An analysis technique for enriching one or more target regions in molecules of deoxyribonucleic acid (DNA) in a sample (such as a tissue sample or cell-free DNA) is described. Notably, in this analysis technique, adapters are attached to ends of the molecules of DNA. Then, the molecules of DNA are selectively cut in one or more off-target regions in the molecules of DNA. The selective cutting may use a Cas9 protein or a restriction enzyme. Moreover, the one or more off-target regions in the molecules of DNA are depleted or removed, where the off-target regions are different from the target regions. Next, after the depleting or removing operation, motor adapters are attached to a remainder of the molecules of DNA. In some embodiments, the one or more target regions are analyzed by pulling or extracting the remainder of the molecules of DNA through an analysis membrane using the motor adapters.
C12Q 1/683 - Hybridisation assays for detection of mutation or polymorphism involving restriction enzymes, e.g. restriction fragment length polymorphism [RFLP]
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
2.
SIGNIFICANCE MODELING OF CLONAL-LEVEL TARGET VARIANTS USING METHYLATION DETECTION
Provided herein are methods of making negative predictions. In some aspects, methods of determining, including via epigenomic detection, that a first target nucleic acid variant is absent at a first genetic locus in a cell-free nucleic acid (cfNA) sample obtained from a subject having a given cancer type at least partially using a computer are provided. Certain of these methods include determining that the first target nucleic acid variant is not detected in the cfNA sample obtained from the subject, generating, by the computer, at least one tumor fraction based value including methylation based estimation; generating, by the computer, at least one mutual exclusivity value; and determining that the first target nucleic acid variant is absent at the first genetic locus in the cfNA sample using the tumor fraction based value and/or the mutual exclusivity value. Additional methods and related systems and computer readable media are also provided.
Described herein are gene signatures providing prognostic, diagnostic, treatment and molecular subtype classifications of cancers through genomic and epigenomic profiling, Methods and compositions for determining cancer and subtypes, including breast cancer are described and specific and sensitive detection of biomarkers of interest is provided. Such biomarkers are indicative of disease pathogenesis, which provides opportunity for selection of treatment, including treatment regimes directed at identifying candidates for responsiveness and overcoming resistance mechanisms.
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
4.
CLASSIFICATION OF COLORECTAL TUMORS USING DNA METHYLATION FROM LIQUID BIOPSY
Described herein are gene signatures providing prognostic, diagnostic, treatment and molecular subtype classifications of cancers through genomic and epigenomic profiling, Methods and compositions for determining cancer and subtypes, including breast cancer are described and specific and sensitive detection of biomarkers of interest is provided. Such biomarkers are indicative of disease pathogenesis, which provides opportunity for selection of treatment, including treatment regimes directed at identifying candidates for responsiveness and overcoming resistance mechanisms.
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
5.
MOLECULAR INDEXING METHODS TO INCREASE THROUGHPUT OF NGS-BASED MULTIPLEX IMMUNOASSAYS
Methods are disclosed for detecting and identifying target molecules, such as proteins, in a plurality of biological samples using high throughput methods. A molecular indexing approach is incorporated into next generation sequencing-based immunoassay workflows that allows for pooling of probe panels targeting molecules of interest to be mixed prior to sequencing, thus increasing throughput and reducing costs.
Disclosed herein are methods, compositions, and devices for use in early detection of cancer. The methods include sequencing a panel of regions in cell-free nucleic acid molecules and detecting one or more biomarkers that are indicative of a cancer.
Described herein are gene signatures providing prognostic, diagnostic, treatment and molecular subtype classifications of cancers through genomic and epigenomic profiling, including immune checkpoint regulators such as programmed death ligand 1 (PDL-1). Using methods and compositions described herein, specific and sensitive detection of biomarkers of interest is provided. Such biomarkers are indicative of disease pathogenesis, which provides opportunity for selection of treatment, including treatment regimes directed at overcoming resistance mechanisms.
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 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
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 15/00 - ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
9.
METHODS AND COMPOSITIONS FOR QUANTIFYING IMMUNE CELL NUCLEIC ACIDS
Provided herein is an RNA analysis method for detecting and quantifying RNA (such as RNA from an immune cell or from a cancer cell) and/or for identifying and quantifying immune cell types from which the RNA originated. In some embodiments, expression levels of genes differentially expressed between healthy subjects and subjects having a disease or disorder are determined based on the RNA. In some embodiments, immune cell types from which the RNA originated are identified and quantified. Provided herein are also methods for determining the likelihood that a subject has the disease or disorder, such as a cancer.
C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
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
10.
METHOD FOR HRD DETECTION IN TARGETED cfDNA SAMPLES USING DE NOVO MUTATIONAL SIGNATURES
Described herein are method for determining homologous recombination repair deficiency (HRD) status in a subject, including use of samples containing cell free nucleic acid such as cell free DNA (cfDNA). As such nucleic acid in samples such as blood are small quantities, described herein are techniques to analyze signatures present in cell free nucleic acids to provide metrics related to the presence or absence of a homologous recombination repair deficiency in a given subject.
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
G16H 50/50 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for simulation or modelling of medical disorders
11.
METHOD FOR HRD DETECTION IN TARGETED CFDNA SAMPLES USING DE NOVO MUTATIONAL SIGNATURES
Described herein are method for determining homologous recombination repair deficiency (HRD) status in a subject, including use of samples containing cell free nucleic acid such as cell free DNA (cfDNA). As such nucleic acid in samples such as blood are small quantities, described herein are techniques to analyze signatures present in cell free nucleic acids to provide metrics related to the presence or absence of a homologous recombination repair deficiency in a given subject.
The disclosure provides methods for processing nucleic acid populations containing different forms (e.g., RNA and DNA, single-stranded or double-stranded) and/or extents of modification (e.g., cytosine methylation, association with proteins). These methods accommodate multiple forms and/or modifications of nucleic acid in a sample, such that sequence information can be obtained for multiple forms. The methods also preserve the identity of multiple forms or modified states through processing and analysis, such that analysis of sequence can be combined with epigenetic analysis.
