A device for determining a HRD index of presence of Homologous Recombination Deficiency, HRD, in a genome of a subject, the device being configured for: receiving shallow WGS data and non-shallow sequencing data relative to a group of genes in the subject genome, obtaining at least one first parameter from the shallow WGS data and at least one second parameter from non-shallow sequencing data, and determining, by applying a HRD prediction Machine Learning Model to the obtained at least first and second parameters, an HRD index representative of presence of HRD in the subject genome.
A computer-implemented method for decision support of a user to standardize phenotyping in genomic analysis of a subject, wherein the method includes: receiving a list of symptoms having at least one symptom observed for the subject; receiving a first graph having nodes and weighted links; receiving a second graph being previously obtained applying a matrix factorization to a gene-symptom matrix; and outputting at least one gene associated to the list of symptoms based on the first graph and on the second graph.
G16H 50/20 - TIC spécialement adaptées au diagnostic médical, à la simulation médicale ou à l’extraction de données médicalesTIC spécialement adaptées à la détection, au suivi ou à la modélisation d’épidémies ou de pandémies pour le diagnostic assisté par ordinateur, p. ex. basé sur des systèmes experts médicaux
G06N 5/022 - Ingénierie de la connaissanceAcquisition de la connaissance
G16B 20/00 - TIC spécialement adaptées à la génomique ou protéomique fonctionnelle, p. ex. corrélations génotype-phénotype
G16B 40/00 - TIC spécialement adaptées aux biostatistiquesTIC spécialement adaptées à l’apprentissage automatique ou à l’exploration de données liées à la bio-informatique, p. ex. extraction de connaissances ou détection de motifs
G16H 50/30 - TIC spécialement adaptées au diagnostic médical, à la simulation médicale ou à l’extraction de données médicalesTIC spécialement adaptées à la détection, au suivi ou à la modélisation d’épidémies ou de pandémies pour le calcul des indices de santéTIC spécialement adaptées au diagnostic médical, à la simulation médicale ou à l’extraction de données médicalesTIC spécialement adaptées à la détection, au suivi ou à la modélisation d’épidémies ou de pandémies pour l’évaluation des risques pour la santé d’une personne
3.
DEVICE AND METHOD FOR AUTOMATIC IDENTIFICATION OF REARRANGEMENTS IN GENOMIC REGIONS
The present invention relates to devices and methods for automatic identification of rearrangements in genomic regions, and in particular, to devices and methods able to identify rearrangements in genomic regions with high sequence homology. The present invention also relates to methods for diagnosing diseases, and methods of treatment of diseases, comprising a step of automatic identification of rearrangements in genomic regions.
The present invention relates to a device for determining a HRD index of presence of Homologous Recombination Deficiency, HRD, in a genome of a subject, said device being configured for: receiving shallow WGS data and non-shallow sequencing data relative to a group of genes in the subject genome, obtaining at least one first parameter from the shallow WGS data and at least one second parameter from non-shallow sequencing data, and determining, by applying a HRD prediction Machine Learning Model to the obtained at least first and second parameters, an HRD index representative of presence of HRD in said subject genome.
The present invention relates to a device for determining a HRD index of presence of Homologous Recombination Deficiency, HRD, in a genome of a subject, said device being configured for: receiving shallow WGS data and non-shallow sequencing data relative to a group of genes in the subject genome, obtaining at least one first parameter from the shallow WGS data and at least one second parameter from non-shallow sequencing data, and determining, by applying a HRD prediction Machine Learning Model to the obtained at least first and second parameters, an HRD index representative of presence of HRD in said subject genome.
The present invention relates to a computer-implemented method for decision support of a user to standardize phenotyping in genomic analysis of a subject, wherein the method comprises: - receiving a list of symptoms comprising at least one symptom observed for the subject; - receiving a first graph comprising nodes and weighted links; - receiving a second graph being previously obtained applying a matrix factorization to a gene-symptom matrix; - outputting at least one gene associated to the list of symptoms based on the first graph and on the second graph.
