SG11202103410TA - Analysis of nanopore signal using a machine-learning technique - Google Patents

Analysis of nanopore signal using a machine-learning technique

Info

Publication number
SG11202103410TA
SG11202103410TA SG11202103410TA SG11202103410TA SG11202103410TA SG 11202103410T A SG11202103410T A SG 11202103410TA SG 11202103410T A SG11202103410T A SG 11202103410TA SG 11202103410T A SG11202103410T A SG 11202103410TA SG 11202103410T A SG11202103410T A SG 11202103410TA
Authority
SG
Singapore
Prior art keywords
analysis
machine
learning technique
nanopore signal
nanopore
Prior art date
Application number
SG11202103410TA
Other languages
English (en)
Inventor
Timothy Lee Massingham
Original Assignee
Oxford Nanopore Tech Ltd
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 Tech Ltd filed Critical Oxford Nanopore Tech Ltd
Publication of SG11202103410TA publication Critical patent/SG11202103410TA/en

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    • 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
    • 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
    • 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; CALCULATING OR 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; CALCULATING OR COUNTING
    • G06N—COMPUTING ARRANGEMENTS BASED ON SPECIFIC COMPUTATIONAL MODELS
    • G06N20/00—Machine learning
    • G06N20/20—Ensemble learning
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR 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
    • G06N3/045—Combinations of networks
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING OR 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
    • 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)
  • Health & Medical Sciences (AREA)
  • Physics & Mathematics (AREA)
  • Chemical & Material Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Molecular Biology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Organic Chemistry (AREA)
  • Data Mining & Analysis (AREA)
  • Medical Informatics (AREA)
  • Biotechnology (AREA)
  • Analytical Chemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Artificial Intelligence (AREA)
  • Evolutionary Computation (AREA)
  • General Physics & Mathematics (AREA)
  • Software Systems (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Biochemistry (AREA)
  • Immunology (AREA)
  • Genetics & Genomics (AREA)
  • Microbiology (AREA)
  • Computing Systems (AREA)
  • Mathematical Physics (AREA)
  • Bioethics (AREA)
  • Public Health (AREA)
  • Signal Processing (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Hematology (AREA)
SG11202103410TA 2018-11-28 2019-11-26 Analysis of nanopore signal using a machine-learning technique SG11202103410TA (en)

Applications Claiming Priority (2)

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
PCT/GB2019/053334 WO2020109773A1 (fr) 2018-11-28 2019-11-26 Analyse de signal de nanopore à l'aide d'une technique d'apprentissage automatique

Publications (1)

Publication Number Publication Date
SG11202103410TA true SG11202103410TA (en) 2021-06-29

Family

ID=65024631

Family Applications (1)

Application Number Title Priority Date Filing Date
SG11202103410TA SG11202103410TA (en) 2018-11-28 2019-11-26 Analysis of nanopore signal using a machine-learning technique

Country Status (11)

Country Link
US (1) US20200176082A1 (fr)
EP (1) EP3887543B1 (fr)
JP (2) JP2022509589A (fr)
KR (1) KR20210095641A (fr)
CN (1) CN113166804A (fr)
AU (1) AU2019389841A1 (fr)
BR (1) BR112021008198A2 (fr)
CA (1) CA3118632A1 (fr)
GB (1) GB201819378D0 (fr)
SG (1) SG11202103410TA (fr)
WO (1) WO2020109773A1 (fr)

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US11210554B2 (en) 2019-03-21 2021-12-28 Illumina, Inc. Artificial intelligence-based generation of sequencing metadata
US11423306B2 (en) 2019-05-16 2022-08-23 Illumina, Inc. Systems and devices for characterization and performance analysis of pixel-based sequencing
US11593649B2 (en) 2019-05-16 2023-02-28 Illumina, Inc. Base calling using convolutions
US10911471B1 (en) * 2019-11-27 2021-02-02 The Florida International University Board Of Trustees Systems and methods for network-based intrusion detection
EP4107735A2 (fr) 2020-02-20 2022-12-28 Illumina, Inc. Appel de base de plusieurs à plusieurs basé sur l'intelligence artificielle
GB202103605D0 (en) 2021-03-16 2021-04-28 Oxford Nanopore Tech Ltd Alignment of target and reference sequences of polymer units
US20220336054A1 (en) 2021-04-15 2022-10-20 Illumina, Inc. Deep Convolutional Neural Networks to Predict Variant Pathogenicity using Three-Dimensional (3D) Protein Structures
WO2022243692A1 (fr) 2021-05-19 2022-11-24 Oxford Nanopore Technologies Plc Procédés de séquençage de brin complémentaire
WO2023115550A1 (fr) 2021-12-24 2023-06-29 GeneSense Technology Inc. Procédés et systèmes basés sur l'apprentissage profond pour le séquençage d'acide nucléique
US20240118269A1 (en) * 2022-09-28 2024-04-11 Massachusetts Institute Of Technology High Throughput Stochastic Bio-Molecular Sensor
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WO2024094966A1 (fr) 2022-11-01 2024-05-10 Oxford Nanopore Technologies Plc Système d'analyse biochimique et procédé de commande d'un système d'analyse biochimique

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Also Published As

Publication number Publication date
CN113166804A (zh) 2021-07-23
WO2020109773A1 (fr) 2020-06-04
AU2019389841A1 (en) 2021-05-20
JP2022509589A (ja) 2022-01-21
CA3118632A1 (fr) 2020-06-04
EP3887543A1 (fr) 2021-10-06
KR20210095641A (ko) 2021-08-02
BR112021008198A2 (pt) 2021-08-03
EP3887543B1 (fr) 2024-08-28
GB201819378D0 (en) 2019-01-09
US20200176082A1 (en) 2020-06-04
JP2023126856A (ja) 2023-09-12

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