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
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
13.
METHODS AND SYSTEMS FOR ANALYZING NUCLEIC ACID MOLECULES
The disclosure provides methods for processing nucleic acid populations containing different forms (e.g., RNA and DNA, single-stranded or double-stranded) and/or extents of modification (e.g., cytosine methylation, association with proteins). These methods accommodate multiple forms and/or modifications of nucleic acid in a sample, such that sequence information can be obtained for multiple forms. The methods also preserve the identity of multiple forms or modified states through processing and analysis, such that analysis of sequence can be combined with epigenetic analysis.
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
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
14.
DETECTING HOMOLOGOUS RECOMBINATION DEFICIENCES BASED ON METHYLATION STATUS OF CELL-FREE NUCLEIC ACID MOLECULES
In implementations described herein, methylation information is determined with respect to classification regions of a reference genome that are related to the presence of a homologous recombination repair deficiency in a subject. The methylation information can be analyzed using a number of computational techniques to provide metrics related to the presence or absence of a homologous recombination repair deficiency in a given subject.
A disease classification method includes determining, using a predictive model, whether cell-free nucleic acid samples are tumor-derived or non-tumor derived based on at least one of the cell-free nucleic acid score or a tumor fraction regression (TFR) score satisfying a respective threshold. The TFR score is determined based on a quantification of an observed tumor-associated aberrant methylation of each of a plurality of cell-free nucleic acid samples using a TFR model. The TFR score includes a fraction of molecules of the plurality of cell-free nucleic acid samples that indicate a tumor. The cell-free nucleic acid score is indicative of the presence of a tumor, and is based on at least one of epigenetic factors or genomic alterations of the cell-free nucleic acid samples.
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 20/00 - 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
Provided herein are methods for monitoring false negative and/or false positive detection of modified nucleosides in DNA in a sample using an enzymatic base-pairing conversion procedure. The methods use nucleosides having known nucleoside identity and known modification status in adapters ligated to the DNA. In certain aspects, the disclosure relates to methods for improving the quality control of such methods.
C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
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
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
Disclosed herein are methods for isolating DNA, such as cell-free DNA (cfDNA) or DNA from a tissue sample, e.g., in which the DNA is partitioned into hypermethylated and hypomethylated partitions. After differential tagging of the partitions, portions of the hypomethylated partition are pooled with the hypermethylated partition or pooled separately. Epigenetic and sequence-variable target regions are captured from the pool comprising DNA from the hypermethylated and hypomethylated partitions, and sequence-variable target regions are captured from the pool comprising DNA from the hypomethylated partition. This approach can reduce costs and/or bandwidth by limiting sequencing of epigenetic target regions from the hypomethylated partition, which may be less informative than other DNA.
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
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
19.
METHODS AND COMPOSITIONS FOR QUANTIFYING IMMUNE CELL DNA
Provided herein is a DNA analysis method for detecting and quantifying immune cell types from which the DNA originated. Provided herein are also methods for determining the likelihood that a subject has a disease or condition, such as cancer.
C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
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
Described herein are methods such as diagnoses to select therapies for personalized cancer treatment by simultaneously detecting genomic and epigenomic attributes from a single patient sample, including quantifying promoter methylation and applications for ascertaining methylation patterns associated with epigenetic allelic status.
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
21.
COMPOSITIONS AND METHODS FOR ASSAYING CIRCULATING MOLECULES
Provided herein are methods of detecting and quantifying target molecules associated with cell debris. Provided herein are also methods for determining the likelihood that a subject has a disease or condition, such as cancer.
G01N 33/92 - Chemical analysis of biological material, e.g. blood, urineTesting involving biospecific ligand binding methodsImmunological testing involving lipids, e.g. cholesterol
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
Multiplex analysis methods and systems for accurately detecting and quantitating multiple analytes in a sample are disclosed. The sample is contacted with an analyte capturing agent and immobilized on a magnetic particle, followed by magnetic separation and washing of the particle and bound analyte. This complex is then contacted with a detection agent labeled with an oligonucleotide barcode specific to the analyte target, followed by quantitative measurement of the barcode by qPCR or NGS. The combination of a plurality of analyte capture particles and cognate detection probes allows multiple analytes to be assayed simultaneously and in a multiplex manner.
In implementations described herein, methylation information is determined with respect to classification regions of a reference genome that are related to the presence of a tumor in a subject. The methylation information can be analyzed using a number of computational techniques to provide metrics related to the presence or absence of a tumor in a given subject, including a determination of tumor fraction.
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.
Methods and systems for hybrid library preparation to improve molecular recovery, provide DNA molecule topology, and/or enable novel multiomic workflows. The methods can improve identification of tumor specific biomarkers which can inform therapy selection.
The disclosure provides methods for processing nucleic acid populations containing different forms (e.g., RNA and DNA, single-stranded or double-stranded) and/or extents of modification (e.g., cytosine methylation, association with proteins). These methods accommodate multiple forms and/or modifications of nucleic acid in a sample, such that sequence information can be obtained for multiple forms. The methods also preserve the identity of multiple forms or modified states through processing and analysis, such that analysis of sequence can be combined with epigenetic analysis.
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
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
28.
CHARACTERIZATION OF WHOLE GENOME DUPLICATION IN A GENOMIC COHORT OF OVER 14000 CELL FREE DNA SAMPLES
Described herein are methods and compositions related to whole gene duplication (WGD). Methods are described for detecting and determining the presence of WGD in a sample, including cell free nucleic acids derived from a subject, such as a liquid sample (e.g., blood, plasma), as well as chromosomal instability and genomic alterations. In various embodiments, the aforementioned methods are used in diagnosis, prognosis and treatment. In other embodiments, processing of samples characterized by WGD is described to confer increased accuracy and precision of detection.
