36 results about "Differential Methylation" patented technology

The invention discloses a sperm genome methylation detection method for safety evaluation of biological breeding crops by using primates and application, and relates to the technical field of safety evaluation of crops, the sperm genome methylation detection method comprises the following steps: dividing non-human primates into three groups, collecting sperms after long-term feeding, and extracting DNA (Deoxyribose Nucleic Acid); carrying out whole genome sequencing and quality control after bisulfite treatment; the epigenetic safety of crops is comprehensively evaluated by analyzing the methylation level of a whole genome and a functional region and functional enrichment of a differential methylation region and related genes thereof; according to the sperm genome methylation detection method for evaluating the safety of the biologically bred crops by utilizing the primates and the application, by utilizing a high-resolution WGBS technology, subtle epigenetic changes which are difficult to find by traditional toxicology can be detected, and the sperm genome methylation detection method has important significance in cross-generation reproduction effect evaluation, and has a wide application prospect. A food safety evaluation system can be perfected, and a more scientific and reliable safety interpretation basis can be established.

The present application relates to a kind of sgRNA targeting Plagl1 gene DMR, epigenetic editing system and its application.Specifically, the present application provides sgRNA targeting Plagl1 gene differential methylation region, which forms epigenetic editing system with dCas9-Tet1-CD fusion protein.The system is loaded in injectable type light-cured silk fibroin hydrogel, the expression of Plagl1 gene in periosteum stem / progenitor cells is accurately activated by targeted demethylation modification, thereby promoting osteogenic differentiation.The present application combines epigenetic regulation with biomaterial delivery, and provides a safe, efficient new strategy for jaw bone defect regeneration and repair.

Low background regions (LBRs) refer to genomic regions comprising one or more CpG sites that are differentially methylated in cancer and non-cancer samples. Disclose methods involve identifying LBRs comprising one or more CpG sites whose methylation statuses sufficiently distinguish between samples that contain a presence of a cancer signature and samples that do not contain a presence of a cancer signature. LBRs enable improved detection of presence or absence of cancer signatures while using smaller samples and fewer consumable reagents.

It has been discovered that differential methylation in DNA can be used to distinguish between malignant and non-malignant skin lesions. Seven genes, 3 that are hypermethylated in melanoma, 1 that is hypermethylated in melanocytes and remains methylated in melanoma, and 3 that are hypermethylated in all tissues are provided as biomarkers. The panel demonstrates a 93% sensitivity, 97% specificity and an AUC of 95% in distinguishing between melanoma and benign lesions. Thus provided herein are melanoma biomarkers and methods of detecting them and using them to diagnose and guide treatment of subjects with the same, and monitor melanoma tumor dynamics during and after treatment.

The invention discloses a biological age assessment method and system based on full life cycle DNA methylation and application, and belongs to the technical field of bioinformatics. The method comprises the following steps: firstly, carrying out quality control and standardization treatment on obtained original DNA methylation data; then, screening differential methylation sites significantly related to calendar age as features; then, by taking calendar age as a target variable, constructing a regression model by adopting a LightGBM gradient lifting framework to obtain a methylated clock model; then, predicting the DNA methylation age of the individual by using the model, and calculating an epigenetic age acceleration value based on the deviation between the DNA methylation age and the calendar age; and finally, carrying out correlation analysis on the age acceleration value and health or physiological indexes of different life stages, so as to evaluate the biological aging state of the individual and predict related health risks. The method covers the whole life cycle, is suitable for Chinese population, and can provide an effective tool for clinical disease risk prediction, health management and anti-aging intervention effect evaluation.

The present disclosure includes a method comprising: (a) obtaining free DNA (cfDNA) from a sample from a subject; (b) selectively enriching a subset of the cfDNA or derivatives thereof from (a) having one or more target regions to obtain an enriched DNA, wherein the target regions are differentially methylated in cancer; (c) sequencing the enriched DNA from (b) to obtain a sequence read; and (d) dividing a plurality of said sequence reads into two or more groups based on the methylation status thereof, and determining the fragment length distribution of said sequence reads in at least one of said groups.

