502 results about "Free dna" patented technology

The invention provides a methylation detection combined marker based on free DNA (cfDNA) in pulmonary alveolar lavage fluid (BAL) and application of the methylation detection combined marker. The methylation combination marker optimizes methylation detection targets in early screening of lung cancer, reduces detection difficulty and cost, and has high diagnosis accuracy, sensitivity and specificity.

Methods and systems disclosed herein can improve inference of gene expression using cell-free DNA fragments. In an aspect, the present disclosure provides a computer-implemented method for inferring gene expression, the method comprising: obtaining a biological sample from a subject; extracting cell-free deoxyribonucleic acid (cfDNA) from the biological sample, wherein the cfDNA comprises a plurality of cfDNA fragments; performing a sequencing assay on the plurality of cfDNA fragments to generate a plurality of cfDNA sequencing fragments; computer processing the plurality of cfDNA sequencing fragments; and calculating, based at least in part on the computer processing, a gene expression score for a gene in a plurality of genes, wherein the gene expression score indicates a probability of expression or non-expression of the gene in the plurality of genes.

The invention discloses a screening method of a gene region set for detecting small residual focuses of ovarian cancer, the gene region set and a detection system of the gene region set, and belongs to the technical field of gene molecular diagnosis. According to the method, a preoperative blood sample, an intraoperative multipoint tumor tissue sample and postoperative daily peritoneal drainage liquid of an ovarian cancer patient on the first to sixth days are taken as detection samples, a novel ovarian cancer nuclear genome hot spot region screening method is developed, a gene region for ovarian cancer tumor DNA detection is constructed, and tumor tissue mutation information is taken as a tracing basis, so that an ovarian cancer tumor DNA detection result is obtained. The characteristics of tumor tissue specific mutation in the free DNA of the peritoneal drainage liquid are analyzed, and the purpose of detecting the free tumor DNA of the peritoneal drainage liquid is achieved. The method can be applied to the postoperative residual focus detection of the ovarian cancer patient, can sensitively and accurately evaluate the postoperative residual focus state of the patient at an early stage, and provides timely prognosis judgment basis for clinic, so as to support the adjustment of clinical decisions.

The invention relates to the field of noninvasive prenatal diagnosis, and particularly discloses a preeclampsia noninvasive screening method based on deep sequencing 8bp oligonucleotide double-fragment characteristics, which comprises the following steps: collecting preeclampsia and healthy pregnant woman peripheral blood samples, and extracting free DNA for high-throughput sequencing; the method comprises the following steps: extracting core 8-mer sequences' GTGCGCCC 'and' GATGGGGT 'in a long fragment of 150-200bp through bioinformatics analysis; an integrated support vector machine, K-nearest neighbor, extreme gradient lifting, a random forest and a multi-layer perceptron are combined with a logistic regression element classifier to construct a stacking model, the frequency of a core sequence is normalized, machine learning analysis is carried out, and the preeclampsia risk is predicted. According to the invention, two 8bp oligonucleotide characteristic fragments are specifically screened, and a deep learning architecture of multi-model fusion is combined, so that the limitations of low specificity and invasive detection of a traditional screening method are effectively broken through.

Methods for non-invasive cancer detection use a combination of genome-wide mutation and fragmentation features of cfDNA that facilitate cancer screening.

Systems and method as described herein may determine and use methylation levels associated with various tissues and samples. For example, a method may include receiving sequence reads including methylation statuses at sites of cell-free DNA molecules. The method may further include aligning the sequence reads to N sets of one or more CpG sites or genes. Then, for each set of the N sets of one or more CpG sites or genes, the method may include identifying a group of sequence reads aligning to the set of one or more CpG sites or genes and determining a methylation level using the methylation statuses of the group of sequence reads.