A network bandwidth architecture controls data transfers between a life science service provider, a local network data repository, and a remote data repository. The data transfers may include patient data and patient metadata that are analyzed by a bioinformatics system of the life science service provider.
G16B 50/00 - ICT programming tools or database systems specially adapted for bioinformatics
G06F 9/50 - Allocation of resources, e.g. of the central processing unit [CPU]
H04L 47/76 - Admission controlResource allocation using dynamic resource allocation, e.g. in-call renegotiation requested by the user or requested by the network in response to changing network conditions
H04J 3/16 - Time-division multiplex systems in which the time allocation to individual channels within a transmission cycle is variable, e.g. to accommodate varying complexity of signals, to vary number of channels transmitted
H04L 12/28 - Data switching networks characterised by path configuration, e.g. LAN [Local Area Networks] or WAN [Wide Area Networks]
The present disclosure provides methods for determining a probability that after any of a number of therapeutic interventions, an initial state of a subject, such as somatic cell mutational status of a subject with cancer, will develop a subsequent state. Such probabilities can be used to inform a health care provider as to particular courses of treatment to maximize probability of a desired outcome for the subject.
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
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 20/00 - 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 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
31.
METHODS AND COMPOSITIONS FOR COPY-NUMBER INFORMED TISSUE-OF-ORIGIN ANALYSIS
Provided herein are methods of analyzing nucleic acids for detecting DNA comprising cell or tissue type-specific epigenetically variable regions, such as differentially methylated regions, that are also copy number variants. Provided herein are also methods for determining the likelihood that a subject has a disease or condition, such as cancer.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
Disclosed herein are methods, compositions, and devices for use in the early detection of cancer. The methods include preparing cell-free nucleic acid molecules from a subject for sequencing, sequencing a panel of regions in the cell-free nucleic acid molecules, and detecting one or more markers that are indicative of a cancer.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
C12M 1/00 - Apparatus for enzymology or microbiology
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
33.
NON-INVASIVE MONITORING OF GENOMIC ALTERATIONS INDUCED BY GENE-EDITING THERAPIES
Non-invasive, post-gene editing methods for determining the reduced efficacy of a genome-editing drug and/or for detecting diseases induced by a genome-editing drug.
G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
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
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
G16B 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
C12N 15/11 - DNA or RNA fragmentsModified forms thereof
C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
The disclosure relates to methods for determining the methylation profile of nucleic acids. The methods use base conversion methods in combination with methylation-based partitioning methods to resolve multiple types of methylation in a single workflow.
C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
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
05 - Pharmaceutical, veterinary and sanitary products
10 - Medical apparatus and instruments
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Diagnostic kits comprising diagnostic agents, preparations and substances for medical purposes Blood collection kit comprised of blood collection bag, holder for medical sample tubes and vials, and medical sample tubes and vials Medical research services in the field of cancer; Providing an on-line searchable database in the field of cancer for scientific research purposes; Providing information about medical research in the field of cancer; Structural and functional analysis of genomes Health care; Cancer screening services; Medical diagnostic testing, monitoring and reporting services; Medical testing for diagnostic or treatment purposes in the field of cancer; Medical testing services; Providing medical information; Health care services, namely, providing a database in the field of cancer information and featuring inputting and collection of data and information all for treatment and diagnostic purposes; Providing healthcare information; Providing a website featuring information in the field of the diagnosis and treatment of cancer; Providing information in the field of cancer prevention, screening, diagnosis and treatment
36.
MICROSATELLITE INSTABILITY DETECTION IN CELL-FREE DNA
Provided herein are methods for determining the microsatellite instability status of samples. In one aspect, the methods include quantifying a number of different repeat lengths present at each of a plurality of microsatellite loci from sequence information to generate a site score for each of the plurality of the microsatellite loci. The methods also include comparing the site score of a given microsatellite locus to a site specific trained threshold for the given microsatellite locus for each of the plurality of the microsatellite loci and calling the given microsatellite locus as being unstable when the site score of the given microsatellite locus exceeds the site specific trained threshold for the given microsatellite locus to generate a microsatellite instability score, which includes a number of unstable microsatellite loci from the plurality of the microsatellite loci.
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
The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.
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
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
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 15/00 - ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
39.
JOINT MODELING OF LONGITUDINAL AND TIME-TO-EVENT DATA TO PREDICT PATIENT SURVIVAL
Changes in ctDNA levels can fluctuate significantly over time from patient to patient, and the results can be difficult to interpret. Described herein are methods and techniques capable of capturing these complexities while accounting for a diverse set of patient traits. Furthermore, analyzing an observational dataset consisting of patients with cancer who received therapy, analytic results are capable of being presented graphically. These results demonstrate the utility of the described methods and techniques in acquiring a comprehensive understanding of how response patterns evolve and how different patient characteristics influence these evolutions.
G16B 20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
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
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
40.
METHODS FOR THE NON-INVASIVE DETECTION AND MONITORING OF THERAPEUTIC NUCLEIC ACID CONSTRUCTS
Methods, systems, and compositions for non-invasively detecting and/or monitoring therapeutic nucleic acid constructs in a sample comprising cell-free nucleic acids from a subject. Detection of therapeutic nucleic acid constructs in samples comprising cell-free nucleic acids allows for verifying therapeutic nucleic acid construct administration, determining the persistence or biological efficacy of the therapeutic nucleic acid construct, and/or ascertaining the efficacy of the therapy in the subject.
Provided herein is a DNA analysis method for detecting a presence or absence of a DNA molecule that comprises a structural variation, comprising contacting the DNA with at least two primers that anneal in a parallel orientation to a target region and contacting the primer-annealed DNA with a 5′ to 3′ exonuclease negative, strand displacement negative DNA polymerase.
C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
42.
