A device and method for monitoring alleles in samples may involve obtaining lists of variants with support metrics from the samples, reconciling and combining the variant information into a single list with support metrics, transmitting the combined list to a dynamic user interface, selecting markers of interest based on user criteria from the interface, and generating an interpretation and displaying metrics based on user-defined parameters. The method may streamline the process of analyzing genetic data by consolidating variant information, facilitating user interaction through a dynamic interface, and providing customizable interpretation options for efficient and user-friendly allele monitoring.
A device and method for monitoring alleles in samples may involve obtaining lists of variants with support metrics from the samples, reconciling and combining the variant information into a single list with support metrics, transmitting the combined list to a dynamic user interface, selecting markers of interest based on user criteria from the interface, and generating an interpretation and displaying metrics based on user-defined parameters. The method may streamline the process of analyzing genetic data by consolidating variant information, facilitating user interaction through a dynamic interface, and providing customizable interpretation options for efficient and user-friendly allele monitoring.
G16B 40/10 - Signal processing, e.g. from mass spectrometry [MS] or from PCR
G16H 10/40 - ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis
G16H 15/00 - ICT specially adapted for medical reports, e.g. generation or transmission thereof
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
G16H 50/70 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for mining of medical data, e.g. analysing previous cases of other patients
3.
MACHINE LEARNING PREDICTIVE MODELS OF TREATMENT RESPONSE
The present invention is directed to a computer-implemented method of predicting treatment result (treatment response or treatment efficacy of a patient) based on the patient's multimodal features collected at least at two different time points. In particular, the invention relates to methods for predicting lung cancer patients' response to immunotherapy treatment.
G16H 20/00 - ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
G16H 10/60 - ICT specially adapted for the handling or processing of patient-related medical or healthcare data for patient-specific data, e.g. for electronic patient records
4.
SYSTEM AND METHODS FOR GENERATING CLINICAL PREDICTIONS BASED ON MULTIMODAL MEDICAL DATA
Systems and methods for training predictive models for generating clinical predictions from multimodal medical data include receiving multimodal medical data of one or more medical subjects, and preprocessing and aggregating one or more features of the multimodal medical data. Further, for each cohort of medical subjects from the medical subjects, the method includes training one or more predictive models to generate a clinical prediction for each of the diseases based on the features of the multimodal medical data and deploying the predictive models to a model bank. The predictive models are used for making clinical predictions based on multimodal medical data of individual medical subjects. Use of multimodal medical data improves accuracy of the clinical predictions. Further, deploying predictive models on the model bank improves accessibility and useability of the predictive models.
G16H 10/20 - ICT specially adapted for the handling or processing of patient-related medical or healthcare data for electronic clinical trials or questionnaires
G16H 10/60 - ICT specially adapted for the handling or processing of patient-related medical or healthcare data for patient-specific data, e.g. for electronic patient records
G16H 15/00 - ICT specially adapted for medical reports, e.g. generation or transmission thereof
G16H 20/00 - ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
G16H 50/50 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for simulation or modelling of medical disorders
G16H 50/70 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for mining of medical data, e.g. analysing previous cases of other patients
5.
SYSTEM AND METHODS FOR GENERATING CLINICAL PREDICTIONS BASED ON MULTIMODAL MEDICAL DATA
Systems and methods for training predictive models for generating clinical predictions from multimodal medical data include receiving multimodal medical data of one or more medical subjects, and preprocessing and aggregating one or more features of the multimodal medical data. Further, for each cohort of medical subjects from the medical subjects, the method includes training one or more predictive models to generate a clinical prediction for each of the diseases based on the features of the multimodal medical data and deploying the predictive models to a model bank. The predictive models are used for making clinical predictions based on multimodal medical data of individual medical subjects. Use of multimodal medical data improves accuracy of the clinical predictions. Further, deploying predictive models on the model bank improves accessibility and useability of the predictive models.
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
NAltiNAlti, comprising: computing a number of reads supporting the presence of the variant, and computing a depth of sequencing at the locus; modeling, over each of the at least one genomic loci, according to a normalized coverage and an observed variant fraction, an allele-specific copy number for the at least one genomic loci; and outputting, for each of the at least one genomic loci, at least one of an absolute copy number or an allelic composition.
The present invention is directed to the probes for detecting known and unknown fusion genes, related methods of detection of fusion genes, uses and kits related thereto. In particular, the invention relates to methods of diagnosing and monitoring of a cancer.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
8.
METHODS FOR DETECTING VARIANTS IN NEXT-GENERATION SEQUENCING GENOMIC DATA
A genomic data analyzer may be configured to detect and characterize, with a variant calling module, genomic variant scenarios on sequencing reads from an enriched patient genomic sample comprising a combination of a first repeat pattern and a second repeat pattern, such as repeats of homopolymer (single nucleotide) and/or heteropolymer (multiple nucleotide) basic motifs. The variant calling module may estimate the probability distribution of the length of the first repeat pattern and the probability distribution of the repeat pattern length measurements in patient data to the distribution of the repeat pattern length measurements in control data, in order to remove biases possibly induced by the next generation sequencing laboratory setup both in control and patient data. The variant calling module may further measure, read by read, the joint probability distribution for the first and the second repeat patterns lengths, and compare it with the expected joint probability distribution for various genomic variant scenarios for the patient, each variant scenario being characterized by a first length of the first repeat pattern and a second length of the second repeat pattern, to select the most likely patient genomic variant scenario as the scenario for which the measured joint probability distribution best matches the expected joint probability distribution.
Provided may be a computer-implemented method for estimating a tumor fraction in a patient sample, comprising the steps of obtaining a catalog of tumor specific variants and whole genome sequencing data from the patient sample. Further, the method may comprise aligning reads to a reference genome; determining a measure of the signal supporting the presence, in the patient sample read alignment file, of variants in the catalog of tumor specific variants; and determining a measure of the noise associated with variants similar to variants in the catalog of tumor specific variants in the patient sample read alignment file. The method may comprise estimating, over iterations, k, the fraction of tumor (eTF) DNA in the patient sample given the measure of the signal and the measure of the noise at all tumor specific positions; and generating a final eTF and a list of somatic variants in the patient sample.
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
Provided may be a computer-implemented method for estimating a tumor fraction in a patient sample, comprising the steps of obtaining a catalog of tumor specific variants and whole genome sequencing data from the patient sample. Further, the method may comprise aligning reads to a reference genome; determining a measure of the signal supporting the presence, in the patient sample read alignment file, of variants in the catalog of tumor specific variants; and determining a measure of the noise associated with variants similar to variants in the catalog of tumor specific variants in the patient sample read alignment file. The method may comprise estimating, over iterations, k, the fraction of tumor (eTF) DNA in the patient sample given the measure of the signal and the measure of the noise at all tumor specific positions; and generating a final eTF and a list of somatic variants in the patient sample.
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
A genomic data analyzer system method to analyze next generation sequencing genomic data from a sourcing laboratory. The method includes receiving, with a processor, a next generation sequencing analysis request from a sourcing laboratory, the next generation sequencing request comprising at least a raw next generation sequencing data file and the sourcing laboratory identification; identifying, with a processor, a first set of characteristics associated with the next generation sequencing analysis request, the first set of characteristics comprising at least a target enrichment technology identifier, a sequencing technology identifier, and a genomic context identifier; configuring, with a processor, a data alignment module to align the input raw sequencing data file in accordance with at least one characteristic of said first set of characteristics; and aligning, with the data alignment module processor, the input sequencing data to a genomic sequence.
A genomic data analyzer may be configured to detect and characterize, with a variant analysis module, biallelic genomic alterations for at least one gene in next generation sequencing variant calling information for patient tumor samples characterized by different purity ratios of somatic genomic material. The variant analysis module may compare the observed variant fraction distributions of putative heterozygous germline mutations to the theoretical distributions corresponding to different chromosomal aberration events to detect a combination of genomic alteration events possibly causing the biallelic loss of function of the gene. The variant analysis module may be used in cost effective, fully automated next-generation-sequencing oncogenomics testing to identify biallelic loss of function on tumor suppressor genes to facilitate the biological understanding and choice of a personalized oncology treatment targeting the analyzed patient tumor solely from next generation sequencing data variant information, without requiring complementary germline analysis or biological assays. The proposed genomic data analyzed may for instance help determine whether certain PARP inhibitors such as Olaparib are a recommended chemotherapy treatment to target ovarian or breast cancers in accordance with the BRCA1 and/or BRCA2 biallelic loss of function analysis.
Clinical decisions are now based on large amounts of data from diverse sources and modalities. The medical personnel (MP) or user is now facing the challenge of leveraging available data to ensure clinical and patient management decisions are based on the most relevant and up-to-date data for the condition and are adapted to the patient profile. One aim of the present invention is to provide the medical personnel or a user with a system for monitoring patient clinical outcome and for supporting clinical decision in a system for monitoring the patient clinical data and allowing to compare the clinical data of the patient with patients showing similar pattern.
G16H 10/60 - ICT specially adapted for the handling or processing of patient-related medical or healthcare data for patient-specific data, e.g. for electronic patient records
G16H 50/70 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for mining of medical data, e.g. analysing previous cases of other patients
14.
MACHINE LEARNING PREDICTIVE MODELS OF TREATMENT RESPONSE
The present invention is directed to a computer-implemented method of predicting treatment result (treatment response or treatment efficacy of a patient) based on the patient's multimodal features collected at least at two different time points. In particular, the invention relates to methods for predicting lung cancer patients' response to immunotherapy treatment.
G16H 50/50 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for simulation or modelling of medical disorders
G16H 50/70 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for mining of medical data, e.g. analysing previous cases of other patients
15.
MACHINE LEARNING PREDICTIVE MODELS OF TREATMENT RESPONSE
The present invention is directed to a computer-implemented method of predicting treatment result (treatment response or treatment efficacy) of a patient based on the patient's multimodal features. In particular, the invention relates to methods for predicting lung cancer patients' response to immunotherapy treatment.
G16H 50/50 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for simulation or modelling of medical disorders
G16H 50/70 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for mining of medical data, e.g. analysing previous cases of other patients
A multi-purpose automated radiomics workflow is proposed which facilitates the extraction of a bank of radiomics features for a diversity of imaging modalities and patient pathologies. It is versatile enough to provide a robust extraction of the radiomics features without requiring manual corrections even when the patient pathology is characterized by multisite lesions and thus multiple segmented sites, such as for instance multiple tumors or metastasis sites in late cancer stages.
