116 results about "Methylation Site" 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.

The invention belongs to the technical field of bioinformatics and deep learning, and particularly relates to a DNA methylation site prediction method, system and device and an electronic medium, and the method comprises the following steps: respectively coding single bases in a DNA sequence into four molecular fingerprints, and constructing each base into a molecular map structure; performing high-order feature extraction on the four molecular fingerprints through a multi-layer perceptron to generate molecular fingerprint features; modeling the molecular graph structure by adopting a multi-head graph attention network, calculating and normalizing attention scores among nodes, carrying out weighted summation on neighbor node features, and carrying out multi-head attention fusion to generate molecular graph features; splicing the molecular fingerprint features and molecular map features, and inputting the spliced molecular fingerprint features and molecular map features into a deep convolution gated channel attention module to generate fused features; and obtaining a prediction probability of the fused features, and judging whether the features are methylation sites or not according to the prediction probability. According to the invention, the identification capability of methylation sites can be improved.

A method for detecting a methylated genomic locus is provided. In certain embodiments, the method comprises: a) treating a nucleic acid sample that contains both unmethylated and methylated copies of a genomic locus with an agent that modifies cytosine to uracil to produce a treated nucleic acid; b) amplifying a product from the treated nucleic acid using a first primer and a second primer, wherein the first primer hybridizes to a site in the locus that contain methylcytosines and the amplifying preferentially amplifies the methylated copies of the genomic locus, to produce an amplified sample; and c) detecting the presence of amplified methylated copies of the genomic locus in the amplified sample using a flap assay that employs an invasive oligonucleotide having a 3′ terminal G or C nucleotide that corresponds to a site of methylation in the genomic locus.

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.

A method, apparatus, storage medium, and program product for tracing the source of disease-affected tissues or organs, the tracing method comprising: acquiring methylation data of multiple tissues or organs, wherein the methylation data of the tissues or organs are methylation data of healthy tissues or organs; establishing an average methylation rate matrix based on the methylation data of multiple tissues or organs, wherein the average methylation rate matrix includes the average methylation rate of each tissue or organ at multiple methylation sites or methylation regions; determining specific methylation sites or specific methylation regions based on the average methylation rate matrix; acquiring methylation data of a sample to be traced; and performing tracing based on the average methylation rate of multiple tissues or organs at the specific methylation sites or specific methylation regions and the methylation data of the sample to be traced.

The application belongs to the technical field of molecular biology and medicine, and discloses a methylation marker for detecting the benignity and malignancy of thyroid nodules and an application. 780 new methylation sites are identified, 273 tumor occurrence and development related genes are associated, and the Fc gamma R-mediated phagocytosis signal pathway is involved. The methylation marker for detecting the benignity and malignancy of thyroid nodules comprises multiple genes and multiple methylation sites. The methylation level of multiple genes and multiple sites is detected, the problem of low and unstable methylation signal of single gene or single site is overcome, and thus the sensitivity and specificity of detection are improved.

The invention relates to a tumor-related DNA methylation marker combination, which is selected from at least one of the following: a target sequence as shown in SEQ ID NO: 1-SEQ ID NO: 10, a nucleic acid fragment with the length of at least 15 oligonucleotides or a complementary nucleic acid fragment thereof, and the nucleic acid fragment comprises at least one methylation site indicated by CG. The invention also relates to a detection kit for the methylation marker combination. According to the invention, the combination of the co-methylation states of a plurality of specific methylation regions is used for distinguishing and analyzing the occurrence of tumors, especially kidney cancer, the specific methylation combination has high sensitivity for distinguishing the occurrence of kidney cancer, and the detection method is simple, convenient and feasible. The primer pair combination of the kit overcomes the defect of false positive caused by detection mismatch of a single methylation site in the aspect of primer sequence design, and the interaction between a plurality of methylation biomarker primers and probe pair combinations is considered.

