AU2019221549C1 - Methods and reagents for detecting and assessing genotoxicity - Google Patents

Methods and reagents for detecting and assessing genotoxicity

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Publication number
AU2019221549C1
AU2019221549C1 AU2019221549A AU2019221549A AU2019221549C1 AU 2019221549 C1 AU2019221549 C1 AU 2019221549C1 AU 2019221549 A AU2019221549 A AU 2019221549A AU 2019221549 A AU2019221549 A AU 2019221549A AU 2019221549 C1 AU2019221549 C1 AU 2019221549C1
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AU
Australia
Prior art keywords
nucleic acid
mutation
dna
sequence
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.)
Active
Application number
AU2019221549A
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English (en)
Other versions
AU2019221549A1 (en
AU2019221549B2 (en
Inventor
Jesse J. SALK
Charles Clinton VALENTINE III
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.)
Twinstrand Biosciences Inc
Original Assignee
Twinstrand Biosciences 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 Twinstrand Biosciences Inc filed Critical Twinstrand Biosciences Inc
Publication of AU2019221549A1 publication Critical patent/AU2019221549A1/en
Application granted granted Critical
Publication of AU2019221549B2 publication Critical patent/AU2019221549B2/en
Priority to AU2025263841A priority Critical patent/AU2025263841A1/en
Publication of AU2019221549C1 publication Critical patent/AU2019221549C1/en
Active legal-status Critical Current
Anticipated expiration legal-status Critical

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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
    • C12Q1/68—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
    • C12Q1/6869—Methods for sequencing
    • 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
    • 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
    • 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
    • G16B20/50—Mutagenesis
    • 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
    • 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
    • C12Q2525/00—Reactions involving modified oligonucleotides, nucleic acids, or nucleotides
    • C12Q2525/10—Modifications characterised by
    • C12Q2525/191—Modifications characterised by incorporating an adaptor
    • 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
    • C12Q2600/142—Toxicological screening, e.g. expression profiles which identify toxicity

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Genetics & Genomics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Pathology (AREA)
  • Medical Informatics (AREA)
  • Theoretical Computer Science (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Oncology (AREA)
  • Hospice & Palliative Care (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Pharmaceuticals Containing Other Organic And Inorganic Compounds (AREA)
  • Enzymes And Modification Thereof (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
AU2019221549A 2018-02-13 2019-02-13 Methods and reagents for detecting and assessing genotoxicity Active AU2019221549C1 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
AU2025263841A AU2025263841A1 (en) 2018-02-13 2025-11-07 Methods And Reagents For Detecting And Assessing Genotoxicity

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US201862630228P 2018-02-13 2018-02-13
US62/630,228 2018-02-13
US201862737097P 2018-09-26 2018-09-26
US62/737,097 2018-09-26
PCT/US2019/017908 WO2019160998A1 (en) 2018-02-13 2019-02-13 Methods and reagents for detecting and assessing genotoxicity

Related Child Applications (1)

Application Number Title Priority Date Filing Date
AU2025263841A Division AU2025263841A1 (en) 2018-02-13 2025-11-07 Methods And Reagents For Detecting And Assessing Genotoxicity

Publications (3)

Publication Number Publication Date
AU2019221549A1 AU2019221549A1 (en) 2020-09-24
AU2019221549B2 AU2019221549B2 (en) 2025-08-07
AU2019221549C1 true AU2019221549C1 (en) 2025-11-27

Family

ID=67619087

Family Applications (2)

Application Number Title Priority Date Filing Date
AU2019221549A Active AU2019221549C1 (en) 2018-02-13 2019-02-13 Methods and reagents for detecting and assessing genotoxicity
AU2025263841A Pending AU2025263841A1 (en) 2018-02-13 2025-11-07 Methods And Reagents For Detecting And Assessing Genotoxicity

Family Applications After (1)

Application Number Title Priority Date Filing Date
AU2025263841A Pending AU2025263841A1 (en) 2018-02-13 2025-11-07 Methods And Reagents For Detecting And Assessing Genotoxicity

Country Status (13)

Country Link
US (1) US20210355532A1 (https=)
EP (1) EP3752639A4 (https=)
JP (2) JP7420388B2 (https=)
KR (1) KR20200123159A (https=)
CN (1) CN111836905A (https=)
AU (2) AU2019221549C1 (https=)
BR (1) BR112020016516A2 (https=)
CA (1) CA3091022A1 (https=)
IL (1) IL276637A (https=)
MX (1) MX2020008472A (https=)
RU (1) RU2020130024A (https=)
SG (1) SG11202007648WA (https=)
WO (1) WO2019160998A1 (https=)

