13 results about "Bisulfite sequencing" patented technology

Aspects of the present disclosure are directed to methods, compositions, and kits for detection and analysis of DNA and RNA cytosine methylation. Certain aspects include methods, compositions and kits useful in bisulfite sequencing of methylated nucleic acids, including methylated nucleic acids from low-input samples such as cell-free DNA and cell-free RNA. Also disclosed are methods and compositions for detection and quantification of 5-hydroxymethylcytosine in DNA.

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.

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.

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.

Aspects of the present disclosure relate to methods, compositions and kits for detecting and analyzing the cytosine methylation of DNA and RNA.Certain aspects include methods, compositions and kits that are useful in bisulfite sequencing of methylated nucleic acids from low-input samples, such as methylated nucleic acids including cell-free DNA and cell-free RNA.Methods and compositions for detecting and quantifying 5-hydroxymethylcytosine in DNA are also disclosed. TIFF2025502057000016.tif86129

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.

Aspects of the present disclosure relate to methods, compositions, and kits for the detection and analysis of DNA and RNA cytosine methylation. Certain aspects include methods, compositions, and kits for hydrosulfite sequencing of methylated nucleic acids, including methylated nucleic acids from low input samples such as cell free DNA and cell free RNA. Also disclosed are methods and compositions for the detection and quantification of 5-hydroxymethylcytosine in DNA.

Provided herein is a method of detecting cancer through generalized loss of stability of epigenetic domains as well as compositions useful therein. The present invention is based on the discovery that generalized loss of stability of epigenetic domains was determined to be a characteristic across various cancer types. Genome-scale bisulfite sequencing of cancers revealed a surprising loss of methylation stability in the cancer methylome, involving both CpG islands and shores, as well as large (up to several megabases) blocks of hypomethylation affecting more than half of the genome, with concomitant stochastic variability in gene expression.

The invention discloses a method and primer pair for quantitatively detecting different levels of classical swine fever antibodies. The invention uses Oligo 6.0 software and MethyPrimer online software to design self-designed primers, uses Bisulfite sequencing, and combines with a classical bisulfite sequencing method for verification, so that different classical swine fever antibody levels can be quickly, accurately and efficiently determined. The primer pair provided by the invention is a primer pair composed of DNAs shown in SEQ ID NO.5, SEQ ID NO.6, SEQ ID NO.7, SEQ ID NO.8, SEQ ID NO.9 and SEQ ID NO.10 in a sequence table. The method provided by the invention is to perform PCR amplification on genomic DNA of a pig to be tested treated with bisulfite by using the primer pair, and then judge whether a CD4 gene promoter region of the pig to be tested is highly methylated or moderately methylated according to a pyrophosphate sequencing result, and the classical swine fever antibody level of a highly methylated pig is higher than that of a moderately methylated pig. The classical swine fever antibody level is detected by using a test paper. The method provided by the invention is convenient to use, accurate and highly sensitive, and can be used for detecting the level of classical swine fever antibodies in Landrace and Large White pigs.

The invention discloses a methylation vector-based lung cancer subtype specific methylation region identification method, a biomarker and application, and relates to the technical field of sequence analysis, the method comprises the following steps: obtaining and preprocessing bisulfite sequencing data of a to-be-analyzed sample; sliding a window on the reference genome for scanning, and coding reads covering all CpG sites in the window into methylation vectors according to a site sequence; collecting same window vectors, clustering to form a vector cluster, calculating a group specificity vector proportion and a sample proportion, screening according to rules, combining adjacent window intervals, and outputting subtype specificity methylation vector areas; the first 500 genes are screened from a low-methylation region as biomarkers and are used for molecular typing and early detection, and prognosis evaluation and curative effect monitoring are supported. Through the technical scheme of the invention, the read-level joint methylation configuration is reserved, the coverage fluctuation and heterogeneity interference are reduced, and the stability and discrimination precision of region identification are improved.

The invention belongs to the field of mitochondrial genetic defect disease diagnosis, and particularly relates to a mitochondrial genome methylation level detection method. According to the invention, a mitochondrial separation and purification technology suitable for single-molecule DNA sequencing is innovatively researched and developed, a mitochondrial genome DNA ring is innovatively opened for single-molecule direct sequencing, and mitochondrial genome DNA methylation analysis is further developed. Statistic difference analysis is respectively carried out on a methylation result of a CpG site of a sample mitochondrial genome DNA (mtDNA) obtained by adopting the detection method and a methylation result obtained by adopting a bisulfate Sequencing technology, and the methylation results obtained by the two methods have no significant difference. Compared with bisulfate Sequencing, the method disclosed by the invention has the obvious value advantages of low cost, high flux and short period.

The invention provides a method and a kit for detecting methylation and expression level of a PRSS33 gene. The method is realized by detecting methylation level and / or mRNA expression level of a PRSS33 gene promoter region from bone marrow or a peripheral blood sample. In an MDS patient, the PRSS33 shows characteristic promoter hypermethylation and gene expression down-regulation; the methylation level is preferably detected by adopting a bisulfite sequencing method, and the mRNA expression level is determined by reverse transcription real-time fluorescent quantitative PCR (Polymerase Chain Reaction); furthermore, the detection result can be used for risk stratification and prognosis evaluation of MDS and monitoring of demethylation drug treatment response; on the other hand, the invention also provides a kit containing the specific primer pair for implementing the detection, and the kit is used for detecting the methylation and expression level of the PRSS33 gene.

Methods and systems of single-cell bisulfite sequencing are provided. The single-cell bisulfite sequencing techniques of the disclosure involve single-cell DNA (scDNA) droplets, where the scDNA are fragmented within the scDNA droplets prior to bisulfite conversion. The methods and systems further include barcode droplets, and fusing the scDNA droplets with the barcode droplets to form barcoded scDNA droplets for bisulfite conversion. The bisulfite conversion beneficially occurs within the bisulfite droplets to reduce DNA degradation. The single-cell bisulfite sequencing method and systems provide for bisulfite sequenced nucleic acid libraries.