AU2016297096B2 - Locked nucleic acids for capturing fusion genes - Google Patents

Locked nucleic acids for capturing fusion genes Download PDF

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Publication number
AU2016297096B2
AU2016297096B2 AU2016297096A AU2016297096A AU2016297096B2 AU 2016297096 B2 AU2016297096 B2 AU 2016297096B2 AU 2016297096 A AU2016297096 A AU 2016297096A AU 2016297096 A AU2016297096 A AU 2016297096A AU 2016297096 B2 AU2016297096 B2 AU 2016297096B2
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Australia
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nucleotides
length
polynucleotide
breakpoint
probe
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AU2016297096A
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AU2016297096A1 (en
AU2016297096A9 (en
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Stefanie Ann Ward Mortimer
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Guardant Health Inc
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Guardant Health Inc
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    • 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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
    • 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
    • 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

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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • General Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Biophysics (AREA)
  • Pathology (AREA)
  • Oncology (AREA)
  • Hospice & Palliative Care (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
AU2016297096A 2015-07-21 2016-07-21 Locked nucleic acids for capturing fusion genes Active AU2016297096B2 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US201562195280P 2015-07-21 2015-07-21
US62/195,280 2015-07-21
PCT/US2016/043430 WO2017015513A1 (en) 2015-07-21 2016-07-21 Locked nucleic acids for capturing fusion genes

Publications (3)

Publication Number Publication Date
AU2016297096A1 AU2016297096A1 (en) 2018-02-15
AU2016297096A9 AU2016297096A9 (en) 2019-07-25
AU2016297096B2 true AU2016297096B2 (en) 2021-03-18

Family

ID=57835293

Family Applications (1)

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AU2016297096A Active AU2016297096B2 (en) 2015-07-21 2016-07-21 Locked nucleic acids for capturing fusion genes

Country Status (8)

Country Link
US (3) US20190071730A9 (enExample)
EP (2) EP3828292A1 (enExample)
JP (1) JP7074661B2 (enExample)
CN (1) CN108138230B (enExample)
AU (1) AU2016297096B2 (enExample)
CA (1) CA2993019A1 (enExample)
ES (1) ES2844852T3 (enExample)
WO (1) WO2017015513A1 (enExample)

Families Citing this family (18)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
EP3907297A1 (en) 2011-04-15 2021-11-10 The Johns Hopkins University Safe sequencing system
US11525163B2 (en) 2012-10-29 2022-12-13 The Johns Hopkins University Papanicolaou test for ovarian and endometrial cancers
US11286531B2 (en) 2015-08-11 2022-03-29 The Johns Hopkins University Assaying ovarian cyst fluid
US9850523B1 (en) 2016-09-30 2017-12-26 Guardant Health, Inc. Methods for multi-resolution analysis of cell-free nucleic acids
ES2840003T3 (es) 2016-09-30 2021-07-06 Guardant Health Inc Métodos para análisis multi-resolución de ácidos nucleicos libres de células
US20200165687A1 (en) * 2017-06-27 2020-05-28 The University Of Tokyo Probe and method for detecting transcript resulting from fusion gene and/or exon skipping
SG11202001010UA (en) 2017-08-07 2020-03-30 Univ Johns Hopkins Methods and materials for assessing and treating cancer
CN108642159B (zh) * 2018-06-27 2022-07-01 上海宏滩生物科技有限公司 生物芯片检测系统
CN113661249B (zh) 2019-01-31 2025-07-01 夸登特健康公司 用于分离无细胞dna的组合物和方法
JP2022521766A (ja) * 2019-02-25 2022-04-12 ツイスト バイオサイエンス コーポレーション 次世代シーケンシングのための組成物および方法
CN110195098A (zh) * 2019-05-10 2019-09-03 广州安必平医药科技股份有限公司 用于检测braf相关融合基因的探针组、试剂盒及其应用
US12173282B2 (en) 2019-09-23 2024-12-24 Twist Bioscience, Inc. Antibodies that bind CD3 epsilon
CA3170345A1 (en) 2020-02-14 2021-08-19 The Johns Hopkins University Methods and materials for assessing nucleic acids
US11475981B2 (en) 2020-02-18 2022-10-18 Tempus Labs, Inc. Methods and systems for dynamic variant thresholding in a liquid biopsy assay
US11211144B2 (en) 2020-02-18 2021-12-28 Tempus Labs, Inc. Methods and systems for refining copy number variation in a liquid biopsy assay
US11211147B2 (en) 2020-02-18 2021-12-28 Tempus Labs, Inc. Estimation of circulating tumor fraction using off-target reads of targeted-panel sequencing
CN111979307B (zh) * 2020-08-31 2022-07-08 伯科生物科技有限公司 用于检测基因融合的靶向测序方法
CN116240268B (zh) * 2023-02-27 2024-04-26 北京大学口腔医学院 用于检测多个基因重排探针系统