COMPOSITIONS AND METHODS FOR ANALYZING CELL-FREE DNA IN METHYLATION PARTITIONING ASSAYS
Provided herein is a DNA analysis method comprising partitioning a sample into at least a first subsample and a second subsample, wherein the first subsample comprises DNA (e.g., cell-free DNA) with a cytosine modification in a greater proportion; the first subsample undergoes a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the first subsample; and DNA is sequenced to distinguish the first nucleobase from the second nucleobase. Also provided is a combination comprising first and second populations of captured DNA, wherein the first population comprises or was derived from DNA with a cytosine modification in a greater proportion than the second population, and wherein the first population comprises a form of a first nucleobase originally present in the DNA with altered base pairing specificity and a second nucleobase without altered base pairing specificity.
The present disclosure provides a method for enriching for multiple genomic regions using a first bait set that selectively hybridizes to a first set of genomic regions of a nucleic acid sample and a second bait set that selectively hybridizes to a second set of genomic regions of the nucleic acid sample. These bait set panels can selectively enrich for one or more nucleosome-associated regions of a genome, said nucleosome-associated regions comprising genomic regions having one or more genomic base positions with differential nucleosomal occupancy, wherein the differential nucleosomal occupancy is characteristic of a cell or tissue type of origin or disease state.
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
C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
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 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
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 15/00 - ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
45.
METHODS INVOLVING METHYLATION PRESERVING AMPLIFICATION WITH ERROR CORRECTION
Provided herein is a DNA analysis method comprising methylation-specific amplification with error correction. Provided herein are also methods for determining the likelihood that a subject has a disease or condition, such as cancer.
Provided herein are methods of analyzing DNA comprising dividing a DNA sample into a plurality of subsamples, treating at least one of the plurality of subsamples, combining at least a portion of the DNA of at least two of the subsamples, and sequencing the combined subsample. Some such methods facilitate detection of both epigenetic and genetic characteristics of the DNA within a combined workflow.
In implementations described herein, methylation information is determined with respect to classification regions of a reference genome that are related to the presence of a homologous recombination repair deficiency in a subject. The methylation information can be analyzed using a number of computational techniques to provide metrics related to the presence or absence of a homologous recombination repair deficiency in a given subject.
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] 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
48.
Systems and methods to detect rare mutations and copy number variation
The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.
The present disclosure provides a method for monitoring residual disease in a subject. Generally, the method comprises determining a frequency of cancer mutations from a first sample obtained from a tumor biopsy from the subject; determining a frequency of the cancer mutations discovered in the first sample from a second sample comprising cell-free deoxyribonucleic acid (cfDNA) molecules that is obtained from the subject after the subject has undergone a course of treatment for cancer; and determining a presence or absence of cancer in the subject based on an analysis of the frequency of the cancer mutations from sequence data from the second sample.
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 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
The disclosure relates to improved sequencing reactions. Specifically, the disclosure provides methods which allow for the identification of regions of a DNA molecule that were synthesized during an end repair and/or A-tailing reaction. Sequence data deriving from such synthesized regions may not be representative of the corresponding region in the original DNA molecules, for example it may contain artifactual methylation statuses. Accordingly, the identification of these synthesized regions allows for such potentially artifactual data to be identified and filtered accordingly.
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
Disclosed herein are methods, compositions, and devices for use in the early detection of cancer. The methods include preparing cell-free nucleic acid molecules from a subject for sequencing, sequencing a panel of regions in the cell-free nucleic acid molecules, and detecting one or more markers that are indicative of a cancer.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
C12M 1/00 - Apparatus for enzymology or microbiology
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
Disclosed herein are methods, compositions, and devices for use in the early detection of cancer. The methods include preparing cell-free nucleic acid molecules from a subject for sequencing, sequencing a panel of regions in the cell-free nucleic acid molecules, and detecting one or more markers that are indicative of a cancer.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
C12M 1/00 - Apparatus for enzymology or microbiology
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
Methods, systems, and apparatuses for securely delivering software artifacts. A first computing device may be configured to encrypt one or more software artifacts into an encrypted data file and encrypt a key and a policy file associated with the encrypted data file and send the encrypted data file, key, and policy file to a second computing device. The policy file may comprise policy information for authenticating access to the encrypted data file. The second computing device may use the key and the policy information to access and authenticate a software application of the second computing device. The software application may be used to decrypt the data file and access the one or more software artifacts.
Provided herein is a method of analyzing DNA comprising a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA; sequence-specifically degrading target sequences in the DNA; and detecting target sequences that are not degraded. Also provided is a combination comprising a population of DNA and a sequence-specific nuclease, wherein the population comprises or was derived from DNA with a cytosine modification, and wherein the population comprises a first, converted nucleobase and a second nucleobase without altered base pairing specificity; wherein the form of the first nucleobase originally present in the DNA prior to alteration of base pairing specificity and the second nucleobase have the same base pairing specificity.
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 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
55.
VALIDATION OF A BIOINFORMATIC MODEL FOR CLASSIFYING NON-TUMOR VARIANTS IN A CELL-FREE DNA LIQUID BIOPSY ASSAY
Provided herein are methods of differentiating tumor and non-tumor origin nucleic acid variants in cell-free nucleic acid (cfNA) samples. Certain of these methods include generating a tumor variant dataset comprising a population of reference tumor-related genetic variants in which the tumor variant dataset comprises frequency of observance data among reference samples that comprises reference plasma only samples and reference white blood samples for tumor-related genetic variants in the population of reference tumor-related genetic variants and determining ratios of the frequency of observance data between the reference samples for tumor-related genetic variants in the population of reference tumor-related genetic variants to produce a relative prevalence dataset. Additional methods and related systems and computer readable media are also provided.
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
56.
