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WO2023049212A3 - State-based base calling - Google Patents

State-based base calling Download PDF

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Publication number
WO2023049212A3
WO2023049212A3 PCT/US2022/044290 US2022044290W WO2023049212A3 WO 2023049212 A3 WO2023049212 A3 WO 2023049212A3 US 2022044290 W US2022044290 W US 2022044290W WO 2023049212 A3 WO2023049212 A3 WO 2023049212A3
Authority
WO
WIPO (PCT)
Prior art keywords
base calling
state
data
technology disclosed
based base
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
PCT/US2022/044290
Other languages
French (fr)
Other versions
WO2023049212A2 (en
Inventor
Gavin Derek PARNABY
Eric Jon Ojard
Dorna KASHEFHAGHIGHI
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
Illumina Software Inc
Original Assignee
Illumina Inc
Illumina Software 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
Priority claimed from US17/944,948 external-priority patent/US20230087698A1/en
Priority claimed from US17/944,809 external-priority patent/US12412387B2/en
Application filed by Illumina Inc, Illumina Software Inc filed Critical Illumina Inc
Priority to EP22801909.7A priority Critical patent/EP4405956A2/en
Priority to JP2023579829A priority patent/JP2024536665A/en
Priority to CN202280046324.1A priority patent/CN117581305A/en
Publication of WO2023049212A2 publication Critical patent/WO2023049212A2/en
Publication of WO2023049212A3 publication Critical patent/WO2023049212A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

Links

Classifications

    • 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
    • G16B40/20—Supervised data analysis
    • 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

Landscapes

  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Medical Informatics (AREA)
  • Health & Medical Sciences (AREA)
  • Evolutionary Biology (AREA)
  • Theoretical Computer Science (AREA)
  • Biophysics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • General Health & Medical Sciences (AREA)
  • Data Mining & Analysis (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Public Health (AREA)
  • Artificial Intelligence (AREA)
  • Evolutionary Computation (AREA)
  • Epidemiology (AREA)
  • Databases & Information Systems (AREA)
  • Software Systems (AREA)
  • Bioethics (AREA)
  • Chemical & Material Sciences (AREA)
  • Analytical Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Image Analysis (AREA)
  • Mobile Radio Communication Systems (AREA)

Abstract

The technology disclosed relates to state-based base calling. In particular, the technology disclosed relates to incorporating state information about data from previous sequencing cycles into the analysis of data from a current sequencing cycle when generating a base call for the current sequencing cycle. For example, when generating a base call for an Nth sequencing cycle, the technology disclosed can incorporate into the base calling logic state information about data from sequencing cycles 1 to N-1.
PCT/US2022/044290 2021-09-22 2022-09-21 State-based base calling Ceased WO2023049212A2 (en)

Priority Applications (3)

Application Number Priority Date Filing Date Title
EP22801909.7A EP4405956A2 (en) 2021-09-22 2022-09-21 State-based base calling
JP2023579829A JP2024536665A (en) 2021-09-22 2022-09-21 State-based base calling
CN202280046324.1A CN117581305A (en) 2021-09-22 2022-09-21 State-based base calling

Applications Claiming Priority (8)

Application Number Priority Date Filing Date Title
US202163247301P 2021-09-22 2021-09-22
US202163247296P 2021-09-22 2021-09-22
US63/247,296 2021-09-22
US63/247,301 2021-09-22
US17/944,809 2022-09-14
US17/944,948 US20230087698A1 (en) 2021-09-22 2022-09-14 Compressed state-based base calling
US17/944,809 US12412387B2 (en) 2021-09-22 2022-09-14 State-based base calling
US17/944,948 2022-09-14

Publications (2)

Publication Number Publication Date
WO2023049212A2 WO2023049212A2 (en) 2023-03-30
WO2023049212A3 true WO2023049212A3 (en) 2023-04-27

Family

ID=83690333

Family Applications (2)

Application Number Title Priority Date Filing Date
PCT/US2022/044293 Ceased WO2023049215A1 (en) 2021-09-22 2022-09-21 Compressed state-based base calling
PCT/US2022/044290 Ceased WO2023049212A2 (en) 2021-09-22 2022-09-21 State-based base calling

Family Applications Before (1)

Application Number Title Priority Date Filing Date
PCT/US2022/044293 Ceased WO2023049215A1 (en) 2021-09-22 2022-09-21 Compressed state-based base calling

Country Status (1)

Country Link
WO (2) WO2023049215A1 (en)

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WO2021168353A2 (en) * 2020-02-20 2021-08-26 Illumina, Inc. Artificial intelligence-based many-to-many base calling

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Also Published As

Publication number Publication date
WO2023049215A1 (en) 2023-03-30
WO2023049212A2 (en) 2023-03-30

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