by examiner, † Cited by third party
Title
C. VRANKEN ET AL: "Super-resolution optical DNA Mapping via DNA methyltransferase-directed click chemistry", NUCLEIC ACIDS RESEARCH, vol. 42, no. 7, 21 January 2014 (2014-01-21), GB, pages e50 - e50, XP055230984, ISSN: 0305-1048, DOI: 10.1093/nar/gkt1406 *
GLENN E. PALOMAKI ET AL: "DNA sequencing of maternal plasma to detect Down syndrome: An international clinical validation study", GENETICS IN MEDICINE, vol. 13, no. 11, 1 November 2011 (2011-11-01), New York, pages 913 - 920, XP055228393, ISSN: 1098-3600, DOI: 10.1097/GIM.0b013e3182368a0e *
NAZARI ZEINAB ESMAIL ET AL: "Molecular Combing of DNA: Methods and Applications", JOURNAL OF SELF ASSEMBLY AND MOLECULAR ELECTRONICS, 1 January 2013 (2013-01-01), XP093038930, ISSN: 2245-4551, Retrieved from the Internet <URL:https://www.journal.riverpublishers.com/index.php/jsame/article/download/190/236> DOI: 10.13052/same2245-4551.116 *
NIEVES DANIEL ET AL: "DNA-Based Super-Resolution Microscopy: DNA-PAINT", GENES, vol. 9, no. 12, 11 December 2018 (2018-12-11), pages 621, XP093040230, Retrieved from the Internet <URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6315775/pdf/genes-09-00621.pdf> DOI: 10.3390/genes9120621 *
PAUL M LIZARDI: "Next-generation sequencing-by-hybridization", NATURE BIOTECHNOLOGY, vol. 26, no. 6, 1 June 2008 (2008-06-01), pages 649 - 650, XP055154438, DOI: 10.1038/nbt0608-649 *
PIHLAK A ET AL: "Rapid genome sequencing with short universal tiling probes", NATURE BIOTECHNOLOGY, NATURE PUBLISHING GROUP US, NEW YORK, vol. 26, no. 6, 1 June 2008 (2008-06-01), pages 676 - 684, XP002601637, ISSN: 1087-0156, [retrieved on 20080525], DOI: 10.1038/NBT1405 *
See also references of WO2020243187A1 *

Also Published As

Publication number Publication date
AU2020282704A1 (en) 2022-01-27
WO2020243187A1 (fr) 2020-12-03
JP2022534920A (ja) 2022-08-04
CA3140900A1 (fr) 2020-12-03
EP3976828A1 (fr) 2022-04-06
CN114207149A (zh) 2022-03-18
KR20220034054A (ko) 2022-03-17

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RIC1 Information provided on ipc code assigned before grant

Ipc: G11C 13/00 20060101ALI20230524BHEP

Ipc: G11C 13/04 20060101ALI20230524BHEP

Ipc: G16B 25/20 20190101ALI20230524BHEP

Ipc: C12Q 1/6869 20180101ALI20230524BHEP

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Ipc: C12Q 1/6874 20180101AFI20230524BHEP