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1. WO2020089337 - SINGLE MOLECULE READER FOR IDENTIFICATION OF BIOPOLYMERS

Publication Number WO/2020/089337
Publication Date 07.05.2020
International Application No. PCT/EP2019/079736
International Filing Date 30.10.2019
IPC
G01N 33/68 2006.01
GPHYSICS
01MEASURING; TESTING
NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
33Investigating or analysing materials by specific methods not covered by groups G01N1/-G01N31/131
48Biological material, e.g. blood, urine; Haemocytometers
50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
68involving proteins, peptides or amino acids
C12Q 1/6869 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
6869Methods for sequencing
G16B 30/00 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
30ICT specially adapted for sequence analysis involving nucleotides or amino acids
G16B 40/00 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
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
CPC
C12Q 1/6869
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
6869Methods for sequencing
C12Q 2537/165
CCHEMISTRY; METALLURGY
12BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
QMEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS
2537Reactions characterised by the reaction format or use of a specific feature
10the purpose or use of
165Mathematical modelling, e.g. logarithm, ratio
G01N 33/6818
GPHYSICS
01MEASURING; TESTING
NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
33Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
48Biological material, e.g. blood, urine
50Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
68involving proteins, peptides or amino acids
6803General methods of protein analysis not limited to specific proteins or families of proteins
6818Sequencing of polypeptides
G16B 30/00
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
30ICT specially adapted for sequence analysis involving nucleotides or amino acids
G16B 40/00
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
40ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
Applicants
  • KATHOLIEKE UNIVERSITEIT LEUVEN [BE]/[BE]
Inventors
  • HOFKENS, Johan
  • JANSSEN, Kris
  • BOUWENS, Arno
  • VITALE, Raffaele
  • DEEN, Jochem
Priority Data
1817786.531.10.2018GB
Publication Language English (EN)
Filing Language English (EN)
Designated States
Title
(EN) SINGLE MOLECULE READER FOR IDENTIFICATION OF BIOPOLYMERS
(FR) LECTEUR À MOLÉCULE UNIQUE POUR L'IDENTIFICATION DE BIOPOLYMÈRES
Abstract
(EN)
The invention relates to methods for the identification of a biopolymer comprising the steps of: (a) measuring the linear pattern of sequence specific markers on a biopolymer, (b) calculating the similarity score between the measured linear pattern and an expected linear pattern for each individual member of a user- defined set of potential target biopolymers, (c) calculating the significance for each of the obtained similarity scores, thereby obtaining a set of target biopolymers with significant similarity of the expected linear pattern to the measured linear pattern, (d) modifying the expected linear pattern of the set of target biopolymers of step c) by reshuffling, adding or removing marker positions from the expected pattern of said target biopolymers, (e) calculating the similarity score between the measured linear pattern and the modified expected linear pattern of step d) for each individual member of the significant set of potential target biopolymers of step b), and (f) calculating the significance for each of the obtained similarity scores, thereby obtaining, compared to the set of target biopolymers of step c, a reduced set of target biopolymers with significant similarity, resulting in improved specificity without loss of sensitivity for the identification of the measured sequence.
(FR)
La présente invention concerne des procédés d'identification d'un biopolymère comprenant les étapes suivantes : (a) mesure du motif linéaire de marqueurs spécifiques de séquence sur un biopolymère, (b) calcul du score de similarité entre le motif linéaire mesuré et un motif linéaire attendu pour chaque membre individuel d'un ensemble défini par l'utilisateur de biopolymères cibles potentiels, (c) calcul de la signification pour chacun des scores de similarité obtenus, obtenant ainsi un ensemble de biopolymères cibles ayant une similarité significative du motif linéaire attendu avec le motif linéaire mesuré, (d) modification du motif linéaire attendu de l'ensemble de biopolymères cibles de l'étape c) par remaniement, ajout ou retrait de positions de marqueur par rapport au motif attendu desdits biopolymères cibles, (e) calcul du score de similarité entre le motif linéaire mesuré et le motif linéaire attendu modifié de l'étape d) pour chaque élément individuel de l'ensemble significatif de biopolymères cibles potentiels de l'étape b), et (f) calcul de la signification pour chacun des scores de similarité obtenus, ce qui permet d'obtenir, par comparaison avec l'ensemble de biopolymères cibles de l'étape c, un ensemble réduit de biopolymères cibles ayant une similarité significative, ce qui permet d'obtenir une spécificité améliorée sans perte de sensibilité pour l'identification de la séquence mesurée.
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