The present invention relates to a method of evaluating the effect of at least one test component of an animal feed on at least the performance and / or the overall health of a test animal consuming an animal feed having the test component, the method comprising the steps of: (a) determining a test methylation profile of one or more preselected methylation sites within the DNA of the test animal; (b) comparing the test methylation profile from (a) to at least one control methylation profile from a control animal consuming animal feed free of the test component belonging to the same biologic classification unit as the test animal; and wherein the results of (a) are used to determine the performance and / or overall health of the test animal; and (c) comparing the test methylation profile from (a) to (i) a first reference methylation profile from a control animal having good performance and / or overall health belonging to the same biologic classification unit as the test animal; and / or (ii) a second reference methylation profile derived from a control animal having poor performance and / or overall health, belonging to the same bioclassification unit as the test animal; and wherein a significant similarity of the test methylation profile of (a) compared to the control methylation profile indicates that the test component has no effect on the performance and / or overall health of the test animal; and wherein a significant difference in the test methylation profile of (a) compared to the control methylation profile indicates that the test component has an effect on the performance and / or overall health of the test animal; and wherein a significant similarity of the test methylation profile of (a) to the first reference methylation profile and / or a difference of the test methylation profile of (a) to the second reference methylation profile indicates that the test animal has good performance and / or overall health as a control cell; and / or wherein the difference in the test methylation profile of (a) compared to the first reference methylation profile and / or the significant similarity of the test methylation profile of (a) to the second reference methylation profile indicates that the test animal has poor performance and / or overall health as a control animal; and wherein the test animal is selected from livestock or poultry.

Systems and methods of identifying methylation patterns discriminating or indicating a cancer condition are provided. First and second datasets are obtained. Each dataset comprises a plurality of fragment methylation patterns determined by methylation sequencing of nucleic acids obtained from a first or second set of subjects and comprising a methylation state of each CpG site in a corresponding plurality of CpG sites. Each plurality of subjects has a respective first or second state of the cancer condition. First and second interval maps are generated for each respective dataset, each comprising a plurality of nodes characterized by a start methylation site, an end methylation site, a representation of each different fragment methylation pattern and a count of fragments. The first and second interval maps are scanned for qualifying methylation patterns within a predetermined range of CpG sites, satisfying one or more selection criteria, thereby identifying methylation patterns discriminating a cancer condition.

The application discloses a kind of based on DNA methylation's construction method of biological age prediction model, the application is downloaded from GEO data website, derived from Chinese population, contains calendar age data, whole blood sample 450k methylation chip data, by the method of elastic network combined bootstrap, 31 methylation sites of modeling candidate are screened, multiple linear regression, support vector machine, random forest and gradient boosting regression tree are used to carry out preliminary construction and evaluation of model, then further filter methylation sites using full subset regression, obtain methylation age prediction model based on 18 methylation sites.Finally, using any provincial team natural population data, methylation age prediction model is optimized, and finally the biological age prediction model based on 18 methylation sites is obtained.The model is suitable for Chinese population, the number of methylation sites contained is less, is not affected by blood cell components, and the prediction accuracy is good.

The application discloses a DNA methylation site marker for detecting hepatocellular carcinoma, a multiplex dPCR kit and a diagnostic model construction method. The DNA methylation site marker comprises cg02829688, cg13080379, cg03760839, cg10703826, cg12664119, cg16990168 and cg23371746 sites. The application designs a primer probe group for the above sites, constructs a multiplex dPCR kit of a double reaction system, realizes quantification of target DNA methylation sites, takes the methylation levels of the 7 sites as characteristic variables, adopts an XGBoost algorithm and / or an LR algorithm to construct a diagnostic model. Experimental verification shows that the model can effectively distinguish hepatocellular carcinoma patients from liver cirrhosis, chronic hepatitis B, metabolic dysfunction-related fatty liver disease patients and healthy individuals, especially shows good efficiency in auxiliary diagnosis of early hepatocellular carcinoma, and provides a new technical scheme for clinical diagnosis and screening of hepatocellular carcinoma.

This invention relates to the field of biotechnology, and in particular to a primer-probe combination for detecting methylation sites in cancer and its applications. This invention is the first to discover that abnormal methylation at specific sites of the TRIB3 gene is significantly associated with the occurrence and development of colorectal cancer, and abnormal methylation at specific sites of the MAPT gene is significantly associated with the occurrence and development of gastric cancer. This correlation has not been publicly reported in the prior art, possessing novelty and significant clinical application value. The primer-probe combination provided by this invention is used to detect the methylation status of the TRIB3 gene or the MAPT gene in a sample. Specifically, when the primer-probe combination is used to detect the methylation level at specific sites of the TRIB3 gene, it can be used for the auxiliary diagnosis, early screening, or risk assessment of colorectal cancer; when the primer-probe combination is used to detect the methylation level at specific sites of the MAPT gene, it can be used for the auxiliary diagnosis, early screening, or risk assessment of gastric cancer.

