Abstract

Disclosed herein are methods for improving detection and monitoring of human diseases. The methods can be used to provide spatial and/or developmental localization of the source of each differential mutation within the body. The methods can also be used to generate a mutation map of a subject. And the mutation map can be used to monitoring state(s) of health of one or more tissues of a subject.

IPC Classes  ?

• 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
• A61K 31/7068 - Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
• C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
• G16B 45/00 - ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• 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
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16C 20/60 - In silico combinatorial chemistry

Abstract

A method of predicting a classification of a disease of a subject based on fragmentomic signatures can include accessing sequence data of a biological sample of a subject. The method can also include generating, based on the sequence data, a set of sequence-size values. Each sequence-size value of the set can correspond to a size of a sequence of the sequence data. The method can also include determining fragmentomic signature amplitudes of the subject by projecting the set of sequence-size values onto latent variables of a fragmentomic signature. The latent variables can be generated by applying one or more signal-separation algorithms to other sequence-size values obtained from one or more reference biological samples. The method can also include generating a result by processing the fragmentomic signature amplitudes using a machine-learning model. The result can include a classification predictive of whether the subject has a particular disease.

IPC Classes  ?

• G16B 30/10 - Sequence alignmentHomology search
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 40/30 - Unsupervised data analysis

Abstract

The disclosure provides methods for estimating tumor purity from tumor samples without use of matched-normal controls. A set of genomic regions are identified based on a nucleic acid sequence data that is aligned to a reference genome. Each genomic region of the set of genomic regions includes one or more nucleotide-sequence variants relative to a corresponding genomic region of the reference genome. A B-allele frequency distribution for the biological sample is determined based on a B-allele frequency determined for each genomic region of the set of genomic regions. The B-allele frequency distribution is processed using a trained machine-learning model to estimate a metric identifying tumor purity in the biological sample.

IPC Classes  ?

• G16B 40/20 - Supervised data analysis
• C12Q 1/686 - Polymerase chain reaction [PCR]
• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• 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
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• 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
• G16B 35/10 - Design of libraries
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16C 20/60 - In silico combinatorial chemistry

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• 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
• G16B 35/10 - Design of libraries
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16C 20/60 - In silico combinatorial chemistry

Abstract

A computer-implemented method for processing and/or analyzing nucleic acid sequencing data comprises receiving a first data input and a second data input. The first data input comprises untargeted sequencing data generated from a first nucleic acid sample obtained from a subject. The second data input comprises target-specific sequencing data generated from a second nucleic acid sample obtained from the subject. Next, with the aid of a computer processor, the first data input and the second data input are combined to produce a combined data set. Next, an output derived from the combined data set is generated. The output is indicative of the presence or absence of one or more polymorphisms of the first nucleic acid sample and/or the second nucleic acid sample.

IPC Classes  ?

• G16B 30/10 - Sequence alignmentHomology search
• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• G06N 3/126 - Evolutionary algorithms, e.g. genetic algorithms or genetic programming
• 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 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16H 50/00 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics

Abstract

Disclosed herein are methods for improving detection and monitoring of human diseases. The methods can be used to provide spatial and/or developmental localization of the source of each differential mutation within the body. The methods can also be used to generate a mutation map of a subject. And the mutation map can be used to monitoring state(s) of health of one or more tissues of a subject.

IPC Classes  ?

• 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
• A61K 31/7068 - Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
• C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
• G16B 45/00 - ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• 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
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16C 20/60 - In silico combinatorial chemistry

Abstract

A method of detecting loss of heterozygosity in HLA alleles is provided. The method can include accessing a trained machine-learning model, which was trained using a training data set that included at least a training data set that includes an adjusted B allele frequency that represents a ratio between a first B allele frequency of heterozygous alleles in the tumor sample that correspond to the genomic region and a second B allele frequency of heterozygous alleles in the genomic region and associated with one or more control samples. The method can also include using the machine-learning model to generate a result corresponding to a probability of whether a loss of heterozygosity exists in an HLA allele identified in the biological sample of the particular subject by processing the sequence data using the machine-learning model.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 20/10 - Ploidy or copy number detection
• G16B 40/20 - Supervised data analysis

Abstract

Provided herein are compositions, methods, and systems for sample processing and/or data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample from a human, non-human, and combinations thereof.

IPC Classes  ?

