27 results about "Methylation analysis" patented technology

The present invention discloses an in vitro method for obtaining DNA methylation biomarkers as exquisite DNA methylation positions in the human genome (i.e., CGIDs) that predict cervical cancer especially at as yet inaccessible early stages by examining progression of “categorical” DNA methylation alterations in three stages of premalignant lesions (cervical intraepithelial neoplasia (CIN)), progressing from CIN1 to CIN3. The present invention discloses combinations of CGIDs for detecting with high specificity and sensitivity cervical cancer by measuring their DNA methylation status and deriving a “methylation score”, which is useful as a biomarker for cervical cancer. Also disclosed are kits for predicting cervical cancer using such CGIDs using multiplexed next generation sequencing methylation assays, pyrosequencing assays and methylation specific PCR. The DNA methylation markers (CGIDs) described in the present invention are useful for cervical screening and early detection of cervical cancer by any person skilled in the art to detect cervical cancer.

Described herein are methods of preparing dual-indexed nucleic acid libraries for methylation profiling using bisulfite conversion sequencing. In various embodiments, the methods use a two-step indexing process to tag bisulfite-treated DNA with unique molecular identifiers (UMIs).

The present disclosure provides methods for generating mbias corrected sequence fragment data comprising correcting one or more strand displacement mbias instances in one or more nucleic acid fragments from a sample obtained from a subject, performing a methylation analysis, and correcting one or more end-repair bias instances in sequence fragment data from the methylation analysis.

A method is provided for probabilistically assigning a tissue of origin to a nucleic acid in a sample, e.g., DNA in a cell-free fluid sample obtained from a human subject. A hydroxymethylation profile is generated for the sample DNA and then compared across a reference data set of hydroxymethylation profile vectors, where each hydroxymethylation profile vector identifies the hydroxymethylation profile at a specific reference locus, the tissue-specific gene associated with the reference locus, and the tissue with which the gene and reference locus are associated. A tissue of origin can be probabilistically assigned to the sample nucleic acid using the results of the comparison. Other methods of use are also provided.

This invention discloses a method for constructing a gene methylation diagnostic model for differentiated thyroid cancer (PTC). The method includes the following steps: S1, obtaining a test sample; S2, extracting and storing DNA from the test sample; S3, performing methylation analysis; S4, establishing a diagnostic model based on DNA methylation, where the model shows that patients with cg03596178, cg06033721, cg06688989, cg07209244, cg07485775, cg14484681, cg19979108, and cg20943461 are more likely to experience disease progression and are considered risk factors; S5, cross-validating and evaluating the performance to obtain the gene methylation diagnostic model. This model, by detecting and statistically analyzing specific methylation sites, can differentiate patients with recurrent or metastatic characteristics in differentiated thyroid cancer. The relevant model can assist in the clinical diagnosis and follow-up of thyroid patients.

The invention discloses a gene level DNA methylation, transcriptome and proteome conjoint analysis method based on a snkemake framework, which comprises the following steps: preprocessing original data of DNA methylation and / or transcriptome and / or proteome, analyzing gene methylation, analyzing transcriptome and / or proteome, and analyzing the transcriptome and proteome. Based on gene methylation analysis data, the preprocessed transcriptome data and the preprocessed proteome data, correlation analysis and / or difference intersection analysis and / or enrichment pathway conjoint analysis are / is carried out, finally analysis results are sorted, and a visual report is generated. The method has comprehensive results, and relates to quantification, difference analysis and pathway enrichment analysis of gene methylation, and correlation analysis, difference intersection analysis and enrichment pathway joint analysis of integrated DNA methylation and / or transcriptome and / or proteome data; automatic arrangement, verification, visualization and report generation of analysis results are realized; all operation steps can be traced, and corresponding analysis log records are generated. The invention further discloses a related system and application.

The present disclosure provides a method for methylation analysis of genomic fragments.

The application discloses a nucleic acid sequence construction method for cfDNA multiplex gene methylation detection and application thereof. The construction method comprises the following steps: using a methylation-sensitive restriction endonuclease to perform enzyme cutting on to-be-detected cfDNA to obtain enzyme cutting fragments, using a ligase to connect an adapter to a nick end of the enzyme cutting fragments to form an adapter product; and using the adapter product as a template to perform PCR amplification to construct a recombined nucleic acid sequence for target gene methylation site detection. The construction method can be used for cfDNA level methylation qPCR analysis and low-abundance sample quantitative analysis, has small sample demand, has a wide methylation analysis coverage, and has high methylation enrichment efficiency.

