CA3240445A1 - Analyse primaire dans le cadre d'un sequencage de nouvelle generation - Google Patents

Analyse primaire dans le cadre d'un sequencage de nouvelle generation Download PDF

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Publication number
CA3240445A1
CA3240445A1 CA3240445A CA3240445A CA3240445A1 CA 3240445 A1 CA3240445 A1 CA 3240445A1 CA 3240445 A CA3240445 A CA 3240445A CA 3240445 A CA3240445 A CA 3240445A CA 3240445 A1 CA3240445 A1 CA 3240445A1
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Prior art keywords
sequence
sample index
cycles
flow cell
sequencing
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Pending
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CA3240445A
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English (en)
Inventor
Chunhong Zhou
Semyon Kruglyak
Francisco Garcia
Minghao GUO
Haosen WANG
Ryan Kelly
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Element Biosciences Inc
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Individual
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Publication date
Priority claimed from US17/547,602 external-priority patent/US11397870B2/en
Priority claimed from US17/725,065 external-priority patent/US12371743B2/en
Priority claimed from US17/725,042 external-priority patent/US12359193B2/en
Application filed by Individual filed Critical Individual
Publication of CA3240445A1 publication Critical patent/CA3240445A1/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
    • 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
    • G06T7/10—Segmentation; Edge detection
    • G06T7/11—Region-based segmentation
    • 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
    • G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
    • G16B25/20—Polymerase chain reaction [PCR]; Primer or probe design; Probe optimisation
    • 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
    • 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
    • G06T2207/10056—Microscopic 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)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Organic Chemistry (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Medical Informatics (AREA)
  • Molecular Biology (AREA)
  • Wood Science & Technology (AREA)
  • Zoology (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Genetics & Genomics (AREA)
  • Analytical Chemistry (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • General Physics & Mathematics (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • General Engineering & Computer Science (AREA)
  • Biochemistry (AREA)
  • Signal Processing (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Artificial Intelligence (AREA)
  • Bioethics (AREA)
  • Data Mining & Analysis (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • Evolutionary Computation (AREA)
  • Public Health (AREA)
  • Software Systems (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)

Abstract

L'invention concerne une analyse de données d'image, en particulier l'identification de positions de grappe afin d'effectuer une opération de base-calling dans une image de cuve à circulation numérique pendant un séquençage d'ADN. Chaque molécule patron d'acide nucléique immobilisée sur un support peut comprendre une séquence d'insert et une séquence d'indice d'échantillon. La séquence d'indice d'échantillon peut comprendre une séquence k-mère. Un système de séquençage peut conduire k cycles de réactions de séquençage de la séquence k-mère avant de conduire un ou plusieurs cycles des réactions de séquençage de séquence d'insert et générer une première pluralité d'images de cuve à circulation. Des intensités de pixel peuvent être déterminées pour des pixels de la première pluralité d'images de cuve à circulation. Un modèle de base-calling peut être déterminé et comprendre des positions de base-calling sur la base des intensités de pixel et des puretés de couleur respectives des intensités de pixel. Le modèle de base-calling peut enregistrer une seconde pluralité d'images de cuve à circulation du support dans un ou plusieurs cycles après les k cycles.
CA3240445A 2021-12-10 2022-12-09 Analyse primaire dans le cadre d'un sequencage de nouvelle generation Pending CA3240445A1 (fr)

Applications Claiming Priority (15)

Application Number Priority Date Filing Date Title
US17/547,602 2021-12-10
US17/547,602 US11397870B2 (en) 2020-08-31 2021-12-10 Single-pass primary analysis
US202263316790P 2022-03-04 2022-03-04
US202263316784P 2022-03-04 2022-03-04
US63/316,784 2022-03-04
US63/316,790 2022-03-04
US17/725,065 US12371743B2 (en) 2022-03-04 2022-04-20 Double-stranded splint adaptors and methods of use
US17/725,042 US12359193B2 (en) 2022-03-04 2022-04-20 Single-stranded splint strands and methods of use
US17/725,042 2022-04-20
US17/725,065 2022-04-20
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
PCT/US2022/052449 WO2023107720A1 (fr) 2021-12-10 2022-12-09 Analyse primaire dans le cadre d'un séquençage de nouvelle génération

Publications (1)

Publication Number Publication Date
CA3240445A1 true CA3240445A1 (fr) 2023-06-15

Family

ID=86731140

Family Applications (1)

Application Number Title Priority Date Filing Date
CA3240445A Pending CA3240445A1 (fr) 2021-12-10 2022-12-09 Analyse primaire dans le cadre d'un sequencage de nouvelle generation

Country Status (6)

Country Link
EP (1) EP4445327A4 (fr)
JP (1) JP2025500808A (fr)
KR (1) KR20240162477A (fr)
AU (1) AU2022407176A1 (fr)
CA (1) CA3240445A1 (fr)
WO (1) WO2023107720A1 (fr)

Families Citing this family (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US10704094B1 (en) 2018-11-14 2020-07-07 Element Biosciences, Inc. Multipart reagents having increased avidity for polymerase binding
US12391929B2 (en) 2019-05-24 2025-08-19 Element Biosciences, Inc. Polymerase-nucleotide conjugates for sequencing by trapping
AU2022316142A1 (en) 2021-07-21 2024-02-22 Element Biosciences, Inc. Optical systems for nucleic acid sequencing and methods thereof

Family Cites Families (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US8965076B2 (en) * 2010-01-13 2015-02-24 Illumina, Inc. Data processing system and methods
EP3051450A1 (fr) * 2015-02-02 2016-08-03 Applied Maths Procédé de typage d'acides nucléiques ou de séquences d'acides aminés basé sur une analyse de séquence
CN111655855B (zh) * 2017-09-14 2025-09-09 生命明疗法股份有限公司 人治疗靶标及其调节剂
US20190130999A1 (en) * 2017-10-26 2019-05-02 Indigo Ag, Inc. Latent Representations of Phylogeny to Predict Organism Phenotype
US12009060B2 (en) * 2018-12-14 2024-06-11 Merck Sharp & Dohme Llc Identifying biosynthetic gene clusters
EP3924505B1 (fr) * 2019-02-12 2025-12-17 10X Genomics, Inc. Procédés de traitement de molécules d'acides nucléiques

Also Published As

Publication number Publication date
AU2022407176A1 (en) 2024-06-27
WO2023107720A1 (fr) 2023-06-15
EP4445327A1 (fr) 2024-10-16
KR20240162477A (ko) 2024-11-15
EP4445327A4 (fr) 2026-01-14
JP2025500808A (ja) 2025-01-15

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Effective date: 20260226