This invention provides an esophageal cancer diagnostic kit based on multi-gene methylation level detection. It detects the methylation status of esophageal cancer gene methylation sites, including ZNF154, RNF126, C2ORF27A, OTOP2, TM4SF19, and P16, thereby enabling early screening of esophageal cancer samples. Furthermore, this kit, combined with digital PCR, offers advantages such as absolute quantification, high batch-to-batch stability, and high sensitivity, accurately distinguishing the relationship between sample gene methylation and esophageal cancer. Simultaneously, it employs fluorescently labeled probes for genotyping, demonstrating high specificity and applicability to esophageal cancer patients at different stages. Therefore, it provides a convenient, rapid, and accurate detection method for early screening, diagnosis, and prognosis of esophageal cancer, possessing significant clinical value.

The invention provides target sections S6-1, S6-2 and S6-3 for identifying multiple cancer species and application of the target sections S6-1, S6-2 and S6-3. A group of unprecedented gene methylation sites are successfully identified through an innovative screening strategy and large-scale cross-cancer omics data analysis. The invention also comprises a detection reagent (such as a primer) and a kit for detecting the target segment of the genome. The methylation degrees of the target segment between a plurality of cancer tissues and para-carcinoma tissues have significant differences, so that the subject can be judged to belong to tumor high-risk groups. The cancer tissue and para-carcinoma tissue differential methylation state presented by the target segment can be widely applied to various different types of cancers.

The invention relates to a methylation site marker for assisting in early diagnosis of esophageal squamous cell carcinoma and application of the methylation site marker, and belongs to the technical field of biomedicine. The methylation site marker is one or a combination of human peripheral blood mononuclear cell methylation sites cg05064044, cg03395511 and cg21548813, and the nucleotide sequence of the methylation site marker is as shown in SEQ ID NO. 1-3. According to the present invention, the methylation chip detection results show that the methylation levels of the cg05064044, the cg03395511 and the cg21548813 in the peripheral blood mononuclear cells of the esophageal squamous cell carcinoma patient are significantly increased compared to the health control group; the methylation levels of cg05064044, cg03395511 and cg21548813 sites in PBMC of esophageal squamous cell carcinoma patients in a training queue and a verification queue are all obviously higher than those of a healthy control group through further analysis. Finally, through ROC curve analysis, it is determined that the three methylation sites cg05064044, cg03395511 and cg21548813 have good specificity and sensitivity, have high diagnosis efficiency when being independently or jointly used for esophageal squamous cell carcinoma diagnosis and can be used as potential molecular markers for esophageal squamous cell carcinoma diagnosis.

The invention discloses a methylation marker combination for detecting gastric cancer, a corresponding primer probe combination, a kit and application thereof. The methylation marker combination related to the gastric cancer comprises a CpG methylation site cg08630279 of a ZNF569 gene, a CpG methylation site cg24773720 of a GHR gene and a CpG methylation site cg20622089 of a CNR1 gene, wherein the CpG methylation site cg08630279 of the ZNF569 gene, the CpG methylation site cg24773720 of the GHR gene and the CpG methylation site The methylation levels of the ZNF569, GHR and CNR1 sites are related to gastric cancer staging, and the ZNF569, GHR and CNR1 sites can be used as high-specificity markers for early screening of gastric cancer. A primer probe combination for detecting the marker combination comprises specific upstream primers, downstream primers and probes aiming at methylation sites of all markers. The kit comprises a primer probe combination, and also comprises a positive control, a negative control and a quality control reagent. Three-site combined detection is adopted, the detection sensitivity in a gastric cancer blood sample reaches 91% or above, the specificity reaches up to 100%, the kit is used for auxiliary screening, detection or molecular analysis related to gastric cancer and precancerous lesions of the gastric cancer, and a technical scheme high in sensitivity, high in specificity and good in repeatability is provided for clinical detection.

A method of determining percentages of twelve blood cell subtypes in a blood specimen, includes steps of: (a) obtaining genomic DNA from the blood specimen of a human subject, (b) observing unmethylated CG loci, in the genomic DNA of the human subject, wherein said observing includes performing a bisulfate conversion process on the genomic DNA of the human subject so that cytosine residues in the genomic DNA of the human subject are transformed to uracil, while 5-methylcytosine residues in the genomic DNA of the human subject are not transformed to uracil, (c) comparing the unmethylated CG loci observed in (b) to unmethylated CG loci observed in genomic DNA collected from a reference group of human individuals and (d) correlating the unmethylated CG loci observed in (b) with the unmethylated CG loci observed in the reference group of human individuals to determine the percentage of the twelve blood cell subtypes in the blood specimen.