Methods, systems, and software for estimating circulating tumor fraction are provided. A first plurality of nucleic acid sequences for a plurality of loci in genomic DNA from a solid tumor sample is obtained. A second plurality of nucleic acid sequences for a plurality of cell-free DNA fragments obtained from a liquid biopsy sample from the same subject is obtained. One or more somatic mutations is identified in the first plurality of nucleic acid sequences. A variant allele frequency (VAF) is determined for each somatic mutation based on a frequency of the respective somatic mutation in the liquid biopsy sample and a frequency of the corresponding wild type allele in the liquid biopsy sample, thereby determining a set of VAFs. An estimate of the circulating tumor fraction for the test subject is determined based on the set of VAFs for the one or more somatic mutations.

Systems and methods for determining a blood tumor mutational burden (bTMB) for a test subject are provided in which there is obtained, from a panel-enriched sequencing reaction, a plurality of nucleic acid sequences. The plurality of nucleic acid sequences comprises a corresponding sequence for each cell-free DNA fragment in a plurality of cell-free DNA fragments obtained from a liquid biopsy sample from the test subject. Each respective cell-free DNA fragment in the plurality of cell-free DNA fragments corresponds to a respective probe sequence in a plurality of probe sequences used to enrich cell-free DNA fragments in the liquid biopsy sample in the panel-enriched sequencing reaction. There is determined, using the panel-enriched sequencing reaction, that a circulating tumor fraction (ctFE) is above a threshold ctFE value. Responsive to this determination, the bTMB is calculated for the test subject from the panel-enriched sequencing reaction and reported.

Described herein are methods of preparing an enriched library of nucleic acids, comprising: (a) identifying a patient-specific panel of somatic variants present in a tumor sample from a patient, (b) generating a subset panel of somatic variants from the patient-specific panel, wherein the subset of somatic variants comprises one or more of: multi -nucleotide variants, insertions and deletions, and genomic rearrangements; (c) preparing a sample of cell-free DNA (cfDNA) fragments from the patient for sequencing; and (d) selectively enriching the cfDNA for the subset of somatic variants to generate an enriched library.

Disclosed herein in some embodiments are methods, compositions, and systems for distinguishing between ulcerative colitis (UC), Crohn's disease (CD) and other Inflammatory Bowel Disorders (IBD) by sequencing cell free nucleic acids. In some embodiments, microbial cell-free nucleic acid sequencing can provide data that can determine whether UC, CD, or other IBD are asymptomatic, in remission, or active. In some embodiments, microbial cell-free nucleic acid sequencing can provide data that can determine whether an active form of UC, CD, or other IBD is mild, moderate, or severe.

The present disclosure provides methods and systems that utilize analysis of cell-free DNA (cfDNA) fragmentation profiles in a sample obtained from a patient, determining a ratio of short to long fragments and a fragment size distribution from the fragmentation profile and determining a divergence score based on the ratio of short to long fragments in the sample as correlated to a ratio from a sample from a healthy patient, and determining, by the machine learning model, a monitoring score for the sample based on the fragmentation score, the divergence score, and the model weights, the monitoring score being indicative of a level of a tumor-derived nucleic acid in the cfDNA of the sample to detect, monitor, diagnose, predict cancer status, determine the likelihood of the presence of cancer and administer treatment to the patient.

The present disclosure provides a method for obtaining a cancer risk prediction marker, a cancer risk assessment method, an electronic device, and a storage medium performed by a machine. The method for obtaining a cancer risk prediction marker includes: analyzing a plurality of peripheral blood circulating cell-free DNA (cfDNA) fragments of a biological sample of a subject to obtain sequence reads; obtaining data of a distribution of a nucleosome, and determining a predetermined interval upstream and downstream of a nucleosome center position as a nucleosome protection region; screening sequence reads of partial cfDNA fragments whose ends are located in the nucleosome protection region from the sequence reads of the plurality of cfDNA fragments; calculating a first fragmentation feature in the sequence reads of the plurality of cfDNA fragments, and calculating a second fragmentation feature in the sequence reads of the screened partial cfDNA fragments; and calculating one or more difference values of a change level of the second fragmentation feature relative to the first fragmentation feature as a cancer risk prediction marker.

