43 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).

Described herein are dual-indexed nucleic acid libraries for methylation profiling using bisulfite conversion sequencing and methods of preparing same..

This disclosure provides methods for cost-effective bisulfite-free identification in DNA, including whole genomic DNA, of the locations of one or more of 5-methylcytosine, 5-hydroxymethylcytosine, 5-carboxylcytosine and 5-formylcytosine. The methods described herein are based on the conversion of modified cytosine (5mC, 5hmC, 5fC, 5caC) to dihydrouracil (DHU), for example by TET-assisted pyridine borane treatment, followed by endonuclease cleavage of the DHU, and identification of the cleavage site, which corresponds to the location of the modified cytosine.

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 screening method influencing drought adaptability of Hu sheep, and relates to the technical field of molecular breeding. The method comprises the following steps: step 1, selection and treatment of experimental sheep; step 2, transcriptome analysis; step 3, carrying out methylation analysis on the whole genome; and step 4, carrying out transcriptome and whole genome methylation conjoint analysis. The LOC121817420 gene is mined through a transcriptome and whole genome methylation method, the expression quantity of the gene in Hu sheep whole blood in two regions is detected through a real-time fluorescence quantification method, the expression quantity of the gene in Hu sheep in the Hetian region of Xinjiang is high, and it is proved that the gene is one of main candidate genes, different from Hu sheep in the Taihu Lake basin, of the Hu sheep in Xinjiang.

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.

In an aspect, the present disclosure provides a method comprising (a) providing a cell-free deoxyribonucleic acid (cfDNA) sample derived from a subject; and (b) sequencing the cfDNA sample or a derivative thereof to determine a methylation pattern or a methylation level of DNA molecules of the cfDNA sample.

The present invention relates to a real-time polymerase chain reaction method for determining a degree and pattern of DNA methylation at a specific DNA sequence site and to a use thereof. More specifically, the present invention relates to a method for determining a degree and pattern of methylation by determining respective Ct values obtained from performing qPCR in two buffer systems (buffer 1 and buffer 2), in which differences occur depending on the presence or absence of methylation, using DNA obtained from a biological sample, calculating a difference between the Ct values of the two buffer systems, and more specifically, calculating a relative ratio of copy number calculation values obtained from tests in the two buffer systems, and to a use thereof.

Methods for mitigation of methylation bias during preparation of sequencing libraries are described. The methods may comprise, e.g., extracting DNA fragments from a sample; performing at least one of: (i) a first end repair reaction, where the first end repair reaction comprises the use of a non-strand-displacing DNA polymerase; or (ii) a second end repair reaction, where the second end repair reaction comprises the use of a chain termination mechanism; performing at least one of: (iii) a tailing reaction to add an overhanging polynucleotide strand to the end-repaired DNA fragments, where the tailing reaction comprises the use of a single deoxynucleotide triphosphate (dNTP); or (iv) a nick / gap repair reaction using a DNA ligase to fill in single- stranded nicks or gaps in the end-repaired DNA fragments, to generate a plurality of modified DNA fragments; and performing methylation analysis of nucleic acid molecules derived from the plurality of modified DNA 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.

The present invention relates to the field of bioinformatics, and in particular to a methylome and metagenomics analysis method. The method comprises: obtaining data to be analyzed after preprocessing the whole genome sulfite sequencing data of the sample to be tested; and performing methylation analysis, bacterial and fungal microecological analysis, and phage analysis on the data to be analyzed. The present invention combines methylome and microbial metagenomics to analyze the whole genome sulfite sequencing data, and can effectively screen biological factors related to sepsis identification and related analysis. These biological factors can be used in sepsis identification, sepsis infection site prediction, and mortality analysis, and are of great value in the field of sepsis detection.

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 disclosure provides methods for detecting a molecule of tumor DNA (tDNA) in a sample of cell-free DNA (cfDNA). In certain embodiments, cfDNA is sequenced using a single molecule sequencing to obtain a methylation profile of a sequence read. Such methylation profile is compared to a reference methylation profile from a cancer cell and / or a non-cancer cell to identify the sequence read as being from a molecule of tDNA. Further embodiments provide estimating the number of molecules of tDNA in the sample of cfDNA and, to determine as a tumor load of the cfDNA, the proportion of the number of molecules of tDNA to the total number of molecules of cfDNA in the sample. Such tumor load can be used to monitor cancer progression in a subject or efficacy of a cancer therapy administered to a subject.

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.

The present invention relates to gene methylation analysis methods, products, and uses. A DNA methylation analysis method is provided, comprising: 1) simultaneously contacting a biological sample containing DNA with a carrier capable of adsorbing nucleic acids and a lysis solution to enrich the DNA on the carrier; 2) directly contacting the DNA-adsorbed carrier obtained in step 1) with a conversion reagent to convert at least one unmethylated cytosine base in the DNA enriched on the carrier to uracil or another base different from cytosine that is detectable by hybridization; and 3) treating the mixed solution obtained in step 2) with a binding solution to re-enrich the converted DNA on the carrier. The present invention also provides corresponding gene methylation detection methods, kits, and uses.

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.

A methylation data processing and analysis method and platform, a storage medium, and a program product. The method comprises: receiving a plurality of pieces of sample information, and generating a task script on the basis of the received sample information, wherein the plurality of pieces of sample information comprises sample queue information, queue comparison information, and sample methylation sequencing data, the sample queue information comprises a sample and a queue to which the sample belongs, the queue comparison information comprises one or more groups of queues to be compared, and one group of queues comprise two queues; on the basis of the generated task script, performing data processing and data analysis, wherein 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 table on the basis of the results of the data processing and the data analysis; and outputting an interactive report on the basis of the generated graph and / or table.

The invention discloses a preparation method of Bupleurum marginatum polysaccharide (BMP-1), and relates to a process method for extracting, separating and purifying plant polysaccharide. The method comprises the following steps: firstly, obtaining a crude extract from bupleurum chinense through a petroleum ether, 90% ethanol and hot water reflux extraction method; then, deproteinizing and decolorizing the extract, and removing impurities; then, carrying out primary separation by adopting DEAE-52 cellulose column chromatography so as to enrich polysaccharide components; and finally, carrying out further purification by using Sephadex G-200 gel, so as to obtain the high-purity Bupleurum marginatum polysaccharide BMP-1. Further, methylation analysis is combined with a gas chromatography-mass spectrometry method, and it is shown that a main chain structure in the bupleurum marginatum polysaccharide contains fragments alpha-D-GalpA-6OMe-(1-> 4)-beta-D-Glcp-(1->, alpha-D-Galp-(1-> 4)-alpha-D-Galp-(1-> and-> 4)-alpha-L-Rhap-(1-> 3)-alpha-L-Rhap-(1->. In-vitro DPPH, ABTS and hydroxyl radical scavenging activity results show that the Bupleurum marginatum polysaccharide BMP-1 has certain antioxidant activity.

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.