G06V 10/82 - Arrangements for image or video recognition or understanding using pattern recognition or machine learning using neural networks
G06V 10/44 - Local feature extraction by analysis of parts of the pattern, e.g. by detecting edges, contours, loops, corners, strokes or intersectionsConnectivity analysis, e.g. of connected components
G06V 20/70 - Labelling scene content, e.g. deriving syntactic or semantic representations
G06V 20/90 - Identifying an image sensor based on its output data
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers; data banks
(software); software (recorded programs); software for data
analysis integrating automatic learning and artificial
intelligence components; computer programs for data search,
collection, management, storage and analysis; data
processing apparatus; integrated circuits containing
programs for audio, video or computer data processing;
recorded or downloaded sounds, images or data. Project studies, technical research and appraisals; writing,
design, development and updating of software; technical
support concerning the use of software; hosting of online
platforms; provision of non-downloadable software on line;
providing temporary use of non-downloadable software on
platforms, enabling users to access software, computer
networks, computer servers and computer and electronic data
storage systems; providing temporary use of non-downloadable
software for importing, management and analysis of data,
incorporating automatic learning and artificial intelligence
components; providing software (Software as a Service,
SaaS); software as a service [SaaS] featuring software for
automatic learning and artificial intelligence to be used
for data analysis; providing scientific information via
web-based platforms; electronic data storage and cloud
computing services for bioinformatics analysis;
bioinformatic analysis services, development of software and
pipeline architectures; providing methods and tools for
calculations and bioinformatics for data analysis;
development and maintenance of data management software,
database construction; development of genomic and
bioinformatic applications; computerized electronic data
storage; providing advice and information for the aforesaid
services or those relating thereto. Medical services; health services; medical analysis services
related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers; data banks
(software); software (recorded programs); software for data
analysis integrating automatic learning and artificial
intelligence components; computer programs for data search,
collection, management, storage and analysis; data
processing apparatus; integrated circuits containing
programs for audio, video or computer data processing;
recorded or downloaded sounds, images or data. Project studies, technical research and appraisals; writing,
design, development and updating of software; technical
support concerning the use of software; hosting of online
platforms; provision of non-downloadable software on line;
providing temporary use of non-downloadable software on
platforms, enabling users to access software, computer
networks, computer servers and computer and electronic data
storage systems; providing temporary use of non-downloadable
software for importing, management and analysis of data,
incorporating automatic learning and artificial intelligence
components; providing software (Software as a Service,
SaaS); software as a service [SaaS] featuring software for
automatic learning and artificial intelligence to be used
for data analysis; providing scientific information via
web-based platforms; electronic data storage and cloud
computing services for bioinformatics analysis;
bioinformatic analysis services, development of software and
pipeline architectures; providing methods and tools for
calculations and bioinformatics for data analysis;
development and maintenance of data management software,
database construction; development of genomic and
bioinformatic applications; computerized electronic data
storage; providing advice and information for the aforesaid
services or those relating thereto. Medical services; health services; medical analysis services
related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers; data banks
(software); software (recorded programs); software for data
analysis integrating automatic learning and artificial
intelligence components; computer programs for data search,
collection, management, storage and analysis; data
processing apparatus; integrated circuits containing
programs for audio, video or computer data processing;
recorded or downloaded sounds, images or data. Project studies, technical research and appraisals; writing,
design, development and updating of software; technical
support concerning the use of software; hosting of online
platforms; provision of non-downloadable software on line;
providing temporary use of non-downloadable software on
platforms, enabling users to access software, computer
networks, computer servers and computer and electronic data
storage systems; providing temporary use of non-downloadable
software for importing, management and analysis of data,
incorporating automatic learning and artificial intelligence
components; providing software (Software as a Service,
SaaS); software as a service [SaaS] featuring software for
automatic learning and artificial intelligence to be used
for data analysis; providing scientific information via
web-based platforms; electronic data storage and cloud
computing services for bioinformatics analysis;
bioinformatic analysis services, development of software and
pipeline architectures; providing methods and tools for
calculations and bioinformatics for data analysis;
development and maintenance of data management software,
database construction; development of genomic and
bioinformatic applications; computerized electronic data
storage; providing advice and information for the aforesaid
services or those relating thereto. Medical services; health services; medical analysis services
related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
20.
METHODS AND SYSTEMS FOR DETECTING TUMOR MUTATIONAL BURDEN
A computer-implemented method may obtain variant calling data for the tumor sample. The method may identify, in the variant calling data and in view of at least one population database, a list of germline variants for the tumor sample along each chromosome. The method may identify, in the variant calling data, a list of candidate somatic variants. The method may filter out likely germline variants from the list of candidate somatic variants to retain only likely somatic variants, filtering out the likely germline variants further comprising the steps of estimating a probability of each candidate somatic variant i being a germline variant (“Pgermline(i)”); and determine whether a candidate somatic variant i is germline or somatic, to retain only the likely somatic variants in the list of candidate somatic variants, determining the tumor mutational burden (TMB) value for the tumor sample.
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers; data banks being software, namely, recorded and downloadable software for medical and health research; software in the nature of recorded and downloadable software for database management and medical and health research; recorded and downloadable software for data analysis integrating automatic learning and artificial intelligence components; recorded and downloadable computer programs for data search, collection, management, storage and analysis; data processing apparatus; integrated circuits containing programs for audio, video or computer data processing; recorded or downloaded sounds, images or data, namely, downloadable and recorded audio files, downloadable and recorded image files, and downloadable and recorded data files all featuring information in the field of liquid biopsy DNA analysis for medical diagnostics and scientific research purposes Project studies, technical research and appraisals, namely, medical and pharmaceutical project studies, medical and pharmaceutical technical research and medical and pharmaceutical appraisals; writing, design, development and updating of software; technical support concerning the use of software, namely, troubleshooting of computer software problems and help desk services; hosting of online platforms for medical and pharmaceutical purposes; provision of non-downloadable software on line for medical and health research; providing temporary use of non-downloadable software on platforms, enabling users to access software, computer networks, computer servers and computer and electronic data storage systems; providing temporary use of non-downloadable software for importing, management and analysis of data, incorporating automatic learning and artificial intelligence components; providing software as a service (SAAS) featuring software for medical and health research; software as a service (SAAS) featuring software for automatic learning and artificial intelligence to be used for data analysis; providing scientific information in the field of medical and health research, and artificial intelligence via web- based platforms; electronic data storage and cloud computing services in the nature of providing, integration, hosting, and management of private and public cloud computing environments for bioinformatics analysis; bioinformatic analysis services, development of software and data pipeline architectures; providing methods and tools for calculations and bioinformatics for data analysis, namely, research and development services related to bioinformatics for data analysis; development and maintenance of data management software, database construction; development of genomic and bioinformatic applications; computerized electronic data storage; providing advice and information for the aforesaid services Medical services; medical analysis services related to the treatment of individuals; medical diagnostic services, diagnostics in the field of medicine in the nature of medical diagnostic services
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers; data banks being software, namely, recorded and downloadable software for medical and health research; software in the nature of recorded and downloadable software for database management and medical and health research; recorded and downloadable software for data analysis integrating automatic learning and artificial intelligence components; recorded and downloadable computer programs for data search, collection, management, storage and analysis; data processing apparatus; integrated circuits containing programs for audio, video or computer data processing; recorded or downloaded sounds, images or data, namely, downloadable and recorded audio files for medical, pharmaceutical, and health research, in the nature of information regarding Non-Genetic Inheritance (NGI) based detection of microsatellite instability for medical diagnostic and scientific research purposes; downloadable and recorded image files for medical, pharmaceutical, biopharmaceuticals and health research, in the nature of in the nature of information regarding Non-Genetic Inheritance (NGI) based detection of microsatellite instability for medical diagnostic and scientific research purposes; and downloadable and recorded data files for medical, pharmaceutical, biopharmaceuticals and health research in the nature of information regarding Non-Genetic Inheritance (NGI) based detection of microsatellite instability for medical diagnostic and scientific research purposes) Project studies, technical research and appraisals, namely, medical, pharmaceutical, and biopharmaceutical project studies, medical, pharmaceutical, and biopharmaceutical technical research and medical and pharmaceutical and biopharmaceutical appraisals; writing, design, development and updating of software; technical support concerning the use of software, namely, troubleshooting of computer software problems and help desk services; hosting of online platforms for medical, pharmaceutical, and biopharmaceutical purposes; provision of non-downloadable software on line for medical and health research; providing temporary use of non-downloadable software on platforms, enabling users to access software, computer networks, computer servers and computer and electronic data storage systems; providing temporary use of non-downloadable software for importing, management and analysis of data, incorporating automatic learning and artificial intelligence components; providing software as a service (SAAS) featuring software for medical and health research; software as a service (SAAS) featuring software for automatic learning and artificial intelligence to be used for data analysis; providing scientific information in the field of medical and health research, and artificial intelligence via web- based platforms; electronic data storage and cloud computing services in the nature of providing, integration, hosting, and management of private and public cloud computing environments for bioinformatics analysis; bioinformatic analysis services, development of software and data pipeline architectures; providing methods and tools for calculations and bioinformatics for data analysis, namely, research and development services related to bioinformatics for data analysis; development and maintenance of data management software, database construction; development of genomic and bioinformatic applications; computerized electronic data storage; providing advice and information for the aforesaid services Medical services; medical analysis services related to the treatment of individuals; medical diagnostic services, diagnostics in the field of medicine in the nature of medical diagnostic services
09 - Scientific and electric apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers; data banks being software, namely, recorded and downloadable software for medical and health research; software in the nature of recorded and downloadable software for database management and medical and health research; recorded and downloadable software for data analysis integrating automatic learning and artificial intelligence components; recorded and downloadable computer programs for data search, collection, management, storage and analysis; data processing apparatus; integrated circuits containing programs for audio, video or computer data processing; recorded or downloaded sounds, images or data, namely, downloadable and recorded audio files for medical, pharmaceutical, biopharmaceutical, and health research, downloadable and recorded image files for medical, pharmaceutical, biopharmaceutical, and health research, and downloadable and recorded data files for medical, pharmaceutical, biopharmaceutical, and health research Project studies, technical research and appraisals, namely, medical, pharmaceutical, and biopharmaceutical project studies, medical, pharmaceutical, and biopharmaceutical technical research and medical and pharmaceutical and biopharmaceutical appraisals; writing, design, development and updating of software; technical support concerning the use of software, namely, troubleshooting of computer software problems and help desk services; hosting of online platforms for medical, pharmaceutical, and biopharmaceutical purposes; provision of non-downloadable software on line for medical and health research; providing temporary use of non-downloadable software on platforms, enabling users to access software, computer networks, computer servers and computer and electronic data storage systems; providing temporary use of non-downloadable software for importing, management and analysis of data, incorporating automatic learning and artificial intelligence components; providing software as a service (SAAS) featuring software for medical and health research; software as a service (SAAS) featuring software for automatic learning and artificial intelligence to be used for data analysis; providing scientific information in the field of medical and health research, and artificial intelligence via web- based platforms; electronic data storage and cloud computing services in the nature of providing, integration, hosting, and management of private and public cloud computing environments for bioinformatics analysis; bioinformatic analysis services, development of software and data pipeline architectures; providing methods and tools for calculations and bioinformatics for data analysis, namely, research and development services related to bioinformatics for data analysis; development and maintenance of data management software, database construction; development of genomic and bioinformatic applications; computerized electronic data storage; providing advice and information for the aforesaid services Medical services; health services, namely, healthcare research services; medical analysis services related to the treatment of individuals; medical diagnostic services, diagnostics in the field of medicine in the nature of medical diagnostic services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Commercial business management; commercial administration;
office functions; collection of data in a central file;
compilation and systematization of data in data banks;
compilation of information into computer databases; data
processing service by computer; systematization of data in a
central file; professional consultations for organization
and administration of means of recording, transcription,
transformation, composition, compilation and systemization
of computer data (company management and data processing
services). Project studies, technical research and appraisals; writing,
design, development and updating of software; technical
support concerning the use of software; hosting of online
platforms; provision of non-downloadable software on line;
providing software on platforms enabling users to access
software, computer networks, computer servers and computer
and data storage systems and to use them; providing
temporary use of non-downloadable software for importing,
management and analysis of data, incorporating automatic
learning and artificial intelligence components; providing
Software as a Service [SaaS]; software as a service [SaaS]
featuring software for automatic learning and artificial
intelligence to be used for data analysis; providing
scientific information via web-based platforms; data storage
and cloud computing for bioinformatic analysis;
bioinformatic analysis services, development of software and
pipeline architectures; providing methods and tools for
calculations and bioinformatics for data analysis;
development and maintenance of data management software,
database construction; development of genomic and
bioinformatic applications; storage of data by computer;
providing advice and information for the aforesaid services
or those relating thereto. Medical services; health services; medical analysis services
related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
42 - Scientific, technological and industrial services, research and design
Goods & Services
(1) Gestion des affaires commerciales; administration commerciale; fonctions de bureau, à savoir des services de secrétariat et de bureautique; recueil de données dans un fichier central nommément, compilation de données d'affaires dans le domaine médical; compilation et systématisation de données dans des bases de données informatisées; compilation de l'information statistiques commerciales dans le domaine médical dans des bases de données informatiques; service de traitement de données par ordinateur dans le domaine médical; systématisation de données dans un fichier central; services de gestion d'entreprise et de conseil dans le domaine médical concernant l'organisation et l'administration de moyens d'enregistrement, de transcription, de transformation, de composition, de la compilation et systématisation d'une base de données informatique.