METHODS AND SYSTEMS FOR ANALYZING METHYLATED POLYNUCLEOTIDES
In an aspect, a method for detecting the presence or absence of cancer, comprising: (a) obtaining the polynucleotide sample from the subject; (b) partitioning the polynucleotide sample based on methylation status into plurality of partitioned sets to generate partitioned polynucleotides; (c) fragmenting the partitioned polynucleotides from at least one of the plurality of partitioned sets to generate fragmented polynucleotides; (d) tagging the fragmented polynucleotides to generate tagged polynucleotides; (e) concatenating the tagged polynucleotides to generate concatenated polynucleotides; (f) processing the concatenated polynucleotides to generate processed polynucleotides, wherein the processing comprises amplification; (g) sequencing the processed polynucleotides to generate a set of sequencing reads; (h) analyzing the set of sequencing reads to detect a methylation status of a plurality of genomic regions; and (i) detecting the presence or absence of cancer from the methylation status of the plurality of genomic regions.
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
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
Disclosed herein are methods, compositions, and devices for use in the early detection of cancer. The methods include preparing cell-free nucleic acid molecules from a subject for sequencing, sequencing a panel of regions in the cell-free nucleic acid molecules, and detecting one or more markers that are indicative of a cancer.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
C12M 1/00 - Apparatus for enzymology or microbiology
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
58.
METHOD OF PREDICTING NON-SMALL CELL LUNG CANCER (NSCLC) PATIENT DRUG RESPONSE OR TIME UNTIL DEATH OR CANCER PROGRESSION FROM CIRCULATING TUMOR DNA (CTDNA) UTILIZING SIGNALS FROM BOTH BASELINE CTDNA LEVEL AND LONGITUDINAL CHANGE OF CTDNA LEVEL OVER TIME
Provided herein are methods of determining a molecular response score for use in predictive models. The molecular response score may be used to monitor and guide administration of treatment to a subject.
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
G16B 20/40 - Population geneticsLinkage disequilibrium
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
59.
COMPOSITIONS AND METHODS FOR ENRICHING METHYLATED POLYNUCLEOTIDES
Provided herein is a DNA analysis method comprising a procedure that affects a first nucleobase in the DNA differently from a second nucleobase in the DNA of the first subsample; partitioning a sample into at least a first subsample and a second subsample, wherein the first subsample comprises DNA (e.g., cell-free DNA) with a nucleobase modification in a different proportion than the second subsample; and DNA is sequenced to distinguish the first nucleobase from the second nucleobase. Also provided is a combination comprising first and second populations of captured DNA, wherein the first population comprises or was derived from DNA with a nucleobase modification in a different proportion than the second population, and wherein the first population comprises a form of a first nucleobase originally present in the DNA with altered base pairing specificity and a second nucleobase without altered base pairing specificity.
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
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
60.
POPULATION BASED TREATMENT RECOMMENDER USING CELL FREE DNA
Systems and methods are disclosed for generating a therapeutic response predict or detecting a disease, by: using a genetic analyzer to generate genetic information; receiving into computer memory a training dataset comprising, for each of a plurality of individuals having a disease, (1) genetic information from the individual generated at first time point and (2) treatment response of the individual to one or more therapeutic interventions determined at a second, later, time point; and implementing a machine learning algorithm using the dataset to generate at least one computer implemented classification algorithm, wherein the classification algorithm, based on genetic information from a subject, predicts therapeutic response of the subject to a therapeutic intervention.
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 40/00 - ICT specially adapted for biostatisticsICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
G16B 50/00 - ICT programming tools or database systems specially adapted for bioinformatics
G16H 20/00 - ICT specially adapted for therapies or health-improving plans, e.g. for handling prescriptions, for steering therapy or for monitoring patient compliance
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
61.
CORRECTING FOR DEAMINATION-INDUCED SEQUENCE ERRORS
Sequencing nucleic acids can identify variations associated with presence, susceptibility or prognosis of disease. However, the value of such information can be compromised by errors introduced by or before the sequencing process including preparing nucleic acids for sequencing. Blunting single-stranded overhangs on nucleic acids in a sample can introduce deamination-induced sequencing errors. The disclosure provides methods of identifying and correcting for such deamination-induced sequencing errors and distinguishing them from real sequence variations.
This disclosure provides, among other things, methods for generating and applying therapeutic interventions. The methods involve, for example, (a) sequencing polynucleotides from cancer cells from a subject; (b) identifying and quantifying somatic mutations in the polynucleotides; (c) developing a profile of tumor heterogeneity in the subject indicating the presence and relative quantity of a plurality of the somatic mutations in the polynucleotides, wherein different relative quantities indicates tumor heterogeneity; and (d) determining a therapeutic intervention for a cancer exhibiting the tumor heterogeneity, wherein the therapeutic intervention is effective against a cancer having the profile of tumor heterogeneity determined.
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
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
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 15/00 - ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
Provided herein is a DNA analysis method for detecting and quantifying immune cell types from which the DNA originated. Provided herein are also methods for determining the likelihood that a subject has a disease or condition, such as cancer.
C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
C12Q 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
65.
SYSTEMS AND METHODS TO DETECT RARE MUTATIONS AND COPY NUMBER VARIATION
The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.
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
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
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
Provided herein are methods for monitoring false negative and/or false positive detection of modified nucleosides in DNA in a sample using a base-pairing conversion procedure. The methods use nucleosides having known nucleoside identity and known modification status in adapters ligated to the DNA. In certain aspects, the disclosure relates to methods for improving the quality control of such methods.
Provided herein are methods of analyzing post-translationally modified proteins. The methods may comprise pre-enriching proteins using lectins and/or multiplexed detection of multiple proteins and/or multiple post-translational modifications. Provided herein are also methods for determining the likelihood that a subject has a disease or condition, such as cancer.