SpRYc is a grafted ScCas9++-SpRY chimeric Cas9 possessing minimal 5′-NNN-3′ PAM specificity. SpRYc comprises the N-terminus (residues 1-1119) of ScCas9++ (Sc++), including the flexible loop, followed by the region of SpRY (residues 1111-1368) spanning its PAM-interacting domain mutations. Methods of altering gene expression include use of SpRYc in complex with guide RNA in a CRISPR-Cas9 system.

The invention discloses a primer for diagnosis of early pregnancy of sows. The nucleotide sequence of the primer is shown as follows: SRY-O-F: 5 '-CAGCAAAATATTCTCGCCTTGG-3', and the nucleotide sequence of the primer is shown as follows. And SRY-O-R: 5 '-CATCCTCTCTCTACGC-3', and SRY-O-R: 5 '- SRY-I-F: 5 '-ATATTCTCGCCTTGGGG-3', SRY-I-F: 5 '- And SRY-I-R is 5 '-GCTTTCGGCTTCTGTA-3', and the formula is shown in the description. Two pairs of primers with high sensitivity and strong specificity are designed through comparative analysis of pig SRY gene sequences, fetal free DNA in peripheral blood of sows is used as a template, and the specificity and sensitivity of PCR are enhanced through amplification of the two pairs of primers. Through two rounds of PCR amplification, whether the sow is pregnant or not can be detected on the 18th day of pregnancy, and the accuracy of the detection result is extremely high and reaches 100%. Compared with the prior art that the ZFY gene is used for detecting the sows on the twentieth breeding day, the method has the advantages that the detection time can be advanced to the eighteenth breeding day, and the detection accuracy is greatly improved (100% vs 10%). According to the method, powerful technical support is provided for early and accurate identification of the non-pregnant sows, reduction of non-production days and feeding cost and smooth execution of a production plan.

The present disclosure provides systems and methods to detect somatic or germline variants by providing a predetermined genomic DNA (gDNA) to an assay mixture, and capturing a sample of a subject's genetic information using a DNA sequencer and detecting genetic variants from the genetic information. A mutation may then be classified as being from a germline source if gDNA derived molecules have lengths inconsistent with those expected from cell-free DNA (cfDNA) derived molecules.

The invention provides a nano-drug based on cfDNA, ROS and Ca < 2 + > removal and NO release promotion strategies and a preparation method and application thereof, the preparation method comprises the following steps: weighing polyethyleneimine PEI and L-arginine in deionized water to prepare a template PEI-arg; adding a calcium ion chelating agent into the template, uniformly mixing, freezing and standing; a polyethyleneimine arginine template simulates biomineralization reaction catalysis and is doped with a calcium ion chelating agent to prepare the nano-drug PEI-arg (at) MON (at) BA. The bionic silicon dioxide nano-drug is successfully prepared by adopting a one-step method, and the nano-system removes free DNA through electrostatic adsorption, eliminates ROS through redox reaction, chelates excessive Ca < 2 + > by virtue of complexation, and continuously releases NO through arginine biotransformation. Benefited from the passive targeting characteristic of the liver, the nano scavenger is enriched to the liver after intravenous injection, so that the liver microcirculation can be remarkably improved, the oxidative stress level can be reduced, the inflammatory cascade reaction can be reduced, and the tissue pathological injury can be effectively relieved.

The present disclosure provides a method for the preparation and analysis of a biological sample of a xenograft receptor wherein the method comprises extracting fragmented or intact cell-free DNA, RNA (such as mRNA or miRNA) or protein of a sample derived from the xenograft receptor, and measuring the amount of cell-free DNA, RNA (such as mRNA or miRNA) or protein derived from said xenograft enables the assessment of xenograft rejection. The detection of the cell-free DNA or RNA can be carried out by preparing a sequencing library and carrying out whole genome sequencing.

