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WO2023107719A3 - Primary analysis in next generation sequencing - Google Patents

Primary analysis in next generation sequencing Download PDF

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Publication number
WO2023107719A3
WO2023107719A3 PCT/US2022/052448 US2022052448W WO2023107719A3 WO 2023107719 A3 WO2023107719 A3 WO 2023107719A3 US 2022052448 W US2022052448 W US 2022052448W WO 2023107719 A3 WO2023107719 A3 WO 2023107719A3
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WO
WIPO (PCT)
Prior art keywords
flow cell
pixel intensities
cycles
base
base calling
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/US2022/052448
Other languages
French (fr)
Other versions
WO2023107719A2 (en
Inventor
Connor THOMPSON
Tsung-li LIU
Semyon Kruglyak
Minghao GUO
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.)
Element Biosciences Inc
Original Assignee
Element Biosciences 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 US17/547,602 external-priority patent/US11397870B2/en
Application filed by Element Biosciences Inc filed Critical Element Biosciences Inc
Priority to AU2022407175A priority Critical patent/AU2022407175A1/en
Priority to CN202280090448.XA priority patent/CN118679523A/en
Priority to EP22905191.7A priority patent/EP4444911A2/en
Priority to CA3240450A priority patent/CA3240450A1/en
Priority to KR1020247023028A priority patent/KR20240159875A/en
Priority to JP2024534541A priority patent/JP2025500815A/en
Publication of WO2023107719A2 publication Critical patent/WO2023107719A2/en
Publication of WO2023107719A3 publication Critical patent/WO2023107719A3/en
Anticipated expiration legal-status Critical
Ceased legal-status Critical Current

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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
    • 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
    • G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T7/00—Image analysis
    • G06T7/30—Determination of transform parameters for the alignment of images, i.e. image registration
    • G06T7/33—Determination of transform parameters for the alignment of images, i.e. image registration using feature-based methods
    • 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
    • G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T2207/00—Indexing scheme for image analysis or image enhancement
    • G06T2207/10—Image acquisition modality
    • G06T2207/10064—Fluorescence image
    • G—PHYSICS
    • G06—COMPUTING OR CALCULATING; COUNTING
    • G06T—IMAGE DATA PROCESSING OR GENERATION, IN GENERAL
    • G06T2207/00—Indexing scheme for image analysis or image enhancement
    • G06T2207/30—Subject of image; Context of image processing
    • G06T2207/30004—Biomedical image processing
    • G06T2207/30024—Cell structures in vitro; Tissue sections in vitro

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  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Theoretical Computer Science (AREA)
  • Medical Informatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Organic Chemistry (AREA)
  • Analytical Chemistry (AREA)
  • Molecular Biology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Epidemiology (AREA)
  • Databases & Information Systems (AREA)
  • Data Mining & Analysis (AREA)
  • Bioethics (AREA)
  • Artificial Intelligence (AREA)
  • Signal Processing (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Software Systems (AREA)
  • General Physics & Mathematics (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Genetics & Genomics (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

Image data analysis, and particularly identifying cluster or polony locations for performing base-calling in a digital image of a flow cell during DNA sequencing is described. A method may include generating a first plurality of flow cell images of a cellular sample immobilized on a support by conducting one or more cycles of sequencing reactions. The cellular sample may include a plurality of concatemer molecules therewithin. For the first plurality of flow cell image, pixel intensities, and a respective color purity of each of the pixel intensities may be determined. A base calling template may include base calling locations based on the pixel intensities and the respective color purity of the pixel intensities. The base calling template may be for registering a second plurality of flow cell images of the support in one or more subsequent cycles of the one or more cycles.
PCT/US2022/052448 2021-12-10 2022-12-09 Primary analysis in next generation sequencing Ceased WO2023107719A2 (en)

Priority Applications (6)

Application Number Priority Date Filing Date Title
AU2022407175A AU2022407175A1 (en) 2021-12-10 2022-12-09 Primary analysis in next generation sequencing
CN202280090448.XA CN118679523A (en) 2021-12-10 2022-12-09 Preliminary analysis in next generation sequencing
EP22905191.7A EP4444911A2 (en) 2021-12-10 2022-12-09 Primary analysis in next generation sequencing
CA3240450A CA3240450A1 (en) 2021-12-10 2022-12-09 Primary analysis in next generation sequencing
KR1020247023028A KR20240159875A (en) 2021-12-10 2022-12-09 Primary analysis of next-generation sequencing
JP2024534541A JP2025500815A (en) 2021-12-10 2022-12-09 Primary Analysis in Next Generation Sequencing

