GB201819378D0 - Analysis of nanopore signal using a machine-learning technique - Google Patents

Analysis of nanopore signal using a machine-learning technique

Info

Publication number
GB201819378D0
GB201819378D0 GBGB1819378.9A GB201819378A GB201819378D0 GB 201819378 D0 GB201819378 D0 GB 201819378D0 GB 201819378 A GB201819378 A GB 201819378A GB 201819378 D0 GB201819378 D0 GB 201819378D0
Authority
GB
United Kingdom
Prior art keywords
analysis
machine
learning technique
nanopore signal
nanopore
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.)
Ceased
Application number
GBGB1819378.9A
Other languages
English (en)
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.)
Oxford Nanopore Technologies PLC
Original Assignee
Oxford Nanopore Technologies PLC
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 Oxford Nanopore Technologies PLC filed Critical Oxford Nanopore Technologies PLC
Priority to GBGB1819378.9A priority Critical patent/GB201819378D0/en
Publication of GB201819378D0 publication Critical patent/GB201819378D0/en
Priority to AU2019389841A priority patent/AU2019389841B2/en
Priority to CA3118632A priority patent/CA3118632A1/en
Priority to JP2021525061A priority patent/JP2022509589A/ja
Priority to BR112021008198-4A priority patent/BR112021008198A2/pt
Priority to SG11202103410TA priority patent/SG11202103410TA/en
Priority to KR1020217016563A priority patent/KR103002542B1/ko
Priority to US16/696,010 priority patent/US12264360B2/en
Priority to CN201980076121.5A priority patent/CN113166804A/zh
Priority to PCT/GB2019/053334 priority patent/WO2020109773A1/en
Priority to EP19816401.4A priority patent/EP3887543B1/en
Priority to JP2023106581A priority patent/JP2023126856A/ja
Priority to US19/057,377 priority patent/US20250197929A1/en
Priority to JP2025139101A priority patent/JP2025172079A/ja
Ceased legal-status Critical Current

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
    • C12Q1/6869—Methods for sequencing
    • 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
    • G16B30/10—Sequence alignment; Homology search
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/483—Physical analysis of biological material
    • G01N33/487—Physical analysis of biological material of liquid biological material
    • G01N33/48707—Physical analysis of biological material of liquid biological material by electrical means
    • G01N33/48721—Investigating individual macromolecules, e.g. by translocation through nanopores
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F18/00—Pattern recognition
    • G06F18/20—Analysing
    • G06F18/21—Design or setup of recognition systems or techniques; Extraction of features in feature space; Blind source separation
    • G06F18/214—Generating training patterns; Bootstrap methods, e.g. bagging or boosting
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00—Machine learning
    • G06N20/20—Ensemble learning
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/044—Recurrent networks, e.g. Hopfield networks
    • G06N3/0442—Recurrent networks, e.g. Hopfield networks characterised by memory or gating, e.g. long short-term memory [LSTM] or gated recurrent units [GRU]
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/04—Architecture, e.g. interconnection topology
    • G06N3/0464—Convolutional networks [CNN, ConvNet]
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/08—Learning methods
    • G06N3/084—Backpropagation, e.g. using gradient descent
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N3/00—Computing arrangements based on biological models
    • G06N3/02—Neural networks
    • G06N3/08—Learning methods
    • G06N3/09—Supervised learning
    • 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
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • 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
    • 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
    • G16B40/00—ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
    • G16B40/10—Signal processing, e.g. from mass spectrometry [MS] or from PCR
    • 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
    • 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
    • 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
    • C12Q2565/00—Nucleic acid analysis characterised by mode or means of detection
    • C12Q2565/60—Detection means characterised by use of a special device
    • C12Q2565/631—Detection means characterised by use of a special device being a biochannel or pore

Landscapes

  • Engineering & Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Data Mining & Analysis (AREA)
  • General Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Artificial Intelligence (AREA)
  • Evolutionary Computation (AREA)
  • Organic Chemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Medical Informatics (AREA)
  • Software Systems (AREA)
  • Biotechnology (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Evolutionary Biology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Mathematical Physics (AREA)
  • Computing Systems (AREA)
  • Immunology (AREA)
  • Biochemistry (AREA)
  • Genetics & Genomics (AREA)
  • Computational Linguistics (AREA)
  • Microbiology (AREA)
  • Signal Processing (AREA)
  • Public Health (AREA)
  • Epidemiology (AREA)
  • Databases & Information Systems (AREA)
  • Bioethics (AREA)
GBGB1819378.9A 2018-11-28 2018-11-28 Analysis of nanopore signal using a machine-learning technique Ceased GB201819378D0 (en)

