252 results about "Free dna" patented technology

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 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.

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.

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.

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.

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.

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.

Aspects of the present disclosure includes methods to quantify methylation in a DNA sample, where the method includes treating the sample to encode the presence or absence of DNA methylation, adding to the sample a set of synthetic molecules (e.g., quality control template (QCT) molecules), generating a co-amplification mixture, sequencing the co-amplification mixture, determining a number of methylated molecules in the sample based on the number of methylated reads from the sample and a number of reads from the set of synthetic molecules.

The invention relates to the technical field of nucleic acid detection, in particular to a lysis buffer solution, a kit and an extraction method for extracting free DNA of peripheral blood. The lysis buffer solution for extracting the free DNA of the peripheral blood comprises a first lysis solution and a second lysis solution, the first lysis solution takes guanidine hydrochloride as a main chaotropic agent and at least one of ammonium thiocyanate and guanidine isothiocyanate as an auxiliary chaotropic agent, and is compounded with a metal ion chelating agent, trehalose, dithiothreitol, digestive enzyme, sodium dodecyl sarcosinate, borate and ascorbic acid; the second lysis solution takes guanidine hydrochloride as a main chaotropic agent and urea as an auxiliary chaotropic agent, and is compounded with a metal ion chelating agent, trehalose, dithiothreitol, digestive enzyme, sodium dodecyl sarcosinate, borate, ascorbic acid and polyethylene glycol. The buffer solution of the lysate does not contain SDS (sodium dodecyl sulfate), so that the residue of SDS in an extracted product can be avoided, and the amount of extracted free DNA (deoxyribonucleic acid) is more.

A method of sequencing a nucleic acid of interest (NAOI) is provided. In some embodiments, the method may comprise providing a sample from a patient, the sample having cell-free DNA molecules comprising NAOIs, amplifying the NAOIs, ligating adapters to the NAOIs, and sequencing the NAOIs. A method of labelling a NAOIs is also provided. In some embodiments, the method may comprise providing a sample from a patient having the NAOIs, amplifying the NAOIs, contacting the amplified NAOIs with a pool of oligonucleotides, attaching oligonucleotides to each of the amplified NAOIs to label the NAOIs. The method may further comprise sequencing the labelled NAOIs and grouping the resulting sequencing reads.

The invention belongs to the field of protein hydrogel, and relates to protein adhesive hydrogel for promoting diabetic oral soft tissue injury repair and a preparation method of the protein adhesive hydrogel. The hydrogel is prepared by mixing an aqueous solution of recombinant fusion protein and an aqueous solution of polyethylene glycol bissuccinimide succinate. The sequence of the recombinant fusion protein is as shown in SEQ ID NO: 1: [PAATAVSHTTHAP (VPGKG) 5] 36. The hydrogel disclosed by the invention has good biocompatibility and excellent adhesion performance, can form a lasting antibacterial barrier, and is electrostatically combined with free DNA (Deoxyribonucleic Acid) in NETs, so that inflammatory factor expression induced by the NETs is inhibited, and finally diabetes wound healing is accelerated.

Disclosed herein includes a method of determining the RhD genotype of a fetus, comprising: (a) extracting cell-free DNA from a sample of a pregnant person, wherein the extracted DNA comprises a mixture of maternal cell-free DNA and fetal cell-free DNA; (b) performing targeted multiplex amplification on the extracted DNA to amplify a plurality of target loci together in the same reaction mixture using a plurality of primer pairs, wherein at least three of the primer pairs each targets a different exon or intron of the RhD gene and the RhCE homologue gene and is each designed to amplify a target locus that comprises a variant between the RhD gene and the RhCE homologue gene; and (c) sequencing the amplicons by high-throughput sequencing and determine the RhD genotype of the fetus using the sequencing reads of the amplicons targeting the RhD gene and the RhCE homologue gene.

1. Name of the product in this design: Packaging box (Free DNA Library Preparation Kit JKEasy). 2. Purpose of this design: As a packaging box. 3. The key design elements of this product are the combination of shape, pattern, and color. 4. The image or photograph that best illustrates the key design points: Design 1 3D view. 5. The design for which protection is sought includes color. 6. The bottom surface of this design product is a part that is not easily seen or not visible during use, so the bottom view of Design 1 is omitted; the bottom surface of this design product is a part that is not easily seen or not visible during use, so the bottom view of Design 2 is omitted. 7. Design 1 is designated as the basic design.

The present disclosure provides methods for detecting the presence or absence of cancer in a subject. In some embodiments, samples are obtained from the subject, and a panel capable of detecting multiple biological molecules, such as RNA, cDNA, and cell-free DNA (cfDNA) is utilized to processing a ample to determine tumor variants in the first sample. A mixture of these biological molecules are detected via oligonucleotide probes in order to detect as a particular sensitivity within a sequencing read budget, further including exon related probe designs for RNA.

