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1. WO2020109356 - VECTOR-BASED HAPLOTYPE IDENTIFICATION

Publication Number WO/2020/109356
Publication Date 04.06.2020
International Application No. PCT/EP2019/082673
International Filing Date 27.11.2019
IPC
G16B 20/00 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
20ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
G16B 45/00 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
45ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
CPC
G16B 20/00
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
20ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
G16B 45/00
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
45ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
Applicants
  • KWS SAAT SE & CO. KGAA [DE]/[DE]
Inventors
  • WAGNER, Christian
  • NEMRI, Adnane
  • REINHARDT, Franz-Josef
Priority Data
18208717.127.11.2018EP
Publication Language English (EN)
Filing Language English (EN)
Designated States
Title
(EN) VECTOR-BASED HAPLOTYPE IDENTIFICATION
(FR) IDENTIFICATION D'HAPLOTYPE BASÉE SUR UN VECTEUR
Abstract
(EN)
The invention relates to a computer-implemented method for identifying haplotypes in a set of sources of genetic information. The method comprises: ‐ providing (102) a 2D matrix (202) comprising a first (304) and a second (302) dimension and a plurality of 2D matrix cells (306, 308); the first dimension represents a sequence of genomic positions, the second dimension represents an ordered list of the sources of genetic information, each of the cells comprising a genomic feature that was observed in the cell's assigned source of genetic information at the cell's assigned genomic position; ‐ computing (104), for each of the cells, a vector (404) comprising multiple elements respectively comprising an identity indicator; ‐ comparing (106) the vectors with each other for identifying two or more continuous or discontinuous blocks of cells in the 2D matrix that have similar vectors; and ‐ outputting (108) the identified blocks of cells, each identified block of cells representing a haplotype.
(FR)
L'invention concerne un procédé mis en œuvre par ordinateur pour identifier des haplotypes dans un ensemble de sources d'informations génétiques. Le procédé comprend : - fournir (102) une matrice bidimensionnelle (2D) (202) comprenant une première (304) et une seconde (302) dimension et une pluralité de cellules de matrice 2D (306, 308) ; la première dimension représente une séquence de positions génomiques, la seconde dimension représente une liste ordonnée des sources d'informations génétiques, chacune des cellules comprenant une caractéristique génomique qui a été observée dans la source d'informations génétiques attribuée à la cellule à la position génomique attribuée à la cellule ; - calculer (104), pour chacune des cellules, un vecteur (404) comprenant de multiples éléments comprenant respectivement un indicateur d'identité ; - comparer (106) les vecteurs les uns aux autres pour identifier au moins deux blocs continus ou discontinus de cellules dans la matrice 2D qui ont des vecteurs similaires ; et - délivrer (108) les blocs identifiés de cellules, chaque bloc identifié de cellules représentant un haplotype.
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