The invention discloses ulva pertusa polysaccharide UPP and ulva pertusa homogeneous polysaccharide UPP-5 as well as a preparation method and application thereof. The single-component polysaccharide UPP-5 is obtained by adopting DEAE-52 anion exchange chromatography in combination with ultrafiltration purification. The structure of the UPP-5 is systematically characterized by high performance gel permeation chromatography, infrared spectroscopy, methylation analysis, nuclear magnetic resonance and other methods, and the result shows that the UPP-5 is acidic heteropolysaccharide with a novel structure. Based on an AOM / DSS induced colorectal cancer mouse model, the effect of the mouse model is evaluated from the aspects of disease activity index, colon length, tumor number, histological observation, gene and protein expression and the like. Results show that the UPP can significantly improve inflammation and pathological states and reduce the incidence of tumors, and has the potential of preventing and treating colorectal cancer. The invention provides a new thought and theoretical basis for structural research and medical function development of algal polysaccharides.

Systems and methods of the disclosure may include a computer-implemented method, the computer-implemented method including: receiving, at a computer system, nucleic acid sequencing data derived from a methylation assay performed on a biological sample associated with at least one subject; computing, using a processor associated with the computer system, a beta value matrix based on the nucleic acid sequencing data, wherein the beta value matrix comprises one or more missing beta values; addressing, using the processor, the one or more missing beta values in the beta value matrix using a missing beta value completion approach; identifying, using the processor, one or more principal components in the completed beta value matrix; and training, using the one or more principal components in combination with a predetermined set of clinical variables, a classifier to predict a survival outcome for a target subject associated with a disease type.

This invention discloses a method for constructing a gene methylation prognostic assessment model for differentiated thyroid cancer, characterized by the following steps: S1, obtaining a test sample; S2, extracting and storing DNA from the test sample; S3, performing methylation analysis; S4, constructing a prognostic classification model based on DNA methylation, calculating the risk value of the prognostic model as Risk Score = 0.15411928*cg03190661 - 0.10405129*cg15676916 + 0.06108015; S5, cross-validating to evaluate performance and obtain the gene methylation prognostic assessment model. This model uses the Risk Score to assess the prognosis of differentiated thyroid cancer: low-risk group, normal follow-up is recommended; medium-risk group, follow-up time can be reduced to half; high-risk group, close follow-up is required.

A method is provided for probabilistically assigning a tissue of origin to a nucleic acid in a sample, e.g., DNA in a cell-free fluid sample obtained from a human subject. A hydroxymethylation profile is generated for the sample DNA and then compared across a reference data set of hydroxymethylation profile vectors, where each hydroxymethylation profile vector identifies the hydroxymethylation profile at a specific reference locus, the tissue-specific gene associated with the reference locus, and the tissue with which the gene and reference locus are associated. A tissue of origin can be probabilistically assigned to the sample nucleic acid using the results of the comparison. Other methods of use are also provided.

The invention discloses a CpG methylation single cell whole genome analysis method and related equipment based on sequencing reads, and the method comprises the following steps: obtaining to-be-analyzed single cell data, and carrying out methylation data sequencing read comparison on the to-be-analyzed single cell to obtain a methylation site statistical result; screening a methylation specific interval based on a random sampling strategy and the methylation Hamming distance of the sequencing read; calculating a Hamming distance matrix of every two to-be-analyzed single cell CpG sites according to a methylation site statistical result and a methylation specific interval, and performing initial clustering based on the Hamming distance matrix; and obtaining cell DNA methylation heterogeneity measurement according to an initial clustering result, extracting a cell type or state specific DNA methylation mode panorama, calculating the similarity between a read segment and each cell type according to a specific methylation mode, and calculating the proportion of cells from a mixed sample sequencing result. According to the embodiment of the invention, the cell methylation analysis efficiency and sensitivity can be improved. The method can be widely applied to the technical field of gene analysis.

A method is provided for probabilistically assigning a tissue of origin to a nucleic acid in a sample, e.g., DNA in a cell-free fluid sample obtained from a human subject. A hydroxymethylation profile is generated for the sample DNA and then compared across a reference data set of hydroxymethylation profile vectors, where each hydroxymethylation profile vector identifies the hydroxymethylation profile at a specific reference locus, the tissue-specific gene associated with the reference locus, and the tissue with which the gene and reference locus are associated. A tissue of origin can be probabilistically assigned to the sample nucleic acid using the results of the comparison. Other methods of use are also provided.