The present application relates to the technical field of medical detection, and particularly relates to a marker combination, a primer probe combination, a kit and application for detecting multiple subtypes of ovarian cancer and borderline ovarian tumors. The marker combination comprises at least 3 of the following differential methylation regions: a differential methylation region of IFFO1, a differential methylation region of TFAP2E-AS1, a differential methylation region of WNT6, and a differential methylation region of AC104801.1. The present application can comprehensively cover the detection of multiple subtypes of ovarian cancer and borderline ovarian tumors, is suitable for liquid biopsy, and has high sensitivity and high specificity.

The invention discloses a DNA methylation regulatory gene identification method related to formation of cold resistance of Brassica campestris L. and application of the DNA methylation regulatory gene identification method. The method belongs to the technical field of winter rape cold resistance epigenetic regulation mechanism analysis. According to the invention, a methylation sensitive amplification polymorphism technology is utilized, four Chinese cabbage type winter rape materials with large cold resistance difference after the same variety is domesticated in different breeding environments are selected as research objects, the change rule of DNA methylation after treatment at 4 DEG C for 24 hours and recovery growth for 2 days is analyzed, and finally differential methylation gene expression is verified by utilizing a qPCR technology. The invention provides a reference method for DNA methylation research of plants under adversity stress, and compared with other epimics research such as DNA methylation, the method is simple and convenient to operate and low in cost, does not need high-throughput sequencing, and only needs one-generation sequencing. The candidate gene identified by the invention provides a genetic basis for explaining a cold resistance evolution molecular mechanism of Brassica campestris L. and guiding cold resistance improvement of northern winter rapes.

The application belongs to the field of aquatic molecular breeding and epigenetic marker development, and particularly relates to a group of DNA methylation markers related to loss of Chinese mitten crab in summer extreme high temperature and application thereof in breeding. The methylation markers include 8 differentially methylated cytosine sites located on the reference genome ASM2467909v1, adjacent to LOC126983793 (ADCY9), LOC126997354 (UNC79), LOC126998428 (UBN1), LOC126997943 (IFT52), LOC126991093 (ACO2), LOC126986070, LOC127001126 and LOC126997895 respectively. Among them, the high temperature damage group shows high methylation at part of the sites, low methylation at part of the sites, and abnormal expression of the corresponding adjacent genes. The above markers can be used for molecular detection and assisted selection of heat tolerance, survival rate maintenance ability, large-size crab output stability and high temperature damage risk of Chinese mitten crab.

For various purposes, a nucleosome signal pattern using fragmentation at a location around a target site is provided. For example, a nucleosome signal pattern may be used to determine methylation levels of a target site (e.g., a CpG site). The signal may be associated with a nucleosome pattern of a cfDNA molecule within a genomic region that is differentially methylated in a target tissue type by having different methylation levels (or levels, e.g., as a pattern) relative to one or more other tissue types (e.g., blood cells). The nucleosome signal pattern can be compared to one or more reference patterns with known methylation levels. Another exemplary method may determine a lesion level in a subject. Another example may determine a proportional concentration of DNA for a particular tissue type.

The application discloses a methylation biomarker for diagnosing lung cancer and application thereof, and belongs to the technical field of biomedical detection. The methylation biomarker is composed of 16 differential methylation regions (DMRs), and specific differential methylation regions are shown in Table 2. The application also provides products and devices for diagnosing lung cancer based on the 16 differential methylation regions, and the lung cancer diagnosis has the advantages of high sensitivity and strong specificity, and has important application value for clinical lung cancer diagnosis.

The present invention belongs to the field of bio-pharmaceuticals. Disclosed are a differentially methylated region of an ADHFE1 gene, a detection primer, a probe, a kit, and use of the differentially methylated region in the detection of colorectal cancer or precancerous lesions of colorectal cancer and in the evaluation of prognostic risks of colorectal cancer patients. The differentially methylated region is chr8:67344198-67345563. The differentially methylated region of the present invention can be used for effectively detecting colorectal cancer or precancerous lesions of colorectal cancer, or for evaluating prognostic risks of colorectal cancer patients.