The invention relates to the technical field of biology, and discloses a multiplex fluorescent PCR detection system and application thereof, the multiplex fluorescent PCR detection system comprises 22 primer pairs, and primer sequences aiming at 22 sites are disclosed and are respectively used for simultaneously amplifying 15 detection sites and 7 internal reference sites. The multiplex fluorescent PCR detection system provided by the invention realizes effective detection of a plurality of methylation sites by combining capillary electrophoresis detection, performs high-sensitivity and specific detection on colorectal cancer by combining a corresponding detection method and a result judgment method, and has important clinical application value and wide market prospect.

The invention discloses a screening method of skeletal muscle senescence markers, clock construction and a kit, and belongs to the technical field of biomedical engineering. The method comprises the following steps: acquiring multi-modal biomarker data of an individual, wherein the multi-modal biomarker data comprises an inflammatory marker, a metabolic marker, a hormone marker and a muscle function marker; inputting the data into a trained skeletal muscle biological age prediction model to obtain skeletal muscle biological age (SMBA); based on the skeletal muscle biological age (SMBA), screening out a specific methylation site set related to the skeletal muscle senescence state from the methylation sites of the whole genome; constructing a methylation aging clock model by using methylation data of the site set; and finally, accurately predicting and evaluating the skeletal muscle senescence state of an individual by using the model. According to the invention, conversion from multi-modal clinical indexes to specific single-dimensional molecular markers is realized, and the constructed senescence clock model and derivative products can be used for personalized evaluation and early risk early warning of skeletal muscle senescence.

Provided are a method and a combination for one-tube simultaneous detection of tumor-specific gene mutation and methylation, and the use thereof. The method comprises searching a database to select mutation and methylation sites of a cancer driver gene and a cancer suppressor gene, synthesizing capture probes correspondingly paired with a target interval, performing hybrid capture on an amplification product of a sample treated with a restriction endonuclease by using a probe set comprising tumor-specific gene mutation and methylation capture probes, constructing a high-throughput sequencing library containing a target region, and performing high-throughput sequencing to obtain the sequence of a target fragment, so as to obtain the results of methylation, point mutations and indel variation of a cancer-associated gene. The provided method enables one-tube simultaneous detection of mutation and methylation states of a cancer-associated gene in one assay, requires a low content of a gene to be detected, can be used for methylation and mutation detection of a tumor-specific DNA, and has low detection costs and high efficiency.

Provided herein are methods and compositions for an epigenetic clock comprising differentiation-independent methylation sites to asses biological age of a human subject.

The application discloses a methylation marker combination for detecting early gastric cancer and application thereof. The marker combination comprises 146 methylation sites of 11 DNA regions and a transformation rate control marker region, and the methylation levels of the target regions are significantly different between early gastric cancer patients and healthy people. The kit of the application contains reagents for detecting the methylation degree of the above sites, and supports various high-throughput sequencing methods. The detection system adopts a logistic regression model to calculate a prediction value, multiplies the average methylation rate of each region by a corresponding weight coefficient, adds them together, and compares the sum with a threshold value to make a positive judgment. The application realizes high sensitivity and high specificity for non-invasive early detection, is particularly suitable for non-invasive screening of plasma free DNA samples, can effectively improve the survival rate of gastric cancer patients, can significantly reduce medical expenses, and has a wide clinical application and industrial utilization prospect.

The embodiments of the present specification provide a DNA methylation site combination as a bladder cancer marker, a detection reagent of the DNA methylation site combination, and a use of the DNA methylation site combination or the detection reagent thereof in the preparation of a kit for bladder cancer screening, bladder cancer risk prediction, evaluation of bladder cancer treatment effect, and / or screening of bladder cancer treatment drugs. The DNA methylation site combination described in the present specification has good sensitivity and specificity, shows significant differences in methylation levels between known bladder cancer patients and non-bladder cancer patients, and can be used as a marker for bladder screening, bladder cancer risk prediction, etc., and can also be used to design diagnostic reagents or kits. The embodiments of the present specification also provide devices and kits for bladder cancer screening or bladder cancer risk prediction.