The application relates to the technical field of biological medicine, and discloses a tumor marker micro-detection and analysis method based on liquid biopsy. The method comprises the following steps: extracting peripheral blood free DNA and performing double-end sequencing; jointly extracting multi-dimensional features such as ctDNA fragment length distribution, end sequence preference, nucleosome positioning signal and CpG methylation state from the sequencing data; constructing a feature matrix under unified genomic coordinates through space-time alignment; inputting a pre-trained cross-scale graph neural network model, taking a genomic region as a node and physical and functional proximity as an edge, learning a coupling mode of multi-modal features in a local chromatin structure, and outputting a malignant risk score; and combining a threshold to distinguish early lung cancer and benign and malignant nodules. The application comprises corresponding functional units and supports efficient parallel analysis. The system significantly improves detection sensitivity and specificity, reduces the false negative rate by 36%, and realizes non-invasive and accurate early lung cancer screening.

The present disclosure generally relates to the use of linear nucleic acid primers for the amplification of a target nucleic acid sequence, for example, in a cell-free environment. In some embodiments, compositions of the linear nucleic acid primers are provided. For example, in some embodiments, the linear nucleic acid primers comprise a guanosine or a cytidine at 3′ terminal end. In some embodiments, the linear nucleic acid primers have been optimized to prevent primer-homodimer and / or hairpin formation and to exclude cumbersome codon sequences. In some embodiments, methods are provided for the amplification of a DNA template fragment using the linear nucleic acid primers. Thus, in some cases, the use of the nucleic acid primers, as described herein, may allow for the reduction in amplification of non-specific hybridization events while allowing for the amplification of the target nucleic acid sequence.

The present disclosure includes, among other things, methods, kits, and systems for determining a status of lung cancer. In various embodiments, the present disclosure relates to the use of one or more histone modifications, chromatin accessibility, binding of one or more transcription factors, and / or DNA methylation as features of a status of lung cancer. In some embodiments, differential modifications and / or differential accessibility are detected and quantified at one or more genomic loci in a biological sample, e.g., cell-free DNA (cfDNA), from a liquid biopsy sample obtained or derived from a subject having lung cancer. In various embodiments, the determined status can be used, e.g., to select a treatment for lung cancer and / or to treat lung cancer.

Systems and methods are disclosed for determining gene fusion by determining a fused read containing sequencing data of a portion of a fused chromosome DNA molecule; determining a predetermined point on the genome with least one mapped portion of the fused read clipped at the predetermined point (a breakpoint); identifying two mapped read portions from two breakpoints (breakpoint pair) as a potential fusion candidate; creating one or more fusion sets based on breakpoint pairs and clustering the fusion sets into one or more fusion clusters; and identifying each fusion cluster meeting a predetermined criterion as a gene fusion.

Aspects of the present disclosure are directed to methods, compositions, and kits for detection and analysis of DNA and RNA cytosine methylation and / or RNA pseudouridylation. Certain aspects include methods, compositions and kits useful in bisulfite sequencing of methylated and / or pseudouridinylated nucleic acids, including methylated and / or pseudouridinylated nucleic acids from low-input samples such as cell-free DNA (cfDNA) and cell-free RNA, long fragment polynucleotides, and / or cfDNA and DNA from formalin-fixed paraffin-embedded (FFPE) samples. Also disclosed herein are methods, compositions and kits useful in bisulfite sequencing of methylated and / or pseudouridinylated nucleic acids with low nucleic acid damage, higher true positive results, and / or lower false negative results.

The present application relates to the field of paternity determination, and provides a non-invasive prenatal paternity relationship determination method and system and electronic equipment, the method comprising: obtaining a paternal DNA sample and a pregnant woman's plasma free DNA sample, the pregnant woman's plasma free DNA sample including a fetal DNA sample; performing genomic sequencing on the paternal DNA sample and the pregnant woman's plasma free DNA sample; after genotype filling, determining the paternal genotype and the fetal genotype; calculating the kinship coefficient of the paternal genotype and the fetal genotype; based on the kinship coefficient of the paternal genotype and the fetal genotype and a pre-constructed corresponding relationship between the kinship coefficient and the paternity relationship, determining the paternity relationship between the father and the fetus. The present application solves the defects of low detection efficiency and high technical cost in the related art, and is convenient to operate, completely non-invasive, and does not cause any physiological interference to the pregnant woman and the fetus; the detection can be carried out from the seventh week of pregnancy, and is suitable for precise identification of the biological father of the fetus and unrelated individuals.

The present disclosure provides methods and systems for screening or detecting colorectal cancer or subsequent colorectal disease progression, which can be applied to cell-free nucleic acids, such as cell-free DNA. The methods can train a machine learning model using detection of methylation signals within single sequencing reads in identified genomic regions as input features, and generate a classifier suitable for stratifying a population of individuals. The methods can include extracting DNA from a cell-free sample obtained from a subject, transforming the DNA for methylation sequencing, generating sequencing reads, and detecting colon proliferative cell disorder related signals in the sequencing information, and training a machine learning model to provide a discriminator capable of distinguishing between groups such as healthy, cancer, etc. in a population of subjects, or distinguishing between disease subtypes or stages. The methods can be used, for example, to predict, prognosticate, and / or monitor response to treatment, tumor burden, recurrence, or progression of colorectal cancer.