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

Locked nucleic acids for capturing fusion genes Download PDF

Info

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
Authority
AU
Australia
Prior art keywords
nucleotides
length
polynucleotide
breakpoint
probe
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.)
Active
Application number
AU2016297096A
Other languages
English (en)
Other versions
AU2016297096A1 (en
AU2016297096A9 (en
Inventor
Stefanie Ann Ward Mortimer
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.)
Guardant Health Inc
Original Assignee
Guardant Health 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 Guardant Health Inc filed Critical Guardant Health Inc
Publication of AU2016297096A1 publication Critical patent/AU2016297096A1/en
Publication of AU2016297096A9 publication Critical patent/AU2016297096A9/en
Application granted granted Critical
Publication of AU2016297096B2 publication Critical patent/AU2016297096B2/en
Active legal-status Critical Current
Anticipated expiration legal-status Critical

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
    • 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

Landscapes

  • 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)
  • Immunology (AREA)
  • Analytical Chemistry (AREA)
  • Genetics & Genomics (AREA)
  • Physics & Mathematics (AREA)
  • Pathology (AREA)
  • Biotechnology (AREA)
  • Microbiology (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • General Engineering & Computer Science (AREA)
  • Biophysics (AREA)
  • Biochemistry (AREA)
  • Bioinformatics & Cheminformatics (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)

Application Number Title Priority Date Filing Date
AU2016297096A Active AU2016297096B2 (en) 2015-07-21 2016-07-21 Locked nucleic acids for capturing fusion genes

Country Status (7)

Country Link
US (3) US20190071730A9 (enExample)
EP (2) EP3325667B1 (enExample)
JP (1) JP7074661B2 (enExample)
CN (1) CN108138230B (enExample)
AU (1) AU2016297096B2 (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
PL3246416T3 (pl) 2011-04-15 2024-09-30 The Johns Hopkins University Bezpieczny system sekwencjonowania
CN109457030B (zh) 2012-10-29 2022-02-18 约翰·霍普金斯大学 卵巢和子宫内膜癌的帕帕尼科拉乌测试
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
KR20240155386A (ko) 2016-09-30 2024-10-28 가던트 헬쓰, 인크. 무세포 핵산의 다중-해상도 분석 방법
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
EP3665308A1 (en) 2017-08-07 2020-06-17 The Johns Hopkins University 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
EP3918089B1 (en) 2019-01-31 2025-01-15 Guardant Health, Inc. Method for isolating and sequencing cell-free dna
EP3938505A4 (en) * 2019-02-25 2022-11-30 Twist Bioscience Corporation COMPOSITIONS AND METHODS FOR SEQUENCING THE NEXT GENERATION
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
WO2021061842A1 (en) 2019-09-23 2021-04-01 Twist Bioscience Corporation Variant nucleic acid libraries for single domain antibodies
BR112022015909A2 (pt) 2020-02-14 2022-10-04 Univ Johns Hopkins Métodos e materiais para avaliação de ácidos nucleicos
US11211144B2 (en) 2020-02-18 2021-12-28 Tempus Labs, Inc. Methods and systems for refining copy number variation in a liquid biopsy assay
US11475981B2 (en) 2020-02-18 2022-10-18 Tempus Labs, Inc. Methods and systems for dynamic variant thresholding 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
US9562259B2 (en) * 2011-03-14 2017-02-07 Ventana Medical Systems, Inc. Method of analyzing chromosomal inversions
WO2012163541A1 (en) * 2011-06-01 2012-12-06 Medical Prognosis Institute A/S Methods and devices for prognosis of cancer relapse
WO2013006195A1 (en) * 2011-07-01 2013-01-10 Htg Molecular Diagnostics, Inc. Methods of detecting gene fusions
CN104364391A (zh) * 2012-02-08 2015-02-18 因赛特遗传学公司 用于诊断和治疗癌症的涉及ros1融合的方法和组合物
US9512477B2 (en) * 2012-05-04 2016-12-06 Boreal Genomics Inc. Biomarker anaylsis using scodaphoresis
IL269097B2 (en) * 2012-09-04 2024-01-01 Guardant Health Inc Systems and methods to detect rare mutations and copy number variation
EP4439566A3 (en) 2013-03-15 2024-12-04 Guardant Health, Inc. Systems and methods to detect rare mutations and copy number variation
EP3795696B1 (en) * 2013-03-15 2023-04-26 The Board of Trustees of the Leland Stanford Junior University Identification and use of circulating nucleic acid tumor markers
CN118910253A (zh) * 2013-04-17 2024-11-08 生命技术公司 与癌症相关的基因融合体和基因变异体
EP3378952B1 (en) * 2013-12-28 2020-02-05 Guardant Health, Inc. Methods and systems for detecting genetic variants

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

Similar Documents

Publication Publication Date Title
US20220411877A1 (en) Locked nucleic acids for capturing fusion genes
US20220356527A1 (en) Methods to determine tumor gene copy number by analysis of cell-free dna
CN105518151B (zh) 循环核酸肿瘤标志物的鉴别和用途
CN113661249A (zh) 用于分离无细胞dna的组合物和方法
WO2018005811A1 (en) Differential tagging of rna for preparation of a cell-free dna/rna sequencing library
CN114616343A (zh) 用于在甲基化分区测定中分析无细胞dna的组合物和方法
WO2019236478A1 (en) Methods and systems for determining the cellular origin of cell-free nucleic acids
EP3976822A1 (en) Methods and systems for improving patient monitoring after surgery
JP2023551292A (ja) メチル化されたポリヌクレオチドを富化するための組成物および方法
JP2024056984A (ja) エピジェネティック区画アッセイを較正するための方法、組成物およびシステム
ES3031713T3 (en) Methods, compositions and systems for improving the binding of methylated polynucleotides
EP3880845B1 (en) Directional targeted sequencing
WO2025029475A1 (en) Methods to enrich nucleotide variants by negative selection
CA2993019C (en) Locked nucleic acids for capturing fusion genes
AU2019252947A1 (en) Methods for detecting and suppressing alignment errors caused by fusion events
JP7304852B2 (ja) 脱アミノ化に誘導される配列エラーの補正
CN120500545A (zh) 肿瘤核酸识别方法
WO2024229433A1 (en) Methods for analysis of dna methylation
WO2025076452A1 (en) Detecting tumor-related information based on methylation status of cell-free nucleic acid molecules

Legal Events

Date Code Title Description
SREP Specification republished
FGA Letters patent sealed or granted (standard patent)