(2) Études de projets, expertises et recherches techniques nommément, études de projets techniques dans le domaine de la médecine et pharmacologie, recherche technique dans le domaine de la médecine et pharmacologie, et expertises de médecine et pharmacologie; rédaction, conception, développement et mise à jour de logiciels; support technique concernant l'utilisation de logiciels; hébergement de plateformes en ligne nommément, hébergement de plateformes de logiciels d'autrui sur Internet; fourniture d'une utilisation temporaire de logiciels non téléchargeables permettant d'accéder à des bases de données dans le cadre de services de recherche et de développement dans le domaine de la médecine; fourniture d'une utilisation temporaire d'un logiciel non téléchargeable permettant aux utilisateurs d'accéder à des logiciels, des réseaux informatiques, des serveurs informatiques, des systèmes informatiques et de stockage de données dans le domaine de la médecine; fourniture d'une utilisation temporaire d'un logiciel non téléchargeable qui utilise l'intelligence artificielle et de l'apprentissage automatique pour l'importation, la gestion et l'analyse de données dans le domaine de la médecine; logiciel-service (saas) fourni pour accéder à des renseignements médicaux et à des renseignements sur la santé; logiciel en tant que service (SAAS) comprenant un logiciel informatique non téléchargeable pour l'intégration de l'intelligence artificielle et de l'apprentissage automatique dans le domaine des services de soins de santé pour l'analyse des données commerciales; mise à disposition d'informations scientifiques dans le domaine des services de soins de santé et recherches médicales par le biais d'un site Web; fournisseur d'informatique en nuage pour le stockage de données pour l'analyse de données biologiques; fourniture d'une utilisation temporaire d'un logiciel non téléchargeable pour l'analyse de données biologiques, développement de logiciels et d'architectures pipeline; mise à disposition de méthodes et d'outils de calcul et de bioinformatique pour l'analyse de données nommément, fourniture de services de recherche et de développement dans les domaines de la biotechnologie; développement et maintenance de logiciels de gestion de données, construction de bases de données; développement d'applications logicielles pour des tiers dans le domaine de la biologie moléculaire et biotechnologie; fournisseur d'informatique en nuage pour le stockage de données par ordinateur.
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Commercial business management; commercial administration, namely, business administration services; providing office functions; collection of data in a central file, namely, business data compilation services; compilation and systematization of data in data banks; compilation of information into computer databases; data processing service by computer; systematization of data in a central file; professional consultations for organization and administration of means of recording, transcription, transformation, composition, compilation and systemization of computer data Project studies, technical research and appraisals, namely, medical, pharmaceutical, and biopharmaceutical project studies, medical, pharmaceutical, biopharmaceutical technical research and medical, pharmaceutical, and biopharmaceutical appraisals; writing, design, development and updating of software; technical support concerning the use of software, namely, troubleshooting of computer software problems and help desk services; hosting of online platforms for medical, pharmaceutical, and biopharmaceutical purposes; provision of non-downloadable software on line for medical and health research; providing temporary use of non-downloadable software on platforms, enabling users to access software, computer networks, computer servers and computer and electronic data storage systems; providing temporary use of non-downloadable software for importing, management and analysis of data, incorporating automatic learning and artificial intelligence components; providing software as a service (SAAS) featuring software for medical and health research; software as a service (SAAS) featuring software for automatic learning and artificial intelligence to be used for data analysis; providing scientific information in the field of medical and health research, and artificial intelligence via web- based platforms; electronic data storage and cloud computing services in the nature of providing, integration, hosting, and management of private and public cloud computing environments for bioinformatics analysis; bioinformatic analysis services, development of software and data pipeline architectures; providing methods and tools for calculations and bioinformatics for data analysis, namely, research and development services related to bioinformatics for data analysis; development and maintenance of data management software, database construction; development of genomic and bioinformatic applications; computerized electronic data storage; providing advice and information for the aforesaid services Medical services; health services, namely, healthcare services; medical analysis services related to the treatment of individuals; medical diagnostic services, diagnostics in the field of medicine in the nature of medical diagnostic services
The present invention is directed to the probes for detecting known and unknown fusion genes, related methods of detection of fusion genes, uses and kits related thereto. In particular, the invention relates to methods of diagnosing and monitoring of a cancer.
Methods are disclosed for adding adapters to fragmented nucleic acids for next generation sequencing, including providing numerical codes based on variable adapter molecular barcode lengths on both sides of the fragmented nucleic acids and identifying reads from the same fragment based on both barcodes. The methods and products allow for the amplification of the fragmented nucleic acids when there is a low yield of isolated fragmented nucleic acids and also for efficient and reliable detection of low-frequency mutations including in subpopulations of cells within a subject.
A genomic data decoder may jointly compress and encrypt genomic data alignment information while preserving the privacy of sensitive genomic data elements at retrieval stage. Genomic data alignment information organized as a read-based alignment data stream may be transposed into a position-based alignment data stream. The position-based alignment information may be encoded into a reference-based alignment data stream. The reference-based alignment data stream may be encrypted with a combination of order-preserving encryption of the genomic position information and symmetric encryption of the reference-based alignment differential data. Differential encoding and entropy coding schemes may further compress the reference-based alignment data stream. The resulting compressed and encrypted stream may be indexed and stored in a biobank storage unit. A genomic data decoder may efficiently retrieve, decrypt and decode a specific subset of the resulting compressed and encrypted stream without leaking information on the other genomic data subsets in the resulting stream.
G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
G06F 7/78 - Arrangements for rearranging, permuting or selecting data according to predetermined rules, independently of the content of the data for changing the order of data flow, e.g. matrix transposition or LIFO buffersOverflow or underflow handling therefor
G06F 21/62 - Protecting access to data via a platform, e.g. using keys or access control rules
H04L 9/06 - Arrangements for secret or secure communicationsNetwork security protocols the encryption apparatus using shift registers or memories for blockwise coding, e.g. D.E.S. systems
30.
METHODS FOR IDENTIFYING CHROMOSOMAL SPATIAL INSTABILITY SUCH AS HOMOLOGOUS REPAIR DEFICIENCY IN LOW COVERAGE NEXT- GENERATION SEQUENCING DATA
A genomic data analyzer may be configured to detect and characterize, with a machine learning model such as a trained convolutional neural network, the presence of a genomic instability in a tumor sample. The genomic data analyzer may use whole genome sequencing reads as input data even at low sequencing coverage in a high throughput sequencing workflow as may be routinely employed in a diversity of clinical oncology setups. The genomic data analyzer may arrange the aligned read data coverage from chromosome arms or full chromosomes to form a coverage data signal array possibly as an image. The trained machine learning model may process the coverage data signal array to determine whether a chromosomal spatial instability (CSI) such as for instance a genomic instability caused by a homologous repair or recombination deficiency (HRD) is present in the tumor sample. The latter indication may guide the choice of a preferred anticancer treatment for the tumor.
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers; data banks;
software (recorded programs); software for data analysis
integrating automatic learning and artificial intelligence
components; computer programs for data search, collection,
management, storage and analysis; data processing apparatus;
integrated circuits containing programs for audio, video or
computer data processing; recorded or downloadable sound,
images or data. Commercial business management; commercial administration;
office functions; collection of data in a central file;
compilation and systematization of data in data banks;
compilation of information into computer databases; computer
data processing services; systematization of data in a
central file; professional consulting for the organization
and administration of means of computer data recording,
transcription, conversion, composition, compilation and
systematization. Project studies, technical research and appraisals; writing,
design, development and updating of software; technical
support concerning the use of software; hosting of online
platforms; provision of non-downloadable software on line;
providing software on platforms enabling users to access
software, computer networks, computer servers and computer
and data storage systems and to use them; providing
temporary use of non-downloadable software for importing,
management and analysis of data, incorporating automatic
learning and artificial intelligence components; providing
software (Software as a Service, SaaS); software as a
service [SaaS] featuring software for automatic learning and
artificial intelligence to be used for data analysis;
providing scientific information via web-based platforms;
data storage and cloud computing for bioinformatic analysis;
bioinformatic analysis services, development of software and
pipeline architectures; providing methods and tools for
calculations and bioinformatics for data analysis;
development and maintenance of data management software,
database construction; development of genomic and
bioinformatic applications; storage of data by computer;
providing advice and information for the aforesaid services
or those relating thereto. Medical services; health services; medical analysis services
related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers; data banks
(software); software (recorded programs); software for data
analysis integrating automatic learning and artificial
intelligence components; computer programs for data search,
collection, management, storage and analysis; data
processing apparatus; integrated circuits containing
programs for audio, video or computer data processing;
recorded or downloaded sounds, images or data. Commercial business management; commercial administration;
office functions; collection of data in a central file;
compilation and systematization of data in data banks;
compilation of information into computer databases; data
processing service by computer; systematization of data in a
central file; professional consulting for the organization
and administration of means of computer data recording,
transcription, conversion, composition, compilation and
systematization. Project studies, technical research and appraisals; writing,
design, development and updating of software; technical
support concerning the use of software; hosting of online
platforms; providing online non-downloadable software;
providing software on platforms enabling users to access
software, computer networks, computer servers and computer
and data storage systems and to use them; providing
temporary use of non-downloadable software for importing,
management and analysis of data, incorporating automatic
learning and artificial intelligence components; providing
software (Software as a Service, SaaS); software as a
service [SaaS] featuring software for automatic learning and
artificial intelligence to be used for data analysis;
providing scientific information via web-based platforms;
data storage and cloud computing for bioinformatic analysis;
bioinformatic analysis services, development of software and
pipeline architectures; providing methods and tools for
calculations and bioinformatics for data analysis;
development and maintenance of data management software,
database construction; development of genomic and
bioinformatic applications; electronic storage of data, by
computer; providing advice and information for the aforesaid
services or those relating thereto. Medical services; health services; medical analysis services
related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
33.
METHODS FOR DETECTING AND CHARACTERIZING MICROSATELLITE INSTABILITY WITH HIGH THROUGHPUT SEQUENCING
The characterization, classification and reporting of MSI status of patient genomic samples may be provided by high throughput genomic analysis of a set of microsatellite marker loci. The patient sample may only comprise a low fraction of somatic DNA relative to germline DNA. A multi-parametric background model may be used to infer at least two parameters respectively characterizing the sample variant fraction and the MSI genomic alterations of the patient DNA sample relative to a reference background model of the MSS repeat length distribution, without the need to use a germline control sample. A local MSI score may be calculated as a function of the at least two parameters to characterize the MSI status at each locus, and a global composite MSI score may be calculated over all tested loci to characterize and report the overall MSI status for the patient sample. The proposed methods facilitate the deployment of high-throughput genomic data analysis testing for large pools of patients with comparable sensitivity and specificity to prior art biological MSI-status characterization assays.
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
G16H 10/40 - ICT specially adapted for the handling or processing of patient-related medical or healthcare data for data related to laboratory analysis, e.g. patient specimen analysis
34.
METHODS FOR DETECTING COPY-NUMBER VARIATIONS IN NEXT-GENERATION SEQUENCING
Copy Number Variants (CNV) detection methods may integrate CNV detection into workflow for next generation sequencer (NGS) data processing, in parallel with SNP and INDEL variant calling. CNV detection methods may analyze coverage patterns across a set of genomic regions and across samples from different patients. The methods do not require specifically chosen reference samples as, but automatically select reference samples from the same batch, for each sample tested. CNV detection methods may detect CNVs in a set of samples without assumptions about CNV status of any of those samples. Embodiments herein may apply the CNV detection scheme iteratively to improve detection performance. The proposed methods may further comprise the step of iteratively feeding back information about the CNVs in the samples into the next iteration step. The methods may also use information from the NGS workflow, such as information on SNP fractions, as input to the NGS CNV detection.
A genomic data analyser may process the next generation sequencing data of a patient sample to identify whether a variant is present (positive variant calling), absent at a high confidence (negative variant calling), or equivocal (possible false negative calling) as falling under a calculated limit of detection (LOD). This LOD estimate corresponds the lowest variant allele fraction (VAF) detectable at the required sensitivity (true positive rate). The presently disclosed genomic data analyser may improve any legacy variant caller of the prior art by automatically calculating the limitations of variant calling detection for a user-defined sensitivity and minimal VAF of interest for any variant genomic position and/or mutation, depending on analytical factors of the NGS assay and workflow such as the sample type, the DNA sample amount and the NGS assay library conversion rate (LCR), and/or its molecular barcoding capability, as well as its NGS assay error profile.
