394 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 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.

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.

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 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.

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.

Methods are provided for detecting gene deletions and driver mutations using tumor-specific methylation patterns from cell-free DNA and tissue biopsies. The methods exploit the mutual exclusivity between tumor-specific methylation and homozygous gene deletion, enabling detection through absence of expected methylation signals. Applications include detection of MTAP, PTEN, and RB1 deletions, as well as prediction of EGFR single nucleotide (SNV) and small (up to 50 base pair) insertions and deletions (indel) driver mutations, enabling identification of patients eligible for targeted therapies.

This invention discloses a method for paternity testing using homozygous loci, belonging to the field of paternity testing technology. The method includes: S101: sequencing the pregnant woman's cell-free DNA sample S and the father's DNA sample F, and genotyping S and F based on sequencing depth; S102: calculating the inefficiency P of the two samples based on the genotyping results. 无 or inefficient P 无 With efficiency P 有 The ratio is used to perform paternity testing; the effectiveness P 有 The effective loci represent the proportion of the homozygous loci in the set X of opposite homozygous loci. Effective loci are those in S that conform to the set X of opposite homozygous loci and can detect fetal signals. Loci in S and F are selected according to Formula I to form the set X of opposite homozygous loci; inefficiency P 无 The percentage of invalid loci in the same homozygous locus set X' is defined as the proportion of invalid loci in S that conform to the same homozygous locus set X' and can detect fetal signals. Loci in S and F are selected according to Formula II to form the same homozygous locus set X'.

The application discloses a free DNA methylation and fragmentomics combined analysis method based on targeted CpG bisulfite sequencing, and belongs to the technical field of liquid biopsy and epigenetic detection. The application extracts cfDNA from blood plasma, carries out high-throughput sequencing after library construction by a methylation adapter, bisulfite conversion, and biotin probe targeted capture of a CpG enrichment region, and simultaneously realizes single-base resolution methylation accurate quantification and FRAGMA fragmentomics analysis by using the same sequencing data, so that the accuracy of methylation quantification results is inferred, and the optimal detection region is iteratively selected; multi-dimensional characteristics such as a methylation ratio, an 11nt cutting map, a CGN / NCG motif ratio and a fragment length distribution are fused to construct a machine learning / deep learning model to output a unified disease risk score. The application realizes the bimodal integration of methylation chemical signals and fragmentomics structural signals in a targeted sequencing system for the first time, and has the advantages of low cost, high sensitivity and strong clinical adaptability.

Disclosed herein are methods and systems for targeted detection of circulating tumor DNA (ctDNA) molecules. In some cases, a methylated DNA depleted molecular sequencing library can be generated and used to reliably detect ctDNA in cell-free DNA samples at lower sequencing depths and at lower costs than existing methods.

The invention provides a method for judging a sib relationship through DNA of a born child and cfDNA of a fetus, and belongs to the technical field of biological identification. According to the non-invasive prenatal sib relation identification method, the risk of traditional invasive detection on pregnant women and fetuses is remarkably reduced, meanwhile, through a high-sensitivity genetic information analysis technology, the problems of maternal DNA interference and low fetal free DNA concentration are effectively solved, and the non-invasive prenatal sib relation identification method is suitable for clinical application. And high-reliability determination of the genetic relationship between the fetus and the born child under a non-invasive condition is realized. The method not only provides a scientific basis for confirming the complex family relationship, but also can be extensively applied to the fields of legal identification and medical assisted reproduction, fills the blank of non-invasive antenatal sib relationship identification in the prior art, and has wide social value and industrialization potential.

The invention relates to methods of determining a tissue of origin, a cell type of origin, origination from a cancerous or immune cell, or a combination thereof of cell-free DNA by using fragment length data.

This document provides methods and materials for assessing and / or treating subjects (e.g., humans) suspected of having cancer. For example, this document provides methods and materials for a nucleic acid sequence analysis which can determine a sequence of B cell receptor. In some cases, determining a sequence of B cell receptor (and, optionally, identifying the presence of one or more mutations and / or identifying the presence of aneuploidy) in DNA (e.g., cell-free DNA (cfDNA)) in a fluid sample (e.g., a cerebrospinal fluid sample) obtained from a subject (e.g., a human subject such as a human suspected of having cancer) can be used to identify the subject as having cancer.

The invention provides methods for simultaneously enriching multiple target regions of interest in one reaction volume, from cell-free DNA isolated from a blood or plasma sample, followed by high-thought sequencing and sequence read analysis. The invention also provides library of target-specific oligonucleotide primers or probes for the multiplexed target enrichment.

Provided herein are biomarkers present in cell-free DNA (cfDNA) for the early detection of preclinical Alzheimer's disease (AD), mild cognitive impairment (MCI), or AD in a subject. The detection of such biomarkers in a subject may be used to convey a method of treating a subject with a therapy (e.g., a drug or a biological agent) for preclinical Alzheimer's disease (AD), mild cognitive impairment (MCI), or AD. The biomarkers disclosed herein may also be used in methods of monitoring the progression of preclinical AD, MCI, or AD.

The present invention provides a method and means for isolating or recovering short-chain DNA such as cell-free DNA (cfDNA) from a blood sample. Specifically, the present invention provides a method for isolating or recovering short-chain DNA of 100-250 bp from a DNA sample, the method comprising: a step for introducing the DNA sample into a column equipped with an ultrafiltration filter and centrifuging the DNA sample; and a step for recovering a filtrate containing the short-chain DNA.