36 results about "DNA methylation" patented technology

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 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 present disclosure includes, among other things, methods, kits, and systems for determining a status of lung cancer. In various embodiments, the present disclosure relates to the use of one or more histone modifications, chromatin accessibility, binding of one or more transcription factors, and / or DNA methylation as features of a status of lung cancer. In some embodiments, differential modifications and / or differential accessibility are detected and quantified at one or more genomic loci in a biological sample, e.g., cell-free DNA (cfDNA), from a liquid biopsy sample obtained or derived from a subject having lung cancer. In various embodiments, the determined status can be used, e.g., to select a treatment for lung cancer and / or to treat lung cancer.

This invention discloses the application of substances that increase LSH content or activity in improving heterochromatin stability and enhancing the efficacy of cell therapy, belonging to the field of biomedical technology. This invention, through overexpression of LSH in IMR90 fibroblasts and T lymphocytes, successfully achieved for the first time complete inhibition of DNA methylation loss in heterochromatin regions during cell expansion. The innovative research results of this invention strongly demonstrate that the insufficient DNA methylation maintenance efficiency caused by the dense chromatin environment in heterochromatin regions is the reason for the continuous loss of DNA methylation during sustained cell expansion. Overexpression of LSH can effectively improve the DNA methylation maintenance efficiency in heterochromatin regions to prevent DNA methylation loss, thereby improving several phenotypic defects caused by sustained cell expansion. This provides a new strategy for effectively maintaining cell function in adoptive cell therapy and has broad application value in enhancing the efficacy of various cell therapies.

The present application relates to the field of second-generation sequencing, in particular to the field of methylation sequencing, and more particularly to a marker sequence, a linker comprising the marker sequence, a kit comprising the sequence or the linker, and a DNA methylation sequencing method using the linker or the kit. The marker sequence comprises a polycytosine sequence on one side or both sides of an insert, wherein each cytosine at each site on each side has two states of modification or no modification. The present application can reduce cross-contamination between sequencing samples, and can be applied to DNA methylation detection.

The present application relates to the technical field of molecular biology, and discloses DNA methylation markers and application thereof in an acute ischemic stroke diagnosis kit, including methylation regions of CDH2, PCDHB10, PCDHB11, PCDHB14, PCDHB16, PCDHB3 and PCDHB9 genes. The present application screens and obtains a combination of 12 methylation regions of 7 marker genes with high specificity and high sensitivity and highly related to early onset risk of acute ischemic stroke, and the combination of the methylation regions is used as a marker for early detection of acute ischemic stroke, and the result is highly accurate, and can provide a reference for auxiliary diagnosis for clinicians.

The invention provides that the induction of DNA methylation changes at a target gene that undergoes loss of DNA methylation may reverse this methylation loss to normalize gene function. The present disclosure provides methods of treating a disease or disorder using a pharmaceutical composition comprising: a methylated DNA probe complementary to a target genomic locus comprising a target gene, and a delivery vehicle and methods of forming said pharmaceutical composition.

The present invention relates to a method for diagnosing or identifying colorectal cancer in a subject through the detection of abnormal hypermethylation levels of specific genes in a biological sample. The inventors have identified DNA methylation biomarkers that can be used alone or in combination to aid in the diagnosis or follow-up of colorectal cancer patients. Furthermore, the method can be used to determine and / or adapt an appropriate treatment plan for a subject diagnosed with colorectal cancer. The present invention further relates to a kit comprising primers or probes for detecting, diagnosing, or identifying hypermethylated genes.

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 application relates to the field of biotechnology, and particularly relates to a method for evaluating DNA methylation transformation efficiency. The present application can simply, quickly, directly and comprehensively evaluate DNA methylation transformation efficiency of the sample to be tested by detecting the methylation and non-methylation ΔCt values of four genes GNAS, GPR1, PAX6 and Actin respectively through conventional fluorescent PCR primer design, and calculating (2 ΔCtMSP +2 ΔCtUSP ) / (2 ΔCtMSP +2 ΔCtUSP +1). The method provided by the present application can be used for evaluation and quality control before carrying out methylation experiment or constructing methylation sequencing library, and the sample with low transformation efficiency can be detected in time to avoid carrying out subsequent experiment and causing resource waste such as experimental cost.