A genomic data analyzer may process the next generation sequencing data of a patient sample to identify whether a variant is present (positive variant calling), absent at a high confidence (negative variant calling), or equivocal (possible false negative calling) as falling under a calculated limit of detection (LOD). This LOD estimate corresponds the lowest variant allele fraction (VAF) detectable at the required sensitivity (true positive rate). The presently disclosed genomic data analyzer may improve any legacy variant caller by automatically calculating the limitations of variant calling detection for a user-defined sensitivity and minimal VAF of interest for any variant genomic position and/or mutation, depending on analytical factors of the NGS assay and workflow such as the sample type, the DNA sample amount and the NGS assay library conversion rate (LCR), and/or its molecular barcoding capability, as well as its NGS assay error profile.
Copy Number Variants (CNV) detection methods described herein may efficiently integrate CNV detection into the workflow for a next generation sequencer (NGS) data processing, in parallel with SNP and INDEL variant calling. CNV detection methods as described herein may be performed by analyzing the coverage pattern across a suitable set of genomic regions or amplicons and across a batch of samples from different patients. The proposed methods do not require the use of specifically chosen reference samples as inputs to the workflow, but rather automatically select a set of reference samples from the same batch, for each sample being tested. The CNV detection methods may reliably detect CNVs in a set of samples without prior assumptions about the CNV status of any of those samples. Embodiments described herein may also apply the CNV detection scheme iteratively to further improve the detection performance, especially in the case of more frequent CNV occurrence. Since the knowledge on the CNVs in reference samples may improve their comparison with the sample being tested, the proposed methods may further comprise the step of iteratively feeding back the information about the CNVs found in the samples from any detection step into the next iteration step. The proposed methods may also further use additional information available from the NGS workflow about the samples, such as information on SNP fractions, as input to the NGS CNV detection.
A genomic data analyzer may be configured to detect and characterize, with a machine learning model such as a trained convolutional neural network, the presence of a genomic instability in a tumor sample. The genomic data analyzer may use whole genome sequencing reads as input data even at low sequencing coverage in a high throughput sequencing workflow as may be routinely employed in a diversity of clinical oncology setups. The genomic data analyzer may arrange the aligned read data coverage from chromosome arms or full chromosomes to form a coverage data signal array possibly as an image. The trained machine learning model may process the coverage data signal array to determine whether a chromosomal spatial instability (CSI) such as for instance a genomic instability caused by a homologous repair or recombination deficiency (HRD) is present in the tumor sample. The latter indication may guide the choice of a preferred anticancer treatment for the tumor.
A genomic data analyzer may be configured to detect and characterize, with a machine learning model such as a trained convolutional neural network, the presence of a genomic instability in a tumor sample. The genomic data analyzer may use whole genome sequencing reads as input data even at low sequencing coverage in a high throughput sequencing workflow as may be routinely employed in a diversity of clinical oncology setups. The genomic data analyzer may arrange the aligned read data coverage from chromosome arms or full chromosomes to form a coverage data signal array possibly as an image. The trained machine learning model may process the coverage data signal array to determine whether a chromosomal spatial instability (CSI) such as for instance a genomic instability caused by a homologous repair or recombination deficiency (HRD) is present in the tumor sample. The latter indication may guide the choice of a preferred anticancer treatment for the tumor.
A method to provide personalized data of a patient includes obtaining at least one first personal data for a non-modifiable risk factor, obtaining at least one second personal data for a modifiable risk factor, and normalizing the first and second data using a lookup table, said normalized data representing an increase or decrease versus a neutral value. The method also includes adding the normalized data representing a decrease to a positive parameter, adding the normalized data representing an increase to a negative parameter, displaying the positive and the negative parameters in two distinct colors in a pie shape, the surface of each pie being proportional to the value of each parameter, and displaying in association with the pie shape, the portion of the negative parameter that results from the second personal data.
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
G16H 10/60 - ICT specially adapted for the handling or processing of patient-related medical or healthcare data for patient-specific data, e.g. for electronic patient records
41.
METHODS FOR IDENTIFYING CHROMOSOMAL SPATIAL INSTABILITY SUCH AS HOMOLOGOUS REPAIR DEFICIENCY IN LOW COVERAGE NEXT-GENERATION SEQUENCING DATA
A genomic data analyzer may be configured to detect and characterize, with a machine learning model such as a trained convolutional neural network, the presence of a genomic instability in a tumor sample. The genomic data analyzer may use whole genome sequencing reads as input data even at low sequencing coverage in a high throughput sequencing workflow as may be routinely employed in a diversity of clinical oncology setups. The genomic data analyzer may arrange the aligned read data coverage from chromosome arms or full chromosomes to form a coverage data signal array possibly as an image. The trained machine learning model may process the coverage data signal array to determine whether a chromosomal spatial instability (CSI) such as for instance a genomic instability caused by a homologous repair or recombination deficiency (HRD) is present in the tumor sample. The latter indication may guide the choice of a preferred anticancer treatment for the tumor.
A genomic data analyzer maybe configured to detect and characterize biallelic genomic alterations for at least one gene in next generation sequencing variant calling information for patient tumor samples characterized by different purity ratios of somatic genomic material. The variant analysis module may compare the observed variant fraction distributions of putative heterozygous germline mutations to the theoretical distributions corresponding to different chromosomal aberration events to detect a combination of genomic alteration events. The variant analysis module maybe used in next-generation-sequencing oncogenomics testing to identify biallelic loss of function on tumor suppressor genes to facilitate the biological understanding and choice of a personalized oncology treatment targeting the analyzed patient tumor solely from next generation sequencing data variant information, without requiring complementary germline analysis or biological assays. The proposed genomic data analyzed may help determine whether PARP inhibitors such as Olaparib are a recommended chemotherapy treatment to target ovarian or breast cancers.
Methods and products are disclosed for asymmetrically adapting fragmented nucleic acids for next generation sequencing, including providing strand identifier sequences and index sequences to identify the source strand and sample, respectively, of the fragmented nucleic acids. The methods and products allow for efficient and reliable detection of low-frequency mutations including in subpopulations of cells within a subject and also for the amplification of the fragmented nucleic acids when there is a low yield of isolated fragmented nucleic acids.
The characterization, classification and reporting of MSI status of patient genomic samples may be provided by high throughput genomic analysis of a set of microsatellite marker loci. The patient sample may only comprise a low fraction of somatic DNA relative to germline DNA. A multi-parametric background model may be used to infer at least two parameters respectively characterizing the sample variant fraction and the MSI genomic alterations of the patient DNA sample relative to a reference background model of the MSS repeat length distribution, without the need to use a germline control sample. A local MSI score may be calculated as a function of the at least two parameters to characterize the MSI status at each locus, and a global composite MSI score may be calculated over all tested loci to characterize and report the overall MSI status for the patient sample. The proposed methods facilitate the deployment of high-throughput genomic data analysis testing for large pools of patients with comparable sensitivity and specificity to prior art biological MSI-status characterization assays.
A genomic data analyzer may be configured to detect and characterize, with a variant calling module, genomic variants from next generation sequencing reads out of a pool of enriched genomic patient samples without suffering from next generation sequencing workflow biases such as those introduced by sequencing errors in particular in repeat patterns regions of the human genome such as homopolymers or heteropolymers. The variant calling module may estimate the probability distribution of the length of the repeat pattern for each patient sample and cross-analyze it against other samples in a single experimental pool to identify best-fit variant models for each pair of samples. The variant calling module may further group samples according to their matching best-fit variant models and identify which group of patient samples carries the wild type reference without the need for control data in the pool. The variant calling module may subsequently characterize the homozygous or heterozygous repeat patterns variants for each patient sample with improved specificity and accuracy even in the presence of next generation sequencing biases.
Methods are disclosed for adding adapters to fragmented nucleic acids for next generation sequencing, including providing numerical codes based on variable adapter molecular barcode lengths on both sides of the fragmented nucleic acids and identifying reads from the same fragment based on both barcodes. The methods and products allow for the amplification of the fragmented nucleic acids when there is a low yield of isolated fragmented nucleic acids and also for efficient and reliable detection of low-frequency mutations including in subpopulations of cells within a subject.
A genomic data analyzer workflow may be configured to identify, with a variant annotation module, subsets of patient variants which match at least one medical reference variant database entry, even if tlic variant calling information in genomic data analyzer workflow and the database use different variant representations of SNP. MNP. INDELS and DELINS. In particular. database variants which are included into a subset of patient variants may be identified even if they do not exactly match the corresponding strings. The variant annotation module may be adapted to apply a branch-and-bound-like algorithm to efficiently process all possible subsets of patient variants in a genomic region.
In order to provide comprehensive information about risk factors of a patient, the proposed solution comprises two main phases, the first phase being the determination of the values and the second step being the particular display arrangement of these values in a comprehensive way. It is proposed a method to provide personalized data of a patient comprising : - obtaining at least one first personal data for a non-modifiable risk factor, - obtaining at least one second personal data for a modifiable risk factor, - normalizing the first and second data using a lookup table, said normalized data representing an increase or decrease versus a neutral value, - adding the normalized data representing a decrease to a positive parameter, - adding the normalized data representing an increase to a negative parameter, - displaying the positive and the negative parameters in two distinct colors in a pie shape, the surface of each pie being proportional to the value of each parameter, - displaying in association with the pie shape, the portion of the negative parameter that results from the second personal data.
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
49.
METHODS FOR ASYMMETRIC DNA LIBRARY GENERATION AND OPTIONALLY INTEGRATED DUPLEX SEQUENCING
Methods and products are disclosed for asymmetrically adapting fragmented nucleic acids for next generation sequencing, including providing strand identifier sequences and index sequences to identify the source strand and sample, respectively, of the fragmented nucleic acids. The methods and products allow for efficient and reliable detection of low-frequency mutations including in subpopulations of cells within a subject and also for the amplification of the fragmented nucleic acids when there is a low yield of isolated fragmented nucleic acids.
A genomic data analyzer may be configured to detect and characterize, with a variant calling module, genomic variants from next generation sequencing reads out of a pool of enriched genomic patient samples without suffering from next generation sequencing workflow biases such as those introduced by sequencing errors in particular in repeat patterns regions of the human genome such as homopolymers or heteropolymers. The variant calling module may estimate the probability distribution of the length of the repeat pattern for each patient sample and cross-analyze it against other samples in a single experimental pool to identify best-fit variant models for each pair of samples. The variant calling module may further group samples according to their matching best-fit variant models and identify which group of patient samples carries the wild type reference without the need for control data in the pool. The variant calling module may subsequently characterize the homozygous or heterozygous repeat patterns variants for each patient sample with improved specificity and accuracy even in the presence of next generation sequencing biases.
A genomic data analyzer may be configured to detect and characterize, with a variant calling module, genomic variant scenarios in sequencing reads from an enriched patient genomic sample comprising a combination of a first repeat pattern and a second repeat pattern, such as repeats of homopolymer (single nucleotide) and/or heteropolymer (multiple nucleotide) basic motifs. The variant calling module may estimate the probability distribution of the length of the first repeat pattern and the probability distribution of the length of the second repeat pattern by comparing the distribution of the repeat pattern length measurements in patient data to the distribution of the repeat pattern length measurements in control data, in order to remove biases possibly induced by the next generation sequencing laboratory setup both in control and patient data. The variant calling module may further measure, read by read, the joint probability distribution for the first and the second repeat patterns lengths, and compare it with the expected joint probability distribution for various genomic variant scenarios for the patient, each variant scenario being characterized by a first length of the first repeat pattern and a second length of the second repeat pattern, to select the most likely patient genomic variant scenario as the scenario for which the measured joint probability distribution best matches the expected joint probability distribution.
A genomic data analyzer system method to analyze next generation sequencing genomic data from a sourcing laboratory. The method includes receiving, with a processor, a next generation sequencing analysis request from a sourcing laboratory, the next generation sequencing request comprising at least a raw next generation sequencing data file and the sourcing laboratory identification; identifying, with a processor, a first set of characteristics associated with the next generation sequencing analysis request, the first set of characteristics comprising at least a target enrichment technology identifier, a sequencing technology identifier, and a genomic context identifier; configuring, with a processor, a data alignment module to align the input raw sequencing data file in accordance with at least one characteristic of said first set of characteristics; and aligning, with the data alignment module processor, the input sequencing data to a genomic sequence.
