Abstract

Provided herein are systems and methods for generating an immune-oncology profile from a biological sample. The immune-oncology profile can include the proportion or percentage of immune cells, expression of immune escape genes, and/or mutational burden. The immune-oncology profile may allow the generation of classifiers for making prognostic or diagnostic predictions.

IPC Classes  ?

• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G01N 33/574 - ImmunoassayBiospecific binding assayMaterials therefor for cancer
• G06F 18/2111 - Selection of the most significant subset of features by using evolutionary computational techniques, e.g. genetic algorithms
• G06F 18/2134 - Feature extraction, e.g. by transforming the feature spaceSummarisationMappings, e.g. subspace methods based on separation criteria, e.g. independent component analysis
• G16B 5/00 - ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 25/00 - ICT specially adapted for hybridisationICT specially adapted for gene or protein expression
• G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding

Abstract

Disclosed herein, are systems and methods for analyzing complex data signals using artificial intelligence and/or deconvolution algorithms to determine output pertaining to the state or status of one or more parameters. Data sets may include signals from various sources that can confound or distort the signals of interest. Accordingly, disclosed herein are deconvolution algorithms that enable the determination of the status of sources that correspond to the signals of interest.

IPC Classes  ?

• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G06F 18/213 - Feature extraction, e.g. by transforming the feature spaceSummarisationMappings, e.g. subspace methods
• G06F 18/214 - Generating training patternsBootstrap methods, e.g. bagging or boosting
• G06F 18/24 - Classification techniques
• G06N 3/086 - Learning methods using evolutionary algorithms, e.g. genetic algorithms or genetic programming
• G06N 3/126 - Evolutionary algorithms, e.g. genetic algorithms or genetic programming
• G06N 5/047 - Pattern matching networksRete networks
• G06N 20/00 - Machine learning
• G06V 10/764 - Arrangements for image or video recognition or understanding using pattern recognition or machine learning using classification, e.g. of video objects
• G06V 20/69 - Microscopic objects, e.g. biological cells or cellular parts
• G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation

Abstract

Disclosed herein are platforms, systems, methods, and media for analyzing gene expression data to predict treatment outcome for cancer patients. Machine learning models can be used to evaluate enrichment scores derived from gene set enrichment analysis to provide accurate predictions.

IPC Classes  ?

• G16B 40/20 - Supervised data analysis
• 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
• G16B 25/20 - Polymerase chain reaction [PCR]Primer or probe designProbe optimisation
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 35/00 - ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• 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
• G16B 50/00 - ICT programming tools or database systems specially adapted for bioinformatics
• G06N 20/00 - Machine learning

Abstract

Disclosed herein, are systems and methods for analyzing complex data signals using artificial intelligence and/or deconvolution algorithms to determine output pertaining to the state or status of one or more parameters. Data sets may include signals from various sources that can confound or distort the signals of interest. Accordingly, disclosed herein are deconvolution algorithms that enable the determination of the status of sources that correspond to the signals of interest.

IPC Classes  ?

• C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving virus or bacteriophage

Abstract

Disclosed herein, are systems and methods for analyzing complex data signals using artificial intelligence and/or deconvolution algorithms to determine output pertaining to the state or status of one or more parameters. Data sets may include signals from various sources that can confound or distort the signals of interest. Accordingly, disclosed herein are deconvolution algorithms that enable the determination of the status of sources that correspond to the signals of interest.

IPC Classes  ?

• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G06N 3/126 - Evolutionary algorithms, e.g. genetic algorithms or genetic programming
• G06N 20/00 - Machine learning
• G06N 3/086 - Learning methods using evolutionary algorithms, e.g. genetic algorithms or genetic programming
• G06N 5/047 - Pattern matching networksRete networks
• G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
• G06F 18/24 - Classification techniques
• G06F 18/213 - Feature extraction, e.g. by transforming the feature spaceSummarisationMappings, e.g. subspace methods
• G06F 18/214 - Generating training patternsBootstrap methods, e.g. bagging or boosting
• G06V 10/764 - Arrangements for image or video recognition or understanding using pattern recognition or machine learning using classification, e.g. of video objects
• G06V 20/69 - Microscopic objects, e.g. biological cells or cellular parts

Abstract

Provided herein are systems and methods for generating an immune-oncology profile from a biological sample. The immune-oncology profile can include the proportion or percentage of immune cells, expression of immune escape genes, and/or mutational burden. The immune-oncology profile may allow the generation of classifiers for making prognostic or diagnostic predictions.

IPC Classes  ?

• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G06K 9/62 - Methods or arrangements for recognition using electronic means
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 25/00 - ICT specially adapted for hybridisationICT specially adapted for gene or protein expression
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

Goods & Services

Reagents for research purposes; assays and reagents for use in genetic research, gene expression analysis, biomarker analysis, and RNA-based immune profiling. Pharmaceutical products; kits comprised of reagents and assays for testing and analyzing genes, nucleic acids, and biological molecules. Scientific research and development; scientific research and development in the field of gene expression analysis, biomarker analysis, and RNA-based immune profiling assay, and immune profiling; DNA analysis services for scientific research purposes; product development services, namely, developing reagents and reagent kits for use in preparing, detecting, analyzing, and sequencing nucleic acids and other biological molecules in the field of genetic research.