This article discloses a method for identifying the nature of thyroid nodules, including detecting the DNA methylation level in a sample selected from the following regions (1) and (2): (1) fragments of one or more of the following genes: COL23A1, ILDR2, DHRS3, KIF1A, GDNF, TBX18, and (2) nucleic acid regions within 10 kb upstream and downstream of the genes (1).

The application discloses a method and system for correcting Hi-C sequence alignment by fusing DNA methylation information, and the method comprises the following steps: obtaining a preliminary alignment result of Hi-C sequencing of a sample genome relative to a reference genome and a methylation site map; obtaining a corresponding candidate alignment position and an original sequence alignment score of each read pair; positioning an alignment interval on the reference genome at both ends of each candidate alignment position; based on the methylation site map, counting the number of methylation sites covered at both ends of the candidate alignment position to obtain a methylation penalty score representing biological consistency; obtaining a recalibration comprehensive score based on the methylation penalty score, reordering all candidate alignment positions of the read pair, calculating an alignment quality update value of each candidate position, and outputting a corrected alignment result. The application solves the problem that in a polyploid and a highly repetitive genome, multiple alignment of Hi-C reads cannot accurately determine the real source position.

The present invention provides a method for determining the risk of death and / or the probability of a healthy lifespan of a dog; the method comprising a) providing a DNA methylation map from a sample obtained from the dog; and b) using the DNA methylation map to determine the risk of death and / or the probability of a healthy lifespan of the dog; wherein the DNA methylation map contains at least one methylation site as listed in Table 1.

This article discloses a method for identifying the nature of thyroid nodules, including detecting the DNA methylation level in a sample selected from the following regions (1) and (2): (1) fragments of one or more of the following genes: GAS6, SOX17, ZMIZ1, TSHR, CDH1, MCRIP2, LINC01977, EGR3, and (2) nucleic acid regions within 10 kb upstream and downstream of the genes (1).

Disclosed herein are methods, compositions, and devices for diagnosing and treating cancer. The methods include sequencing a set of regions in cell-free nucleic acid molecules and detecting one or more biomarkers indicative of cancer and cancer subtype typing ability.

The application discloses a recombinant Pfu DNA polymerase resistant to dU template and application thereof in construction of a DNA methylation library. The application discloses a recombinant Pfu DNA polymerase resistant to dU template, and the amino acid sequence of the recombinant Pfu DNA polymerase is shown as SEQ ID NO. 1. Further, a complex for blocking the polymerization activity of the recombinant Pfu DNA polymerase is disclosed, and application thereof in construction of a DNA methylation library is disclosed. The recombinant Pfu DNA polymerase can efficiently amplify the DNA methylation library containing the dU template, and further, through the synergistic effect of the optimized amplification reaction buffer containing an amplification auxiliary factor and the library amplification condition, the yield of the DNA methylation library is significantly improved, the GC distribution deviation problem in the sequencing data analysis is effectively improved, the construction quality of the DNA methylation library is comprehensively improved, and a reliable guarantee is provided for the accurate analysis of subsequent sequencing data.

The present invention relates to a method of diagnosing or identifying colorectal cancer in a subject by detecting abnormal hypermethylation levels of specific genes in a biological sample of the subject. The inventors have indeed identified DNA methylation biomarkers that, alone or in combination, can help diagnose or follow up colorectal cancer patients. In addition, it can be used to determine and / or adapt a suitable treatment regimen for a subject diagnosed with colorectal cancer. The invention also relates to a kit containing the primer or the probe for detecting, diagnosing or identifying the hypermethylated gene.

This disclosure includes, in particular, methods, kits, and systems for determining the ER status of cancers, such as breast cancer. In various embodiments, this disclosure relates to the use of one or more histone modifications, chromatin accessibility, binding of one or more transcription factors, and / or DNA methylation as characteristics of the ER status of cancer. In some embodiments, differential modifications and / or differential accessibility are detected and quantified at one or more genomic sites in a biological sample, such as cell-free DNA (cfDNA), obtained from or derived from a liquid biopsy sample from a subject with cancer. In various embodiments, the determined ER status can be used, for example, to select for treatment and / or therapy for cancer, such as breast cancer.

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.