Methylation arrays and a method of diagnosing or treating a cancer in a subject using differential methylation levels. In one implementation, the method includes the steps of obtaining a cfDNA sample from a subject, probing the cfDNA sample with a plurality of CpG probes, and comparing information from the probed cfDNA sample to a methylation array. The methylation arrays are used to determine a differential methylation level at each of a plurality of limited CpG sites within the cfDNA sample. The plurality of limited CpG sites correspond to the plurality of CpG probes, and two or more of the CpG sites are located on chromosome (2), two or more are located on chromosome (6), and two or more are located on chromosome (16).

The invention discloses a methylation signal detection method, device and equipment based on free DNA sequencing fragments in plasma and a storage medium, and relates to the technical field of non-invasive disease detection.The method comprises the steps that for each free DNA methylation sequencing fragment, the average methylation value of all CpG loci contained in the free DNA methylation sequencing fragment is calculated and discretized into the preset methylation level; carrying out normalization processing on methylation levels corresponding to methylation sequencing fragments in the preset genome region to obtain methylation state distribution characteristics; and screening out significant differential methylation state distribution characteristics, inputting the significant differential methylation state distribution characteristics into an XGBoost classifier, and outputting to obtain a plasma free DNA methylation characteristic score. According to the method, fragment hierarchical coding is adopted, the continuous methylation value of a single fragment is discretized to a limited level, and the distribution of the continuous methylation value in a genome region is counted, so that weak but specific disease signals are effectively amplified and can be detected from a large number of normal backgrounds.

The application provides a human genome T5 series fragment for multi-cancer identification and use thereof. A set of human genome differential methylation regions for multi-cancer identification, referred to as T5 series fragments (T5-1, T5-2, T5-3, T5-4, T5-5, T5-6, T5-7, T5-8) is disclosed. On this basis, the application provides a multi-cancer methylation technology which can cover more than 20 high-incidence cancer types, has high sensitivity (≥90%) and high specificity (≤5% false positive rate), and can realize rapid and micro-sample detection.

The application discloses a biological age evaluation method and system based on whole life cycle DNA methylation and application, and belongs to the technical field of bioinformatics. First, the obtained original DNA methylation data is subjected to quality control and standardization processing; then, differential methylation sites significantly related to calendar age are screened as features; next, taking calendar age as a target variable, a regression model is constructed by adopting a LightGBM gradient boosting framework to obtain a methylation clock model; subsequently, the model is used to predict the DNA methylation age of an individual, and an epigenetic age acceleration value is calculated based on the deviation of the DNA methylation age from the calendar age; finally, the age acceleration value is subjected to correlation analysis with health or physiological indexes in different life stages, so as to evaluate the biological aging state of the individual and predict related health risks. The application covers the whole life cycle, is suitable for Chinese population, and can provide an effective tool for clinical disease risk prediction, health management and anti-aging intervention effect evaluation.

Systems and methods for detecting initiating methylation changes in biological samples are disclosed. One method may include: receiving genomic data associated with a sample; generating a feature value and dataset for the sample and a reference sample; comparing the sample dataset to a reference dataset to determine whether a differentially methylated region is present. The systems and methods may compare the datasets associated feature sets for different samples to determine whether change in datasets over feature values meet a threshold for an initiating methylation change. Other aspects are described and claimed.

Provided herein are methods related to analyzing DNA in a sample from a subject, comprising measuring in the sample or a subsample thereof a level of methylation of one or more variant differentially methylated regions (DMRs) independently of one or more corresponding DMRs, wherein the one or more variant DMRs comprise a somatic mutation that the one or more corresponding DMRs do not comprise.

