[go: up one dir, main page]

Madubata et al., 2017 - Google Patents

Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas

Madubata et al., 2017

View HTML @Full View
Document ID
14171847113994084145
Author
Madubata C
Roshan-Ghias A
Chu T
Resnick S
Zhao J
Arnes L
Wang J
Rabadan R
Publication year
Publication venue
NPJ genomic medicine

External Links

Snippet

Cancer is caused by germline and somatic mutations, which can share biological features such as amino acid change. However, integrated germline and somatic analysis remains uncommon. We present a framework that uses machine learning to learn features of …
Continue reading at www.nature.com (HTML) (other versions)

Classifications

    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/22—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or SNP [Single-Nucleotide Polymorphism] discovery or sequence alignment
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/28—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for programming tools or database systems, e.g. ontologies, heterogeneous data integration, data warehousing or computing architectures
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/18—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology 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
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/30—Medical informatics, i.e. computer-based analysis or dissemination of patient or disease data
    • G06F19/32—Medical data management, e.g. systems or protocols for archival or communication of medical images, computerised patient records or computerised general medical references
    • G06F19/322—Management of patient personal data, e.g. patient records, conversion of records or privacy aspects
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/24—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for machine learning, data mining or biostatistics, e.g. pattern finding, knowledge discovery, rule extraction, correlation, clustering or classification
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/20—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for hybridisation or gene expression, e.g. microarrays, sequencing by hybridisation, normalisation, profiling, noise correction models, expression ratio estimation, probe design or probe optimisation
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/30—Medical informatics, i.e. computer-based analysis or dissemination of patient or disease data
    • G06F19/34—Computer-assisted medical diagnosis or treatment, e.g. computerised prescription or delivery of medication or diets, computerised local control of medical devices, medical expert systems or telemedicine
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F21/00—Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
    • G06F21/60—Protecting data
    • G06F21/62—Protecting access to data via a platform, e.g. using keys or access control rules
    • G06F21/6218—Protecting access to data via a platform, e.g. using keys or access control rules to a system of files or objects, e.g. local or distributed file system or database
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06Q—DATA PROCESSING SYSTEMS OR METHODS, SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES; SYSTEMS OR METHODS SPECIALLY ADAPTED FOR ADMINISTRATIVE, COMMERCIAL, FINANCIAL, MANAGERIAL, SUPERVISORY OR FORECASTING PURPOSES, NOT OTHERWISE PROVIDED FOR
    • G06Q50/00—Systems or methods specially adapted for a specific business sector, e.g. utilities or tourism
    • G06Q50/10—Services
    • G06Q50/22—Health care, e.g. hospitals; Social work
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F21/00—Security arrangements for protecting computers, components thereof, programs or data against unauthorised activity
    • G06F21/50—Monitoring users, programs or devices to maintain the integrity of platforms, e.g. of processors, firmware or operating systems
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/20—Handling natural language data
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES OR MICRO-ORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or micro-organisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or micro-organisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Hybridisation probes
    • C12Q1/6883—Hybridisation probes for diseases caused by alterations of genetic material

Similar Documents

Publication Publication Date Title
Martínez-Jiménez et al. Genetic immune escape landscape in primary and metastatic cancer
Gorelick et al. Respiratory complex and tissue lineage drive recurrent mutations in tumour mtDNA
Sztupinszki et al. Detection of molecular signatures of homologous recombination deficiency in prostate cancer with or without BRCA1/2 mutations
Woo et al. DNA replication timing and selection shape the landscape of nucleotide variation in cancer genomes
Patel et al. Genomic determinants of chronic myelomonocytic leukemia
Tiffin et al. Integration of text-and data-mining using ontologies successfully selects disease gene candidates
Gupta et al. Prioritization of anticancer drugs against a cancer using genomic features of cancer cells: A step towards personalized medicine
Newman et al. FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution
Shihab et al. Predicting the functional consequences of cancer-associated amino acid substitutions
Larson et al. SomaticSniper: identification of somatic point mutations in whole genome sequencing data
Alkodsi et al. Comparative analysis of methods for identifying somatic copy number alterations from deep sequencing data
Huang et al. Lessons from a decade of integrating cancer copy number alterations with gene expression profiles
Shigemizu et al. A practical method to detect SNVs and indels from whole genome and exome sequencing data
Way et al. Comprehensive cross-population analysis of high-grade serous ovarian cancer supports no more than three subtypes
Hofree et al. Challenges in identifying cancer genes by analysis of exome sequencing data
Suo et al. Integration of somatic mutation, expression and functional data reveals potential driver genes predictive of breast cancer survival
Madubata et al. Identification of potentially oncogenic alterations from tumor-only samples reveals Fanconi anemia pathway mutations in bladder carcinomas
Xia et al. Genetic determinants of the molecular portraits of epithelial cancers
Przytycki et al. Differential analysis between somatic mutation and germline variation profiles reveals cancer-related genes
Sollier et al. COMPASS: joint copy number and mutation phylogeny reconstruction from amplicon single-cell sequencing data
Ran et al. Low intratumor heterogeneity correlates with increased response to PD-1 blockade in renal cell carcinoma
WO2018064547A1 (en) Methods for classifying somatic variations
Li et al. An NGS workflow blueprint for DNA sequencing data and its application in individualized molecular oncology
Pyke et al. A machine learning algorithm with subclonal sensitivity reveals widespread pan-cancer human leukocyte antigen loss of heterozygosity
Juul et al. The landscape and driver potential of site-specific hotspots across cancer genomes