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.

This application relates to the field of gene detection technology, and in particular to the application, kit, and method of DNA methylation site in the diagnosis of type 2 diabetes. This application demonstrates through clinical testing that the methylation site cg06087988 shows significant differences between patients with type 2 diabetes and those without, and can be used for the diagnosis / prediction of type 2 diabetes.

The invention discloses a method and a system for predicting the sensitivity of a patient to a calcium preparation based on 28 methylation sites. According to the invention, a risk scoring formula Marker of the sensitive subtype of the calcium preparation is constructed according to the 28 methylation markers. Researches show that the method can accurately and conveniently predict the calcium preparation sensitive subtype of the to-be-detected object and guide a medication scheme by performing methylation site sequencing on the to-be-detected object and calculating the Marker value, and has an application prospect.

The invention belongs to the technical field of gene detection, and discloses application of EVX2 gene methylation in evaluation of cervical carcinoma risk of high-risk HPV infected persons. The biomarker for evaluating the cervical cancer risk of the high-risk HPV infected person is a methylation site of an EVX2 gene. According to the invention, detection of the methylation level of the EVX2 gene is applied to evaluation of cervical cancer risk of high-risk HPV infected people, and the kit can be used for screening and shunting cervical HSIL and cervical cancer and is beneficial to early intervention of high-risk HPV infected people.

The invention relates to the technical field of biology, in particular to a method and a reagent for directly detecting gene methylation based on a Cas12a system and application of the method and the reagent. According to the method for directly detecting the gene methylation of the gene in the Cas12a system, disclosed by the invention, a Cas12a protein and specific Multiplex-gRNAs of a target gene are combined in a CRISPR-Cas12a buffer system to form a compound, the target gene is specifically recognized, the trans-cleavage activity of the Cas12a protein is activated, a fluorescence-labeled reporter probe is cleaved to generate a fluorescence signal, and the methylation of the gene is directly detected in the CRISPR-Cas12a buffer system. Qualitative / quantitative analysis of target gene methylation is carried out by detecting the intensity of a fluorescence signal generated by a Cas12a protein trans-cleavage fluorescence labeled reporter probe. The method has the advantages that hydrosulfite pretreatment and amplification are not needed, and the complex process and sensitivity limitation of a traditional methylation detection technology are remarkably broken through. The methylation state of the target DNA can be quickly distinguished, and the result can be read within 30 minutes in the whole detection process. Compared with the prior art, the method disclosed by the invention has the characteristics of simplicity and convenience in operation, no amplification pollution risk, low requirement on sample concentration and the like, and is particularly suitable for rapid detection of methylation sites in cfDNA samples from clinical plasma and auxiliary diagnosis of cancers.

The invention provides a gene composition for screening or diagnosing Parkinson's syndrome and application of the gene composition, and belongs to the technical field of biology. The invention provides a set of seven genes in brain tissue, a set of eight genes in cerebrospinal fluid, a set of ten genes in blood and a set of eight DNA methylation sites in blood, and at least one of the sets can be used as a marker for screening or diagnosing Parkinson's syndrome. Meanwhile, based on the genotype, expression level or methylation level data of the marker, a model for diagnosing the Parkinson's syndrome is constructed by combining a maximum logic intelligent classifier, and the subtype of the Parkinson's syndrome is determined. The method does not depend on a p value and multiple inspection correction, but establishes the model by searching the minimum and optimal gene combinations capable of perfectly distinguishing cases and contrasts, thereby fundamentally avoiding the problems of overfitting and insufficient statistical efficacy.

The application provides a Septin9 methylation detection composition and application thereof, and the composition comprises a methylation-dependent restriction enzyme, a capture oligonucleotide, a universal primer and a Septin9 methylation-specific primer; the capture oligonucleotide comprises a first universal sequence, a folding sequence and a binding capture sequence from 5' end to 3' end in sequence; the folding sequence is at least partially identical to a 5' end sequence of a Septin9 methylation site after the methylation-dependent restriction enzyme is cut; and the binding capture sequence is specifically bound to a fragment region where the detected Septin9 methylation site is located. The application is based on a methylation-dependent restriction enzyme and a universal primer fluorescence quantitative PCR technology, does not need bisulfite conversion, and realizes accurate and specific Septin9 methylation detection.