A genomic data analyzer workflow may be configured to identify, with a variant annotation module, subsets of patient variants which match at least one medical reference variant database entry, even if the variant calling information in genomic data analyzer workflow and the database use different variant representations of SNP, MNP, INDELS and DELINS. In particular, database variants which are included into a subset of patient variants may be identified even if they do not exactly match the corresponding strings. The variant annotation module may be adapted to apply a branch-and-bound- like algorithm to efficiently process all possible subsets of patient variants in a genomic region.
A genomic data decoder may jointly compress and encrypt genomic data alignment information while preserving the privacy of sensitive genomic data elements at retrieval stage. Genomic data alignment information organized as a read-based alignment data stream may be transposed into a position-based alignment data stream. The position-based alignment information may been coded into a reference-based alignment data stream. The reference-based alignment data stream may be encrypted with a combination of order-preserving encryption of the genomic position information and symmetric encryption of the reference-based alignment differential data. Differential encoding and entropy coding schemes may further compress the reference-based alignment data stream. The resulting compressed and encrypted stream may be indexed and stored in a biobank storage unit. A genomic data decoder may efficiently retrieve, decrypt and decode a specific subset of the resulting compressed and encrypted stream without leaking information on the other genomic data subsets in the resulting stream.
G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
G06F 7/78 - Arrangements for rearranging, permuting or selecting data according to predetermined rules, independently of the content of the data for changing the order of data flow, e.g. matrix transposition or LIFO buffersOverflow or underflow handling therefor
G06F 21/62 - Protecting access to data via a platform, e.g. using keys or access control rules
H04L 9/06 - Arrangements for secret or secure communicationsNetwork security protocols the encryption apparatus using shift registers or memories for blockwise coding, e.g. D.E.S. systems
55.
METHODS FOR DETECTING BIALLELIC LOSS OF FUNCTION IN NEXT-GENERATION SEQUENCING GENOMIC DATA
A genomic data analyzer maybe configured to detect and characterize, with a variant analysis module, biallelic genomic alterations for at least one gene in next generation sequencing variant calling information for patient tumor samples characterized by different purity ratios of somatic genomic material. The variant analysis module may compare the observed variant fraction distributions of putative heterozygous germline mutations to the theoretical distributions corresponding to different chromosomal aberration events to detect a combination of genomic alteration events possibly causing the biallelic loss of function of the gene. The variant analysis module maybe used in cost effective, fully automated next-generation-sequencing oncogenomics testing to identify biallelic loss of function on tumor suppressor genes to facilitate the biological understanding and choice of a personalized oncology treatment targeting the analyzed patient tumor solely from next generation sequencing data variant information, without requiring complementary germline analysis or biological assays. The proposed genomic data analyzed may for instance help determine whether certain PARP inhibitors such as Olaparib are a recommended chemotherapy treatment to target ovarian or breast cancers in accordance with the BRCA1 and/or BRCA2 biallelic loss of function analysis.
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers; data banks
(software); software (recorded programs); software for
data analysis integrating automatic learning and artificial
intelligence components; computer programs for data search,
collection, management, storage and analysis; data
processing apparatus; integrated circuits containing
programs for audio, video or computer data processing;
recorded or downloaded sounds, images or data. Commercial business management; commercial administration;
office functions; collection of data in a central file;
compilation and systematization of data in data banks;
compilation of information into computer databases; data
processing service by computer; systematization of data in
a central file; professional consulting for the
organization and administration of means of computer data
recording, transcription, conversion, composition,
compilation and systematization. DNA screening for the purposes of scientific research;
laboratory testing services; clinical trials;
computer-aided diagnostic testing services; computer-aided
scientific research, testing and analysis services; project
studies, technical research and appraisals; writing, design,
development and updating of software; technical support
concerning the use of software; hosting of online
platforms; provision of online non-downloadable software;
provision of software on platforms enabling users to access
software, computer networks, computer servers and computer
and data storage systems and to use them; provision of
temporary use of non-downloadable software for importing,
management and analysis of data, incorporating automatic
learning and artificial intelligence components; provision
of software (Software as a Service, SaaS); software as a
service [SaaS] featuring software for automatic learning and
artificial intelligence to be used for data analysis; IT
Platform as a Service (PaaS); provision of scientific
information via web-based platforms; data storage and cloud
computing for bioinformatic analysis; bioinformatic
analysis services, development of software and pipeline
architectures; provision of methods and tools for
calculations and bioinformatics for data analysis;
development and maintenance of data management software,
database construction; development of genomic and
bioinformatic applications; storage of data by computer;
provision of advice and information for the aforesaid
services or those relating thereto. Medical services; health services; medical clinic
services; medical care and analysis services relating to
patient treatment; medical analysis services for the
diagnosis and treatment of persons; medical diagnostics,
diagnostics in the field of medicine; medical screening;
DNA screening for medical purposes; genetic testing services
for medical purposes; medical tests for diagnostic or
treatment purposes; medical diagnostic services [testing
and analysis]; medical and health services relating to DNA,
genetics and genetic testing; medical testing services for
prognosis and diagnosis in the field of oncology and
congenital diseases; RNA or DNA analysis for prognosis and
diagnosis in the field of oncology and congenital diseases;
provision of information in the field of prevention,
screening, diagnosis and treatment in the field of oncology
and congenital diseases.
57.
METHODS FOR DETECTING COPY-NUMBER VARIATIONS IN NEXT-GENERATION SEQUENCING
Copy Number Variants (CNV) detection methods described herein may efficiently integrate CNV detection into the workflow for a next generation sequencer (NGS) data processing, in parallel with SNP and INDEL variant calling. CNV detection methods as described herein may be performed by analyzing the coverage pattern across a suitable set of genomic regions or amplicons and across a batch of samples from different patients. The proposed methods do not require the use of specifically chosen reference samples as inputs to the workflow, but rather automatically select a set of reference samples from the same batch, for each sample being tested. The CNV detection methods may reliably detect CNVs in a set of samples without prior assumptions about the CNV status of any of those samples. Embodiments described herein may also apply the CNV detection scheme iteratively to further improve the detection performance, especially in the case of more frequent CNV occurrence. Since the knowledge on the CNVs in reference samples may improve their comparison with the sample being tested, the proposed methods may further comprise the step of iteratively feeding back the information about the CNVs found in the samples from any detection step into the next iteration step. The proposed methods may also further use additional information available from the NGS workflow about the samples, such as information on SNP fractions, as input to the NGS CNV detection.
G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
G06F 19/22 - for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism [SNP] discovery or sequence alignment
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers, namely, computer hardware and computer peripherals which integrate machine learning and artificial intelligence systems; data processing systems consisting primarily of computer hardware, computer peripheral devices, computer software in the fields of genetics, genomics, and oncology, and computer hardware and software which integrate machine learning and artificial intelligence systems; software being recorded programs to receive, store, access, search, collect, display, manage, process, and analyze data in the fields of genetics and genomics; downloadable software for data analysis integrating automatic learning and artificial intelligence components; downloadable computer programs for data search, collection, management, storage and analysis; data processing apparatus; integrated circuits containing programs for audio, video or computer data processing; pre-recorded and downloaded sounds, images and data containing content in the fields of genetics, genomics, and oncology Commercial business management; commercial administration, namely, business administration services; providing office functions; compilation of information into computer databases; compilation and systematization of data in data banks; compilation of information into computer databases; data processing service by computer; systematization of data in a central file; professional business consulting for the organization and administration of means of computer data recording, transcription, conversion, composition, compilation and systematization DNA screening for the purposes of scientific research; scientific laboratory testing services; conducting clinical trials for others; computer diagnostic services; computer-aided scientific research, testing and analysis services in the field of oncology and congenital diseases; technical research in the field of oncology and congenital diseases, conducting studies in oncology and congenital diseases in connection therewith, and appraisals being genetic testing for scientific research purposes; writing, design, development and updating of software; technical support concerning the use of software; hosting of online platforms for others; providing online, non-downloadable computer software for use in database management and data analysis in the fields of genetics, genomics, and oncology ; platform as a service (PAAS) services featuring computer software platforms for enabling users to access computer software, computer networks, computer servers, and online data storage services and allowing the user to use them in the field of bioinformatics; provision of temporary use of non-downloadable software for importing, management and analysis of data, incorporating automatic learning and artificial intelligence components; software as a service (SaaS) services featuring software for use in database management and data analysis in the fields of genetics, genomics, and oncology; software as a service (SaaS) services featuring software for automatic learning and artificial intelligence to be used for data analysis; platform as a Service (PaaS) services featuring software for database management; provision of scientific information in the field of genetics, oncology, and congenital diseases via web-based platforms; computer services, namely, cloud hosting provider services for use in storing data used in bioinformatics analysis; bioinformatic data analysis services; development of software for others; scientific research featuring provision of methods and tools for calculations and bioinformatics for data analysis; development and maintenance of data management software; database development services; development of genomic and bioinformatic software applications; electronic data storage; and provision of advice and information for the aforesaid services Medical services; healthcare services in the field of oncology and congenital diseases; medical clinic services; medical care and analysis services relating to patient treatment; medical analysis services for the diagnosis and treatment of persons; medical diagnostic testing services; diagnostic monitoring services in the field of medicine for medical purposes; medical screening; DNA screening for medical purposes; genetic testing services for medical purposes; medical testing services for diagnostic or treatment purposes; Medical diagnostic testing and analysis services; medical and healthcare services relating to DNA, genetics and genetic testing; medical testing services for prognosis and diagnosis in the field of oncology and congenital diseases; RNA or DNA analysis for medical treatment prognosis and diagnosis in the field of oncology and congenital diseases; provision of information in the field of prevention, screening, diagnosis and treatment in the field of oncology and congenital diseases
59.
Method to manage raw genomic data in a privacy preserving manner in a biobank
A method to manage raw genomic data (SAM/BAM files) in a privacy preserving manner in a biobank. By using order preserving encryption of the reads' positions, the method provides a requested range of nucleotides to a medical unit, without revealing the locations of the short reads (which include the requested nucleotides) to the biobank.
The method prevents the leakage of extra information in the short reads to the medical unit by masking the encrypted short reads at the biobank. That is, specific parts of the genomic data for which the medical unit is not authorized or the patient prefers to keep secret are masked at the biobank, without revealing any information to the biobank.
G06F 21/62 - Protecting access to data via a platform, e.g. using keys or access control rules
G16B 50/00 - ICT programming tools or database systems specially adapted for bioinformatics
H04L 9/06 - Arrangements for secret or secure communicationsNetwork security protocols the encryption apparatus using shift registers or memories for blockwise coding, e.g. D.E.S. systems
05 - Pharmaceutical, veterinary and sanitary products
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Pharmaceutical products; diagnostic reagents and contrast
agents for medical use; chemical reagents for medical use;
diagnostic biomarking reagents for medical use; kits
containing reagents for diagnostic tests for medical use. Equipment for data processing and computers; data banks
(software); software (recorded programs); software for
data analysis integrating automatic learning and artificial
intelligence components; computer programs for data search,
collection, management, storage and analysis; data
processing apparatus; integrated circuits containing
programs for audio, video or computer data processing;
recorded or downloaded sounds, images or data. Commercial business management; commercial administration;
office functions; collection of data in a central file;
compilation and systematization of data in data banks;
compilation of information into computer databases; data
processing service by computer; systematization of data in
a central file; professional consulting for the
organization and administration of means of computer data
recording, transcription, conversion, composition,
compilation and systematization. Project studies, technical research and appraisals; writing,
design, development and updating of software; technical
support concerning the use of software; hosting of online
platforms; provision of online non-downloadable software;
provision of software on platforms enabling users to access
software, computer networks, computer servers and computer
and data storage systems and to use them; provision of
temporary use of non-downloadable software for importing,
management and analysis of data, incorporating automatic
learning and artificial intelligence components; provision
of software (Software as a Service, SaaS); software as a
service [SaaS] featuring software for automatic learning and
artificial intelligence to be used for data analysis;
provision of scientific information via Web-based
plateforms; data storage and cloud computing for
bioinformatic analysis; bioinformatic analysis services,
development of software and pipeline architectures;
provision of methods and tools for calculations and
bioinformatics for data analysis; development and
maintenance of data management software, database
construction; development of genomic and bioinformatic
applications; storage of data by computer; provision of
advice and information for the aforesaid services or those
relating thereto. Medical services; health services; medical analysis
services related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
61.
