79 results about "Cell-Free Nucleic Acids" patented technology

A method for preserving and processing cell-free nucleic acids located within a blood sample is disclosed, wherein a blood sample containing cell-free nucleic acids is treated to reduce both blood cell lysis and nuclease activity within the blood sample. The treatment of the sample aids in increasing the amount of cell-free nucleic acids that can be identified and tested while maintaining the structure and integrity of the nucleic acids.

A method for preserving and processing nucleic acids located within a blood sample is disclosed, wherein a blood sample containing nucleic acids is treated to reduce both blood cell lysis and nuclease activity within the blood sample. The treatment of the sample aids in increasing the integrity and amount of cellular nucleic acids that can be identified and tested while avoiding contamination of the isolated nucleic acids with cell-free nucleic acids.

The present invention provides methods for isolating cell free nucleic acid, e.g., apoptotic or fetal nucleic acids and methods of detecting neoplastic cells or identifying the genetic composition of a fetus. The invention also provides magnetic particles comprising an anti-DNA antibody, and kits comprising the magnetic particles.

The present invention relates, e.g., to a method for detecting a nucleic acid molecule of interest in a sample comprising cell-free nucleic acids, comprising fluorescently labeling the nucleic acid molecule of interest, by specifically binding a fluorescently labeled nanosensor or probe to the nucleic acid of interest, or by enzymatically incorporating a fluorescent probe or dye into the nucleic acid of interest, illuminating the fluorescently labeled nucleic acid molecule, causing it to emit fluorescent light, and measuring the level of fluorescence by single molecule spectroscopy, wherein the detection of a fluorescent signal is indicative of the presence of the nucleic acid of interest in the sample.

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.

Methods for creating a selector of mutated genomic regions and for using the selector set to analyze genetic alterations in a cell-free nucleic acid sample are provided. The methods can be used to measure tumor-derived nucleic acids in a blood sample from a subject and thus to monitor the progression of disease in the subject. The methods can also be used for cancer screening, cancer diagnosis, cancer prognosis, and cancer therapy designation.

The present disclosure relates to methods to deconvolute a mixture sample of genetic material from different origins or sources. The disclosed methods can be used in various applications, including, the non-invasive determination of a fetal genome, a fetal -ome (e.g. exome). or other targeted fetal locus from cell-free nucleic acids in maternal plasma or other body fluids; the de-termination of cancer-associated mutations from cell-free nucleic acids in a body fluid sample that contains a mixture of nucleic acids from normal cells and tumor cells; and quantification of donor cell contamination using a body fluid from a transplantation recipient to monitor and / or predict the outcome of a transplantation procedure.

Disclosed herein are polynucleotide adaptors and methods of use thereof for identifying and analyzing nucleic acids, including cell-free nucleic acids from a patient sample. Also disclosed herein are methods of using the adaptors to detect, diagnose, or determine prognosis of cancers.

The present invention relates, e.g., to a method for determining the size distribution of DNA molecules in a sample comprising cell-free nucleic acid, comprising labeling the DNA with a fluorescent dye in a stoichiometric manner, subjecting the DNA to molecular spectroscopy (e.g., cylindrical illumination confocal spectroscopy), analyzing suitable fluorescent burst parameters of the labeled DNA, and conducting single molecule DNA integrity analysis of the labeled DNA molecules in the sample. In one embodiment of the invention, the method is used as a diagnostic method for detecting cancer.

A method for preserving and protecting cell-free nucleic acids located within blood plasma samples is disclosed, wherein a sample of blood containing nucleic acids is treated to reduce deleterious effects of storage and transport.

Systems, methods, and apparatuses are provided for diagnosing auto-immune diseases such as systemic lupus erythematosus (SLE) based on the sizes, methylation levels, and / or genomic characteristics of circulating DNA molecules. Patients provide blood or other tissue samples containing cell-free nucleic molecules for analysis. Massively parallel and / or methylation-aware sequencing can be used to determine the sizes and methylation levels of individual DNA molecules and identify the number of molecules originating from different genomic regions. A level of SLE can be estimated based on: the amount of molecules having sizes below a threshold value; the methylation level(s) of the entire genome or portions of the genome; correlations between the sizes and methylation levels of DNA molecules; and / or comparing the representation of DNA molecules in each of a plurality of genomic regions with a reference value for that region, and determining an amount of genomic regions having increased or decreased measured genomic representation.