The application relates to the technical field of melanoma prognosis, and provides a construction method and a verification method of a melanoma prognosis model based on a lactation gene methylation feature. The DNA methylation data of a cancer genome atlas database is taken as a training set, and the DNA methylation data of a gene expression comprehensive database is taken as a verification set, so that the lactation-related gene methylation feature prognosis marker model of melanoma constructed has good external applicability. A methylation site pair matrix is constructed through the relative methylation order relationship of the methylation sites, so that the batch effect between different data sets is effectively avoided, and excellent robustness and clinical applicability are achieved. The methylation sites corresponding to the lactation-related gene set are taken as anchor points to perform hierarchical clustering and differential methylation site screening, functional sites related to prognosis are screened out, the reliability of the constructed prognosis marker model is improved, and the accuracy of prognosis prediction is improved.

Provided are a combination of differentially methylated regions, a kit, and use thereof. The combination of differentially methylated regions comprises the following differentially methylated regions: (1) chr8: 145106171-145107467 and (2) chr8:67344198-67345563. The combination of differentially methylated regions can be used for effective detection of colorectal cancer or precancerous lesions of colorectal cancer, or for evaluating prognostic risks of colorectal cancer patients, exhibiting high sensitivity and specificity.

Described herein are methods for the detection of molecular residual disease (MRD) and cancer by analysis of cell‑free nucleic acids. The invention provides a capture panel comprising target‑specific probes that are directed to one or more genomic regions encompassing a spectrum of variant types, namely structural variants (SV), large insertions / deletions, phased single‑nucleotide variants, small insertions / deletions, multi‑nucleotide variants and single‑nucleotide variants. By contacting a nucleic‑acid sample derived from a subject with the probe panel, the method enriches variant‑bearing molecules and subjects the captured set to sequencing. Disease presence or the likelihood thereof is determined on the basis of each target region, optionally integrating epigenetic information (e.g., differential methylation) obtained from a tumour biopsy. The probe design is adapted to technical noise, allocating higher probe concentrations to low‑noise, high‑complexity variants, thereby reducing reliance on molecular barcodes, lowering required read depth and improving analytical sensitivity for both fixed‑panel and patient‑specific MRD assays.

This invention discloses an analytical method integrating small RNA and DNA methylmics to study crop continuous cropping adaptation, comprising the following steps: collecting wheat samples under W1 and WM conditions; identifying 21-24nt-siRNA clusters under W1 and WM conditions; performing differential expression analysis on 24-nt siRNA clusters; for differentially expressed 24-nt siRNAs, screening for clusters overlapping with differentially methylated regions (DMRs), retaining only pairs with consistent regulatory patterns, defining them as RdDM action sites, and then predicting siRNA target genes. This analytical method can systematically identify differentially expressed siRNAs under continuous cropping conditions; combine whole-genome methylation data (WGBS) to analyze the association between siRNAs and differentially methylated regions (DMRs); identify key RdDM target genes and their functional pathways; and construct a multi-level regulatory network of siRNA–DNA methylation–gene expression, providing a theoretical basis and application foundation for crop continuous cropping adaptation and molecular improvement.

Provided herein are methods of analyzing DNA comprising cell or tissue type-specific epigenetically variable regions, such as differentially methylated regions. The methods can comprise sequencing the DNA, determining levels of a plurality of epigenetic target regions of an epigenetic target region set of DNA, determining whether at least one of the plurality of epigenetic target regions overlaps a copy number variant, and adjusting the level of any epigenetic target region that overlaps a copy number variant to compensate for the copy number variant. Provided herein are also methods for determining the likelihood that a subject has a disease or condition, such as cancer.

This invention discloses a gene composition, kit, and application for early diagnosis of renal cell carcinoma, relating to the field of molecular diagnostic technology. The gene composition consists of the PLIN2 gene, SLC25A25 gene, PITX1 gene, and SOX1 gene. The differential methylation site of the PLIN2 gene is cg13990947, the differential methylation site of the SLC25A25 gene is cg14294859, the differential methylation site of the PITX1 gene is cg02037307, and the differential methylation site of the SOX1 gene is cg1. 6705627; This invention, by screening four genes (PLIN2, SLC25A25, PITX1, and SOX1) and specific methylation site combinations, can accurately identify two major subtypes of renal cell carcinoma—clear cell and papillary renal cell carcinoma—compared to single-gene detection. The methylation difference between cancerous and normal tissues, Δβ-value, is greater than 0.2, solving the problem of heterogeneous renal cell carcinoma detection. The optimized urine free DNA lysis buffer and bisulfite conversion system improve the nucleic acid extraction and conversion rates. Combined with dedicated methylation-specific primers and probes, it enables non-invasive detection of urine samples.