METHODS FOR DETECTING VARIANTS IN NEXT-GENERATION SEQUENCING GENOMIC DATA
A genomic data analyzer may be configured to detect and characterize, with a variant calling module, genomic variant scenarios in sequencing reads from an enriched patient genomic sample comprising a combination of a first repeat pattern and a second repeat pattern, such as repeats of homopolymer (single nucleotide) and/or heteropolymer (multiple nucleotide) basic motifs. The variant calling module may estimate the probability distribution of the length of the first repeat pattern and the probability distribution of the length of the second repeat pattern by comparing the distribution of the repeat pattern length measurements in patient data to the distribution of the repeat pattern length measurements in control data, in order to remove biases possibly induced by the next generation sequencing laboratory setup both in control and patient data. The variant calling module may further measure, read by read, the joint probability distribution for the first and the second repeat patterns lengths, and compare it with the expected joint probability distribution for various genomic variant scenarios for the patient, each variant scenario being characterized by a first length of the first repeat pattern and a second length of the second repeat pattern, to select the most likely patient genomic variant scenario as the scenario for which the measured joint probability distribution best matches the expected joint probability distribution.
G06F 19/22 - for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism [SNP] discovery or sequence alignment
G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
05 - Pharmaceutical, veterinary and sanitary products
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Pharmaceutical products; diagnostic reagents and contrast
agents for medical use; chemical reagents for medical use;
biomarker reagents for diagnostics for medical use; kits
containing reagents for diagnostic tests for medical use. Equipment for data processing and computers; data banks;
software (recorded programs); software for data analysis
integrating automatic learning and artificial intelligence
components; computer programs for data search, collection,
management, storage and analysis; data processing apparatus;
integrated circuits containing programs for audio, video or
computer data processing; recorded or downloaded sounds,
images or data. Commercial business management; commercial administration;
office functions; collection of data in a central file;
compilation and systematization of data in data banks;
compilation of information into computer databases; data
processing service by computer; systematization of data in
a central file; professional consulting for the
organization and administration of means of computer data
recording, transcription, conversion, composition,
compilation and systematization. Project studies, technical research and appraisals; writing,
design, development and updating of software; technical
support concerning the use of software; hosting of online
platforms; provision of online non-downloadable software;
provision of software on platforms enabling users to access
software, computer networks, computer servers and computer
and data storage systems and to use them; provision of
temporary use of non-downloadable software for importing,
management and analysis of data, incorporating automatic
learning and artificial intelligence components; provision
of software (Software as a Service, SaaS); software as a
service [SaaS] featuring software for automatic learning and
artificial intelligence to be used for data analysis;
provision of scientific information via web-based platforms;
data storage and cloud computing for bioinformatic analysis;
bioinformatic analysis services, development of software and
pipeline architectures; provision of methods and tools for
calculations and bioinformatics for data analysis;
development and maintenance of data management software,
database design; development of genomic and bioinformatic
applications; storage of data by computer; provision of
advice and information for the aforesaid services or those
relating thereto. Medical services; health services; medical analysis
services related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
05 - Pharmaceutical, veterinary and sanitary products
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Diagnostic reagents and contrast agents for medical use; chemical reagents for medical use; diagnostic biomarker reagents for diagnostics for medical use; kits containing various reagents for diagnostic tests for medical use Equipment for data processing and computers, namely, computer hardware and computer peripherals which integrate machine learning and artificial intelligence systems; data bank management software; software being recorded programs to receive, store, access, search, collect, display, manage, process, and analyze data in the fields of genetics and genomics; computer programs for data search, collection, management, storage and analysis; data processing apparatus; integrated circuits containing programs for audio, video and computer data processing; pre- recorded and downloaded sounds, images and data files containing content in the fields of genetics and genomics Commercial business management; commercial administration, namely, business administration; providing office functions; collection of data in a central file, namely, compilation of information into computer databases; compilation and systematization of data in data banks; compilation of information into computer databases; data processing service by computer; systematization of data in a central file, namely, systemization of information into computer databases; business consulting in the field of organization and administration of means of computer data recording, transcription, conversion, composition, compilation and systematization Conducting project feasibility studies in the field of new technologies and machine learning; technical research in the field of genomics, genetics and bioinformatics, and appraisals being genetic testing for scientific research purposes; writing, design, development and updating of computer software; technical support concerning the use of software, namely, troubleshooting of computer software problems; Software as a service (SAAS) services, namely, hosting software for use by others to provide access to an online internet SaaS platform; provision of online non-downloadable software for use in database management and data analysis in the fields of genetics and genomics; platform as a service (PAAS) featuring computer software platforms enabling users to access software, computer networks, computer servers and computer and data storage systems and to use them; provision of temporary use of non-downloadable software for importing, management and analysis of data, incorporating automatic learning and artificial intelligence components; provision of Software as a Service (Saas) services featuring software for use in database management and data analysis in the fields of genetics and genomics; software as a service (Saas) services featuring software for automatic learning and artificial intelligence to be used for data analysis; provision of scientific information via web-based platforms; electronic data storage and cloud computing featuring software, all for bioinformatic analysis; bioinformatic analysis services being chemical and biological analysis services, development of software, and development of software for data processing pipelines; scientific research featuring provision of methods and tools for calculations and bioinformatics for data analysis; development and maintenance of data management software, database design; computer software development of genomic and bioinformatic mobile applications; electronic storage of data by computer; provision of advice and information for the aforesaid services, namely, genetics and genomics research information Medical services; health care services; medical analysis services related to the treatment of individuals for medical purposes; medical testing for diagnostic and treatment purposes
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers; data banks;
software (recorded programs); software for data analysis
integrating automatic learning and artificial intelligence
components; computer programs for data search, collection,
management, storage and analysis; data processing apparatus;
integrated circuits containing programs for audio, video or
computer data processing; recorded or downloaded sounds,
images or data. Commercial business management; commercial administration;
office functions; collection of data in a central file;
compilation and systematization of data in data banks;
compilation of information into computer databases; data
processing service by computer; systematization of data in
a central file; professional consulting for the
organization and administration of means of computer data
recording, transcription, conversion, composition,
compilation and systematization. Project studies, technical research and appraisals; writing,
design, development and updating of software; technical
support concerning the use of software; hosting of online
platforms; provision of online non-downloadable software;
provision of software on platforms enabling users to access
software, computer networks, computer servers and computer
and data storage systems and to use them; provision of
temporary use of non-downloadable software for importing,
management and analysis of data, incorporating automatic
learning and artificial intelligence components; provision
of software (Software as a Service, SaaS); software as a
service [SaaS] featuring software for automatic learning and
artificial intelligence to be used for data analysis;
provision of scientific information via web-based platforms;
data storage and cloud computing for bioinformatic analysis;
bioinformatic analysis services, development of software and
pipeline architectures; provision of methods and tools for
calculations and bioinformatics for data analysis;
development and maintenance of data management software,
database design; development of genomic and bioinformatic
applications; storage of data by computer; provision of
advice and information for the aforesaid services or those
relating thereto. Medical services; health services; medical analysis
services related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers; data banks
(software); software (recorded programs); computer
programs for data search, collection, management, storage
and analysis; data processing apparatus; integrated
circuits containing programs for audio, video or computer
data processing; recorded or downloaded sounds, images or
data. Commercial business management; commercial administration;
office functions; collection of data in a central file;
compilation and systematization of data in data banks;
compilation of information into computer databases; data
processing service by computer; systematization of data in
a central file; professional consulting for the
organization and administration of means of computer data
recording, transcription, conversion, composition,
compilation and systematization. Project studies, technical research and appraisals; writing,
design, development and updating of software; technical
support concerning the use of software; hosting of online
platforms; provision of online non-downloadable software;
provision of software on platforms enabling users to access
software, computer networks, computer servers and computer
and data storage systems and to use them; provision of
scientific information via web-based platforms; data
storage and cloud computing for bioinformatic analysis;
bioinformatic analysis services, development of software and
pipeline architectures; provision of methods and tools for
calculations and bioinformatics for data analysis;
development and maintenance of data management software,
database construction; development of genomic and
bioinformatic applications; storage of data by computer;
provision of advice and information for the aforesaid
services or those relating thereto. Medical services; health services; medical analysis
services related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
(1) Data processing and computer equipment, namely computers and computer hardware; data bank, namely computer software for database management, computer software for creating searchable databases; software, namely computer operating recorded program; software for data analysis, namely for DNA analysis for diagnostic and treatment purposes which integrates machine learning and artificial intelligence systems in the field of genetics, genomics and bioinformatics; computer programs for data search of medical records, for collection of medical data, for database management, for electronic storage of medical records and medical analysis for diagnostic and treatment purposes in the field of genetics, genomics and bioinformatics; data processing apparatus, namely interface cards for data processing equipment in the form of printed circuits; integrated circuits containing programs for audio, video or computer data processing. (1) Commercial business management and administration; office functions, namely office support staff recruitment services; collection of data in a central file, namely updating and maintenance of data in a computerized central file; compilation and organization of data in data banks; compilation of information into computer databases; data processing service by computer, namely computerized business records management, updating and maintenance of data in computer databases; organization of data in a central file; business organization and management consulting, namely professional consulting for the organization and administration of means of computer data recording, transcription, conversion, composition, compilation and systematization.
(2) Project studies, expert reports and research of a technical nature, namely medical research, scientific research in the field of genetics, genomics and bioinformatics, genetic testing for scientific research purposes, writing, design, development and updating of software, technical support concerning the use of software, hosting of online platforms, namely web hosting, provision of online non-downloadable software, namely cloud computing providing software for database management, platform as a service (PAAS) featuring computer software platforms for use in the field of medical science, namely provision of software, for use in the field of medical science, on platforms enabling users to access software for use in data analysis in the field of genetics, genomics and bioinformatics, providing temporary use of non-downloadable software for importing, managing and analyzing of data, which integrates machine learning and artificial intelligence systems, provision of software (Software as a Service, SaaS), namely, software as a service [SaaS] provider featuring a machine learning and artificial intelligence software for use in data analysis in the field of genetics, genomics and bioinformatics, providing information in the field of medical science via a website, data storage, namely electronic storage of medical records and cloud computing for bioinformatic analysis, bioinformatic analysis services, development of software and pipeline architectures, provision of methods for calculations and bioinformatics for data analysis, development and maintenance of data management software, database construction, development of genomic and bioinformatic applications, storage of data by computer, information and advisory services relating to the aforesaid services.
(3) Medical services and health services, namely medical screening, medical imaging, medical testing services; medical analysis services related to the treatment of individuals, namely medical analysis services for diagnostic and treatment purposes provided by medical laboratories; medical diagnostics services.
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
(1) Data processing and computer equipment, namely computers and computer hardware; data bank, namely computer software for database management, computer software for creating searchable databases; software, namely computer operating recorded program; software for data analysis, namely for DNA analysis for diagnostic and treatment purposes which integrates machine learning and artificial intelligence systems in the field of genetics, genomics and bioinformatics; computer programs for data search of medical records, for collection of medical data, for database management, for electronic storage of medical records and medical analysis for diagnostic and treatment purposes in the field of genetics, genomics and bioinformatics; data processing apparatus, namely interface cards for data processing equipment in the form of printed circuits; integrated circuits containing programs for audio, video or computer data processing. (1) Commercial business management and administration; office functions, namely office support staff recruitment services; collection of data in a central file, namely updating and maintenance of data in a computerized central file; compilation and organization of data in data banks; compilation of information into computer databases; data processing service by computer, namely computerized business records management, updating and maintenance of data in computer databases; organization of data in a central file; business organization and management consulting, namely professional consulting for the organization and administration of means of computer data recording, transcription, conversion, composition, compilation and systematization.