G16H 50/20 - TIC spécialement adaptées au diagnostic médical, à la simulation médicale ou à l’extraction de données médicalesTIC spécialement adaptées à la détection, au suivi ou à la modélisation d’épidémies ou de pandémies pour le diagnostic assisté par ordinateur, p. ex. basé sur des systèmes experts médicaux
G16H 50/20 - TIC spécialement adaptées au diagnostic médical, à la simulation médicale ou à l’extraction de données médicalesTIC spécialement adaptées à la détection, au suivi ou à la modélisation d’épidémies ou de pandémies pour le diagnostic assisté par ordinateur, p. ex. basé sur des systèmes experts médicaux
8.
METHOD AND DEVICE FOR CLINICAL APPLICATION OF A GENOTYPEPHENOTYPE ASSOCIATION ATLAS
The present invention relates to a device (1) for the identification of genes having the highest probability to be associated to symptoms observed for a subject, said device comprising: at least one input adapted to receive subject data (20) representative of at least one symptom observed for the subject; at least one processor configured to calculate a score vector representative of the probability that each gene is associated to the symptoms observed for the subject; and at least one output adapted to provide at least one prediction (31) based on said score vector, said prediction (31) providing an information of the gene(s) that is(are) more likely to be associated to the symptoms observed for the subject.
09 - Appareils et instruments scientifiques et électriques
42 - Services scientifiques, technologiques et industriels, recherche et conception
Produits et services
Software development kits (SDK); downloadable computer
software applications; application programming interface
(API) software; downloadable interface used to set out,
modify, and store instructions to run software applications;
computer programs, mobile device software and downloadable
computer programs for creating other software applications;
computer programs, downloadable mobile device software and
computer programs for monitoring and interacting with other
interfaces and computer programs; computer programs,
downloadable mobile device software and computer programs
for setting out, modifying and storing instructions for
running software applications; computer programs,
downloadable mobile device software and computer programs
for monitoring and documenting other software applications
and the inputs and outputs of such software applications;
computer programs, downloadable mobile device software and
computer programs for connecting and collaborating with
other users; computer programs, downloadable mobile device
software and computer programs for conducting genomic
analyses; computer programs, downloadable mobile device
software and computer programs for uploading, sharing,
storing, analyzing, managing and transferring genomic data;
computer programs, downloadable mobile device software and
computer programs for performing laboratory sequencing
services, cancer diagnosis, assembly of sequence readings,
alignment of sequence readings, detection and description of
gene mutations and variations, genotyping of samples,
isoform identification and quantification, discovery and
description of the genetic background of a population,
discovery and description of disease progression in
organisms and populations, discovery and description of sets
of genetic possibilities for a given population,
subpopulation, species, variant or given disease, generation
and control of versions of simulated data sets and
generation and control of versions of empirical genetic data
sets; software enabling the collection, compilation,
systematization and/or evaluation of genomic data. Research services in the field of genomics; research and
development services in the field of medical diagnostics
tools and software design; software design; software
development; updating of software; software as a service
(SaaS); IT platform as a service [PaaS]; cloud computing;
hosting of servers; design and development of operating
software for access to a computer network in the cloud
[cloud computing] as well as use thereof; electronic
storage of data in the field of DNA sequencing for
diagnostic and therapeutic purposes; technical data
analysis in the field of DNA sequencing for diagnostic and
therapeutic purposes; computer services including online
searchable databases and algorithms for the management and
delivery of results of scientific analysis based on genomic
data; quality control; monitoring of computer systems for
detecting unauthorized access or health data breaches.
