CA3223746A1 - Etalonnage de score de qualite de systemes d'appel de bases - Google Patents

Etalonnage de score de qualite de systemes d'appel de bases Download PDF

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Publication number
CA3223746A1
CA3223746A1 CA3223746A CA3223746A CA3223746A1 CA 3223746 A1 CA3223746 A1 CA 3223746A1 CA 3223746 A CA3223746 A CA 3223746A CA 3223746 A CA3223746 A CA 3223746A CA 3223746 A1 CA3223746 A1 CA 3223746A1
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Prior art keywords
base
range
sensor data
value
intensity
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Pending
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CA3223746A
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Rohan PAUL
Dorna KASHEFHAGHIGHI
John S. Vieceli
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Illumina Inc
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Illumina Inc
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Priority claimed from US17/839,387 external-priority patent/US20230029970A1/en
Application filed by Illumina Inc filed Critical Illumina Inc
Publication of CA3223746A1 publication Critical patent/CA3223746A1/fr
Pending legal-status Critical Current

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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
    • 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
    • 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
    • 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
    • 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
    • G06N3/045—Combinations of networks
    • 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
    • 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
    • G16B40/20—Supervised data analysis

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  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Data Mining & Analysis (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Computation (AREA)
  • Artificial Intelligence (AREA)
  • Software Systems (AREA)
  • Molecular Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • General Engineering & Computer Science (AREA)
  • Chemical & Material Sciences (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Biomedical Technology (AREA)
  • Mathematical Physics (AREA)
  • General Physics & Mathematics (AREA)
  • Computing Systems (AREA)
  • Computational Linguistics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Epidemiology (AREA)
  • Bioethics (AREA)
  • Public Health (AREA)
  • Analytical Chemistry (AREA)
  • Databases & Information Systems (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Organic Chemistry (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Signal Processing (AREA)
  • Biochemistry (AREA)
  • Genetics & Genomics (AREA)

Abstract

L'invention concerne un procédé de génération d'appels de bases par un appelant de base. Le procédé comprend la réception d'une pluralité de données de capteur à partir d'une cellule d'écoulement, la pluralité de données de capteur se trouvant dans une première plage et permettant d'identifier une deuxième plage, de telle sorte qu'au moins un pourcentage de seuil de la pluralité de données de capteur se trouve dans la deuxième plage. Au moins un sous-ensemble de la pluralité de données de capteur, qui se trouvent dans la deuxième plage, sont mappées sur une troisième plage, générant ainsi une pluralité de données de capteur normalisées. La pluralité de données de capteur normalisées est traitée dans un appelant de base, pour appeler, pour la pluralité de données de capteur normalisées, une ou plusieurs bases correspondantes.
CA3223746A 2021-07-28 2022-07-28 Etalonnage de score de qualite de systemes d'appel de bases Pending CA3223746A1 (fr)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US202163226707P 2021-07-28 2021-07-28
US63/226,707 2021-07-28
US17/839,387 2022-06-13
US17/839,387 US20230029970A1 (en) 2021-07-28 2022-06-13 Quality score calibration of basecalling systems
PCT/US2022/038729 WO2023009758A1 (fr) 2021-07-28 2022-07-28 Étalonnage de score de qualité de systèmes d'appel de bases

Publications (1)

Publication Number Publication Date
CA3223746A1 true CA3223746A1 (fr) 2023-02-02

Family

ID=83149575

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3223746A Pending CA3223746A1 (fr) 2021-07-28 2022-07-28 Etalonnage de score de qualite de systemes d'appel de bases

Country Status (7)

Country Link
EP (1) EP4377960A1 (fr)
JP (1) JP2024532049A (fr)
KR (1) KR20240037882A (fr)
AU (1) AU2022319125A1 (fr)
CA (1) CA3223746A1 (fr)
IL (1) IL309786A (fr)
WO (1) WO2023009758A1 (fr)

Families Citing this family (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN118053503B (zh) * 2024-01-11 2024-12-06 中国农业科学院农业基因组研究所 一种入侵生物多组学数据库构建方法及系统

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EP0450060A1 (fr) 1989-10-26 1991-10-09 Sri International Sequen age d'adn
US6090592A (en) 1994-08-03 2000-07-18 Mosaic Technologies, Inc. Method for performing amplification of nucleic acid on supports
US5641658A (en) 1994-08-03 1997-06-24 Mosaic Technologies, Inc. Method for performing amplification of nucleic acid with two primers bound to a single solid support
EP1498494A3 (fr) 1997-04-01 2007-06-20 Solexa Ltd. Procédé de séquencage d'acides nucléiques
EP1591541B1 (fr) 1997-04-01 2012-02-15 Illumina Cambridge Limited Methode de séquençage d'acide nucléique
AR021833A1 (es) 1998-09-30 2002-08-07 Applied Research Systems Metodos de amplificacion y secuenciacion de acido nucleico
US20020150909A1 (en) 1999-02-09 2002-10-17 Stuelpnagel John R. Automated information processing in randomly ordered arrays
ATE377093T1 (de) 2000-07-07 2007-11-15 Visigen Biotechnologies Inc Sequenzbestimmung in echtzeit
US7211414B2 (en) 2000-12-01 2007-05-01 Visigen Biotechnologies, Inc. Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity
AR031640A1 (es) 2000-12-08 2003-09-24 Applied Research Systems Amplificacion isotermica de acidos nucleicos en un soporte solido
US7057026B2 (en) 2001-12-04 2006-06-06 Solexa Limited Labelled nucleotides
US20040002090A1 (en) 2002-03-05 2004-01-01 Pascal Mayer Methods for detecting genome-wide sequence variations associated with a phenotype
AU2003259352A1 (en) 2002-08-23 2004-03-11 Solexa Limited Labelled nucleotides
EP2607369B1 (fr) 2002-08-23 2015-09-23 Illumina Cambridge Limited Nucléotides modifiés pour le séquençage de polynucléotide
GB0321306D0 (en) 2003-09-11 2003-10-15 Solexa Ltd Modified polymerases for improved incorporation of nucleotide analogues
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EP1828412B2 (fr) 2004-12-13 2019-01-09 Illumina Cambridge Limited Procede ameliore de detection de nucleotides
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Also Published As

Publication number Publication date
EP4377960A1 (fr) 2024-06-05
AU2022319125A1 (en) 2024-01-18
KR20240037882A (ko) 2024-03-22
JP2024532049A (ja) 2024-09-05
WO2023009758A1 (fr) 2023-02-02
IL309786A (en) 2024-02-01

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