WO2023049212A3 - State-based base calling - Google Patents

State-based base calling Download PDF

Info

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
Application number
PCT/US2022/044290
Other languages
French (fr)
Other versions
WO2023049212A2 (en
Inventor
Gavin Derek PARNABY
Eric Jon Ojard
Dorna KASHEFHAGHIGHI
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/US20230298339A1/en
Application filed by Illumina, Inc., Illumina Software, Inc. filed Critical Illumina, Inc.
Priority to CN202280046324.1A priority Critical patent/CN117581305A/en
Publication of WO2023049212A2 publication Critical patent/WO2023049212A2/en
Publication of WO2023049212A3 publication Critical patent/WO2023049212A3/en

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 WO2023049212A2 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
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
US17/944,948 2022-09-14
US17/944,948 US20230087698A1 (en) 2021-09-22 2022-09-14 Compressed state-based base calling
US17/944,809 US20230298339A1 (en) 2021-09-22 2022-09-14 State-based base calling
US17/944,809 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/US2022/044290 WO2023049212A2 (en) 2021-09-22 2022-09-21 State-based base calling
PCT/US2022/044293 WO2023049215A1 (en) 2021-09-22 2022-09-21 Compressed state-based base calling

Family Applications After (1)

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

Country Status (1)

Country Link
WO (2) WO2023049212A2 (en)

Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015084985A2 (en) * 2013-12-03 2015-06-11 Illumina, Inc. Methods and systems for analyzing image data
WO2020191390A2 (en) * 2019-03-21 2020-09-24 Illumina, Inc. Artificial intelligence-based quality scoring
US20200302297A1 (en) * 2019-03-21 2020-09-24 Illumina, Inc. Artificial Intelligence-Based Base Calling
WO2020232410A1 (en) * 2019-05-16 2020-11-19 Illumina, Inc. Base calling using convolutions
WO2021167911A1 (en) * 2020-02-20 2021-08-26 Illumina, Inc. Artificial intelligence-based base calling of index sequences
WO2021168353A2 (en) * 2020-02-20 2021-08-26 Illumina, Inc. Artificial intelligence-based many-to-many base calling