09 - Appareils et instruments scientifiques et électriques
42 - Services scientifiques, technologiques et industriels, recherche et conception
Produits et services
Software development kits (SDK); downloadable computer
software applications; application programming interface
(API) software; downloadable interface used to set out,
modify, and store instructions to run software applications;
computer programs, mobile device software and downloadable
computer programs for creating other software applications;
computer programs, downloadable mobile device software and
computer programs for monitoring and interacting with other
interfaces and computer programs; computer programs,
downloadable mobile device software and computer programs
for setting out, modifying and storing instructions for
running software applications; computer programs,
downloadable mobile device software and computer programs
for monitoring and documenting other software applications
and the inputs and outputs of such software applications;
computer programs, downloadable mobile device software and
computer programs for connecting and collaborating with
other users; computer programs, downloadable mobile device
software and computer programs for conducting genomic
analyses; computer programs, downloadable mobile device
software and computer programs for uploading, sharing,
storing, analyzing, managing and transferring genomic data;
computer programs, downloadable mobile device software and
computer programs for performing laboratory sequencing
services, cancer diagnosis, assembly of sequence readings,
alignment of sequence readings, detection and description of
gene mutations and variations, genotyping of samples,
isoform identification and quantification, discovery and
description of the genetic background of a population,
discovery and description of disease progression in
organisms and populations, discovery and description of sets
of genetic possibilities for a given population,
subpopulation, species, variant or given disease, generation
and control of versions of simulated data sets and
generation and control of versions of empirical genetic data
sets; software enabling the collection, compilation,
systematization and/or evaluation of genomic data. Research services in the field of genomics; research and
development services in the field of medical diagnostics
tools and software design; software design; software
development; updating of software; software as a service
(SaaS); computer platform as a service [PaaS]; cloud
computing; hosting of servers; design and development of
operating software for access to a computer network in the
cloud [cloud computing] as well as use thereof; electronic
storage of data in the field of DNA sequencing for
diagnostic and therapeutic purposes; technical data
analysis in the field of DNA sequencing for diagnostic and
therapeutic purposes; computer services including online
searchable databases and algorithms for the management and
delivery of results of scientific analysis based on genomic
data; quality control; monitoring of computer systems for
detecting unauthorized access or health data breaches.
09 - Appareils et instruments scientifiques et électriques
42 - Services scientifiques, technologiques et industriels, recherche et conception
Produits et services
Software development kit [SDK]; Computer software applications, downloadable; application programming interface (API) software; downloadable interface used to describe, modify, and store instructions for the execution of software applications; Computer programs for creating other software applications and downloadable computer programs and mobile device software for use in building other software applications; computer programs, downloadable computer programs and mobile device software for use in monitoring and interacting with other computer programs and interfaces; computer programs, downloadable computer programs and mobile device software for use in describing, modifying, and storing instructions for the execution of software applications; computer programs, downloadable computer programs and mobile device software for use in monitoring and documenting other software applications and the inputs and outputs of those software applications; computer programs, downloadable computer programs and mobile device software for use in connecting and collaborating with other users; Computer programs for conducting genome analysis, downloadable computer programs and mobile device software for use in conducting genomics analysis; computer programs, downloadable computer programs and mobile device software for use in uploading, sharing, storing, analyzing, managing, and transferring genomic data; Software, software for mobile and Downloadable computer programmes, for the following purposes: Laboratory sequencing, cancer diagnosis, assembly of sequence readings, alignment of sequence readings, detection and description of genetic mutations and variations, sample genotyping, identification and quantification of isoforms; Software, software for mobile and Downloadable computer programmes, for the following purposes: Discovery and description of a population's genetic background, discovery and description of disease progression in organisms and populations; Software, software for mobile and Downloadable computer programmes, for the following purposes: Discovery and description of genetic possibility sets for a given population, subpopulation, species, variant, or disease, production and version control of sets of simulated data and production and version control of sets of empirical genetic data; Software, for the following purposes: Genomic data collection, establishment, systematisation and/or evaluation. genomics research; Research and development services, In the field of design of medical diagnostic tools and software; Computer software design; Software development; Updating of computer software; Software as a service [SaaS]; Platform as a service [PaaS]; Cloud computing; Server hosting; Design and development of operating software for accessing and using a cloud computing network; Electronic data storage, In the field of DNA sequencing, for the following purposes: diagnosing and Therapy; Analysis of technical data, In the field of DNA sequencing, for the following purposes: diagnosing and Therapy; Computer services including online searchable databases and algorithms for managing and providing scientific analysis results based on genomics data; Quality control; Monitoring of computer systems for detecting unauthorized access or data breach, In the field of heath.