The invention relates to the technical field of prenatal diagnosis, in particular to a biomarker for early prediction of preeclampsia based on body fluid free DNA and application of the biomarker, and particularly relates to a biomarker for prediction or diagnosis of pregnancy diseases, especially preeclampsia, identified through a machine learning model based on a sample set. The biomarker can be eclampsia specific motif and related motif variation trend, so that early prediction of preeclampsia with low cost, high efficiency and high accuracy is realized.

The utility model relates to the technical field of blood preservation, in particular to a stable preservation liquid device for preserving plasma free DNA for a long time, which comprises a preservation liquid device main body, the upper surface of the preservation liquid device main body is fixedly connected with a supporting material receiving shell, and the inner ring surface of the supporting material receiving shell is fixedly connected with a mounting block. And an extended threaded rod is inserted into the surface of the inner ring of the mounting block in a limiting manner. According to the stable preserving fluid equipment for preserving plasma free DNA for a long time, a preserving test tube can be clamped through a fixing plate, the temperature can be adjusted after ice blocks are added into a supporting material collecting shell, and after the temperature is adjusted, a pull handle needs to be pulled, so that the preserving fluid equipment can be used for preserving plasma free DNA stably. And then a user can take down the piston from the supporting material collecting shell, so that ice blocks in the supporting material collecting shell can be replaced, and the preserving fluid equipment can be conveniently transferred to a site through a plurality of universal wheels fixedly connected to the surface of the bottom of the preserving fluid equipment main body and an operation handrail.

The invention provides a method for the analysis of a biological sample to determine multiple types of information therefrom in a streamlined, combined workflow, where all information is obtained in a sequencing-based analysis. The information includes the presence and concentration of specific plasma proteins in a blood sample: the number, location, and types of histone modifications associated with cell-free DNA obtained from the same sample: the sequence of cfRNA and cfDNA in the cell-free DNA sample; and epigenetic information pertaining to the cell-free DNA, such as hydroxy methylation and methylation profiles, i.e., the distribution of 5-hydroxymethylcytosine (5hmC) and 5-methylcy tosine (5mC) residues, respectively. The invention additionally pertains to a classical sequencing-based method for analyzing a biological sample to determine one or more non-classical sequence features of the sample. Compositions, kits, and related methods are also provided, including an embodiment in which truncated sequencing adapters are used in conjunction with barcoded PCR primers.

Methods for the processing and analysis of blood samples obtained with blood collection tubes that reduce contamination of cfDNA by genomic DNA but that inhibit digestion by methylation-sensitive and / or methylation-dependent restriction enzymes.

Provided herein are computer-implemented methods for assigning maternal or fetal origin to one or more genetic variations in cell-free DNA (cfDNA) of a sample from a pregnant mammal, preferably a pregnant human, it uses a probabilistic model for assigning maternal or fetal origin to genetic variations in DNA from a sample obtained from a pregnant mammal, where the model assigns maternal or fetal origin based on a combination of fetal fraction and DNA fragment size.

The present disclosure provides methods and systems for screening or detecting a colorectal cancer or following colorectal disease progression that may be applied to cell-free nucleic acids such as cell-free DNA. The method may use detection of methylation signals within a single sequencing read in identified genomic regions as input features to train a machine learning model and generate a classifier useful for stratifying populations of individuals. The method may comprise extracting DNA from a cell-free sample obtained from a subject, converting the DNA for methylation sequencing, generating sequencing reads, and detecting colon proliferative cell disorder-associated signals in the sequencing information and training a machine learning model to provide a discriminator capable of distinguishing groups in a subject population such as healthy, cancer or distinguishing disease subtype or stage. The method may be used for, e.g., predicting, prognosticating, and / or monitoring response to treatment, tumor load, relapse, or colorectal cancer development.

The invention relates to a DNA methylation detection method and a reagent. Specifically, the invention relates to a method for diagnosing whether a tumor exists in a subject and whether a tumor postoperative minimal residual focus exists or not by detecting a methylation marker in free DNA in a sample from the subject to judge the methylation level of the DNA, and judging the postoperative prognosis of the subject suffering from the tumor. Methods of predicting postoperative recurrence or assessing the efficacy of a treatment on a subject having a tumor. The invention also relates to a marker, a kit and a detection reagent for the method.