(2) Project studies, expert reports and research of a technical nature, namely medical research, scientific research in the field of genetics, genomics and bioinformatics, genetic testing for scientific research purposes, writing, design, development and updating of software, technical support concerning the use of software, hosting of online platforms, namely web hosting, provision of online non-downloadable software, namely cloud computing providing software for database management, platform as a service (PAAS) featuring computer software platforms for use in the field of medical science, namely provision of software, for use in the field of medical science, on platforms enabling users to access software for use in data analysis in the field of genetics, genomics and bioinformatics, providing temporary use of non-downloadable software for importing, managing and analyzing of data, which integrates machine learning and artificial intelligence systems, provision of software (Software as a Service, SaaS), namely, software as a service [SaaS] provider featuring a machine learning and artificial intelligence software for use in data analysis in the field of genetics, genomics and bioinformatics, providing information in the field of medical science via a website, data storage, namely electronic storage of medical records and cloud computing for bioinformatic analysis, bioinformatic analysis services, development of software and pipeline architectures, provision of methods for calculations and bioinformatics for data analysis, development and maintenance of data management software, database construction, development of genomic and bioinformatic applications, storage of data by computer, information and advisory services relating to the aforesaid services.
(3) Medical services and health services, namely medical screening, medical imaging, medical testing services; medical analysis services related to the treatment of individuals, namely medical analysis services for diagnostic and treatment purposes provided by medical laboratories; medical diagnostics services.
68.
METHODS FOR PROCESSING NEXT-GENERATION SEQUENCING GENOMIC DATA
A genomic data analyzer system detects a set of characteristics that uniquely determine the input next-generation-sequencing (NGS) sample processing and corresponding genomic context for optimizing a genomic analysis workflow in precision medicine applications. Depending on characteristics such as the DNA target enrichment amplicon-based or probe-based assay technology, the sample type or laboratory process characteristics, the NGS sequencing technology and the genomic context, the genomic data analyzer automatically selects and configures a data alignment module and a variant calling module to optimize the sensitivity and the specificity of the detection of genomic mutations of clinical relevance such as SNPs and INDELs in a diversity of pathologies. More characteristics of the sequencing technology, the target enrichment technology, the samples or the genomic context may be identified according to intermediary results of the data alignment module and the variant calling module, and the genomic data analyzer may further adapt accordingly the alignment module and the variant calling module to execute specific genomic data processing methods. The genomic data analyzer system can thus automatically serve a diversity of sourcing laboratories operating with different biological assays and sequencing technologies setups for different pathologies without requiring a dedicated manual configuration of the genomic analysis workflow at each laboratory for each possible personalized medicine genomic analysis request.
G06F 19/28 - for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
G06F 19/22 - for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism [SNP] discovery or sequence alignment
42 - Scientific, technological and industrial services, research and design
Goods & Services
Conducting project feasibility studies in the field of new technologies and machine learning in the field of bioinformatics; technical research in the field of genomics, genetics and bioinformatics, and appraisals being genetic testing for scientific research purposes; writing, design, development and updating of computer software in the field of bioinformatics; technical support concerning the use of software, namely, troubleshooting of computer software problems in the field of bioinformatics; Software as a service (SAAS) services, namely, hosting software for use by others to provide access to an online internet SaaS platform in the field of bioinformatics; provision of online non-downloadable software for use in database management and data analysis in the fields of genetics and genomics; platform as a service (PAAS) featuring computer software platforms enabling users to access software, computer networks, computer servers and computer and data storage systems and to use them in the field of bioinformatics; provision of temporary use of non-downloadable software for importing, management and analysis of data, incorporating automatic learning and artificial intelligence components in the field of bioinformatics; provision of software (Software as a Service, Saas) for use in database management and data analysis in the fields of genetics and genomics; software as a service (Saas) featuring software for automatic learning and artificial intelligence to be used for data analysis in the field of bioinformatics; provision of scientific information via web-based platforms; electronic data storage and cloud computing featuring software, all for bioinformatic analysis; bioinformatic analysis services being chemical and biological analysis services, development of software, and development of software for data processing pipelines; scientific research featuring provision of methods and tools for calculations and bioinformatics for data analysis; development and maintenance of data management software, database design in the field of bioinformatics; computer software development of genomic and bioinformatic mobile applications; electronic storage of data by computer; provision of advice and information for the aforesaid services, namely, genetics and genomics research information
05 - Pharmaceutical, veterinary and sanitary products
42 - Scientific, technological and industrial services, research and design
Goods & Services
Diagnostic reagents and contrast agents for medical use; chemical reagents for medical use; diagnostic biomarker reagents for diagnostics for medical use; kits containing various reagents for diagnostic tests for medical use Conducting project feasibility studies in the field of new technologies and machine learning; technical research in the field of genomics, genetics and bioinformatics, and appraisals being genetic testing for scientific research purposes; writing, design, development and updating of computer software in the field of bioinformatics; technical support concerning the use of software, namely, troubleshooting of computer software problems in the field of bioinformatics; Software as a service (SAAS) services, namely, hosting software for use by others to provide access to an online internet SaaS platform in the field of bioinformatics; provision of online nondownloadable software for use in database management and data analysis in the fields of genetics and genomics; platform as a service (PAAS) featuring computer software platforms enabling users to access software, computer networks, computer servers and computer and data storage systems and allowing the user to use them in the field of bioinformatics; provision of temporary use of non-downloadable software for importing, management and analysis of data, incorporating automatic learning and artificial intelligence components in the field of bioinformatics; provision of software (Software as a Service, SAAS) featuring software for use in database management and data analysis in the fields of genetics and genomics; software as a service (SAAS) featuring software for automatic learning and artificial intelligence to be used for data analysis in the field bioinformatics; providing scientific information in the field of genetics and genomics research information via web-based platforms; electronic data storage and cloud computing, namely, cloud computing featuring software for use in database management for bioinformatics analysis; bioinformatic analysis services being chemical and biological analysis services; development of software, and development of software for data processing in the field of bioinformatics; scientific research featuring provision of methods and tools for calculations and bioinformatics for data analysis; development and maintenance of data management software; database design in the field of bioinformatics; computer software development, namely, development of software of genomic and bioinformatic mobile applications; electronic storage of data by computer in the field of bioinformatics; and provision of advice and information for the aforesaid services
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
[ Equipment for data processing and computers, namely, computer hardware and computer peripherals which integrate machine learning and artificial intelligence systems; data bank management software; software being recorded programs to receive, store, access, search, collect, display, manage, process, and analyze data in the fields of genetics and genomics; computer programs for data search, collection, management, storage and analysis; data processing apparatus; integrated circuits containing programs for audio, video and computer data processing; pre-recorded and downloadable sound recordings, images and electronic data files containing content in the fields of genetics and genomics] [ Commercial business management; commercial business administration; providing office functions; collection of data in a central file being central file management services; compilation and systematization of data in data banks; compilation of information into computer databases; ] data processing service by computer; central file management in the nature of systematization of data in a central file; professional business consulting for the organization and administration of means of computer data recording, transcription, conversion, composition, compilation and systematization Conducting project feasibility studies in the field of new technologies and machine learning; technical research in the field of genomics, genetics and bioinformatics, and appraisals being genetic testing for scientific research purposes; writing, design, development and updating of computer software; technical support concerning the use of software, namely, troubleshooting of computer software problems; Software as a service (SAAS) services, namely, hosting software for use by others to provide access to an online internet SaaS platform; provision of online non-downloadable software for use in database management and data analysis in the fields of genetics and genomics; provision of a website featuring online non-downloadable software enabling users to access and operate software, computer networks, computer servers and computer and data storage systems; provision of scientific information in the field of genetics and genomics via web-based platforms; electronic data storage and cloud computing featuring software, all for bioinformatic analysis; bioinformatic analysis services being chemical and biological analysis services, development of software, and development of software for data processing pipelines; scientific research featuring provision of methods and tools for calculations and bioinformatics for data analysis; development and maintenance of data management computer software; database construction, namely, database design and development; computer software development of genomic and bioinformatic mobile applications; electronic storage of data by computer; provision of advice and information for the aforesaid services, namely, genetics and genomics research information [ Medical services; health care services; medical analysis services related to the treatment of individuals for medical purposes; medical testing for diagnostic and treatment purposes]
72.
METHODS TO COMPRESS, ENCRYPT AND RETRIEVE GENOMIC ALIGNMENT DATA
A genomic data decoder may jointly compress and encrypt genomic data alignment information while preserving the privacy of sensitive genomic data elements at retrieval stage. Genomic data alignment information organized as a read-based alignment data stream may be transposed into a position-based alignment data stream. The position-based alignment information may been coded into a reference- based alignment data stream. The reference-based alignment data stream may be encrypted with a combination of order-preserving encryption of the genomic position information and symmetric encryption of the reference-based alignment differential data. Differential encoding and entropy coding schemes may further compress the reference-based alignment data stream. The resulting compressed and encrypted stream may be indexed and stored in a biobank storage unit. A genomic data decoder may efficiently retrieve, decrypt and decode a specific subset of the resulting compressed and encrypted stream without leaking information on the other genomic data subsets in the resulting stream.
G06F 19/22 - for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism [SNP] discovery or sequence alignment
G06F 19/28 - for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
73.
METHODS FOR DETECTING COPY-NUMBER VARIATIONS IN NEXT-GENERATION SEQUENCING
Copy Number Variants (CNV) detection methods described herein may efficiently integrate CNV detection into the workflow for a next generation sequencer (NGS) data processing, in parallel with SNP and INDEL variant calling. CNV detection methods as described herein may be performed by analyzing the coverage pattern across a suitable set of genomic regions or amplicons and across a batch of samples from different patients. The proposed methods do not require the use of specifically chosen reference samples as inputs to the workflow, but rather automatically select a set of reference samples from the same batch, for each sample being tested. The CNV detection methods may reliably detect CNVs in a set of samples without prior assumptions about the CNV status of any of those samples. Embodiments described herein may also apply the CNV detection scheme iteratively to further improve the detection performance, especially in the case of more frequent CNV occurrence. Since the knowledge on the CNVs in reference samples may improve their comparison with the sample being tested, the proposed methods may further comprise the step of iteratively feeding back the information about the CNVs found in the samples from any detection step into the next iteration step. The proposed methods may also further use additional information available from the NGS workflow about the samples, such as information on SNP fractions, as input to the NGS CNV detection.
G06F 19/18 - for functional genomics or proteomics, e.g. genotype-phenotype associations, linkage disequilibrium, population genetics, binding site identification, mutagenesis, genotyping or genome annotation, protein-protein interactions or protein-nucleic acid interactions
G06F 19/22 - for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or Single-Nucleotide Polymorphism [SNP] discovery or sequence alignment
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Data processing and computer equipment; data bank
management software; software (recorded programs); computer
programs for data search, collection, management, storage
and analysis; data processing apparatus; integrated
circuits containing programs for audio, video or computer
data processing; recorded or downloaded sounds, images or
data. Commercial business management; commercial administration;
office functions; collection of data in a central file;
compilation and systematization of data in data banks;
compilation of information into computer databases; data
processing service by computer; systematization of data in
a central file; professional consulting for the
organization and administration of means of computer data
recording, transcription, conversion, composition,
compilation and systematization. Project studies, expert reports and research of a technical
nature; writing, design, development and updating of
software; technical support concerning the use of software;
hosting of online platforms; provision of online
non-downloadable software; provision of software on
platforms enabling users to access software, computer
networks, computer servers and computer and data storage
systems and to use them; provision of scientific
information via web-based platforms; data storage and cloud
computing for bioinformatic analysis; bioinformatic analysis
services, development of software and pipeline
architectures; provision of methods and tools for
calculations and bioinformatics for data analysis;
development and maintenance of data management software,
database construction; development of genomic and
bioinformatic applications; storage of data by computer;
provision of advice and information for the aforesaid
services or those relating thereto. Medical services; health services; medical analysis
services related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers; data bank
management software; software (recorded programs); computer
programs for data search, collection, management, storage
and analysis; data processing apparatus; integrated
circuits containing programs for audio, video or computer
data processing; recorded or downloaded sounds, images or
data. Commercial business management; commercial administration;
office functions; collection of data in a central file;
compilation and systematization of data in data banks;
compilation of information into computer databases; data
processing service by computer; systematization of data in
a central file; professional consulting for the
organization and administration of means of computer data
recording, transcription, conversion, composition,
compilation and systematization. Project studies, technical research and appraisals; writing,
design, development and updating of software; technical
support concerning the use of software; hosting of online
platforms; provision of online non-downloadable software;
provision of software on platforms enabling users to access
software, computer networks, computer servers and computer
and data storage systems and to use them; provision of
scientific information via web-based platforms; data
storage and cloud computing for bioinformatic analysis;
bioinformatic analysis services, development of software and
pipeline architectures; provision of methods and tools for
calculations and bioinformatics for data analysis;
development and maintenance of data management software,
database construction; development of genomic and
bioinformatic applications; storage of data by computer;
provision of advice and information for the aforesaid
services or those relating thereto. Medical services; health services; medical analysis
services related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
76.
