WO2026072436A1 - Systèmes et procédés de quantification de la connectivité de lectures de séquences - Google Patents

Systèmes et procédés de quantification de la connectivité de lectures de séquences

Info

Publication number
WO2026072436A1
WO2026072436A1 PCT/US2025/046976 US2025046976W WO2026072436A1 WO 2026072436 A1 WO2026072436 A1 WO 2026072436A1 US 2025046976 W US2025046976 W US 2025046976W WO 2026072436 A1 WO2026072436 A1 WO 2026072436A1
Authority
WO
WIPO (PCT)
Prior art keywords
nucleic acid
read
flow cell
read pairs
polynucleotide fragments
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
PCT/US2025/046976
Other languages
English (en)
Inventor
Daniel James ANDREWS
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
Original Assignee
Illumina 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
Application filed by Illumina Inc filed Critical Illumina Inc
Publication of WO2026072436A1 publication Critical patent/WO2026072436A1/fr
Pending legal-status Critical Current
Anticipated expiration legal-status Critical

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
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • G16B30/20—Sequence assembly
    • 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

Landscapes

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

Abstract

Dans certains modes de réalisation, la technologie divulguée concerne un procédé de détermination d'un score de qualité de liaison entre deux paires de lectures. Dans certains modes de réalisation, la technologie divulguée concerne un procédé d'attribution de paires de lectures à des polymères d'acide nucléique cibles. Dans certains modes de réalisation, la technologie divulguée concerne un procédé de production d'un mappage de paires de lectures à une séquence de référence. Dans certains modes de réalisation, la technologie divulguée concerne un procédé de production d'un mappage de paires de lectures à une séquence de référence. Dans certains modes de réalisation, la technologie divulguée concerne un procédé d'amélioration de la précision d'alignements fractionnés de paires de lectures à une séquence de référence.
PCT/US2025/046976 2024-09-27 2025-09-18 Systèmes et procédés de quantification de la connectivité de lectures de séquences Pending WO2026072436A1 (fr)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US202463700049P 2024-09-27 2024-09-27
US63/700,049 2024-09-27

Publications (1)

Publication Number Publication Date
WO2026072436A1 true WO2026072436A1 (fr) 2026-04-02

Family

ID=97600187

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2025/046976 Pending WO2026072436A1 (fr) 2024-09-27 2025-09-18 Systèmes et procédés de quantification de la connectivité de lectures de séquences

Country Status (1)

Country Link
WO (1) WO2026072436A1 (fr)

