GB2613427B - Methods and Systems for Analyzing Nucleic Acid Molecules - Google Patents

Methods and Systems for Analyzing Nucleic Acid Molecules Download PDF

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Publication number
GB2613427B
GB2613427B GB2212061.2A GB202212061A GB2613427B GB 2613427 B GB2613427 B GB 2613427B GB 202212061 A GB202212061 A GB 202212061A GB 2613427 B GB2613427 B GB 2613427B
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Prior art keywords
systems
methods
nucleic acid
acid molecules
analyzing nucleic
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GB202212061D0 (en
GB2613427A (en
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Diehn Maximilian
Ash Alizadeh Arash
M Kurtz David
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Leland Stanford Junior University
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Leland Stanford Junior University
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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
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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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
    • C12Q1/6806—Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
    • C—CHEMISTRY; METALLURGY
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    • 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
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1089—Design, preparation, screening or analysis of libraries using computer algorithms
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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
    • C12Q1/6813—Hybridisation assays
    • C12Q1/6827—Hybridisation assays for detection of mutation or polymorphism
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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
    • C—CHEMISTRY; METALLURGY
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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
    • C12Q1/6874—Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation
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    • G16B30/00—ICT specially adapted for sequence analysis involving nucleotides or amino acids
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
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    • G16B35/20—Screening of libraries
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
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    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
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    • G16H10/00—ICT specially adapted for the handling or processing of patient-related medical or healthcare data
    • G16H10/40—ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis
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    • G16H20/00—ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
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    • G—PHYSICS
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    • G16H50/00—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
    • G16H50/20—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
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    • G16H50/30—ICT specially adapted for medical diagnosis, medical simulation or medical data mining; ICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indices; for individual health risk assessment
    • G—PHYSICS
    • G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
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    • C12Q2537/00—Reactions characterised by the reaction format or use of a specific feature
    • C12Q2537/10—Reactions characterised by the reaction format or use of a specific feature the purpose or use of
    • C12Q2537/165—Mathematical modelling, e.g. logarithm, ratio
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/112—Disease subtyping, staging or classification
    • C—CHEMISTRY; METALLURGY
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    • C12Q2600/00—Oligonucleotides characterized by their use
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
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    • G—PHYSICS
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  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • General Health & Medical Sciences (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Analytical Chemistry (AREA)
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  • Medical Informatics (AREA)
  • Molecular Biology (AREA)
  • Immunology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Pathology (AREA)
  • Public Health (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Epidemiology (AREA)
  • Evolutionary Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Primary Health Care (AREA)
  • Biomedical Technology (AREA)
  • Data Mining & Analysis (AREA)
  • Oncology (AREA)
  • Hospice & Palliative Care (AREA)
  • Databases & Information Systems (AREA)
  • Library & Information Science (AREA)
  • Bioethics (AREA)
  • Crystallography & Structural Chemistry (AREA)
  • Medicinal Chemistry (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Evolutionary Computation (AREA)
GB2212061.2A 2019-11-06 2020-11-06 Methods and Systems for Analyzing Nucleic Acid Molecules Active GB2613427B (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
GB2318607.5A GB2623904B (en) 2019-11-06 2020-11-06 Methods and systems for analyzing nucleic acid molecules

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US201962931688P 2019-11-06 2019-11-06
GB2112217.1A GB2595193B (en) 2019-11-06 2020-11-06 Methods and systems for analyzing nucleic acid molecules

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GB202212061D0 GB202212061D0 (en) 2022-10-05
GB2613427A GB2613427A (en) 2023-06-07
GB2613427B true GB2613427B (en) 2024-01-17