The present disclosure provides a method for enriching for multiple genomic regions using a first bait set that selectively hybridizes to a first set of genomic regions of a nucleic acid sample and a second bait set that selectively hybridizes to a second set of genomic regions of the nucleic acid sample. These bait set panels can selectively enrich for one or more nucleosome-associated regions of a genome, said nucleosome-associated regions comprising genomic regions having one or more genomic base positions with differential nucleosomal occupancy, wherein the differential nucleosomal occupancy is characteristic of a cell or tissue type of origin or disease state.
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
C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
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 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
The present disclosure provides a method for enriching for multiple genomic regions using a first bait set that selectively hybridizes to a first set of genomic regions of a nucleic acid sample and a second bait set that selectively hybridizes to a second set of genomic regions of the nucleic acid sample. These bait set panels can selectively enrich for one or more nucleosome-associated regions of a genome, said nucleosome-associated regions comprising genomic regions having one or more genomic base positions with differential nucleosomal occupancy, wherein the differential nucleosomal occupancy is characteristic of a cell or tissue type of origin or disease state.
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
C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
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 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
This disclosure provides, among other things, methods for compiling and using a database for identifying one or more therapeutic interventions for a cancer and/or the efficacy of a therapeutic intervention for subjects with a tumor genomic profile. The database may include, for each of a plurality of subjects having cancer: (i) tumor genomic testing data, including somatic alterations, collected at two or more time intervals per subject via serial biopsy of cell-free DNA, (ii) one or more therapeutic interventions administered to each of the subjects at one or more times; and (iii) efficacy of the therapeutic interventions.
During operation, a computer system may receive information indicating: a number of genetic molecules associated with normal tissue in a sample, and a number of tumor genetic molecules associated with a tumor in the sample. Then, the computer system may determine a sample-specific dynamic quality metric based at least in part on: a type of cancer, sequencing coverage of one or more cancer-specific genomic targets, and a first ratio of the number of tumor genetic molecules to a sum of the number tumor genetic molecules and the number of genetic molecules or a second ratio of the number of tumor genetic molecules to the number of genetic molecules. Next, based at least in part on a comparison of the sample-specific dynamic quality metric and a threshold, the computer system may selectively provide an indication of whether a mutation or the type of cancer is present in the sample.
This disclosure provides, among other things, methods for generating and applying therapeutic interventions. The methods involve, for example, (a) sequencing polynucleotides from cancer cells from a subject; (b) identifying and quantifying somatic mutations in the polynucleotides; (c) developing a profile of tumor heterogeneity in the subject indicating the presence and relative quantity of a plurality of the somatic mutations in the polynucleotides, wherein different relative quantities indicates tumor heterogeneity; and (d) determining a therapeutic intervention for a cancer exhibiting the tumor heterogeneity, wherein the therapeutic intervention is effective against a cancer having the profile of tumor heterogeneity determined.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
C12Q 1/6874 - Methods for sequencing involving nucleic acid arrays, e.g. sequencing by hybridisation [SBH]
73.
Methods and systems for detecting genetic variants
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
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 15/00 - ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
74.
Computational modeling of loss of function based on allelic frequency
The disclosure relates to computer technology for precision diagnosis of various states of genetic material such as a gene sequenced from cell-free DNA in a sample. The state may include a somatic homozygous deletion, a somatic heterozygous deletion, a copy number variation, or other states. A computer system may generate competing probabilistic models that each output a probability that the genetic material is in a certain state. Each model may be trained on a training sample set to output a probability that the genetic material is in a respective state. In some embodiments, the computer system may use various probabilistic distributions to generate the models. For example, the computer system may use a beta-binomial distribution, a binomial distribution, a normal (also referred to as “Gaussian”) distribution, or other type of probabilistic modeling techniques.
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
C12Q 1/6809 - Methods for determination or identification of nucleic acids involving differential detection
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
75.
METHODS FOR DETECTION AND REDUCTION OF SAMPLE PREPARATION-INDUCED METHYLATION ARTIFACTS
The disclosure relates to improved sequencing reactions. Specifically, the disclosure provides methods which allow for the identification of regions of a DNA molecule that were synthesized during an end repair and/or A-tailing reaction. Sequence data deriving from such synthesized regions may not be representative of the corresponding region in the original DNA molecules, for example it may contain artifactual methylation statuses. Accordingly, the identification of these synthesized regions allows for such potentially artifactual data to be identified and filtered accordingly.
Provided herein are methods for differentiating tumor and non-tumor (e.g., clonal hematopoiesis of indeterminate potential (CHIP)) origin nucleic acid variants from one another in a test sample obtained from a test subject at least partially using a computer. Other aspects are directed to methods of treating disease in subjects. Yet other aspects include related systems and computer readable media used to differentiating tumor and non-tumor origin nucleic acid variants from one another.
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
77.
Methods and systems for detecting genetic variants
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
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 15/00 - ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
78.
METHODS FOR SIMULTANEOUS MOLECULAR AND SAMPLE BARCODING
The present application provides methods of sequencing populations of nucleic acids within multiple pooled samples with tracking of individual molecules and their samples of origin. In such methods, the same sequencing read provides in line sequences of sample and molecular barcodes and a sample molecule allowing deconvolution of sequencing reads to sample of origin and grouping of amplification copies of original molecules into families. The methods are amenable to multiple sequencing platforms, reduce uninformative portions of sequencing reads on adapter sequence common to all adapters, decrease opportunity for labelling samples with the wrong barcode (index hopping), and provide additional multiplexing capacity.
Methods and systems for improving callings of insertions and/or deletions by identifying genetic sequence reads having identical molecular barcodes and sequences among sequence reads from a nucleic acid sequencer, grouping the genetic reads into a family, and processing families comprising split reads to detect the insertion and/or deletion in a sample of polynucleotide molecules.
This disclosure provides methods, sets, and kits for predicting and identifying druggable targets for treating cancer. This disclosure further provides methods of treating cancer.
Provided herein are methods of analyzing DNA comprising degrading forms of DNA sequences that are prevalent in healthy subjects; and detecting sequences that are not degraded. Some such methods facilitate detection of aberrant forms of DNA.