The application discloses a sequencing read-based CpG methylation single-cell whole genome analysis method and related equipment, and the method comprises the following steps: obtaining single-cell data to be analyzed, performing methylation data sequencing read alignment on the single cells to be analyzed, and obtaining methylation site statistical results; screening a methylation-specific interval based on a random sampling strategy and a methylation Hamming distance of the sequencing read; calculating a Hamming distance matrix of CpG sites of each pair of single cells to be analyzed according to the methylation site statistical results and the methylation-specific interval, and performing initial clustering based on the Hamming distance matrix; obtaining a cell DNA methylation heterogeneity metric according to the initial clustering result, extracting a cell type or state-specific DNA methylation pattern panorama, calculating the similarity of a read and each cell type according to the specific methylation pattern, and calculating the proportion of cells from a mixed sample sequencing result. The embodiment of the application can improve the efficiency and sensitivity of cell methylation analysis. The application can be widely applied in the technical field of gene analysis.

The invention discloses a construction method and application of a nucleic acid sequence for cfDNA multiple gene methylation detection. The construction method comprises the following steps: carrying out enzyme digestion on cfDNA to be detected by using methylation sensitive restriction endonuclease to obtain an enzyme digestion fragment, and connecting a joint to a cut end of the enzyme digestion fragment by using ligase to form a joint product; and carrying out PCR amplification by taking the joint product as a template, and constructing a recombinant nucleic acid sequence for detecting the methylation site of the target gene. The construction method disclosed by the invention can be used for methylation qPCR analysis of cfDNA level and quantitative analysis of low-abundance specimens, the demand quantity of samples is small, the coverage range of methylation analysis is wide, and the methylation enrichment efficiency is high.

A methylation data processing analysis method and platform, a storage medium and a program product, the method comprising: receiving a plurality of pieces of sample information, the plurality of pieces of sample information comprising sample queue information, queue comparison information and sample methylation sequencing data, and generating a task script according to the received sample information, the sample queue information comprises samples and queues to which the samples belong, the queue comparison information comprises one or more groups of queues to be compared, and one group of queues comprises two queues; according to the generated task script, data processing and data analysis are carried out, the data processing comprises sequencing data quality control, sequencing data comparison and comparison result statistics, and the data analysis comprises sample methylation analysis, inter-group methylation analysis and differential methylation analysis; generating a graph and / or a table according to results of data processing and data analysis; and outputting the interactive report according to the generated graph and / or table.

Methods and systems for detecting and correcting 3 '-end hypomethylation bias, and for analyzing methyl-seq data to detect or diagnose disease are described. In some examples, the disclosed methods may comprise: determining a methylation state for each sequenced fragment of a plurality of sequenced fragments based on the sequenced fragment data derived from a sample from a subject; determining for each sequenced fragment of the plurality a probability that the methylation state of a sequenced fragment is significantly different from a distribution of methylation states determined for a plurality of sequenced fragments derived from samples from healthy individuals that map to a same genomic interval; determining a disease probability metric for the sample based on the probabilities determined for the plurality of sequenced fragments; and outputting a determination that the subject has the disease based on a comparison of the disease probability metric for the sample to a first predetermined threshold.

Disclosed herein are methods of determining a cell free DNA (cfDNA) methylation profile and a cfDNA fragmentation profile in a single DNA sample from a subject. In one aspect, the disclosed methods relate to identifying methylated cytosine in a target nucleic acid from the DNA sample and obtaining sequenced fragments from the same sample; mapping the sequenced fragments to a genome to obtain genomic intervals of mapped sequences; and, analyzing the genomic intervals of mapped sequences to determine cfDNA fragment lengths and determining the cfDNA fragmentation profile using the lengths.

The invention belongs to the technical field of plant molecular biology and crop genetic breeding, and discloses DNA (deoxyribonucleic acid) methylated transferase ItCMT2 related to sweet potato tuberous root development as well as an encoding gene and application of the DNA methylated transferase ItCMT2. According to the invention, the ItCMT2 gene is cloned and identified from a sweet potato diploid related species Ipomoeatrifidavar.Y22, and the ItCMT2 gene is used for encoding a protein containing BAH and C5MTase structural domains. By constructing an ItCMT2 gene knock-down (KD) transgenic sweet potato model and combining agronomic character identification, methylation analysis, hormone quantification and omics conjoint analysis, it is proved that ItCMT2 can maintain sweet potato genome methylation, the root weight of a single sweet potato plant can be reduced by 51.3%-75.7% when expression of ItCMT2 is reduced, and a unique hormone spectrum of zeatin, auxin and jasmonic acid is presented; meanwhile, the starch is reduced and the starch grain shape is abnormal along with the increase of root tuber lignin.

