EP4444911A4 - PRIMARY ANALYSIS IN NEXT GENERATION SEQUALIZATION - Google Patents

PRIMARY ANALYSIS IN NEXT GENERATION SEQUALIZATION

Info

Publication number
EP4444911A4
EP4444911A4 EP22905191.7A EP22905191A EP4444911A4 EP 4444911 A4 EP4444911 A4 EP 4444911A4 EP 22905191 A EP22905191 A EP 22905191A EP 4444911 A4 EP4444911 A4 EP 4444911A4
Authority
EP
European Patent Office
Prior art keywords
framework
generation sequencing
primary analysis
primary
analysis
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
EP22905191.7A
Other languages
German (de)
English (en)
French (fr)
Other versions
EP4444911A2 (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
Publication of EP4444911A2 publication Critical patent/EP4444911A2/en
Publication of EP4444911A4 publication Critical patent/EP4444911A4/en
Pending 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
    • 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

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Physics & Mathematics (AREA)
  • Health & Medical Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biotechnology (AREA)
  • Theoretical Computer Science (AREA)
  • General Health & Medical Sciences (AREA)
  • Organic Chemistry (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Computer Vision & Pattern Recognition (AREA)
  • Immunology (AREA)
  • Evolutionary Computation (AREA)
  • Signal Processing (AREA)
  • Genetics & Genomics (AREA)
  • Artificial Intelligence (AREA)
  • Bioethics (AREA)
  • Data Mining & Analysis (AREA)
  • Databases & Information Systems (AREA)
  • Epidemiology (AREA)
  • General Physics & Mathematics (AREA)
  • General Engineering & Computer Science (AREA)
  • Public Health (AREA)
  • Software Systems (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
EP22905191.7A 2021-12-10 2022-12-09 PRIMARY ANALYSIS IN NEXT GENERATION SEQUALIZATION Pending EP4444911A4 (en)

Applications Claiming Priority (5)

Application Number Priority Date Filing Date Title
US17/547,602 US11397870B2 (en) 2020-08-31 2021-12-10 Single-pass primary analysis
US202263349421P 2022-06-06 2022-06-06
US17/854,042 US11915444B2 (en) 2020-08-31 2022-06-30 Single-pass primary analysis
US202263388183P 2022-07-11 2022-07-11
PCT/US2022/052448 WO2023107719A2 (en) 2021-12-10 2022-12-09 Primary analysis in next generation sequencing

Publications (2)

Publication Number Publication Date
EP4444911A2 EP4444911A2 (en) 2024-10-16
EP4444911A4 true EP4444911A4 (en) 2025-12-17

Family

ID=86731139

Family Applications (1)

Application Number Title Priority Date Filing Date
EP22905191.7A Pending EP4444911A4 (en) 2021-12-10 2022-12-09 PRIMARY ANALYSIS IN NEXT GENERATION SEQUALIZATION

Country Status (6)

Country Link
EP (1) EP4444911A4 (https=)
JP (1) JP2025500815A (https=)
KR (1) KR20240159875A (https=)
AU (1) AU2022407175A1 (https=)
CA (1) CA3240450A1 (https=)
WO (1) WO2023107719A2 (https=)

Families Citing this family (11)

* 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
WO2020102766A2 (en) 2018-11-15 2020-05-22 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
AU2022316142A1 (en) 2021-07-21 2024-02-22 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
CN120636551B (zh) * 2025-06-05 2026-04-10 上海赛陆生命科学有限公司 基因测序的模板构建方法、产品、基因测序仪及介质

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2021102039A1 (en) * 2019-11-21 2021-05-27 10X Genomics, Inc, Spatial analysis of analytes
WO2021133911A1 (en) * 2019-12-23 2021-07-01 Cold Spring Harbor Laboratory Mixseq: mixture sequencing using compressed sensing for in-situ and in-vitro applications

Family Cites Families (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2001061044A1 (en) * 2000-02-15 2001-08-23 Lynx Therapeutics, Inc. Data analysis and display system for ligation-based dna sequencing
EP3257949A1 (en) * 2005-06-15 2017-12-20 Complete Genomics Inc. Nucleic acid analysis by random mixtures of non-overlapping fragments
US8965076B2 (en) * 2010-01-13 2015-02-24 Illumina, Inc. Data processing system and methods
US11859246B2 (en) * 2013-12-11 2024-01-02 Accuragen Holdings Limited Methods and compositions for enrichment of amplification products
WO2016060974A1 (en) * 2014-10-13 2016-04-21 Life Technologies Corporation Methods, systems, and computer-readable media for accelerated base calling

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2021102039A1 (en) * 2019-11-21 2021-05-27 10X Genomics, Inc, Spatial analysis of analytes
WO2021133911A1 (en) * 2019-12-23 2021-07-01 Cold Spring Harbor Laboratory Mixseq: mixture sequencing using compressed sensing for in-situ and in-vitro applications

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
FU XIAONAN ET AL: "Continuous Polony Gels for Tissue Mapping with High Resolution and RNA Capture Efficiency", BIORXIV, 17 March 2021 (2021-03-17), XP055983312, Retrieved from the Internet <URL:https://www.biorxiv.org/content/10.1101/2021.03.17.435795v1.full> [retrieved on 20221121], DOI: 10.1101/2021.03.17.435795 *
LEE JE HYUK ET AL: "Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues", NATURE PROTOCOLS, vol. 10, no. 3, 12 February 2015 (2015-02-12), GB, pages 442 - 458, XP093280058, ISSN: 1754-2189, Retrieved from the Internet <URL:http://www.nature.com/articles/nprot.2014.191> DOI: 10.1038/nprot.2014.191 *

Also Published As

Publication number Publication date
EP4444911A2 (en) 2024-10-16
CA3240450A1 (en) 2023-06-15
WO2023107719A3 (en) 2023-07-20
KR20240159875A (ko) 2024-11-07
JP2025500815A (ja) 2025-01-15
AU2022407175A1 (en) 2024-06-27
WO2023107719A2 (en) 2023-06-15

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Ipc: C12Q 1/6869 20180101AFI20251111BHEP

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