Citations (26)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1991006678A1 (fr) 1989-10-26 1991-05-16 Sri International Sequençage d'adn
WO1992002258A1 (fr) 1990-07-27 1992-02-20 Isis Pharmaceuticals, Inc. Oligonucleotides, a pyrimidine modifiee et resistants a la nuclease, detectant et modulant l'expression de genes
WO1993010820A1 (fr) 1991-11-26 1993-06-10 Gilead Sciences, Inc. Formation amelioree de triple et double helices a l'aide d'oligomeres contenant des pyrimidines modifiees
WO1994022892A1 (fr) 1993-03-30 1994-10-13 Sterling Winthrop Inc. Oligonucleotides modifies contant des nucleosides 7-deazapurines
US5432272A (en) 1990-10-09 1995-07-11 Benner; Steven A. Method for incorporating into a DNA or RNA oligonucleotide using nucleotides bearing heterocyclic bases
US6150510A (en) 1995-11-06 2000-11-21 Aventis Pharma Deutschland Gmbh Modified oligonucleotides, their preparation and their use
WO2004018497A2 (fr) 2002-08-23 2004-03-04 Solexa Limited Nucleotides modifies
US20050100900A1 (en) 1997-04-01 2005-05-12 Manteia Sa Method of nucleic acid amplification
WO2005065814A1 (fr) 2004-01-07 2005-07-21 Solexa Limited Arrangements moleculaires modifies
US7057026B2 (en) 2001-12-04 2006-06-06 Solexa Limited Labelled nucleotides
WO2006064199A1 (fr) 2004-12-13 2006-06-22 Solexa Limited Procede ameliore de detection de nucleotides
US20060240439A1 (en) 2003-09-11 2006-10-26 Smith Geoffrey P Modified polymerases for improved incorporation of nucleotide analogues
US20060281109A1 (en) 2005-05-10 2006-12-14 Barr Ost Tobias W Polymerases
WO2007002744A2 (fr) 2005-06-27 2007-01-04 Applied Thin Films, Inc. Microspheres a base de phosphate d'aluminium
WO2007010251A2 (fr) 2005-07-20 2007-01-25 Solexa Limited Preparation de matrices pour sequencage d'acides nucleiques
US7211414B2 (en) 2000-12-01 2007-05-01 Visigen Biotechnologies, Inc. Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity
US7315019B2 (en) 2004-09-17 2008-01-01 Pacific Biosciences Of California, Inc. Arrays of optical confinements and uses thereof
US7329492B2 (en) 2000-07-07 2008-02-12 Visigen Biotechnologies, Inc. Methods for real-time single molecule sequence determination
US20080108082A1 (en) 2006-10-23 2008-05-08 Pacific Biosciences Of California, Inc. Polymerase enzymes and reagents for enhanced nucleic acid sequencing
US7405281B2 (en) 2005-09-29 2008-07-29 Pacific Biosciences Of California, Inc. Fluorescent nucleotide analogs and uses therefor
US20100111168A1 (en) 2007-02-19 2010-05-06 Freescale Semiconductor, Inc. Data communication unit, data communication network and method of decoding
US20100120098A1 (en) 2008-10-24 2010-05-13 Epicentre Technologies Corporation Transposon end compositions and methods for modifying nucleic acids
WO2012025250A1 (fr) 2010-08-27 2012-03-01 Illumina Cambridge Ltd. Méthodes de séquençage de polynucléotides
US20120270305A1 (en) 2011-01-10 2012-10-25 Illumina Inc. Systems, methods, and apparatuses to image a sample for biological or chemical analysis
US20130260372A1 (en) 2012-04-03 2013-10-03 Illumina, Inc. Integrated optoelectronic read head and fluidic cartridge useful for nucleic acid sequencing
US10246746B2 (en) 2013-12-20 2019-04-02 Illumina, Inc. Preserving genomic connectivity information in fragmented genomic DNA samples