• C40B 20/04 - Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes
• 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 1/689 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
• C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving virus or bacteriophage

Goods & Services

Diagnostic biomarker reagents for medical purposes Providing data analysis and interpretation of nucleic-acid sequence data and analyzing and sequencing nucleic acids and other biological molecules to identify biomarkers usable for medical diagnosis and treatment, and scientific and medical research and design services relating to the sequencing nucleic acids and other biological molecules, all in the field of bioinformatics, genomics and gene expression research and development Providing medical genomics testing and reporting services in the field of biomarkers for the susceptibility, risk, diagnosis, prognosis, treatment or management of cancer and other diseases; medical information services, namely, providing biomarker scores for treatment and diagnostic information

Abstract

Provided herein are methods and system for using methylation data to improve disease detection.

IPC Classes  ?

• C12Q 1/689 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
• C12Q 1/6883 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 30/10 - Sequence alignmentHomology search
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• 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
• G16B 35/10 - Design of libraries
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16C 20/60 - In silico combinatorial chemistry

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• 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
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16C 20/60 - In silico combinatorial chemistry

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• 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
• G16B 35/10 - Design of libraries
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16C 20/60 - In silico combinatorial chemistry

Abstract

A method of predicting a classification of a disease of a subject based on fragmentomic signatures can include accessing sequence data of a biological sample of a subject. The method can also include generating, based on the sequence data, a set of sequence-size values. Each sequence-size value of the set can correspond to a size of a sequence of the sequence data. The method can also include determining fragmentomic signature amplitudes of the subject by projecting the set of sequence-size values onto latent variables of a fragmentomic signature. The latent variables can be generated by applying one or more signal-separation algorithms to other sequence-size values obtained from one or more reference biological samples. The method can also include generating a result by processing the fragmentomic signature amplitudes using a machine-learning model. The result can include a classification predictive of whether the subject has a particular disease.

IPC Classes  ?

• 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
• G16B 30/10 - Sequence alignmentHomology search
• G16B 40/30 - Unsupervised data analysis

Abstract

The disclosure provides methods for predicting surface-presenting peptides using binding and surface-presentation characteristics. The method can include accessing a trained machine-learning model that is configured to generate an output that indicates an extent to which the one or more expression levels and the one or more peptide-presentation metrics are related in accordance with a population-level relationship between expression and presentation. For each peptide of the set of peptides for a tissue sample, a score can be determined using the machine-learning model and genomic and transcriptomic data corresponding to the peptide. The score is predictive of whether a corresponding peptide is a surface-presenting peptide that binds to an MHC molecule and is presented on a cell surface.

IPC Classes  ?

• G16B 40/20 - Supervised data analysis
• G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
• G06N 20/20 - Ensemble learning

Abstract

The present disclosure provides methods and systems for personalized genetic testing of disease in a subject, in particular for identifying and tracking genetic mutations identified in an individual subject to monitor for cancer or for the spread or recurrence of the disease. In some embodiments, custom assays, including custom panels designed to target sequence data corresponding to both subject-specific loci and other loci known for cancer-causing or therapy resistance mutations, are designed based upon the sequencing of a screening biopsy sample. Such custom assays are then run on subsequently obtained tissue samples, such as tissue obtained from a surgical resection of a primary or metastatic tumor or from a lymph node biopsy. The subsequently obtained tissue samples can be taken from the subject at various time points after an initial screening biopsy to further allow for extended monitoring of the subject for spread or recurrence of the disease.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• C12Q 1/6869 - Methods for sequencing

Abstract

The present disclosure provides methods and systems for personalized genetic testing of disease in a subject, in particular for identifying and tracking genetic mutations identified in an individual subject to monitor for cancer or for the spread or recurrence of the disease. In some embodiments, custom assays, including custom panels designed to target sequence data corresponding to both subject-specific loci and other loci known for cancer-causing or therapy resistance mutations, are designed based upon the sequencing of a screening biopsy sample. Such custom assays are then run on subsequently obtained tissue samples, such as tissue obtained from a surgical resection of a primary or metastatic tumor or from a lymph node biopsy. The subsequently obtained tissue samples can be taken from the subject at various time points after an initial screening biopsy to further allow for extended monitoring of the subject for spread or recurrence of the disease.

IPC Classes  ?

