FR3099183B1 - Method for detecting and quantifying a biological species of interest by metagenomic analysis, and determining an associated level of confidence - Google Patents

Method for detecting and quantifying a biological species of interest by metagenomic analysis, and determining an associated level of confidence Download PDF

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Publication number
FR3099183B1
FR3099183B1 FR1908364A FR1908364A FR3099183B1 FR 3099183 B1 FR3099183 B1 FR 3099183B1 FR 1908364 A FR1908364 A FR 1908364A FR 1908364 A FR1908364 A FR 1908364A FR 3099183 B1 FR3099183 B1 FR 3099183B1
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Prior art keywords
interest
biological species
species
confidence
detecting
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FR1908364A
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French (fr)
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FR3099183A1 (en
Inventor
Vladimir Lazarevic
Sébastien Hauser
Maud Tournoud
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Biomerieux SA
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Biomerieux SA
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    • 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
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/689—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
    • 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
    • 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
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • 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

Abstract

Procédé de détection d'une espèce biologique d'intérêt (SOI) présente dans un échantillon d'analyse, l'espèce biologique d'intérêt présentant un génome connu, l'échantillon d'analyse comportant un mélange de différentes espèces biologiques, le procédé comportant les étapes suivantes : extraction de séquences de nucléotides de l'échantillon d'analyse ; séquençage des séquences de nucléotides extraites lors de l'étape a) ; à partir du séquençage, obtention de séquences normalisées assignées à l'espèce biologique d'intérêt et à l'espèce de contrôle ; comparaison des séquences normalisées respectivement assignées à l'espèce biologique d'intérêt et à l'espèce de contrôle à des seuils de détection respectivement associés à l'espèce biologique d'intérêt et à l'espèce de contrôle, de façon à déterminer un niveau de confiance à la quantité de séquence déterminée lors de l'étape c), suite aux étapes a) et b), le niveau de confiance étant soit suffisant, soit insuffisant.Method for detecting a biological species of interest (SOI) present in an analysis sample, the biological species of interest having a known genome, the analysis sample comprising a mixture of different biological species, the method comprising the following steps: extraction of nucleotide sequences from the analysis sample; sequencing of the nucleotide sequences extracted during step a); from the sequencing, obtaining standardized sequences assigned to the biological species of interest and to the control species; comparison of the normalized sequences respectively assigned to the biological species of interest and to the control species with detection thresholds respectively associated with the biological species of interest and to the control species, so as to determine a level of confidence in the quantity of sequence determined during step c), following steps a) and b), the level of confidence being either sufficient or insufficient.

FR1908364A 2019-07-23 2019-07-23 Method for detecting and quantifying a biological species of interest by metagenomic analysis, and determining an associated level of confidence Active FR3099183B1 (en)

Priority Applications (1)

Application Number Priority Date Filing Date Title
FR1908364A FR3099183B1 (en) 2019-07-23 2019-07-23 Method for detecting and quantifying a biological species of interest by metagenomic analysis, and determining an associated level of confidence

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
FR1908364 2019-07-23
FR1908364A FR3099183B1 (en) 2019-07-23 2019-07-23 Method for detecting and quantifying a biological species of interest by metagenomic analysis, and determining an associated level of confidence

Publications (2)

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FR3099183A1 FR3099183A1 (en) 2021-01-29
FR3099183B1 true FR3099183B1 (en) 2022-11-18

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FR1908364A Active FR3099183B1 (en) 2019-07-23 2019-07-23 Method for detecting and quantifying a biological species of interest by metagenomic analysis, and determining an associated level of confidence

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Family Cites Families (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
FR3001464B1 (en) 2013-01-25 2016-02-26 Biomerieux Sa METHOD FOR SPECIFIC ISOLATION OF NUCLEIC ACIDS OF INTEREST
EP2985350B1 (en) * 2014-08-14 2017-10-04 microBIOMix GmbH Method for microbiome analysis
CA2998381A1 (en) * 2015-09-21 2017-03-30 The Regents Of The University Of California Pathogen detection using next generation sequencing
US11749381B2 (en) 2016-10-13 2023-09-05 bioMérieux Identification and antibiotic characterization of pathogens in metagenomic sample

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Publication number Publication date
FR3099183A1 (en) 2021-01-29

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