SG10201810862YA - Method for identification and enumeration of nucleic acid sequence, expression, copy, or dna methylation changes, using combined nuclease, ligase, polymerase, and sequencing reactions - Google Patents

Method for identification and enumeration of nucleic acid sequence, expression, copy, or dna methylation changes, using combined nuclease, ligase, polymerase, and sequencing reactions

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Publication number
SG10201810862YA
SG10201810862YA SG10201810862YA SG10201810862YA SG10201810862YA SG 10201810862Y A SG10201810862Y A SG 10201810862YA SG 10201810862Y A SG10201810862Y A SG 10201810862YA SG 10201810862Y A SG10201810862Y A SG 10201810862YA SG 10201810862Y A SG10201810862Y A SG 10201810862YA
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Singapore
Prior art keywords
nucleic acid
copy
polymerase
expression
methylation changes
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SG10201810862YA
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Francis Barany
John Efcavitch
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Univ Cornell
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    • 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
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    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1068—Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
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    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
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    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
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    • 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

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  • Chemical & Material Sciences (AREA)
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Abstract

METHOD FOR IDENTIFICATION AND ENUMERATION OF NUCLEIC ACID SEQUENCE, EXPRESSION, COPY, OR DNA METHYLATION CHANGES, USING COMBINED NUCLEASE, LIGASE, POLYMERASE, AND SEQUENCING REACTIONS The present invention relates to a method for the highly specific, targeted capture of regions of human genomes and transcriptomes from the blood, i.e. from cell free circulating DNA, exosomes, microRNA, circulating tumor cells, or total blood cells, to allow for the highly sensitive detection of mutation, expression, copy number, translocation, alternative splicing, and methylation changes using combined nuclease, ligation, polymerase, and massively parallel sequencing reactions. The method generates a collection of different circular chimeric single- stranded nucleic acid constructs, suitable for sequencing on multiple platforms. In some embodiments, each construct of the collection comprised a first single stranded segment of original genomic DNA from a host organism and a second single stranded synthetic nucleic acid segment that is linked to the first single stranded segment and comprises a nucleotide sequence that is exogenous to the host organism. These chimeric constructs are suitable for identifying and enumerating mutations, copy changes, translocations, and methylation changes. In other embodiments, input mRNA, IncRNA, or miRNA is used to generate circular DNA products that reflect the presence and copy number of specific mRNA's, IncRNA's splice-site variants, translocations, and miRNA. Figure for publication: None
SG10201810862YA 2014-06-06 2015-06-08 Method for identification and enumeration of nucleic acid sequence, expression, copy, or dna methylation changes, using combined nuclease, ligase, polymerase, and sequencing reactions SG10201810862YA (en)

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US201462009047P 2014-06-06 2014-06-06
US201562136093P 2015-03-20 2015-03-20

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US (3) US10407722B2 (en)
EP (4) EP3889271B1 (en)
JP (3) JP7008407B2 (en)
CN (2) CN113046413A (en)
AU (2) AU2015269103B2 (en)
CA (2) CA2950295C (en)
DK (1) DK3152331T3 (en)
ES (3) ES2864531T3 (en)
IL (1) IL249126B (en)
PT (3) PT3152331T (en)
SG (2) SG10201810862YA (en)
WO (1) WO2015188192A2 (en)

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DK3152331T3 (en) 2019-11-04
US20230295718A1 (en) 2023-09-21
US10407722B2 (en) 2019-09-10
US20190345552A1 (en) 2019-11-14
CA2950295A1 (en) 2015-12-10
WO2015188192A2 (en) 2015-12-10
CN106661631A (en) 2017-05-10
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AU2022201907A1 (en) 2022-04-07
EP3889271B1 (en) 2022-11-23
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JP7008407B2 (en) 2022-01-25
WO2015188192A3 (en) 2016-05-26
ES2864531T3 (en) 2021-10-14
CA2950295C (en) 2023-10-17
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US20170204459A1 (en) 2017-07-20
EP4170044A1 (en) 2023-04-26
CA3213538A1 (en) 2015-12-10
EP3567122A1 (en) 2019-11-13
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