• 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 1/6827 - Hybridisation assays for detection of mutation or polymorphism
• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• G16B 30/10 - Sequence alignmentHomology search
• 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

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 35/10 - Design of libraries
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 35/00 - ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• G16C 20/60 - In silico combinatorial chemistry

Abstract

Methods for generating a composite biomarker that identifies a predicted level of responsiveness of a subject to a particular type of an immunotherapy treatment is provided. The method can include generating genomic metrics that represent one or more characteristics corresponding to one or more DNA sequences. The method can also include generating transcriptomic metrics represent one or more characteristics corresponding to a set of peptides that are translated from a corresponding RNA sequence of the one or more RNA sequences. The method can also include generating a composite biomarker score derived from the set of genomic metrics and the set of transcriptomic metrics. The method can also include determining, based on the composite biomarker score, a predicted level of responsiveness of the subject to a particular type of an immunotherapy treatment.

IPC Classes  ?

• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• 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 40/20 - Supervised data analysis

Abstract

The present disclosure provides methods of treating cancer with a specific KRAS mutation subtype with a combination treatment with a CD40 agonist and one or more chemotherapy drugs.

IPC Classes  ?

• 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
• A61P 35/00 - Antineoplastic agents
• C07K 16/28 - Immunoglobulins, e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
• G01N 33/50 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing

Abstract

A computer-implemented method for processing and/or analyzing nucleic acid sequencing data comprises receiving a first data input and a second data input. The first data input comprises untargeted sequencing data generated from a first nucleic acid sample obtained from a subject. The second data input comprises target-specific sequencing data generated from a second nucleic acid sample obtained from the subject. Next, with the aid of a computer processor, the first data input and the second data input are combined to produce a combined data set. Next, an output derived from the combined data set is generated. The output is indicative of the presence or absence of one or more polymorphisms of the first nucleic acid sample and/or the second nucleic acid sample.

IPC Classes  ?

• G16B 30/10 - Sequence alignmentHomology search
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16H 50/00 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
• G06N 3/12 - Computing arrangements based on biological models using genetic models
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

(1) Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. (2) Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Abstract

A method of detecting loss of heterozygosity in HLA alleles is provided. The method can include accessing a trained machine-learning model, which was trained using a training data set that included at least a training data set that includes an adjusted B allele frequency that represents a ratio between a first B allele frequency of heterozygous alleles in the tumor sample that correspond to the genomic region and a second B allele frequency of heterozygous alleles in the genomic region and associated with one or more control samples. The method can also include using the machine-learning model to generate a result corresponding to a probability of whether a loss of heterozygosity exists in an HLA allele identified in the biological sample of the particular subject by processing the sequence data using the machine-learning model.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 40/20 - Supervised data analysis

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Abstract

Disclosed herein are methods for improving detection and monitoring of human diseases. The methods can be used to provide spatial and/or developmental localization of the source of each differential mutation within the body. The methods can also be used to generate a mutation map of a subject. And the mutation map can be used to monitoring state(s) of health of one or more tissues of a subject.

IPC Classes  ?

• 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
• A61K 31/7068 - Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
• C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
• G16B 45/00 - ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks

Abstract

Methods for somatic variant calling from an unmatched biological samples is provided. The method can include obtaining nucleic acid sequence data corresponding to a biological sample of a subject. The method can also include aligning the nucleic acid sequence data to a reference genome. The method can also include identifying, based on the aligned nucleic acid sequence data, a set of candidate variants in said nucleic acid sequence data. The set of candidate variants may include one or more somatic variants and one or more germline variants. The method can also include, without using a nucleic acid sequencing data from a matching biological sample of the subject, processing the set of candidate variants using a trained machine-learning model to identify the somatic variants. The method can also include outputting a report that identifies the somatic variants.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 40/20 - Supervised data analysis

Abstract

A computer-implemented method for processing and/or analyzing nucleic acid sequencing data comprises receiving a first data input and a second data input. The first data input comprises untargeted sequencing data generated from a first nucleic acid sample obtained from a subject. The second data input comprises target-specific sequencing data generated from a second nucleic acid sample obtained from the subject. Next, with the aid of a computer processor, the first data input and the second data input are combined to produce a combined data set. Next, an output derived from the combined data set is generated. The output is indicative of the presence or absence of one or more polymorphisms of the first nucleic acid sample and/or the second nucleic acid sample.