Goods & Services

Reagents for research purposes; assays and reagents for use in genetic research, gene expression analysis, biomarker analysis, and RNA-based immune profiling. Pharmaceutical products; kits comprised of reagents and assays for testing and analyzing genes, nucleic acids, and biological molecules. Scientific research and development; scientific research and development in the field of gene expression analysis, biomarker analysis, and RNA-based immune profiling assay, and immune profiling; DNA analysis services for scientific research purposes; product development services, namely, developing reagents and reagent kits for use in preparing, detecting, analyzing, and sequencing nucleic acids and other biological molecules in the field of genetic research; scientific and technological services, namely, collaborative scientific research and development services for researchers in the fields of agricultural genetics, epigenetics, gene expression analysis, single nucleotide polymorphism detection and insertion-deletion detection, namely, preparation, detection, analysis and sequence characterization of nucleic acids, among other biochemical entities; development of proprietary bioinformatic analysis software pipelines and computer systems for collecting, storing, characterizing, sorting, viewing, and delivering genetic information to clients in an increasingly navigable format; designing genomic experiments in context of client driven strategic goals; DNA/RNA sequencing using Next Generation Sequencing, and the forthcoming subsequent technologies of biological material for scientific research purposes; providing scientific research data in the field of genomics, including custom, proprietary bioinformatic analysis of data generated by NGS technology or unanalyzed biological data.

Goods & Services

Reagents for research purposes; assays and reagents for use in genetic research, gene expression analysis, biomarker analysis, and RNA-based immune profiling. Kits comprised of reagents and assays for testing and analyzing genes, nucleic acids, and biological molecules. Scientific research and development; scientific research and development in the field of gene expression analysis, biomarker analysis, and RNA-based immune profiling assay, and immune profiling; DNA analysis services for scientific research purposes; product development services, namely, developing reagents and reagent kits for use in preparing, detecting, analyzing, and sequencing nucleic acids and other biological molecules in the field of genetic research.

Goods & Services

Assays and reagents for use in genetic research, gene expression analysis, biomarker analysis, and RNA-based immune profiling other than for medical or veterinary use Medical diagnostic kits comprised of reagents and assays for testing and analyzing genes, nucleic acids, and biological molecules Scientific research and development; scientific research and development in the field of gene expression analysis, biomarker analysis, and RNA-based immune profiling assay, and immune profiling; DNA analysis services for scientific research purposes; product development services, namely, developing reagents and reagent kits for use in preparing, detecting, analyzing, and sequencing nucleic acids and other biological molecules in the field of genetic research

Abstract

Provided herein are systems and methods for generating an immune-oncology profile from a biological sample. The immune-oncology profile can include the proportion or percentage of immune cells, expression of immune escape genes, and/or mutational burden. The immune-oncology profile may allow the generation of classifiers for making prognostic or diagnostic predictions.

IPC Classes  ?

• G01N 33/48 - Biological material, e.g. blood, urineHaemocytometers
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G06K 9/62 - Methods or arrangements for recognition using electronic means
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 25/00 - ICT specially adapted for hybridisationICT specially adapted for gene or protein expression
• G16B 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G01N 33/574 - ImmunoassayBiospecific binding assayMaterials therefor for cancer
• G16B 5/00 - ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks

Abstract

Provided herein are systems and methods for generating an immune-oncology profile from a biological sample. The immune-oncology profile can include the proportion or percentage of immune cells, expression of immune escape genes, and/or mutational burden. The immune-oncology profile may allow the generation of classifiers for making prognostic or diagnostic predictions.

IPC Classes  ?

• 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
• G06F 19/26 - for data visualisation, e.g. graphics generation, display of maps or networks or other visual representations
• 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

Abstract

Provided herein are methods of amplifying nucleic acids. In particular, methods are provided for amplifying circular RNA molecules. In certain embodiments, circular DNA molecules for amplification are generated from circular RNA molecules.

IPC Classes  ?

• C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
• C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• A41C 3/00 - Brassières
• A41C 3/02 - Brassières with front closures

Abstract

Provided herein are methods of amplifying nucleic acids. In particular, methods are provided for amplifying circular RNA molecules. In certain embodiments, circular DNA molecules for amplification are generated from circular RNA molecules.

IPC Classes  ?

• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

Abstract

Provided herein are methods of amplifying nucleic acids. In particular, methods are provided for amplifying circular RNA molecules. In certain embodiments, circular DNA molecules for amplification are generated from circular RNA molecules. Provided herein are methods for amplifying a nucleic acid. In certain embodiments, a method comprises priming a circular RNA template molecule with one or more DNA primers and extending the primers with a reverse transcriptase to generate a cDNA strand that is a copy of the circular RNA molecule. In certain embodiments, the cDNA strand generated is linear.

IPC Classes  ?

• C12P 19/34 - Polynucleotides, e.g. nucleic acids, oligoribonucleotides

Goods & Services

Scientific and technological services, namely, collaborative scientific research and development services for researchers in the fields of agricultural genetics, epigenetics, gene expression analysis, single nucleotide polymorphism detection and insertion-deletion detection, namely, preparation, detection, analysis and sequence characterization of nucleic acids, among other biochemical entities; development of proprietary bioinformatic analysis software pipelines and computer systems for collecting, storing, characterizing, sorting, viewing, and delivering genetic information to clients in an increasingly navigable format; designing genomic experiments in context of client driven strategic goals; DNA/RNA sequencing using Next Generation Sequencing, and the forthcoming subsequent technologies of biological material for scientific research purposes; providing scientific research data in the field of genomics, including custom, proprietary bioinformatic analysis of data generated by NGS technology or unanalyzed biological data