09 - Appareils et instruments scientifiques et électriques
42 - Services scientifiques, technologiques et industriels, recherche et conception
Produits et services
(1) Kits de développement logiciel (SDK) dans le domaine de l'analyse génomique; applications logicielles informatiques téléchargeables pour l'analyse scientifique de séquences génétiques; logiciels destiné à être utilisé comme d'interface de programmation d'applications (API) dans le domaine de l'analyse scientifique de séquences génétiques; logiciel téléchargeable d'interface utilisateur graphique utilisée pour décrire, modifier et stocker des instructions informatiques permettant l'exécution d'applications logicielles; programmes informatiques, logiciels d'applications mobiles et programmes informatiques téléchargeables pour la création d'autres applications logicielles dans le domaine de l'analyse génomique; programmes informatiques, logiciels d'applications mobiles et programmes informatiques téléchargeables pour la surveillance à distance du fonctionnement du matériel et du réseau informatique et l'interaction avec d'autres interfaces de programmation d'applications (API) et programmes informatiques; programmes informatiques, logiciels d'applications mobiles et programmes informatiques téléchargeables pour l'identification, la modification et le stockage d'instructions informatiques permettant l'exécution d'applications logicielles; programmes informatiques, logiciels d'applications mobiles et programmes informatiques téléchargeables pour la surveillance et la documentation du fonctionnement, de l'état et de l'utilisation d'autres applications logicielles et les entrées et sorties d'instructions informatiques de ces applications logicielles; programmes informatiques, logiciels d'applications mobiles et programmes informatiques téléchargeables pour la connexion d'ordinateurs et la collaboration avec d'autres utilisateurs pour accéder à des données dans le domaine de l'analyse génomique; programmes informatiques, logiciels de dispositifs mobiles et programmes informatiques téléchargeables pour la conduite d'analyses génomiques; programmes informatiques, logiciels de dispositifs mobiles et programmes informatiques téléchargeables pour le téléchargement en amont, le partage, le stockage, l'analyse, la gestion et le transfert de données génomiques; programmes informatiques, logiciels de dispositifs mobiles et programmes informatiques téléchargeables pour la réalisation de services de séquençage en laboratoire, le diagnostic du cancer, l'assemblage de lectures de séquence, l'alignement de lectures de séquence, la détection et la description de mutations et variations génétiques, le génotypage d'échantillons, l'identification et la quantification d'isoformes, la découverte et la description des antécédents génétiques d'une population, la découverte et la description de la progression d'une maladie dans des organismes et populations, la découverte et la description d'ensembles de possibilités génétiques pour une population donnée, une sous-population, une espèce, une variante ou une maladie donnée, la production et le contrôle des versions d'ensembles de données simulées et la production et le contrôle des versions d'ensembles de données génétiques empiriques; logiciels permettant la collecte, l'établissement, la systématisation et l'évaluation de données génomiques. (1) Services de recherche dans le domaine de la génomique; services de recherche et développement dans le domaine de la conception d'outils et de logiciels de diagnostic médical; conception de logiciels; développement de logiciels; mise à jour de logiciels; logiciel-service (SaaS) pour l'analyse scientifique de séquences génétiques, logiciel-service (SaaS) permettant d'évaluer, d'analyser et de recueillir des données dans le domaine de l'analyse génomique; plateforme informatique en tant que service [PaaS] pour l'analyse scientifique de séquences génétiques et permettant d'évaluer, d'analyser et de recueillir des données dans le domaine de l'analyse génomique; informatique en nuage offrant des logiciels de gestion de bases de données, informatique en nuage comprenant des logiciels destinés à être utilisés dans le domaine de l'analyse génomique; hébergement de serveurs; conception et développement de logiciels d'exploitation permettant l'accès à un réseau d'informatique dans le nuage [cloud computing] ainsi que son utilisation; stockage électronique de données dans le domaine du séquençage d'ADN à des fins diagnostiques et thérapeutiques; analyse de données techniques dans le domaine du séquençage d'ADN à des fins diagnostiques et thérapeutiques; services informatiques nommément conception et développement de bases de données consultables en ligne et d'algorithmes pour la gestion et la fourniture de résultats d'analyses scientifiques basés sur des données génomiques; contrôle de qualité de résultats d'analyses scientifiques basés sur des données génomiques; surveillance de systèmes informatiques pour la détection d'accès non autorisés ou d'atteintes à la protection de données de santé.
13.
System for analysing genomic data comprising a plurality of application nodes and a knowledge database
A genomic data analysis architecture includes a plurality of application nodes, each application node including a calculation system including at least one calculation node, the calculation system being constructed and arranged so as to carry out genomic calculations, a human-machine interface constructed and arranged so as to communicate with the calculation system, and a knowledge base access interface, and including a knowledge base constructed and arranged so as to communicate with the plurality of application nodes. The knowledge base contains genomic data.