Priority Applications (14)

Application Number Priority Date Filing Date Title
GBGB1819378.9A GB201819378D0 (en) 2018-11-28 2018-11-28 Analysis of nanopore signal using a machine-learning technique
EP19816401.4A EP3887543B1 (en) 2018-11-28 2019-11-26 Analysis of nanopore signal using a machine-learning technique
KR1020217016563A KR103002542B1 (ko) 2018-11-28 2019-11-26 머신러닝 기술을 이용한 나노기공 신호 분석
CN201980076121.5A CN113166804A (zh) 2018-11-28 2019-11-26 使用机器学习技术分析纳米孔信号
JP2021525061A JP2022509589A (ja) 2018-11-28 2019-11-26 機械学習技術を使用するナノ細孔シグナルの分析
BR112021008198-4A BR112021008198A2 (pt) 2018-11-28 2019-11-26 método e aparelho de análise para analisar um sinal derivado a partir de um polímero durante a translocação do polímero em relação a um nanoporo, e, sistema de medição e análise de nanoporo.
SG11202103410TA SG11202103410TA (en) 2018-11-28 2019-11-26 Analysis of nanopore signal using a machine-learning technique
AU2019389841A AU2019389841B2 (en) 2018-11-28 2019-11-26 Analysis of nanopore signal using a machine-learning technique
US16/696,010 US12264360B2 (en) 2018-11-28 2019-11-26 Analysis of nanopore signal using a machine-learning technique
CA3118632A CA3118632A1 (en) 2018-11-28 2019-11-26 Analysis of nanopore signal using a machine-learning technique
PCT/GB2019/053334 WO2020109773A1 (en) 2018-11-28 2019-11-26 Analysis of nanopore signal using a machine-learning technique
JP2023106581A JP2023126856A (ja) 2018-11-28 2023-06-29 機械学習技術を使用するナノ細孔シグナルの分析
US19/057,377 US20250197929A1 (en) 2018-11-28 2025-02-19 Analysis of nanopore signal using a machine-learning technique
JP2025139101A JP2025172079A (ja) 2018-11-28 2025-08-22 機械学習技術を使用するナノ細孔シグナルの分析

Applications Claiming Priority (1)

Application Number Priority Date Filing Date Title
GBGB1819378.9A GB201819378D0 (en) 2018-11-28 2018-11-28 Analysis of nanopore signal using a machine-learning technique

Publications (1)

Publication Number Publication Date
GB201819378D0 true GB201819378D0 (en) 2019-01-09

Family

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Family Applications (1)

Application Number Title Priority Date Filing Date
GBGB1819378.9A Ceased GB201819378D0 (en) 2018-11-28 2018-11-28 Analysis of nanopore signal using a machine-learning technique

Country Status (10)

Country Link
US (2) US12264360B2 (enExample)
EP (1) EP3887543B1 (enExample)
JP (3) JP2022509589A (enExample)
CN (1) CN113166804A (enExample)
AU (1) AU2019389841B2 (enExample)
BR (1) BR112021008198A2 (enExample)
CA (1) CA3118632A1 (enExample)
GB (1) GB201819378D0 (enExample)
SG (1) SG11202103410TA (enExample)
WO (1) WO2020109773A1 (enExample)

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Also Published As

Publication number Publication date
SG11202103410TA (en) 2021-06-29
JP2023126856A (ja) 2023-09-12
BR112021008198A2 (pt) 2021-08-03
CA3118632A1 (en) 2020-06-04
US20250197929A1 (en) 2025-06-19
AU2019389841A1 (en) 2021-05-20
JP2025172079A (ja) 2025-11-20
US12264360B2 (en) 2025-04-01
EP3887543B1 (en) 2024-08-28
EP3887543A1 (en) 2021-10-06
AU2019389841B2 (en) 2026-05-07
US20200176082A1 (en) 2020-06-04
KR20210095641A (ko) 2021-08-02
WO2020109773A1 (en) 2020-06-04
CN113166804A (zh) 2021-07-23
JP2022509589A (ja) 2022-01-21

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