Applications Claiming Priority (8)

Application Number Priority Date Filing Date Title
US17/547,602 US11397870B2 (en) 2020-08-31 2021-12-10 Single-pass primary analysis
US17/547,602 2021-12-10
US202263349421P 2022-06-06 2022-06-06
US63/349,421 2022-06-06
US17/854,042 US11915444B2 (en) 2020-08-31 2022-06-30 Single-pass primary analysis
US17/854,042 2022-06-30
US202263388183P 2022-07-11 2022-07-11
US63/388,183 2022-07-11

Publications (2)

Publication Number Publication Date
WO2023107719A2 WO2023107719A2 (en) 2023-06-15
WO2023107719A3 true WO2023107719A3 (en) 2023-07-20

Family

ID=86731139

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2022/052448 Ceased WO2023107719A2 (en) 2021-12-10 2022-12-09 Primary analysis in next generation sequencing

Country Status (6)

Country Link
EP (1) EP4444911A2 (en)
JP (1) JP2025500815A (en)
KR (1) KR20240159875A (en)
AU (1) AU2022407175A1 (en)
CA (1) CA3240450A1 (en)
WO (1) WO2023107719A2 (en)

Families Citing this family (10)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2019241305A1 (en) 2018-06-12 2019-12-19 Element Biosciences, Inc. Improved reverse transcriptase for nucleic acid sequencing
US10704094B1 (en) 2018-11-14 2020-07-07 Element Biosciences, Inc. Multipart reagents having increased avidity for polymerase binding
US10768173B1 (en) 2019-09-06 2020-09-08 Element Biosciences, Inc. Multivalent binding composition for nucleic acid analysis
GB2598656B (en) 2018-11-15 2023-10-04 Element Biosciences Inc Methods for generating circular nucleic acid molecules
US12313627B2 (en) 2019-05-01 2025-05-27 Element Biosciences, Inc. Multivalent binding composition for nucleic acid analysis
US12391929B2 (en) 2019-05-24 2025-08-19 Element Biosciences, Inc. Polymerase-nucleotide conjugates for sequencing by trapping
US11287422B2 (en) 2019-09-23 2022-03-29 Element Biosciences, Inc. Multivalent binding composition for nucleic acid analysis
GB2629259B (en) 2021-07-21 2025-05-28 Element Biosciences Inc Optical systems for nucleic acid sequencing and methods thereof
WO2025136957A1 (en) * 2023-12-18 2025-06-26 Pleno, Inc. Systems and methods for decoding by sequencing
WO2025212654A1 (en) * 2024-04-02 2025-10-09 Element Biosciences, Inc. Library molecule titration for tunable surface density in polony sequencing

Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030224419A1 (en) * 1997-05-23 2003-12-04 Lynx Therapeutics, Inc. Data analysis and display system for ligation-based DNA sequencing
US20160102348A1 (en) * 2014-10-13 2016-04-14 Life Technologies Corporation Methods, systems, and computer-readable media for accelerated base calling
US20200080141A1 (en) * 2013-12-11 2020-03-12 Accuragen Holdings Limited Methods and compositions for enrichment of amplification products
US20200392574A1 (en) * 2005-06-15 2020-12-17 Complete Genomics, Inc Dna array
US20210150715A1 (en) * 2010-01-13 2021-05-20 Illumina, Inc. System and methods for identifying nucleotides

Patent Citations (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030224419A1 (en) * 1997-05-23 2003-12-04 Lynx Therapeutics, Inc. Data analysis and display system for ligation-based DNA sequencing
US20200392574A1 (en) * 2005-06-15 2020-12-17 Complete Genomics, Inc Dna array
US20210150715A1 (en) * 2010-01-13 2021-05-20 Illumina, Inc. System and methods for identifying nucleotides
US20200080141A1 (en) * 2013-12-11 2020-03-12 Accuragen Holdings Limited Methods and compositions for enrichment of amplification products
US20160102348A1 (en) * 2014-10-13 2016-04-14 Life Technologies Corporation Methods, systems, and computer-readable media for accelerated base calling

Also Published As

Publication number Publication date
WO2023107719A2 (en) 2023-06-15
AU2022407175A1 (en) 2024-06-27
EP4444911A2 (en) 2024-10-16
CA3240450A1 (en) 2023-06-15
KR20240159875A (en) 2024-11-07
JP2025500815A (en) 2025-01-15

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