Analysis of nucleic acids, e.g cell-free DNA, extracted from a dried blood sample, preferably dried plasma or dried serum. The analysis may encompass detection of fragmentation patterns and / or sequence characteristics of cfDNA for detecting cancer.

The invention relates to the technical field of molecular diagnosis, in particular to a high-sensitivity peripheral blood free DNA magnetic bead capture system, a methylation transformation method kit and application. The kit is composed of a lysis solution, a protease K diluent, a composite conversion reagent, a washing solution, a scavenger, an eluent and combined magnetic beads. According to the high-sensitivity peripheral blood free DNA magnetic bead capture system and the methylation transformation method kit, the detection limit of early-stage lung cancer ctDNA reaches 0.005% AF, the I-stage cancer ctDNA detection rate is increased to 93% from the industry average 40%, the sample size is reduced to 4 mL from the conventional 10 mL, the batch-to-batch difference of the kit is small, and the kit has very high application value clinically.

This invention relates to the field of medical technology, specifically to a method for preoperative risk assessment and prediction in liver transplant patients with hepatocellular carcinoma, comprising the following steps: Sample collection: selecting plasma samples and corresponding clinicopathological information from liver transplant recipients of hepatocellular carcinoma, and clarifying the inclusion and exclusion criteria for samples; Plasma cell-free DNA extraction and whole-genome sequencing: extracting and quality-controlling cell-free DNA from the plasma samples collected in step S1, constructing a sequencing library, and performing low-coverage whole-genome sequencing. This invention utilizes plasma-extracted cfDNA for whole-genome sequencing, combined with clinical testing information, to construct a preoperative risk assessment and prediction model for postoperative recurrence in liver transplant recipients of hepatocellular carcinoma based on non-invasive testing. This model can be used to predict the probability of recurrence-free survival before liver transplantation. The model derivation cohort integrates clinical records and circulating tumor DNA data for preoperative recurrence risk prediction.

Provided herein, among other things, is a method of treating a cancer patient without the need for a tissue biopsy. In some embodiments, the method may comprise (a) performing or having performed a sequencing assay on cell-free DNA (cfDNA) from a sample of blood from the patient to determine if the cell-free DNA comprises actionable and / or non-actionable sequence variations in one or more target genes, and (b) treating the patient using the following method: i. administering a therapy that is targeted to an actionable sequence variation if the patient is identified as having the actionable sequence variation, and ii. administering a non-targeted therapy in the absence of any follow-up genetic testing on DNA extracted from a tissue biopsy if one or more non-actionable sequence variations and no actionable sequence variations are identified.

The invention discloses a dairy cow early embryo sex identification method, and belongs to the technical field of dairy cow breeding and breeding. The identification method comprises the following steps: (1) culturing a dairy cow embryo to an early blastocyst stage, starting to perform single-embryo single-droplet culture, and after culturing until a blastocyst cavity is formed, punching a blastocyst zona pellucida to promote the blastocyst to shrink and release blastocyst cavity liquid; (2) collecting blastocyst cavity liquid, and extracting embryo free DNA in the blastocyst cavity liquid; (3) by taking the free DNA as a template, designing a primer to amplify a specific repetitive sequence ChrY fragment of the bull Y chromosome; if the amplification product exists, the embryo is identified as a bull, and if the amplification product does not exist, the embryo is identified as a cow. The method can ensure that the embryo free DNA in the obtained blastocyst cavity fluid is only derived from the embryo, and can effectively avoid embryo injury. According to the method disclosed by the invention, the copy number of the amplified target area in the bull Y chromosome is more than 2000 times, a detection signal can be amplified, and the detection accuracy is improved.

A method of performing bisulfite sequencing on ultrashort single-stranded cell-free DNA (uscfDNA) and mononucleosomal cell-free DNA (mncfDNA) is described as well as methods of using the methylation profile of uscfDNA and / or mncfDNA for detecting biomarkers and diagnosing diseases and disorders.