The invention is directed to a method of monitoring a mantle cell lymphoma residual disease in an immunotransplant patient by post-treatment analysis of clonotype profiles from patient blood samples. In some embodiments, methods of the invention comprising steps of (a) treating a patient by immunotransplanting the patient with vaccine-primed autologous T cells; (b) obtaining a peripheral blood sample from the patient comprising B-cells and / or cell-free nucleic acids; (c) amplifying molecules of nucleic acid from the B-cells of the sample and / or cell-free nucleic acids in the sample, the molecules of nucleic acid comprising recombined DNA sequences from immunoglobulin genes; (d) sequencing the amplified molecules of nucleic acid to form a clonotype profile; and (e) determining from the clonotype profile a presence, absence and / or level of the one or more patient-specific clonotypes correlated with the mantle cell lymphoma, including phylogenic clonotypes thereof.

A processing system uses a Bayesian inference based model for targeted sequencing or variant calling. In an embodiment, the processing system generates candidate variants of a cell free nucleic acid sample. The processing system determines likelihoods of true alternate frequencies for each of the candidate variants in the cell free nucleic acid sample and in a corresponding genomic nucleic acid sample. The processing system filters or scores the candidate variants by the model using at least the likelihoods of true alternate frequencies. The processing system outputs the filtered candidate variants, which may be used to generate features for a predictive cancer or disease model.

The present disclosure provides a probabilistic model for accurate and sensitive somatic single nucleotide variant (SNV) detection in cell-free nucleic acid samples comprising a set of sequence data.A joint genotype may be determined for each locus in the set of sequence data, and germline mutations may be intrinsically removed. A set of filtrations can be applied to eliminate low quality somaticvariant calls. Further, a global tumor cell-free deoxyribonucleic acid (cfDNA) fraction and overlapping read mates can be considered, thereby enabling accurate SNV detection and variant allele frequency estimation from samples with low tumor cfDNA fraction. A sensitive early detection of minimal residual disease (MRD) is designed by using the probabilistic model and the machine learning model fordistinguishing true variants from sequencing errors.

Cell free nucleic acids from a test sample obtained from an individual are analyzed to identify possible fusion events. Cell free nucleic acids are sequenced and processed to generate fragments. Fragments are decomposed into kmers and the kmers are either analyzed de novo or compared to targeted nucleic acid sequences that are known to be associated with fusion gene pairs of interest. Thus, kmers that may have originated from a fusion event can be identified. These kmers are consolidated to generate gene ranges from various genes that match sequences in the fragment. A candidate fusion event can be called given the spanning of one or more gene ranges across the fragment.

The present invention relates to methods for predicting the survival time of patients suffering from cancer. Said methods are based on the quantification and analysis of the cell free nucleic acids that are present in a sample from the patient and typically include the determination of the level of the mutant nucleic acid which contains a mutation of interest, the calculation of the mutation load for said mutation of interest, the calculation of the DNA integrity index or a combination thereof.

The invention provides methods to monitor cell free nucleic acids. The method comprises obtaining a plasma sample from a subject known to have a cancer characterized by a pair of mutually exclusive mutations specific to the cancer; isolating cell free nucleic acids from the plasma sample obtained from the subject; measuring the amount a housekeeping gene and / or total DNA in the cell free nucleic acids isolated from the plasma sample to confirm that the amount of housekeeping gene and / or total DNA in the sample is within a selected range; measuring the amount of a first of the pair of mutually exclusive mutations specific to the cancer in the cell free nucleic acids isolated from the plasma sample; and indicating in a report that the subject has the first mutation when (a) the amount of the housekeeping gene and / or total DNA in the cell free nucleic acids isolated from the plasma sample is within the selected range and (b) the amount of the first mutation is increased as compared to a control amount, wherein the control amount is determined by measuring the apparent amount of the first mutation in control cell free nucleic acids isolated from plasma samples obtained from control subjects known to have the second of the pair of mutually exclusive mutations specific to the cancer using measuring conditions substantially the same as those used to measure the amount of the first mutation in the cell free nucleic acids isolated from the plasma sample from the subject.

A composition and method for preserving a urine sample and a preservative delivery vessel are disclosed wherein treatment of the urine sample aids in preserving circulating cell-free nucleic acids in urine over a wide range of dilution ratios within temperature fluctuations that can occur during urine sample handling, storage and transportation. The urine sample preservation composition and method and preservative delivery vessel provide a method for obtaining high quality stabilized urinary cell-free nucleic acids for clinical diagnostics development and application.

The present disclosure provides cell-free nucleic acid standards comprising genomic polynucleotides and methods of using cell-free nucleic acid standards comprising genomic polynucleotides for developing, optimizing, and validating cell-free nucleic acid assays.