A method for measuring a fractional concentration of DNA from a first tissue type in a biological sample of a subject, the biological sample comprising cell-free DNA, the method comprises analysing a plurality of cell-free DNA molecules from the biological sample of the subject by (a) determining a genomic position in a reference genome corresponding to at least one end of the cell-free DNA molecule, (b) identifying a first set of CpG sites that all have a first differential methylation for the first tissue type in the reference genome, wherein the first set of CpG sites includes one or more CpG sites, (c) determining a first amount of cell-free DNA molecules ending at one of 0 or -1 position of any one of the first set of CpG sites or alternatively, (c) determining an end sequence motif of at least one end of the cell-free DNA molecule, wherein an end of the cell-free DNA molecule has a first position at an outermost position, a second position that is next to the first position, and a third position that is next to the second position; and (d) determining the fractional concentration of DNA from the first tissue type in the biological sample by comparing the first amount to a calibration value, wherein the calibration value is determined from one or more calibration samples having known fractional concentrations of DNA from the first tissue type.

The application discloses a clustering-based multiple differential methylation region predicted set integration method, which comprises the following steps: dividing a genome into a plurality of non-overlapping genomic blocks; setting a threshold and evaluating the reliability of all predicted sets under the threshold to construct a reliability weight matrix; calculating the weight of each genomic block; and clustering all genomic blocks to obtain a final integrated differential methylation region set. The application also discloses a system for implementing the clustering-based multiple differential methylation region predicted set integration method. The application calculates the weight of the genomic block based on the influence of the method coverage and the methylation difference on the differential methylation region distinguishing capability, improves the reliability of the integrated set, and can provide a more reliable, comprehensive and significant differential methylation region set by reasonably integrating the differential methylation region sets predicted by different methods. Moreover, the application is high in reliability, good in accuracy and objective and scientific.

The disclosure provides methods for identifying genomic loci (e.g., vimentin and / or SqBE18) that are differentially methylated in metaplasias (e.g., Barrett's esophagus) and / or neoplastic cancers (e.g., esophageal cancers). Identification of methylated genomic loci has numerous uses, including for example, to characterize disease risk, to predict responsiveness to therapy, to non-invasively diagnose subjects and to treat subjects determined to have gastrointestinal metaplasias and / or neoplasias.

Provided is a methylation marker for gastric cancer detection. Provided are 28 differentially methylated regions (DMRs) for diagnosing or assisting with the diagnosis of cancer, and an ELMO1 gene and a KCNA3 gene with a better performance are selected from these 28 DMRs as preferred methylation markers for detecting gastric cancer. Provided is an accurate, simple and economical means for the early screening of gastric cancer, which can improve the detection rate of gastric cancer, particularly early gastric cancer, in gastric cancer high-risk populations and populations undergoing routine physical examinations, thereby improving the survival rate of gastric cancer patients, while saving on substantial medical expenses and alleviating the medical burden.

The invention discloses a cancer marker screening method and system combining a co-methylation module and cellular component correlation analysis, and relates to the technical field of bioinformatics, the method comprises the following steps: obtaining DNA methylation sequencing data of a cancer tissue sample group and a control tissue sample group, and preprocessing to generate a methylation matrix; performing differential methylation analysis to obtain differential sites, and forming differential methylation fragments according to an adjacent merging rule; a co-methylation network is constructed based on fragment methylation level correlation, and module characteristic values are obtained through division; and estimating cell components by using the methylation reference spectrum and / or single cell data, screening a target module according to a rule that a module characteristic value is related to a cancer cell ratio and is not related to a non-cancer cell ratio, and outputting a cancer cell specific candidate fragment set. By means of the technical scheme, cell mixing and infiltration interference is inhibited, the specificity and stability of the marker are improved, and cross-queue consistency and typing diagnosis performance are improved.