IPC Classes  ?

• G16B 30/10 - Sequence alignmentHomology search
• G06N 3/12 - Computing arrangements based on biological models using genetic models
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• 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
• G16H 50/00 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics
• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• G16C 20/60 - In silico combinatorial chemistry
• G16B 35/00 - ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• C12Q 1/6869 - Methods for sequencing

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 35/10 - Design of libraries
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 35/00 - ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• G16C 20/60 - In silico combinatorial chemistry

Abstract

Disclosed herein are methods for improving detection and monitoring of human diseases. The methods can be used to provide spatial and/or developmental localization of the source of each differential mutation within the body. The methods can also be used to generate a mutation map of a subject. And the mutation map can be used to monitoring state(s) of health of one or more tissues of a subject.

IPC Classes  ?

• 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
• A61K 31/7068 - Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
• G16B 45/00 - ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism

Abstract

The disclosure provides methods for estimating tumor purity from tumor samples without use of matched-normal controls. A set of genomic regions are identified based on a nucleic acid sequence data that is aligned to a reference genome. Each genomic region of the set of genomic regions includes one or more nucleotide-sequence variants relative to a corresponding genomic region of the reference genome. A B-allele frequency distribution for the biological sample is determined based on a B-allele frequency determined for each genomic region of the set of genomic regions. The B-allele frequency distribution is processed using a trained machine-learning model to estimate a metric identifying tumor purity in the biological sample.

IPC Classes  ?

• G16B 40/20 - Supervised data analysis
• 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
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• C12Q 1/686 - Polymerase chain reaction [PCR]
• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 35/10 - Design of libraries
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 35/00 - ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• G16C 20/60 - In silico combinatorial chemistry

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 35/10 - Design of libraries
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 35/00 - ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• G16C 20/60 - In silico combinatorial chemistry

Abstract

Disclosed herein are methods for improving detection and monitoring of human diseases. The methods can be used to provide spatial and/or developmental localization of the source of each differential mutation within the body. The methods can also be used to generate a mutation map of a subject. And the mutation map can be used to monitoring state(s) of health of one or more tissues of a subject.

IPC Classes  ?

• 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 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
• A61K 31/7068 - Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
• G16B 45/00 - ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks

Abstract

The disclosure provides methods for predicting surface-presenting peptides using binding and surface-presentation characteristics. The method can include accessing a trained machine-learning model that is configured to generate an output that indicates an extent to which the one or more expression levels and the one or more peptide-presentation metrics are related in accordance with a population-level relationship between expression and presentation. For each peptide of the set of peptides for a tissue sample, a score can be determined using the machine-learning model and genomic and transcriptomic data corresponding to the peptide. The score is predictive of whether a corresponding peptide is a surface-presenting peptide that binds to an MHC molecule and is presented on a cell surface.

IPC Classes  ?

• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• C12Q 1/6869 - Methods for sequencing
• G01N 33/48 - Biological material, e.g. blood, urineHaemocytometers
• G06F 19/10 - Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology (in silico methods of screening virtual chemical libraries C40B 30/02;in silico or mathematical methods of creating virtual chemical libraries C40B 50/02)
• 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

Abstract

Methods for generating a composite biomarker that identifies a predicted level of responsiveness of a subject to a particular type of an immunotherapy treatment is provided. The method can include generating genomic metrics that represent one or more characteristics corresponding to one or more DNA sequences. The method can also include generating transcriptomic metrics represent one or more characteristics corresponding to a set of peptides that are translated from a corresponding RNA sequence of the one or more RNA sequences. The method can also include generating a composite biomarker score derived from the set of genomic metrics and the set of transcriptomic metrics. The method can also include determining, based on the composite biomarker score, a predicted level of responsiveness of the subject to a particular type of an immunotherapy treatment.

IPC Classes  ?

• C12N 15/09 - Recombinant DNA-technology
• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
• 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
• G01N 33/48 - Biological material, e.g. blood, urineHaemocytometers
• G01N 33/50 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing

Abstract

The disclosure provides methods and systems for analyzing genotype data. In some embodiments, a computer-implemented method comprises receiving data relating to one or more phenotypes of a subject or family members thereof, and ranking genes based on their association score with one or more phenotypes. Next, an output of the data is generated, the output comprising a comparison of the data based on the association score. The comparison can be in at least one of numeric and graphic form.

