6 results about "Bisulfite sequencing" patented technology

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 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 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.