Systems, methods, and apparatuses are provided for diagnosing auto-immune diseases such as systemic lupus erythematosus (SLE) based on the sizes, methylation levels, and / or genomic characteristics of circulating DNA molecules. Patients provide blood or other tissue samples containing cell-free nucleic molecules for analysis. Massively parallel and / or methylation-aware sequencing can be used to determine the sizes and methylation levels of individual DNA molecules and identify the number of molecules originating from different genomic regions. A level of SLE can be estimated based on: the amount of molecules having sizes below a threshold value; the methylation level(s) of the entire genome or portions of the genome; correlations between the sizes and methylation levels of DNA molecules; and / or comparing the representation of DNA molecules in each of a plurality of genomic regions with a reference value for that region, and determining an amount of genomic regions having increased or decreased measured genomic representation.

The present disclosure contemplates various uses of cell-free DNA. Methods provided herein may use sequence information in a macroscale and global manner, with or without somatic variant information, to assess a fragmentome profile that can be representative of a tissue of origin, disease, progression, etc. In an aspect, disclosed herein is a method for determining a presence or absence of a genetic aberration in deoxyribonucleic acid (DNA) fragments from cell-free DNA obtained from a subject, the method comprising: (a) constructing a multi-parametric distribution of the DNA fragments over a plurality of base positions in a genome; and (b) without taking into account a base identity of each base position in a first locus, using the multi-parametric distribution to determine the presence or absence of the genetic aberration in the first locus in the subject.

This invention relates to methods and compositions for assessing risk by measuring total and specific cell-free nucleic acids (such as DNA) in a subject. The methods and compositions provided herein can be used to determine risk of a condition, such as transplant rejection.

A processing system uses a Bayesian inference based model for targeted sequencing or variant calling. In an embodiment, the processing system generates candidate variants of a cell free nucleic acid sample. The processing system determines likelihoods of true alternate frequencies for each of the candidate variants in the cell free nucleic acid sample and in a corresponding genomic nucleic acid sample. The processing system filters or scores the candidate variants by the model using at least the likelihoods of true alternate frequencies. The processing system outputs the filtered candidate variants, which may be used to generate features for a predictive cancer or disease model.

Systems, media, methods, and kits disclosed herein can be used to analyze human microbiota for the detection of a condition (e.g., a disease or condition). Further, the systems, media, methods, and kits disclosed herein can utilize machine learning algorithms to analyze samples with high accuracy. In an aspect, a classifier capable of distinguishing a population of subjects based on microbiome composition may comprise: a plurality of microbiome-associated features associated with two or more classes of subjects inputted into a machine learning model, wherein the features comprise the microbiome species and abundance of microbiome elements, wherein the features are derived from a taxonomic community composition analysis of a cell-free nucleic acid sample in a population of subjects; wherein the features contribute to a classifier sensitivity of greater than 50% and a classifier specificity of greater than 85% to distinguish the population of subjects into two or more classes.

The present invention relates to methods for screening a subject for a cancer. In particular, the present invention relates to a method (A) for screening a subject for a cancer comprising the steps of i) extracting the cell free nucleic acids from a sample obtained from the subject, ii) determining the total concentration of mitochondrial cell free nucleic acids, ii) determining the total concentration of nuclear cell free nucleic acids iv) calculating the ratio of the level determined at step ii) to the concentration determined at step iii), v) comparing ratio determined at step iv) with a predetermined corresponding reference value and vi) concluding that the subject suffers from a cancer when the ratio determined at step iv) is lower than the predetermined corresponding reference value or concluding that the subject does not suffer from a cancer when the ratio determined at step iv) is higher than the predetermined corresponding reference value.

A method is provided for probabilistically assigning a tissue of origin to a nucleic acid in a sample, e.g., DNA in a cell-free fluid sample obtained from a human subject. A hydroxymethylation profile is generated for the sample DNA and then compared across a reference data set of hydroxymethylation profile vectors, where each hydroxymethylation profile vector identifies the hydroxymethylation profile at a specific reference locus, the tissue-specific gene associated with the reference locus, and the tissue with which the gene and reference locus are associated. A tissue of origin can be probabilistically assigned to the sample nucleic acid using the results of the comparison. Other methods of use are also provided.

A processing system uses a Bayesian inference based model for targeted sequencing or variant calling. In an embodiment, the processing system determines first depths and first alternate depths of first sequence reads from a cell free nucleic acid sample of a subject. The processing system determines second depths and second alternate depths of second sequence reads from a genomic nucleic acid sample of the subject. The processing system determines likelihoods of true alternate frequency of the cell free nucleic acid sample and of the genomic nucleic acid sample. Using the first likelihood, the second likelihood, and one or more parameters, the processing system determines a probability that the true alternate frequency of the cell free nucleic acid sample is greater than a function of the true alternate frequency of the genomic nucleic acid sample.