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100279890A1 (en) * 2007-06-27 2010-11-04 Oslo Universitetssykehus Hf Fusion gene microarray

Family Cites Families (16)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5482834A (en) * 1982-05-17 1996-01-09 Hahnemann University Evaluation of nucleic acids in a biological sample hybridization in a solution of chaotrophic salt solubilized cells
US5200313A (en) * 1983-08-05 1993-04-06 Miles Inc. Nucleic acid hybridization assay employing detectable anti-hybrid antibodies
US6582908B2 (en) * 1990-12-06 2003-06-24 Affymetrix, Inc. Oligonucleotides
CN101928767A (zh) * 2009-06-29 2010-12-29 林新华 用于检测慢性粒细胞白血病bcr/abl融合基因的电化学dna生物传感器
EP2494069B1 (en) * 2009-10-30 2013-10-02 Roche Diagniostics GmbH Method for detecting balanced chromosomal aberrations in a genome
US20130059294A1 (en) * 2010-05-16 2013-03-07 Xiangdong Ren Identification of polymorphic hepatitis b viruses and kras oncogene mutations and clinical use
CN103534359B (zh) * 2011-03-14 2016-07-06 文塔纳医疗系统公司 分析染色体易位的方法及其系统
US20140106986A1 (en) * 2011-06-01 2014-04-17 Medical Prognosis Institute A/S Methods and devices for prognosis of cancer relapse
AU2011372509B2 (en) * 2011-07-01 2017-02-09 Htg Molecular Diagnostics, Inc. Methods of detecting gene fusions
AU2013216904A1 (en) * 2012-02-08 2014-08-28 Insight Genetics, Inc. Methods and compositions relating to fusions of ROS1 for diagnosing and treating cancer
EP2844773B1 (en) * 2012-05-04 2017-08-16 Boreal Genomics Corp. Biomarker analysis using scodaphoresis
CN110872617A (zh) * 2012-09-04 2020-03-10 夸登特健康公司 检测稀有突变和拷贝数变异的系统和方法
ES2831148T3 (es) * 2013-03-15 2021-06-07 Univ Leland Stanford Junior Identificación y uso de marcadores tumorales de ácido nucleico circulante
EP4439566A3 (en) 2013-03-15 2024-12-04 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
CN105378110B (zh) * 2013-04-17 2024-06-25 生命技术公司 与癌症相关的基因融合体和基因变异体
ES2784450T3 (es) * 2013-12-28 2020-09-25 Guardant Health Inc Métodos y sistemas para detectar variantes genéticas

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20100279890A1 (en) * 2007-06-27 2010-11-04 Oslo Universitetssykehus Hf Fusion gene microarray

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
LIQING LIN ET AL, SENSORS AND ACTUATORS B: CHEMICAL: INTERNATIONAL JOURNAL DEVOTED TO RESEARCH AND DEVELOPMENT OF PHYSICAL AND CHEMICAL TRANSDUCERS, 2011, vol. 155, no. 1, pages 1 - 7 *
YUN LEI ET AL, "Sequence-specific electrochemical detection of double-strand PCR amplicons of PML/RAR[alpha] fusion gene in acute promyelocytic leuk", ANALYTICAL AND BIOANALYTICAL CHEMISTRY, (2012-10-13), vol. 405, no. 1, pages 423 - 428 *

Also Published As

Publication number Publication date
CN108138230A (zh) 2018-06-08
US20180195131A1 (en) 2018-07-12
JP2018524014A (ja) 2018-08-30
EP3828292A1 (en) 2021-06-02
AU2016297096A1 (en) 2018-02-15
EP3325667B1 (en) 2020-11-11
US20170226590A1 (en) 2017-08-10
WO2017015513A1 (en) 2017-01-26
AU2016297096A9 (en) 2019-07-25
ES2844852T3 (es) 2021-07-22
WO2017015513A9 (en) 2018-04-12
CA2993019A1 (en) 2017-01-26
EP3325667A1 (en) 2018-05-30
EP3325667A4 (en) 2018-12-19
US20220411877A1 (en) 2022-12-29
US20190071730A9 (en) 2019-03-07
JP7074661B2 (ja) 2022-05-25
CN108138230B (zh) 2023-03-10

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