Families Citing this family (18)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10844428B2 (en) 2015-04-28 2020-11-24 Illumina, Inc. Error suppression in sequenced DNA fragments using redundant reads with unique molecular indices (UMIS)
CA3006792A1 (en) 2015-12-08 2017-06-15 Twinstrand Biosciences, Inc. Improved adapters, methods, and compositions for duplex sequencing
SG11201906428SA (en) 2017-01-18 2019-08-27 Illumina Inc Methods and systems for generation and error-correction of unique molecular index sets with heterogeneous molecular lengths
AU2018261332B2 (en) 2017-05-01 2024-12-05 Illumina, Inc. Optimal index sequences for multiplex massively parallel sequencing
EP3622089B1 (en) 2017-05-08 2024-07-17 Illumina, Inc. Method for sequencing using universal short adapters for indexing of polynucleotide samples
US11447818B2 (en) 2017-09-15 2022-09-20 Illumina, Inc. Universal short adapters with variable length non-random unique molecular identifiers
AU2018366213B2 (en) 2017-11-08 2025-05-15 Twinstrand Biosciences, Inc. Reagents and adapters for nucleic acid sequencing and methods for making such reagents and adapters
BR112021000409A2 (pt) * 2018-07-12 2021-04-06 Twinstrand Biosciences, Inc. Métodos e reagentes para caracterizar edição genômica, expansão clonal e aplicações associadas
GB201911095D0 (en) * 2019-08-02 2019-09-18 Randox Laboratories Ltd Biological status classification
IL303423A (en) * 2020-12-07 2023-08-01 Hoffmann La Roche Techniques for generating predictive results related to oncology treatment lines using artificial intelligence
CN112614544B (zh) * 2020-12-28 2024-05-17 杭州瑞普基因科技有限公司 Kraken2软件输出结果的优化方法及鉴定样本中物种类型的方法
CN112553356A (zh) * 2020-12-31 2021-03-26 江苏意诺飞生物科技有限公司 一种高通量检测和判定幽门螺旋杆菌耐药性的方法
CN113554285B (zh) * 2021-07-05 2024-04-26 中国水产科学研究院黄海水产研究所 暴发水母种群波动对渔业资源风险影响的量化评估方法
NL2029132B1 (en) * 2021-09-06 2023-03-21 Prinses Maxima Centrum Voor Kinderoncologie B V Means and methods for assessing genotoxicity
CN115713968A (zh) * 2022-11-21 2023-02-24 苏州新格元生物科技有限公司 一种评估基因毒性的方法、装置、存储介质和设备
US12514461B2 (en) * 2023-08-23 2026-01-06 Wisconsin Alumni Research Foundation System and method for analyzing gene expression using diffusion weighted magnetic resonance imaging (MRI)
KR102698843B1 (ko) * 2024-01-23 2024-08-26 주식회사 이콜트리 유전독성 시험 자동화 시스템 및 방법
WO2025216210A1 (ja) * 2024-04-08 2025-10-16 株式会社ペルセウスプロテオミクス 識別用分子を用いた核酸分子の特定

Family Cites Families (9)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5510099A (en) * 1987-05-01 1996-04-23 Stratagene Mutagenesis testing using transgenic non-human animals carrying test DNA sequences
KR100300932B1 (ko) * 1992-07-06 2001-10-22 조이스 브린톤 리포터유전자에융합된세균의스트레스프로모터를이용하여독성을측정하는방법및진단키트
GB0905410D0 (en) * 2009-03-28 2009-05-13 Gentronix Ltd Genotoxicity testing
PT2828218T (pt) * 2012-03-20 2020-11-11 Univ Washington Through Its Center For Commercialization Métodos para baixar a taxa de erro da sequenciação paralela massiva de adn utilizando sequenciação duplex de consensus
AU2013267609C1 (en) * 2012-05-31 2019-01-03 Board Of Regents, The University Of Texas System Method for accurate sequencing of DNA
EP2706123A1 (en) * 2012-09-05 2014-03-12 Rijksinstituut Voor Volksgezondheid En Milieu In vitro method for determining genotoxic and non-genotoxic carcinogenicity of a compound.
ES2674928T3 (es) * 2012-11-05 2018-07-05 Gmdx Co Pty Ltd Métodos para determinar la causa de la mutagénesis somática
JP6262922B1 (ja) * 2017-02-16 2018-01-17 花王株式会社 物質の遺伝毒性の評価方法
BR112021000409A2 (pt) * 2018-07-12 2021-04-06 Twinstrand Biosciences, Inc. Métodos e reagentes para caracterizar edição genômica, expansão clonal e aplicações associadas

Non-Patent Citations (1)

* Cited by examiner, † Cited by third party
Title
POON, S.L, ET AL. "Mutation signatures of carcinogen exposure: genome-wide detection and new opportunities for cancer prevention", GENOME MED, 2014. 6: 1-14 *

Also Published As

Publication number Publication date
EP3752639A4 (en) 2021-12-01
JP2024038208A (ja) 2024-03-19
JP2021513364A (ja) 2021-05-27
KR20200123159A (ko) 2020-10-28
WO2019160998A1 (en) 2019-08-22
SG11202007648WA (en) 2020-09-29
IL276637A (en) 2020-09-30
BR112020016516A2 (pt) 2020-12-15
US20210355532A1 (en) 2021-11-18
AU2019221549A1 (en) 2020-09-24
AU2025263841A1 (en) 2025-11-27
CA3091022A1 (en) 2019-08-22
AU2019221549B2 (en) 2025-08-07
JP7420388B2 (ja) 2024-01-23
CN111836905A (zh) 2020-10-27
MX2020008472A (es) 2020-11-11
EP3752639A1 (en) 2020-12-23
RU2020130024A (ru) 2022-03-14

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DA2 Applications for amendment section 104

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DA3 Amendments made section 104

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FGA Letters patent sealed or granted (standard patent)