Patent Citations (30)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO1991006678A1 (fr) 1989-10-26 1991-05-16 Sri International Sequençage d'adn
WO1992002258A1 (fr) 1990-07-27 1992-02-20 Isis Pharmaceuticals, Inc. Oligonucleotides, a pyrimidine modifiee et resistants a la nuclease, detectant et modulant l'expression de genes
US5432272A (en) 1990-10-09 1995-07-11 Benner; Steven A. Method for incorporating into a DNA or RNA oligonucleotide using nucleotides bearing heterocyclic bases
WO1993010820A1 (fr) 1991-11-26 1993-06-10 Gilead Sciences, Inc. Formation amelioree de triple et double helices a l'aide d'oligomeres contenant des pyrimidines modifiees
WO1994022892A1 (fr) 1993-03-30 1994-10-13 Sterling Winthrop Inc. Oligonucleotides modifies contant des nucleosides 7-deazapurines
US6150510A (en) 1995-11-06 2000-11-21 Aventis Pharma Deutschland Gmbh Modified oligonucleotides, their preparation and their use
US20050100900A1 (en) 1997-04-01 2005-05-12 Manteia Sa Method of nucleic acid amplification
US7329492B2 (en) 2000-07-07 2008-02-12 Visigen Biotechnologies, Inc. Methods for real-time single molecule sequence determination
US7211414B2 (en) 2000-12-01 2007-05-01 Visigen Biotechnologies, Inc. Enzymatic nucleic acid synthesis: compositions and methods for altering monomer incorporation fidelity
US7057026B2 (en) 2001-12-04 2006-06-06 Solexa Limited Labelled nucleotides
US20060188901A1 (en) 2001-12-04 2006-08-24 Solexa Limited Labelled nucleotides
US20070166705A1 (en) 2002-08-23 2007-07-19 John Milton Modified nucleotides
WO2004018497A2 (fr) 2002-08-23 2004-03-04 Solexa Limited Nucleotides modifies
US20060240439A1 (en) 2003-09-11 2006-10-26 Smith Geoffrey P Modified polymerases for improved incorporation of nucleotide analogues
WO2005065814A1 (fr) 2004-01-07 2005-07-21 Solexa Limited Arrangements moleculaires modifies
US7315019B2 (en) 2004-09-17 2008-01-01 Pacific Biosciences Of California, Inc. Arrays of optical confinements and uses thereof
WO2006064199A1 (fr) 2004-12-13 2006-06-22 Solexa Limited Procede ameliore de detection de nucleotides
US20060281109A1 (en) 2005-05-10 2006-12-14 Barr Ost Tobias W Polymerases
WO2007002744A2 (fr) 2005-06-27 2007-01-04 Applied Thin Films, Inc. Microspheres a base de phosphate d'aluminium
WO2007010251A2 (fr) 2005-07-20 2007-01-25 Solexa Limited Preparation de matrices pour sequencage d'acides nucleiques
US7405281B2 (en) 2005-09-29 2008-07-29 Pacific Biosciences Of California, Inc. Fluorescent nucleotide analogs and uses therefor
US20080108082A1 (en) 2006-10-23 2008-05-08 Pacific Biosciences Of California, Inc. Polymerase enzymes and reagents for enhanced nucleic acid sequencing
US20100111168A1 (en) 2007-02-19 2010-05-06 Freescale Semiconductor, Inc. Data communication unit, data communication network and method of decoding
US20100120098A1 (en) 2008-10-24 2010-05-13 Epicentre Technologies Corporation Transposon end compositions and methods for modifying nucleic acids
WO2012025250A1 (fr) 2010-08-27 2012-03-01 Illumina Cambridge Ltd. Méthodes de séquençage de polynucléotides
EP3205730B1 (fr) * 2010-08-27 2020-05-06 Illumina Cambridge Limited Méthodes de séquencage en «paired end» de polynucléotides
US20120270305A1 (en) 2011-01-10 2012-10-25 Illumina Inc. Systems, methods, and apparatuses to image a sample for biological or chemical analysis
US20130260372A1 (en) 2012-04-03 2013-10-03 Illumina, Inc. Integrated optoelectronic read head and fluidic cartridge useful for nucleic acid sequencing
US10246746B2 (en) 2013-12-20 2019-04-02 Illumina, Inc. Preserving genomic connectivity information in fragmented genomic DNA samples
EP3083994B1 (fr) * 2013-12-20 2021-08-18 Illumina, Inc. Conservation des informations de connectivité génomique dans des échantillons d'adn génomiques fragmentés

Non-Patent Citations (4)

* Cited by examiner, † Cited by third party
Title
BENTLEY ET AL., NATURE, vol. 456, 2008, pages 53 - 59
PEREIRA, ROLIVEIRA, JSOUSA, M: "Bioinformatics and computational tools for next-generation sequencing analysis in clinical genetics", JOURNAL OF CLINICAL MEDICINE, vol. 9, no. 1, 2020, pages 132, XP055870546, DOI: 10.3390/jcm9010132
SAMBROOK ET AL.: "Practical Handbook of Biochemistry and Molecular Biology", 1989, COLD SPRING HARBOR PRESS, pages: 385 - 394
SINGLETON ET AL.: "Dictionary of Microbiology and Molecular Biology", 1994, J. WILEY & SONS

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