IPC Classes  ?

• G06F 16/2457 - Query processing with adaptation to user needs
• G16B 50/00 - ICT programming tools or database systems specially adapted for bioinformatics
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G06F 16/248 - Presentation of query results
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 50/10 - OntologiesAnnotations

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Abstract

Provided herein are compositions, methods, and systems for sample processing and/or data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample from a human, non-human, and combinations thereof.

IPC Classes  ?

• C40B 30/04 - Methods of screening libraries by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• C40B 20/04 - Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes
• 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 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving virus or bacteriophage
• C12Q 1/689 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 35/00 - ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• G16C 20/60 - In silico combinatorial chemistry
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 99/00 - Subject matter not provided for in other groups of this subclass

Abstract

A computer-implemented method for processing and/or analyzing nucleic acid sequencing data comprises receiving a first data input and a second data input. The first data input comprises untargeted sequencing data generated from a first nucleic acid sample obtained from a subject. The second data input comprises target-specific sequencing data generated from a second nucleic acid sample obtained from the subject. Next, with the aid of a computer processor, the first data input and the second data input are combined to produce a combined data set. Next, an output derived from the combined data set is generated. The output is indicative of the presence or absence of one or more polymorphisms of the first nucleic acid sample and/or the second nucleic acid sample.

IPC Classes  ?

• G16B 30/10 - Sequence alignmentHomology search
• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• G06N 3/126 - Evolutionary algorithms, e.g. genetic algorithms or genetic programming
• 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 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16H 50/00 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics

Abstract

The disclosure provides methods for estimating tumor purity from tumor samples without use of matched-normal controls. A set of genomic regions are identified based on a nucleic acid sequence data that is aligned to a reference genome. Each genomic region of the set of genomic regions includes one or more nucleotide-sequence variants relative to a corresponding genomic region of the reference genome. A B-allele frequency distribution for the biological sample is determined based on a B-allele frequency determined for each genomic region of the set of genomic regions. The B-allele frequency distribution is processed using a trained machine-learning model to estimate a metric identifying tumor purity in the biological sample.

IPC Classes  ?

• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• 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
• 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

Methods for somatic variant calling from an unmatched biological samples is provided. The method can include obtaining nucleic acid sequence data corresponding to a biological sample of a subject. The method can also include aligning the nucleic acid sequence data to a reference genome. The method can also include identifying, based on the aligned nucleic acid sequence data, a set of candidate variants in said nucleic acid sequence data. The set of candidate variants may include one or more somatic variants and one or more germline variants. The method can also include, without using a nucleic acid sequencing data from a matching biological sample of the subject, processing the set of candidate variants using a trained machine-learning model to identify the somatic variants. The method can also include outputting a report that identifies the somatic variants.

IPC Classes  ?

• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• G06F 15/00 - Digital computers in generalData processing equipment in general
• 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
• G06N 3/12 - Computing arrangements based on biological models using genetic models

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Design of algorithms and models for use in scientific and medical research, all in the field of bioinformatics, genomics and gene expression research and development; platform as a service (PAAS) featuring computer software platforms for using algorithms to analyze cells, antigens, tissues, gene expressions, gene sequences, genome annotation, antigen characteristics and immunological responses, transcriptome characterization, and genome mapping for medical diagnosis and treatment; platform as a service (PAAS) featuring computer software platforms for using algorithms to predict antigen characteristics and immunological responses; providing data analysis and interpretation regarding antigen characteristics and immunological responses, and research and design relating thereto. Analysis of cells, antigens, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping medical diagnosis and treatment and drug design and development; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, antigen characteristics and immunological response, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment and drug design and development.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, amino acids, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Abstract

Disclosed herein are methods for improving detection and monitoring of human diseases. The methods can be used to provide spatial and/or developmental localization of the source of each differential mutation within the body. The methods can also be used to generate a mutation map of a subject. And the mutation map can be used to monitoring state(s) of health of one or more tissues of a subject.

IPC Classes  ?

• 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
• A61K 31/7068 - Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid
• G16B 45/00 - ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks
• C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
• C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16B 20/10 - Ploidy or copy number detection
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 35/10 - Design of libraries
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 35/00 - ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• G16C 20/60 - In silico combinatorial chemistry

Abstract

Provided herein are compositions, methods, and systems for sample processing and/or data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample from a human, non-human, and combinations thereof.