Provided herein are methods for determining the microsatellite instability status of samples. In one aspect, the methods include quantifying a number of different repeat lengths present at each of a plurality of microsatellite loci from sequence information to generate a site score for each of the plurality of the microsatellite loci. The methods also include comparing the site score of a given microsatellite locus to a site specific trained threshold for the given microsatellite locus for each of the plurality of the microsatellite loci and calling the given microsatellite locus as being unstable when the site score of the given microsatellite locus exceeds the site specific trained threshold for the given microsatellite locus to generate a microsatellite instability score, which includes a number of unstable microsatellite loci from the plurality of the microsatellite loci.
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
Disclosed are methods of detecting the presence or absence of a genomic rearrangement in which a sample of tagged DNA molecules is divided into aliquots. The isolated molecules are linearly amplified with a set of primers that targeting loci of interest and comprise a rearrangement detection barcode, a sequencing adapter, and a non-nucleotide binding partner, thereby producing a first population of processed DNA, which is then captured on a solid support using binding to the non-nucleotide binding partner and amplified or eluted. A second aliquot is enriched for a second plurality of loci of interest, thereby producing a second population of processed DNA. At least a portion of the amplified and/or eluted first population of processed DNA and at least a portion of the second population of processed DNA are sequenced; and the presence or absence of genomic rearrangement(s) in the first population of processed DNA is detected.
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
84.
METHODS FOR IDENTIFYING DRUGGABLE TARGETS AND TREATING CANCER
This disclosure provides methods, sets, and kits for predicting and identifying druggable targets for treating cancer. This disclosure further provides methods of treating cancer.
During operation, a computer system may receive information corresponding to identified molecules of deoxyribonucleic acid (DNA) in a tissue sample. Then, the computer system may determine a symmetric normalized odds ratio, which corresponds to damage of the DNA, based at least in part on the information. Moreover, determining the symmetric normalized odds ratio may include: computing a first odds ratio; computing a second odds ratio, where a numerator and a denominator in the second odds ratio are reversed relative to the first odds ratio; summing the first odds ratio and the second odds ratio; and normalizing the summation. Next, the computer system may calculate a confidence metric of one or more of the molecules based at least in part on the symmetric normalized odds ratio and a threshold, wherein the confidence metric corresponds to a probability that the one or more molecules are identified correctly.
During operation, a computer system may receive information corresponding to identified molecules of deoxyribonucleic acid (DNA) in a tissue sample. Then, the computer system may determine a symmetric normalized odds ratio, which corresponds to damage of the DNA, based at least in part on the information. Moreover, determining the symmetric normalized odds ratio may include: computing a first odds ratio; computing a second odds ratio, where a numerator and a denominator in the second odds ratio are reversed relative to the first odds ratio; summing the first odds ratio and the second odds ratio; and normalizing the summation. Next, the computer system may calculate a confidence metric of one or more of the molecules based at least in part on the symmetric normalized odds ratio and a threshold, wherein the confidence metric corresponds to a probability that the one or more molecules are identified correctly.
The disclosure relates to computer technology for precision diagnosis of various states of genetic material such as a gene sequenced from cell-free DNA in a sample. The state may include a somatic homozygous deletion, a somatic heterozygous deletion, a copy number variation, or other states. A computer system may generate competing probabilistic models that each output a probability that the genetic material is in a certain state. Each model may be trained on a training sample set to output a probability that the genetic material is in a respective state. In some embodiments, the computer system may use various probabilistic distributions to generate the models. For example, the computer system may use a beta-binomial distribution, a binomial distribution, a normal (also referred to as “Gaussian”) distribution, or other type of probabilistic modeling techniques.
Methods and systems for improving callings of insertions and/or deletions by identifying genetic sequence reads having identical molecular barcodes and sequences among sequence reads from a nucleic acid sequencer, grouping the genetic reads into a family, and processing families comprising split reads to detect the insertion and/or deletion in a sample of polynucleotide molecules.
The disclosure provides methods for processing nucleic acid populations containing different forms (e.g., RNA and DNA, single-stranded or double-stranded) and/or extents of modification (e.g., cytosine methylation, association with proteins). These methods accommodate multiple forms and/or modifications of nucleic acid in a sample, such that sequence information can be obtained for multiple forms. The methods also preserve the identity of multiple forms or modified states through processing and analysis, such that analysis of sequence can be combined with epigenetic analysis.
C12Q 1/68 - Measuring or testing processes involving enzymes, nucleic acids or microorganismsCompositions thereforProcesses of preparing such compositions involving nucleic acids
C12N 15/10 - Processes for the isolation, preparation or purification of DNA or RNA
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
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
90.
Systems and methods to detect rare mutations and copy number variation
The present disclosure provides a system and method for the detection of rare mutations and copy number variations in cell free polynucleotides. Generally, the systems and methods comprise sample preparation, or the extraction and isolation of cell free polynucleotide sequences from a bodily fluid; subsequent sequencing of cell free polynucleotides by techniques known in the art; and application of bioinformatics tools to detect rare mutations and copy number variations as compared to a reference. The systems and methods also may contain a database or collection of different rare mutations or copy number variation profiles of different diseases, to be used as additional references in aiding detection of rare mutations, copy number variation profiling or general genetic profiling of a disease.
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 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
Disclosed herein are compositions and methods for isolating DNA, such as cell-free DNA (cfDNA). In some embodiments, the cell-free DNA is from a subject having or suspected of having cancer and/or the cell-free DNA comprises DNA produced by a tumor. In some embodiments, the DNA isolated by the method is captured using a sequence-variable target region set and an epigenetic target region set, wherein the sequence-variable target region set is captured with a greater capture yield than the epigenetic target region set. In some embodiments, captured cfDNA of the sequence-variable target region set is sequenced to a greater depth of sequencing than captured cfDNA of the epigenetic target region set.
