CA3183529A1 - Systems and methods for per-cluster intensity correction and base calling - Google Patents

Systems and methods for per-cluster intensity correction and base calling

Info

Publication number
CA3183529A1
CA3183529A1 CA3183529A CA3183529A CA3183529A1 CA 3183529 A1 CA3183529 A1 CA 3183529A1 CA 3183529 A CA3183529 A CA 3183529A CA 3183529 A CA3183529 A CA 3183529A CA 3183529 A1 CA3183529 A1 CA 3183529A1
Authority
CA
Canada
Prior art keywords
current
intensity
channel
specific
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.)
Pending
Application number
CA3183529A
Other languages
English (en)
French (fr)
Inventor
Eric Jon Ojard
Abde Ali Hunaid Kagalwalla
Rami Mehio
Nitin UDPA
Gavin Derek PARNABY
John S. Vieceli
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.)
Illumina Inc
Original Assignee
Illumina 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 Illumina Inc filed Critical Illumina Inc
Publication of CA3183529A1 publication Critical patent/CA3183529A1/en
Pending legal-status Critical Current

Links

Classifications

    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06F—ELECTRIC DIGITAL DATA PROCESSING
    • G06F18/00—Pattern recognition
    • G06F18/20—Analysing
    • G06F18/24—Classification techniques
    • G06F18/241—Classification techniques relating to the classification model, e.g. parametric or non-parametric approaches
    • G06F18/2411—Classification techniques relating to the classification model, e.g. parametric or non-parametric approaches based on the proximity to a decision surface, e.g. support vector machines
    • 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
    • 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
    • G06F18/213—Feature extraction, e.g. by transforming the feature space; Summarisation; Mappings, e.g. subspace methods
    • G06F18/2135—Feature extraction, e.g. by transforming the feature space; Summarisation; Mappings, e.g. subspace methods based on approximation criteria, e.g. principal component analysis
    • G06F18/21355—Feature extraction, e.g. by transforming the feature space; Summarisation; Mappings, e.g. subspace methods based on approximation criteria, e.g. principal component analysis nonlinear criteria, e.g. embedding a manifold in a Euclidean space
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T7/00—Image analysis
    • G06T7/10—Segmentation; Edge detection
    • G06T7/187—Segmentation; Edge detection involving region growing; involving region merging; involving connected component labelling
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06V—IMAGE OR VIDEO RECOGNITION OR UNDERSTANDING
    • G06V10/00—Arrangements for image or video recognition or understanding
    • G06V10/40—Extraction of image or video features
    • G06V10/50—Extraction of image or video features by performing operations within image blocks; by using histograms, e.g. histogram of oriented gradients [HoG]; by summing image-intensity values; Projection analysis
    • G06V10/507—Summing image-intensity values; Histogram projection analysis
    • 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
    • G16B40/30—Unsupervised data analysis
    • 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
    • G16B45/00—ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Theoretical Computer Science (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Data Mining & Analysis (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Medical Informatics (AREA)
  • Artificial Intelligence (AREA)
  • Evolutionary Computation (AREA)
  • General Physics & Mathematics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioethics (AREA)
  • Software Systems (AREA)
  • Public Health (AREA)
  • Epidemiology (AREA)
  • Databases & Information Systems (AREA)
  • Signal Processing (AREA)
  • Molecular Biology (AREA)
  • Multimedia (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Telephonic Communication Services (AREA)
  • Apparatus For Radiation Diagnosis (AREA)
  • Nuclear Medicine (AREA)
  • Complex Calculations (AREA)
CA3183529A 2020-10-27 2021-10-26 Systems and methods for per-cluster intensity correction and base calling Pending CA3183529A1 (en)

Applications Claiming Priority (3)

Application Number Priority Date Filing Date Title
US202063106256P 2020-10-27 2020-10-27
US63/106,256 2020-10-27
PCT/US2021/056711 WO2022093865A1 (en) 2020-10-27 2021-10-26 Systems and methods for per-cluster intensity correction and base calling

Publications (1)

Publication Number Publication Date
CA3183529A1 true CA3183529A1 (en) 2022-05-05

Family

ID=78822676

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3183529A Pending CA3183529A1 (en) 2020-10-27 2021-10-26 Systems and methods for per-cluster intensity correction and base calling

Country Status (10)

Country Link
US (5) US11361194B2 (https=)
EP (2) EP4459625A3 (https=)
JP (1) JP2023547298A (https=)
KR (1) KR20230098097A (https=)
CN (1) CN115803817A (https=)
AU (1) AU2021369495B2 (https=)
CA (1) CA3183529A1 (https=)
IL (1) IL298884A (https=)
MX (1) MX2022016354A (https=)
WO (1) WO2022093865A1 (https=)

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Also Published As

Publication number Publication date
US20220129711A1 (en) 2022-04-28
WO2022093865A1 (en) 2022-05-05
EP4238098C0 (en) 2024-08-21
EP4459625A2 (en) 2024-11-06
CN115803817A (zh) 2023-03-14
IL298884A (en) 2023-02-01
US20240220584A1 (en) 2024-07-04
US11593595B2 (en) 2023-02-28
EP4238098A1 (en) 2023-09-06
JP2023547298A (ja) 2023-11-10
US20230259588A1 (en) 2023-08-17
EP4238098B1 (en) 2024-08-21
AU2021369495B2 (en) 2026-04-02
US12216741B2 (en) 2025-02-04
US11853396B2 (en) 2023-12-26
US20250265313A1 (en) 2025-08-21
MX2022016354A (es) 2023-01-24
AU2021369495A1 (en) 2023-02-02
EP4459625A3 (en) 2025-01-22
US20220300772A1 (en) 2022-09-22
KR20230098097A (ko) 2023-07-03
US11361194B2 (en) 2022-06-14

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