Family Cites Families (47)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US2073908A (en) 1930-12-29 1937-03-16 Floyd L Kallam Method of and apparatus for controlling rectification
CA2044616A1 (en) 1989-10-26 1991-04-27 Roger Y. Tsien Dna sequencing
DE69530072T2 (en) 1994-12-08 2004-03-04 Molecular Dynamics, Sunnyvale FLUORESCENT IMAGING SYSTEM USING A LENS WITH MACRO SCANNING
US5528050A (en) 1995-07-24 1996-06-18 Molecular Dynamics, Inc. Compact scan head with multiple scanning modalities
US6327410B1 (en) 1997-03-14 2001-12-04 The Trustees Of Tufts College Target analyte sensors utilizing Microspheres
US6023540A (en) 1997-03-14 2000-02-08 Trustees Of Tufts College Fiber optic sensor with encoded microspheres
US7622294B2 (en) 1997-03-14 2009-11-24 Trustees Of Tufts College Methods for detecting target analytes and enzymatic reactions
US20020150909A1 (en) 1999-02-09 2002-10-17 Stuelpnagel John R. Automated information processing in randomly ordered arrays
US20050191698A1 (en) 1999-04-20 2005-09-01 Illumina, Inc. Nucleic acid sequencing using microsphere arrays
EP1923471B1 (en) 1999-04-20 2012-12-19 Illumina, Inc. Detection of nucleic acid reactions on bead arrays
US6355431B1 (en) 1999-04-20 2002-03-12 Illumina, Inc. Detection of nucleic acid amplification reactions using bead arrays
US6770441B2 (en) 2000-02-10 2004-08-03 Illumina, Inc. Array compositions and methods of making same
CN100462433C (en) 2000-07-07 2009-02-18 维西根生物技术公司 Real-time sequence determination
WO2002044425A2 (en) 2000-12-01 2002-06-06 Visigen Biotechnologies, Inc. Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity
GB0127564D0 (en) 2001-11-16 2002-01-09 Medical Res Council Emulsion compositions
US7057026B2 (en) 2001-12-04 2006-06-06 Solexa Limited Labelled nucleotides
WO2004018497A2 (en) 2002-08-23 2004-03-04 Solexa Limited Modified nucleotides for polynucleotide sequencing
CA2513889A1 (en) 2003-01-29 2004-08-19 454 Corporation Double ended sequencing
JP3827015B2 (en) 2003-02-04 2006-09-27 旭硝子株式会社 Molten glass conduit, molten glass connecting conduit and vacuum degassing apparatus
WO2005010145A2 (en) 2003-07-05 2005-02-03 The Johns Hopkins University Method and compositions for detection and enumeration of genetic variations
GB0321306D0 (en) 2003-09-11 2003-10-15 Solexa Ltd Modified polymerases for improved incorporation of nucleotide analogues
DE10355830A1 (en) 2003-11-26 2005-06-09 Röhm GmbH & Co. KG Production of (2-oxo-1,3-dioxolan-4-yl)-methyl methacrylate for use e.g. in adhesives or paint, comprises transesterification of methyl methacrylate with glycerol carbonate using a metal 1,3-diketonate catalyst
KR100955023B1 (en) 2003-12-01 2010-04-27 엘지전자 주식회사 Method for recording data continuous in digital complex recorder
JP2007525571A (en) 2004-01-07 2007-09-06 ソレクサ リミテッド Modified molecular array
US6904876B1 (en) 2004-06-28 2005-06-14 Ford Global Technologies, Llc Sodium cooled pistons for a free piston engine
US7581253B2 (en) 2004-07-20 2009-08-25 Lenovo (Singapore) Pte. Ltd. Secure storage tracking for anti-virus speed-up
CN101914620B (en) 2004-09-17 2014-02-12 加利福尼亚太平洋生命科学公司 Method for analysis of molecules
US8045998B2 (en) 2005-06-08 2011-10-25 Cisco Technology, Inc. Method and system for communicating using position information
GB0514910D0 (en) 2005-07-20 2005-08-24 Solexa Ltd Method for sequencing a polynucleotide template
DE102005036355A1 (en) 2005-07-29 2007-02-01 Cairos Technologies Ag Method for measuring the power and moving ratios on a ball comprises using an electronic device arranged in the ball for measuring the physical forces acting on the ball and an emitter for transferring the forces to an evaluation unit
GB0517097D0 (en) 2005-08-19 2005-09-28 Solexa Ltd Modified nucleosides and nucleotides and uses thereof
US20070059319A1 (en) 2005-09-15 2007-03-15 Caliper Life Sciences, Inc. Methods of screening for immuno-adjuvants and vaccines comprising anti-microtubule immuno-adjuvants
US7405281B2 (en) 2005-09-29 2008-07-29 Pacific Biosciences Of California, Inc. Fluorescent nucleotide analogs and uses therefor
US7329860B2 (en) 2005-11-23 2008-02-12 Illumina, Inc. Confocal imaging methods and apparatus
EP2018622B1 (en) 2006-03-31 2018-04-25 Illumina, Inc. Systems for sequence by synthesis analysis
MX2008016450A (en) 2006-06-21 2009-01-22 Cobarr Spa Recovery of aromatic dicarboxylic acids from waste polyester resin.
US7754429B2 (en) 2006-10-06 2010-07-13 Illumina Cambridge Limited Method for pair-wise sequencing a plurity of target polynucleotides
WO2008051530A2 (en) 2006-10-23 2008-05-02 Pacific Biosciences Of California, Inc. Polymerase enzymes and reagents for enhanced nucleic acid sequencing
US7414716B2 (en) 2006-10-23 2008-08-19 Emhart Glass S.A. Machine for inspecting glass containers
US20080147080A1 (en) 2006-12-13 2008-06-19 Joel Pynson Injector apparatus for use with intraocular lenses and methods of use
US8039817B2 (en) 2008-05-05 2011-10-18 Illumina, Inc. Compensator for multiple surface imaging
US8965076B2 (en) 2010-01-13 2015-02-24 Illumina, Inc. Data processing system and methods
US8951781B2 (en) 2011-01-10 2015-02-10 Illumina, Inc. Systems, methods, and apparatuses to image a sample for biological or chemical analysis
EP2718465B1 (en) 2011-06-09 2022-04-13 Illumina, Inc. Method of making an analyte array
EP3305400A3 (en) 2011-10-28 2018-06-06 Illumina, Inc. Microarray fabrication system and method
BR112014024789B1 (en) 2012-04-03 2021-05-25 Illumina, Inc detection apparatus and method for imaging a substrate
US20210265016A1 (en) * 2020-02-20 2021-08-26 Illumina, Inc. Data Compression for Artificial Intelligence-Based Base Calling