Some embodiments relate to a method for detecting the presence of one or more nucleic acids indicative of a health condition, tissue of origin, germ layer of origin or organ of origin in a mixture of nucleic acids comprising performing methylation analysis on a sample comprising a plurality of nucleic acids and determining whether the sample includes a plurality of methylation haplotype blocks indicative of the presence one or more nucleic acids indicative of a health condition, tissue of origin, germ layer of origin or organ of origin wherein the methylation haplotype blocks comprise a plurality of methylation sites for which the methylation status is coordinated.

The invention belongs to the technical field of biological medicine, and discloses a xenogenic heart transplantation donor source cfDNA quantitative detection kit based on SNP typing. The kit is characterized in that donor-specific SNP sites and myocardial / endothelial cell differential methylation CpG sites are integrated, an SNP anchoring and methylation analysis two-dimensional molecular traceability system is constructed, cfDNA fragments containing SNP-CpG units are amplified or captured in a targeted mode, bioinformatics analysis is combined, circulating free DNA of a myocardial source and circulating free DNA of an endothelial source are quantified respectively, and the molecular traceability of the myocardial / endothelial cell is improved. And judging cellular rejection or antibody-mediated rejection according to the ratio and a threshold value. The kit disclosed by the invention not only has high engineering feasibility and clinical applicability, but also realizes cognitive transition from whether the cells are damaged to what kind of cells are damaged by what mechanism on the molecular diagnosis level, and provides a key tool for precise immune management of xenotransplantation.

The invention provides a screening method using m6A demethylase ALKBH5 as a CAVD biomarker and application thereof, and the screening method comprises the following steps: S1, collecting a tissue sample, taking an aortic valve sample of a CAVD patient, separating the aortic valve sample into a calcified part and a non-calcified part according to the calcification degree of the valve, using the calcified part tissue as a calcified group, using the non-calcified part tissue as a control group, and using the calcified group and the non-calcified part tissue as a control group; each group comprises at least five; s2, RNA extraction and quality control: separating and purifying RNA from tissue samples of a calcification group and a control group by using a TRIzol method; s3, carrying out m6A library construction and sequencing; s4, sequencing data quality control; s5, analyzing sequencing data, including Motif analysis, differential methylation analysis, enrichment analysis and conjoint analysis; s6, construction of a CAVD cell calcification model; s7, carrying out QPCR (Quantitative Polymerase Chain Reaction) detection on methylation regulatory enzymes such as WTAP, FTO (Fluorine-doped Tin Oxide), ALKBH5 and YTHDF3; s8, detecting the protein of the demethylase ALKBH5 and the fluorescence expression level of the demethylase ALKBH5; s9, research on the calcification of the hVIC by knocking down the demethylase ALKBH5; and obtaining the relationship between the methylase ALKBH5 and the CAVD. The invention finds that ALKBH5 may become a novel biomarker for screening or diagnosing CAVD, and a new target for treating CAVD.

Methods for mitigating methylation bias during preparation of a sequencing library are described. The method may include, for example, extracting DNA fragments from a sample; performing at least one of: (i) a first end repair reaction, wherein the first end repair reaction comprises the use of a non-strand displacement DNA polymerase; or (ii) a second end repair reaction, wherein the second end repair reaction comprises the use of a chain termination mechanism; performing at least one of: (iii) a tailing reaction to add a pendant polynucleotide strand to the end-repaired DNA fragment, where the tailing reaction comprises the use of a single deoxynucleoside triphosphate (dNTP); or (iv) a nick / gap repair reaction that uses a DNA ligase to fill a single-stranded nick or gap in the end-repaired DNA fragment to produce a plurality of modified DNA fragments, or (iv) a nick / gap repair reaction that uses a DNA ligase to fill a single-stranded nick or gap in the end-repaired DNA fragment; and performing methylation analysis of nucleic acid molecules derived from the plurality of modified DNA fragments.

Provided herein are compositions and methods for identifying post-transcriptional nucleic acid modifications. Further provided herein are synthetic blocking libraries. Further provided herein are methods for designing synthetic blocking libraries, and application towards methylome analysis.

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.

Systems, methods, and compositions for identifying genomic variants and methylation analysis, including synthetic polynucleotide libraries, are provided. The synthetic polynucleotide libraries may comprise a plurality of polynucleotides. The polynucleotides may comprise sequences corresponding to a genetic abnormality in a genome. The stoichiometry of each of the plurality of polynucleotides is controlled. Systems, methods, and compositions described herein may include standards for determining the analytical sensitivity and / or accuracy of instruments configured to measure nucleic acid variant frequencies. Standards may comprise RNA-fusions and / or CNV mutations related to cancer.