IPC Classes  ?

• C40B 50/06 - Biochemical methods, e.g. using enzymes or whole viable microorganisms
• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• 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 1/689 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
• C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving virus or bacteriophage

Abstract

This disclosure provides systems and methods for sample processing and data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Some or all of a nucleic acid sample may be sequenced to provide sequence information, which may be stored or otherwise maintained in an electronic storage location. The sequence information may be analyzed with the aid of a computer processor, and the analyzed sequence information may be stored in an electronic storage location that may include a pool or collection of sequence information and analyzed sequence information generated from the nucleic acid sample. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample, for producing one or more libraries, and for producing biomedical reports. Methods and systems of the disclosure can aid in the diagnosis, monitoring, treatment, and prevention of one or more diseases and conditions.

IPC Classes  ?

• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
• G16B 35/10 - Design of libraries
• C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
• C12Q 1/6869 - Methods for sequencing
• G16B 35/00 - ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
• G16B 99/00 - Subject matter not provided for in other groups of this subclass
• G16B 20/10 - Ploidy or copy number detection
• G16C 20/60 - In silico combinatorial chemistry

Goods & Services

(1) Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. (2) Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

(1) Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. (2) Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

(1) Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. (2) Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

(1) Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. (2) Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

(1) Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. (2) Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

(1) Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. (2) Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

(1) Design of algorithms and models for use in scientific and medical research, all in the field of bioinformatics, genomics and gene expression research and development; platform as a service (PAAS) featuring computer software platforms for using algorithms to analyze cells, antigens, tissues, gene expressions, gene sequences, genome annotation, antigen characteristics and immunological responses, transcriptome characterization, and genome mapping for medical diagnosis and treatment; platform as a service (PAAS) featuring computer software platforms for using algorithms to predict antigen characteristics and immunological responses; providing data analysis and interpretation regarding antigen characteristics and immunological responses, and research and design relating thereto. (2) Analysis of cells, antigens, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping medical diagnosis and treatment and drug design and development; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, antigen characteristics and immunological response, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment and drug design and development.

Goods & Services

(1) Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. (2) Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

(1) Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. (2) Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

(1) Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. (2) Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

(1) Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. (2) Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

Design of algorithms and models for use in scientific and medical research, all in the field of bioinformatics, genomics and gene expression research and development; platform as a service (PAAS) featuring computer software platforms for using algorithms to analyze cells, antigens, tissues, gene expressions, gene sequences, genome annotation, antigen characteristics and immunological responses, transcriptome characterization, and genome mapping for medical diagnosis and treatment; platform as a service (PAAS) featuring computer software platforms for using algorithms to predict antigen characteristics and immunological responses; providing data analysis and interpretation regarding antigen characteristics and immunological responses, and research and design relating thereto Analysis of cells, antigens, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping medical diagnosis and treatment and drug design and development; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, antigen characteristics and immunological response, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment and drug design and development

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, amino acids, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Abstract

Provided herein are compositions, methods, and systems for sample processing and/or data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample from a human, non-human, and combinations thereof.

IPC Classes  ?

• C40B 50/06 - Biochemical methods, e.g. using enzymes or whole viable microorganisms
• C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
• 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 1/689 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for bacteria
• C12Q 1/70 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving virus or bacteriophage

Abstract

Provided herein are compositions, methods, and systems for sample processing and/or data analysis. Sample processing may include nucleic acid sample processing and subsequent sequencing. Methods and systems of the present disclosure can be used, for example, for the analysis of a nucleic acid sample from a human, non-human, and combinations thereof.

IPC Classes  ?

• C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
• C12N 15/03 - Bacteria
• C12N 15/06 - Animal cells

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

(1) Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development (2) Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development. Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment.

Goods & Services

(1) Providing genome sequencing, data analysis and interpretation, assay development and preparing, amplifying, labeling, detecting, analyzing and sequencing nucleic acids and other biological molecules, and research and design relating thereto, all in the field of bioinformatics, genomics and gene expression research and development (2) Analysis of cells, tissues, gene expressions, gene sequences, genome annotation, transcriptome characterization, and genome mapping for medical diagnosis and treatment; Preparation of reports relating to gene expressions, gene and genome sequences, genome interaction and annotation, transcriptome analysis and characterization, and genome mapping for medical diagnosis and treatment