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 1/6881 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
In implementations described herein, methylation information is determined with respect to classification regions of a reference genome that are related to the presence of a tumor in a subject. The methylation information can be analyzed using a number of computational techniques to provide metrics related to the presence or absence of a tumor in a given subject.
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
G16B 30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
G16B 40/10 - Signal processing, e.g. from mass spectrometry [MS] or from PCR
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
94.
METHODS FOR SEQUENCE DETERMINATION USING PARTITIONED NUCLEIC ACIDS
DNA damage (e.g., cytosine deamination) can appear more frequently in hypermethylated partitions of DNA (e.g., cell-free DNA) samples, than in hypomethylated partitions. Embodiments include sequencing hypermethylated partitions and hypomethylated partitions wherein calling a C to T or G to A transition mutation relative to a reference sequence based on sequences of molecules from the hypermethylated partition requires observation of the transition mutation in a greater number of molecules than calling a C to T or G to A transition mutation relative to the reference sequence based on sequences of molecules from the hypomethylated partition, or C to T or G to A transition mutations are not called relative to a reference sequence based on sequences of molecules of the hypermethylated partition.
Disclosed herein are methods, compositions, and devices for use in the early detection of cancer. The methods include preparing cell-free nucleic acid molecules from a subject for sequencing, sequencing a panel of regions in the cell-free nucleic acid molecules, and detecting one or more markers that are indicative of a cancer.
C12Q 1/6886 - Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
G16H 50/30 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for calculating health indicesICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for individual health risk assessment
C12M 1/00 - Apparatus for enzymology or microbiology
C12Q 1/6806 - Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay
G16H 50/20 - ICT specially adapted for medical diagnosis, medical simulation or medical data miningICT specially adapted for detecting, monitoring or modelling epidemics or pandemics for computer-aided diagnosis, e.g. based on medical expert systems
G01N 33/574 - ImmunoassayBiospecific binding assayMaterials therefor for cancer
C12M 1/34 - Measuring or testing with condition measuring or sensing means, e.g. colony counters
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
42 - Scientific, technological and industrial services, research and design
44 - Medical, veterinary, hygienic and cosmetic services; agriculture, horticulture and forestry services
Goods & Services
Scientific research for medical purposes in the area of cancerous diseases; structural and functional analysis of genomes; providing a website featuring information in the field of cancerous diseases for scientific purposes; providing a website featuring information about scientific research for medical purposes in the field of cancerous diseases Healthcare services, namely, providing a database in the field of cancer related information and featuring inputting and collection of data and information for diagnostic purposes; medical testing of blood for diagnostic or cancer screening purposes; providing cancer screening services in the nature of providing medical diagnostic testing services consisting primarily of chemical analysis and use of bioinformatics tools for cancer detection; providing a website featuring information in the field of cancerous diseases for diagnostic and cancer screening purposes; providing a website featuring information in the field of the prevention, screening, diagnosis, and treatment of cancerous diseases for medical purposes
97.
METHODS FOR ANALYZING CYTOSINE METHYLATION AND HYDROXYMETHYLATION
Provided herein are methods of analyzing DNA molecules in a sample (e.g., including identifying methylated and hydroxymethylated cytosine positions), the DNA molecules comprising first and second strands and asymmetric adapters, the method comprising: synthesizing first complementary strands which are complementary to the first strands and second complementary strands which are complementary to the second strands; optionally glucosylating a 5-hydroxymethylated cytosine in at least one first or second strand before or after synthesizing the first and second complementary strands; methylating a cytosine in at least one first complementary strand or second complementary strand, wherein the methylation converts a hemimethylated CpG to a fully methylated CpG; deaminating an unmodified cytosine in at least one first or second strand, thereby producing treated DNA molecules; and sequencing at least a portion of the treated DNA molecules; optionally wherein the asymmetric adapters are Y-shaped adapters or bubble adapters.
Disclosed herein in are methods and systems for determining genetic variants (e.g., copy number variation) in a polynucleotide sample. A method for determining copy number variations includes tagging double-stranded polynucleotides with duplex tags, sequencing polynucleotides from the sample and estimating total number of polynucleotides mapping to selected genetic loci. The estimate of total number of polynucleotides can involve estimating the number of double-stranded polynucleotides in the original sample for which no sequence reads are generated. This number can be generated using the number of polynucleotides for which reads for both complementary strands are detected and reads for which only one of the two complementary strands is detected.
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 15/00 - ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
99.
Methods for multi-resolution analysis of cell-free nucleic acids
The present disclosure provides a method for enriching for multiple genomic regions using a first bait set that selectively hybridizes to a first set of genomic regions of a nucleic acid sample and a second bait set that selectively hybridizes to a second set of genomic regions of the nucleic acid sample. These bait set panels can selectively enrich for one or more nucleosome-associated regions of a genome, said nucleosome-associated regions comprising genomic regions having one or more genomic base positions with differential nucleosomal occupancy, wherein the differential nucleosomal occupancy is characteristic of a cell or tissue type of origin or disease state.
G16B 20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
C12Q 1/6827 - Hybridisation assays for detection of mutation or polymorphism
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 25/10 - Gene or protein expression profilingExpression-ratio estimation or normalisation
100.
MULTIFUNCTIONAL PRIMERS FOR PAIRED SEQUENCING READS
The invention provides methods of generating forward and reverse reads of an immobilized single-stranded target nucleic acid using multifunctional primers. A multifunctional primer serves to initiate separate syntheses of first and second complementary strands to the single-stranded target nucleic acid, and to tether the first complementary strand to the immobilized target nucleic acid. The first complementary strand serves to provide a primer binding site and template for an extension product to generate a reverse sequencing read. The second complementary strand serves to displace the first complementary strand from duplexing with the target nucleic acid. The first or second complementary strand can provide a forward sequence read.