Patent Citations (6)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2015084985A2 (en) * 2013-12-03 2015-06-11 Illumina, Inc. Methods and systems for analyzing image data
WO2020191390A2 (en) * 2019-03-21 2020-09-24 Illumina, Inc. Artificial intelligence-based quality scoring
US20200302297A1 (en) * 2019-03-21 2020-09-24 Illumina, Inc. Artificial Intelligence-Based Base Calling
WO2020232410A1 (en) * 2019-05-16 2020-11-19 Illumina, Inc. Base calling using convolutions
WO2021167911A1 (en) * 2020-02-20 2021-08-26 Illumina, Inc. Artificial intelligence-based base calling of index sequences
WO2021168353A2 (en) * 2020-02-20 2021-08-26 Illumina, Inc. Artificial intelligence-based many-to-many base calling

Non-Patent Citations (2)

* Cited by examiner, † Cited by third party
Title
KIRCHER M ET AL: "Improved base calling for the Illumina Genome Analyzer using machine learning strategies", GENOME BIOLOGY, BIOMED CENTRAL LTD, vol. 10, no. 8, 14 August 2009 (2009-08-14), pages R83, XP021061445, ISSN: 1465-6906, DOI: 10.1186/GB-2009-10-8-R83 *
WIGODA N: "Illumina Primary Analysis Pipeline & Quality Control", 19 November 2019 (2019-11-19), XP055870543, Retrieved from the Internet <URL:https://dors.weizmann.ac.il/course/course2019-20/Noa_IlluminaPrimaryAnalysisPipeline.pdf> [retrieved on 20211208] *

Also Published As

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

Similar Documents

Publication Publication Date Title
WO2008075329A3 (en) Method and system for automatic quality evaluation
WO2019201511A8 (en) Method and data processing apparatus
CN103713876A (en) Data processing method and electronic equipment
WO2023049212A3 (en) State-based base calling
CN105787710A (en) Information reminding method, reminded terminal and reminding terminal
CN104598067A (en) Information processing method and electronic equipment
US20220358935A1 (en) System with post-conversation evaluation, electronic device, and related methods
CN202748768U (en) Communication terminal for realizing customized operation events
WO2021168353A3 (en) Artificial intelligence-based many-to-many base calling
US9020141B1 (en) Processing an outbound call campaign having multiple abandonment rates
CN102158600A (en) Event reminding method and terminal
CN105530375A (en) Alarm clock reminding method and device and mobile terminal
CN108202440A (en) Ceramic component and its moulding process, electronic equipment
CN104301486A (en) Electronic equipment and conversation control method
CN107277217A (en) A kind of incoming call answering method and terminal device
CN102970449B (en) Method and device for issuing caller information
MXPA04003934A (en) Method for producing repulsion magnetic circuit and its production system.
CN105163288B (en) Cluster communication method and group communication system
DE50006687D1 (en) MAGNESIUM ALLOYS OF HIGH DUCTILITY, METHOD FOR THE PRODUCTION AND USE THEREOF
CN1941959A (en) Method for setting cell-phone calendar and cell phone
CN106453835A (en) Method and terminal for switching answering modes
CN105187650A (en) Intelligent scene mode switching method and system
CN205566446U (en) Voice gateway
TW200642423A (en) Phone and dialing method thereof
CN108447476A (en) Method and device for asking service and service resource allocation

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 22801909

Country of ref document: EP

Kind code of ref document: A2

WWE Wipo information: entry into national phase

Ref document number: 202280046324.1

Country of ref document: CN

WWE Wipo information: entry into national phase

Ref document number: 2022801909

Country of ref document: EP

NENP Non-entry into the national phase

Ref country code: DE

ENP Entry into the national phase

Ref document number: 2022801909

Country of ref document: EP

Effective date: 20240422