Method to manage raw genomic data in a privacy preserving manner in a biobank
A method to manage raw genomic data (SAM/BAM files) in a privacy preserving manner in a biobank. By using order preserving encryption of the reads' positions, the method provides a requested range of nucleotides to a medical unit, without revealing the locations of the short reads (which include the requested nucleotides) to the biobank. The method prevents the leakage of extra information in the short reads to the medical unit by masking the encrypted short reads at the biobank. That is, specific parts of the genomic data for which the medical unit is not authorized or the patient prefers to keep secret are masked at the biobank, without revealing any information to the biobank.
G06F 21/62 - Protecting access to data via a platform, e.g. using keys or access control rules
G06F 19/28 - for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
H04L 9/06 - Arrangements for secret or secure communicationsNetwork security protocols the encryption apparatus using shift registers or memories for blockwise coding, e.g. D.E.S. systems
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Data processing and computer equipment; data banks
(software); software (recorded programs); computer
programs for data search, collection, management, storage
and analysis; data processing apparatus; integrated
circuits containing programs for audio, video or computer
data processing; recorded or downloaded sounds, images or
data. Business management; commercial administration; office
functions; collection of information into computer
databases; compilation and systematization of data in data
banks; compilation of information into computer databases;
data processing service by computer; systematization of
data in a central file; professional consulting for the
organization and administration of means of computer data
recording, transcription, conversion, composition,
compilation and systematization. Project studies, expert reports and research of a technical
nature; writing, design, development and updating of
software; technical support concerning the use of software;
hosting of online platforms; provision of online
non-downloadable software; provision of software on
platforms enabling users to access software, computer
networks, computer servers and computer and data storage
systems and to use them; provision of scientific
information via web-based platforms; data storage and cloud
computing for bioinformatic analysis; bioinformatic analysis
services, development of software and pipeline
architectures; provision of methods and tools for
calculations and bioinformatics for data analysis;
development and maintenance of data management software,
database construction; development of genomic and
bioinformatic applications; storage of data by computer;
provision of advice and information for the aforesaid
services or those relating thereto. Medical services; health services; medical analysis
services related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Data processing and computer equipment, namely, computer hardware and computer peripherals which integrate machine learning and artificial intelligence systems; data processing systems consisting primarily of computer hardware, computer peripheral devices, computer software in the fields of genetics and genomics, and computer hardware and software which integrate machine learning and artificial intelligence systems; software being recorded programs to receive, store, access, search, collect, display, manage, process, and analyze data in the fields of genetics and genomics; data processing apparatus; integrated circuits containing programs for audio, video and computer data processing; pre-recorded and downloaded sounds, images and data containing content in the fields of genetics and genomics [ Business management; business administration; providing office functions; ] compilation of information into computer databases; compilation and systematization of data in data banks; data back-up services; data processing service by computer; central file management in the nature of systematization of information in computer databases; professional business consulting for the organization and administration of means of computer data recording, transcription, conversion, composition, compilation and systematization [ Medical services; health care services; ] medical analysis services related to the treatment of individuals for medical purposes [ ; medical diagnostics for treatment purposes; diagnostics in the field of medicine for treatment purposes ]
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Data processing and computer equipment, namely, computer hardware and computer peripherals which integrate machine learning and artificial intelligence systems; data processing systems consisting primarily of computer hardware, computer peripheral devices, computer software in the fields of genetics and genomics, and computer hardware and software which integrate machine learning and artificial intelligence systems; software being recorded programs to receive, store, access, search, collect, display, manage, process, and analyze data in the fields of genetics and genomics; data processing apparatus; integrated circuits containing programs for audio, video and computer data processing; pre-recorded and downloaded sounds, images and data containing content in the fields of genetics and genomics Business management; business administration; providing office functions; compilation of information into computer databases; compilation and systematization of data in data banks; compilation of information into computer databases; data processing service by computer; central file management in the nature of systematization of data in a central file; professional business consulting for the organization and administration of means of computer data recording, transcription, conversion, composition, compilation and systematization Medical services; health care services; medical analysis services related to the treatment of individuals for medical purposes; medical diagnostics for treatment purposes; diagnostics in the field of medicine for treatment purposes
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
[ Data bank management software in the field of human genome analysis and bioinformatics ] [ Commercial business management; commercial business administration; providing office functions; ] computerized collection of data in a central file being central file management services; compilation and systematization of data in data banks; compilation of information into computer databases; data processing service by computer; computerized central file management in the nature of systematization of data in a central file; [ professional business consulting for the organization and administration of means of computer data recording, transcription, conversion, composition, compilation and systematization; ] all of the aforementioned services in the field of human genome analysis and bioinformatics [ Conducting project feasibility studies in the field of new technologies and machine learning; ] technical research in the field of genomics, genetics and bioinformatics, and appraisals being genetic testing for scientific research purposes; software as a service (SAAS) services, namely, hosting software platforms for use by others, which provide access to an online SaaS platform; provision of online non-downloadable software for use in database management and data analysis in the fields of genetics and genomics; provision of a website featuring online non-downloadable software enabling users to access software, computer networks, computer servers and computer and data storage systems and to use them; provision of scientific information in the field of genetics and genomics via web-based platforms; electronic data storage and cloud computing featuring software, all for bioinformatic analysis; bioinformatic analysis services being chemical and biological analysis services; scientific research featuring provision of methods and tools for calculations and bioinformatics for data analysis; database construction, namely, database design and development; electronic storage of data by computer; all of the aforementioned services in the field of human genome analysis and bioinformatics [ Medical services; health care services; medical analysis services related to the treatment of individuals for medical purposes; medical testing for diagnostic and treatment purposes; all of the aforementioned services in the field of human genome analysis and bioinformatics ]
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers, namely, computer hardware and computer peripherals which integrate machine learning and artificial intelligence systems; data bank management software; software being recorded programs to receive, store, access, search, collect, display, manage, process, and analyze data in the fields of genetics and genomics; computer programs for data search, collection, management, storage and analysis; data processing apparatus; integrated circuits containing programs for audio, video and computer data processing; pre-recorded and downloaded sounds, images and data files containing content in the fields of genetics and genomics Commercial business management; commercial business administration; providing office functions; collection of data in a central file being central file management services; compilation and systematization of data in data banks; compilation of information into computer databases; data processing service by computer; central file management in the nature of systematization of data in a central file; professional business consulting for the organization and administration of means of computer data recording, transcription, conversion, composition, compilation and systematization Conducting project feasibility studies in the field of new technologies and machine learning; technical research in the field of genomics, genetics and bioinformatics, and appraisals being genetic testing for scientific research purposes; writing, design, development and updating of computer software; technical support concerning the use of software, namely, troubleshooting of computer software problems; Software as a service (SAAS) services, namely, hosting software for use by others to provide access to an online internet SaaS platform; provision of online non-downloadable software for use in database management and data analysis in the fields of genetics and genomics; provision of a website featuring online non-downloadable software enabling users to access software, computer networks, computer servers and computer and data storage systems and to use them; provision of scientific information in the field of genetics and genomics via web-based platforms; electronic data storage and cloud computing featuring software, all for bioinformatic analysis; bioinformatic analysis services being chemical and biological analysis services, development of software, and development of software for data processing pipelines; scientific research featuring provision of methods and tools for calculations and bioinformatics for data analysis; development and maintenance of data management computer software, database construction, namely, database design and development; computer software development of genomic and bioinformatic mobile applications; electronic storage of data by computer; provision of advice and information for the aforesaid services, namely, genetics and genomics research information Medical services; health care services; medical analysis services related to the treatment of individuals for medical purposes; medical testing for diagnostic and treatment purposes
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Data processing equipment and computer equipment in the nature of computer hardware; data banks in the nature of software used to store and access data; recorded programs in nature of software used to store and access data; computer programs for data search, collection, management, storage and analysis; data processing apparatus; integrated circuits containing programs for audio, video or computer data processing; recorded or downloaded sound recordings featuring information on genomics and bioinformatics; recorded or downloaded images or data files containing content on genomics and bioinformatics; all of the aforementioned goods used in the field of human genome analysis; none of the aforementioned goods used in the field of robotics Business management; commercial business administration; office functions; collection of information into computer databases; compilation and systematization of data in data banks; compilation of information into computer databases; data processing service by computer; systematization of data in a central file; professional business consulting for the organization and administration of means of computer data recording, transcription, conversion, composition, compilation and systematization; all of the aforementioned services used in the field of human genome analysis; none of the aforementioned services used in the field of robotics Project studies, expert reports and research of a technical nature, namely, development of new technology in the field of genomics and bioinformatics; project studies, expert reports and research of a technical nature, namely, scientific study, research, development and expert reports in the fields of genomics and bioinformatics; writing, design, development and updating of software; technical support concerning the use of software, namely, troubleshooting computer software problems; hosting of online platforms in the nature of websites; provision of online non-downloadable software used to host websites; provision of temporary use of non-downloadable software that enables users to access software, computer networks, computer servers and computer and data storage systems and to use them; provision of scientific information in the fields of genomics and bioinformatics via web-based platforms; electronic data storage and providing temporary use of non-downloadable cloud computing software used to conduct bioinformatic analysis; scientific research in the field of bioinformatic analysis services, development of software and software architectures; scientific research featuring provision of methods and tools for calculations and bioinformatics for data analysis; development and maintenance of data management software, database construction; scientific research, namely, development of genomic and bioinformatic applications; storage of data by computer; provision of advice and information for the aforesaid services; all of the aforementioned services used in the field of human genome analysis; none of the aforementioned services used in the field of robotics Medical services; health assessment services; medical services, namely, analysis services related to the treatment of individuals; medical diagnostic testing in the field of medicine; all of the aforementioned services used in the field of human genome analysis; none of the aforementioned services used in the field of robotics
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Data processing and computer equipment; data processing
systems; software (recorded programs); data processing
apparatus; integrated circuits containing programs for
audio, video or computer data processing; recorded or
downloaded sounds, images or data. Business management; business administration; office
functions; compilation of information into computer
databases; compilation and systematization of data in data
banks; compilation of information into computer databases;
data processing service by computer; systematization of data
in a central file; professional consulting for the
organization and administration of means of computer data
recording, transcription, conversion, composition,
compilation and systematization. Medical services; health care services; medical analysis
services related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
84.
METHOD TO MANAGE RAW GENOMIC DATA IN A PRIVACY PRESERVING MANNER IN A BIOBANK
A method to manage raw genomic data (SAM/BAM files) in a privacy preserving manner in a biobank. By using order preserving encryption of the reads' positions,the method provides a requested range of nucleotides to a medical unit, without revealing the locations of the short reads (which include the requested nucleotides) to the biobank. The method prevents the leakage of extra information in the short reads to the medical unit by masking the encrypted short reads at the biobank. That is, specific parts of the genomic data for which the medical unit is not authorized or the patient prefers to keep secret are masked at the biobank, without revealing any information to the biobank.
09 - Scientific and electric apparatus and instruments
35 - Advertising and business services
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Equipment for data processing and computers; data banks
(computer software); software (recorded programs); data
processing apparatus; integrated circuits containing
programs for audio, video or computer data processing;
recorded or downloaded sounds, images or data. Business management; business administration; office
functions; compilation of information into computer
databases; compilation and systematization of data in data
banks; data back-up service; data processing service by
computer; systematization of information into computer
databases; professional consulting for the organization and
administration of means of computer data recording,
transcription, conversion, composition, compilation and
systematization. Medical services; health care services; medical analysis
services related to the treatment of individuals; medical
diagnostics, diagnostics in the field of medicine.
