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1. WO2020109600 - TUBERCULOSIS RESISTANCE PREDICTION METHOD

Publication Number WO/2020/109600
Publication Date 04.06.2020
International Application No. PCT/EP2019/083171
International Filing Date 29.11.2019
IPC
C12Q 1/689 2018.01
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING 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
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
68involving nucleic acids
6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
6888for detection or identification of organisms
689for bacteria
G16B 20/20 2019.01
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
20ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
20Allele or variant detection, e.g. single nucleotide polymorphism detection
CPC
C12Q 1/689
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
1Measuring or testing processes involving enzymes, nucleic acids or microorganisms
68involving nucleic acids
6876Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
6888for detection or identification of organisms
689for bacteria
C12Q 2600/106
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
2600Oligonucleotides characterized by their use
106Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
C12Q 2600/156
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
2600Oligonucleotides characterized by their use
156Polymorphic or mutational markers
G16B 20/20
GPHYSICS
16INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
BBIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
20ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
20Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
Applicants
  • UNIVERSITÄT ZÜRICH [CH]/[CH]
Inventors
  • BUCH, Thorsten
  • PRAJWAL, Prajwal
  • DÜMCKE, Sebastian
Agents
  • SCHULZ JUNGHANS PATENTANWÄLTE PARTGMBB
Priority Data
18209254.429.11.2018EP
19158962.122.02.2019EP
Publication Language English (EN)
Filing Language English (EN)
Designated States
Title
(EN) TUBERCULOSIS RESISTANCE PREDICTION METHOD
(FR) MÉTHODE DE PRÉDICTION DE RÉSISTANCE À LA TUBERCULOSE
Abstract
(EN)
The invention relates to a method for predicting mycobacterial drug resistance by isolating mycobacterial nucleic acid from a sample, obtaining a sample sequence from the nucleic acid, aligning and comparing the sample sequence to a reference sequence and determining for each reference position whether the sample sequence value is the same as a particular sequence value assigned to the position in a table. If both values are the same, a position weight value is assigned to the position. A predictor value is obtained by adding all position weight values and the predictor value is compared to a threshold value. If the predictor value is smaller than the threshold value, drug resistance is predicted. The invention encompasses a system for practicing the method, and the use of certain antibacterial drugs to treat infections by pathogens, resistance of which has been determined by the method of the invention.
(FR)
L'invention concerne une méthode de prédiction de la résistance aux médicaments mycobactériens consistant à isoler de l'acide nucléique mycobactérien à partir d'un échantillon, à obtenir une séquence d'échantillon à partir de l'acide nucléique, à aligner et comparer la séquence d'échantillon à une séquence de référence et à déterminer, pour chaque position de référence, si la valeur de séquence d'échantillon est identique à une valeur de séquence particulière attribuée à la position dans une table. Si les deux valeurs sont les mêmes, une pondération de position est attribuée à la position. Une valeur de prédiction est obtenue en additionnant toutes les pondérations de position et la valeur de prédiction est comparée à une valeur de seuil. Si la valeur de prédiction est inférieure à la valeur seuil, la résistance aux médicaments est prédite. L'invention concerne un système pour mettre en œuvre la méthode, et l'utilisation de certains médicaments antibactériens pour traiter des infections par des pathogènes, dont la résistance a été déterminée par le procédé de l'invention.
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