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GB2212061.2A Active GB2613427B (en) 2019-11-06 2020-11-06 Methods and Systems for Analyzing Nucleic Acid Molecules
GB2112217.1A Active GB2595193B (en) 2019-11-06 2020-11-06 Methods and systems for analyzing nucleic acid molecules
GB2404419.0A Active GB2627085B (en) 2019-11-06 2020-11-06 Methods and systems for analysing nucleic acid molecules
GB2318607.5A Active GB2623904B (en) 2019-11-06 2020-11-06 Methods and systems for analyzing nucleic acid molecules

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GB2404419.0A Active GB2627085B (en) 2019-11-06 2020-11-06 Methods and systems for analysing nucleic acid molecules
GB2318607.5A Active GB2623904B (en) 2019-11-06 2020-11-06 Methods and systems for analyzing nucleic acid molecules

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US (14) US20210172022A1 (https=)
EP (3) EP4527945A3 (https=)
JP (2) JP7825272B2 (https=)
KR (1) KR20220094218A (https=)
CN (3) CN118374597A (https=)
AU (1) AU2020378435A1 (https=)
BR (1) BR112022008752A2 (https=)
CA (1) CA3156589A1 (https=)
DE (1) DE112020005433T5 (https=)
DK (1) DK4055187T3 (https=)
ES (1) ES3041276T3 (https=)
GB (4) GB2613427B (https=)
MX (1) MX2022005588A (https=)
WO (1) WO2021092476A1 (https=)

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CA2970916C (en) 2014-03-14 2025-02-04 Caredx, Inc. METHODS FOR MONITORING IMMUNOSUPPRESSIVE THERAPIES IN A TRANSPLANT RECIPIENT
WO2021092476A1 (en) 2019-11-06 2021-05-14 The Board Of Trustees Of The Leland Stanford Junior University Methods and systems for analyzing nucleic acid molecules
US11783912B2 (en) 2021-05-05 2023-10-10 The Board Of Trustees Of The Leland Stanford Junior University Methods and systems for analyzing nucleic acid molecules
KR20230064172A (ko) * 2021-11-03 2023-05-10 주식회사 지씨지놈 세포유리 핵산단편 위치별 서열 빈도 및 크기를 이용한 암 진단 방법
MX2024006820A (es) * 2021-12-15 2024-08-15 Univ Johns Hopkins Mutacion del genoma completo de molecula unica y perfiles de fragmentacion de acido desoxirribonucleico (adn) libre de celula.
CN114974421B (zh) * 2022-05-20 2024-04-30 南开大学 基于扩散-降噪的单细胞转录组测序数据补插方法及系统
KR20230172174A (ko) * 2022-06-15 2023-12-22 주식회사 지씨지놈 무세포 핵산의 단일염기변이를 이용한 암 진단 및 암 종 예측방법
CN115181800B (zh) * 2022-07-11 2025-06-13 南京世和基因生物技术股份有限公司 基因标志物在非小细胞肺癌预后效果预测中的应用、预测装置以及计算机可读取介质
GB202212094D0 (en) * 2022-08-19 2022-10-05 Inivata Ltd Method of detecting cancer DNA in a sample
CN116466085A (zh) * 2022-11-28 2023-07-21 中国人民解放军海军军医大学第三附属医院 一种四基因的生物标志物组合及其在肝癌治疗中的应用
KR102630597B1 (ko) * 2023-08-22 2024-01-29 주식회사 지놈인사이트테크놀로지 종양 정보를 활용한 미세 잔존 질환 탐지 방법 및 장치
US20250140343A1 (en) * 2023-10-30 2025-05-01 Myriad Women's Health, Inc. Methods for improving minimal residual disease assays
WO2025245136A1 (en) * 2024-05-22 2025-11-27 Foresight Diagnostics Inc. Methods and systems for adjuvant therapy
WO2026019737A1 (en) * 2024-07-16 2026-01-22 Myriad Women's Health, Inc. Targeted depletion sequencing for use in minimum residual disease assays
WO2026072949A1 (en) * 2024-09-27 2026-04-02 Roche Sequencing Solutions, Inc. Multi-modal risk stratification of minimum residual disease

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