WO2023196925A3 - Méthodes et systèmes de typage d'allèles - Google Patents

Méthodes et systèmes de typage d'allèles Download PDF

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Publication number
WO2023196925A3
WO2023196925A3 PCT/US2023/065469 US2023065469W WO2023196925A3 WO 2023196925 A3 WO2023196925 A3 WO 2023196925A3 US 2023065469 W US2023065469 W US 2023065469W WO 2023196925 A3 WO2023196925 A3 WO 2023196925A3
Authority
WO
WIPO (PCT)
Prior art keywords
systems
methods
allele typing
allele
typing
Prior art date
Application number
PCT/US2023/065469
Other languages
English (en)
Other versions
WO2023196925A2 (fr
Inventor
Sante GNERRE
Original Assignee
Guardant Health, 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 Guardant Health, Inc. filed Critical Guardant Health, Inc.
Publication of WO2023196925A2 publication Critical patent/WO2023196925A2/fr
Publication of WO2023196925A3 publication Critical patent/WO2023196925A3/fr

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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
    • G16B30/10—Sequence alignment; Homology search
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6881—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
    • 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
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • 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
    • G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
    • G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Landscapes

  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Genetics & Genomics (AREA)
  • Zoology (AREA)
  • General Health & Medical Sciences (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • Biophysics (AREA)
  • Molecular Biology (AREA)
  • Immunology (AREA)
  • Spectroscopy & Molecular Physics (AREA)
  • Theoretical Computer Science (AREA)
  • Microbiology (AREA)
  • Bioinformatics & Computational Biology (AREA)
  • Medical Informatics (AREA)
  • Evolutionary Biology (AREA)
  • Biochemistry (AREA)
  • General Engineering & Computer Science (AREA)
  • Pathology (AREA)
  • Cell Biology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

L'invention concerne des méthodes et des systèmes de typage d'allèles et d'appel de variants.
PCT/US2023/065469 2022-04-07 2023-04-06 Méthodes et systèmes de typage d'allèles WO2023196925A2 (fr)

Applications Claiming Priority (4)

Application Number Priority Date Filing Date Title
US202263328681P 2022-04-07 2022-04-07
US63/328,681 2022-04-07
US202363487926P 2023-03-02 2023-03-02
US63/487,926 2023-03-02

Publications (2)

Publication Number Publication Date
WO2023196925A2 WO2023196925A2 (fr) 2023-10-12
WO2023196925A3 true WO2023196925A3 (fr) 2023-11-16

Family

ID=88243801

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2023/065469 WO2023196925A2 (fr) 2022-04-07 2023-04-06 Méthodes et systèmes de typage d'allèles

Country Status (1)

Country Link
WO (1) WO2023196925A2 (fr)

Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150218546A1 (en) * 2011-04-05 2015-08-06 Lars Klareskog Novel peptides that bind to types of mhc class ii and their use on diagnosis and treatment
US20190121940A1 (en) * 2013-10-15 2019-04-25 Regeneron Pharmaceuticals, Inc High resolution allele identification
US20200239952A1 (en) * 2016-05-27 2020-07-30 Human Longevity, Inc. Methods of human leukocyte antigen typing

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20150218546A1 (en) * 2011-04-05 2015-08-06 Lars Klareskog Novel peptides that bind to types of mhc class ii and their use on diagnosis and treatment
US20190121940A1 (en) * 2013-10-15 2019-04-25 Regeneron Pharmaceuticals, Inc High resolution allele identification
US20200239952A1 (en) * 2016-05-27 2020-07-30 Human Longevity, Inc. Methods of human leukocyte antigen typing

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
BENEDICT PATEN;DANIEL R ZERBINO;GLENN HICKEY;DAVID HAUSSLER: "A unifying model of genome evolution under parsimony", BMC BIOINFORMATICS, BIOMED CENTRAL , LONDON, GB, vol. 15, no. 1, 19 June 2014 (2014-06-19), GB , pages 206, XP021189927, ISSN: 1471-2105, DOI: 10.1186/1471-2105-15-206 *
HAVELL MARKUS, CONTENTE-CUOMO TANIA, FAROOQ MARIA, LIANG WINNIE S., BORAD MITESH J., SIVAKUMAR SHIVAN, GOLLINS SIMON, TRAN NHAN L.: "Evaluation of pre-analytical factors affecting plasma DNA analysis", SCIENTIFIC REPORTS, vol. 8, no. 1, XP055495793, DOI: 10.1038/s41598-018-25810-0 *
KIM ET AL.: "Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype", NATURE BIOTECHNOLOGY, vol. 37, no. 8, August 2019 (2019-08-01), pages 907 - 915, XP036850003, DOI: 10.1038/s41587-019-0201-4 *

Also Published As

Publication number Publication date
WO2023196925A2 (fr) 2023-10-12

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