The present invention generally refers to a method of determining the methylation level of a set of biomarkers in a subject suspected of having thyroid cancer, the method comprising: a) from an isolated or extracted genomic DNA obtained from a biological sample from the subject suspected of having thyroid cancer, determining the methylation level of one or more biomarkers selected from the group consisting of cg01378044 (located in TBX18 gene, chr6:85,462,137-85,462,137), cg18305394 (located in the 5' region of PCK1 gene, chr20:56,134,788-56,134,788), cg11925561 (located in an intergenic region of chromosome 5, chr5:3,304,588- 3,304,588), and cg14672100 (located in an intergenic region of chromosome 5, chr5:6,344,259-6,344,259) from the extracted genomic DNA. The present invention also refers to diagnostic, prognostic and patient selection uses of said method.

The present application relates to the technical field of biological diagnosis, and particularly relates to a mutant gene set for tumor molecular typing and application thereof, wherein the mutant gene set comprises 82 mutant genes including DNA methylation modification related genes, histone modification related genes, chromatin remodeling related genes, TCR signal pathway related genes, PI3K-AKT signal pathway related genes, JAK-STAT signal pathway related genes, immune escape related genes, P53 signal pathway related genes, tumor suppressor genes and NOTCH signal pathway related genes. The mutant gene set can be used for molecular typing, targeted therapy and overall survival prediction of intranodal peripheral T-cell lymphoma. The mutant gene set is verified by clinical trials, and is suitable for all primary and relapsed PTCL patients, relapsed or refractory peripheral T-cell lymphoma umbrella study based on genomics typing and PTCL patients receiving different treatment schemes, and has a very wide application range.

The application discloses DNA methylation detection of corn genome target segments, and particularly relates to a method, a kit and a system for constructing a corn genome DNA methylation detection library containing target segments. The method, the kit and the system construct a DNA methylation detection library through twice PCR amplification, and realize detection through sequencing of the DNA methylation detection library and DNA methylation information comparison. The method, the kit and the system can detect DNA methylation information of multiple target segments in multiple corn materials at one time, and can also be applied to detection of DNA methylation of two parent alleles of hybrid materials. Each of the target segments should contain at least one or more SNP sites capable of distinguishing different corn materials or different alleles. The application simplifies complicated experimental operations and greatly reduces detection costs while accurately detecting DNA methylation levels.

The present disclosure provides methods of single-cell DNA methylation analysis that enable high-throughput, whole-genome DNA methylation sequencing of single cells in a variety of tissues.

This invention provides a DNA methylation marker combination, kit, device, and storage medium, belonging to the field of biomedical diagnostics. It includes methylation sites in target regions of the FGGY, LMNA, REST, PLOD2, POLR1D, NFKBIZ, PRKCB, CCSER1, and NEFM genes. The target regions of the FGGY and LMNA genes are selected from Chr1, the target regions of the REST and CCSER1 genes are selected from Chr4, the target regions of the PLOD2 and NFKBIZ genes are selected from Chr3, the target region of the POLR1D gene is selected from Chr13, the target region of the PRKCB gene is selected from Chr16, and the target region of the NEFM gene is selected from Chr8. This invention is applicable to adult diffuse gliomas and offers advantages such as simplicity, economy, speed, and clinical applicability.

The present invention provides a method for determining the risk of death and / or the probability of a healthy lifespan of a dog; the method comprising a) providing a DNA methylation map from a sample obtained from the dog; and b) using the DNA methylation map to determine the risk of death and / or the probability of a healthy lifespan of the dog; wherein the DNA methylation map contains at least one methylation site as listed in Table 3.

The application is in the field of methods using DNA methylation of canines. The present invention relates to a method of determining the contribution of a dog breed to a test dog genome, comprising: a) providing a DNA methylation profile from a sample obtained from the test dog; b) obtaining the identity of one or both alleles for a genetic marker in the test dog genome; and c) determining the contribution of a dog breed to the test dog genome by comparing at least part of the DNA methylation profile and at least one genetic marker of the test dog to reference DNA profiles from different dog breeds. A method for selecting a dietary, pharmacological, or lifestyle regime for a test dog, the method based on the contribution of a dog breed to the test dog genome. A method for preventing or reducing the risk of a test dog developing a disease; the method comprising selecting a dietary, pharmacological, or lifestyle regime for the test dog based on the contribution of the at least one dog breed to the test dog genome. Computer products for carrying out the said methods.

This invention relates to an anti-aging composition of Sophora japonica buds and dried tangerine peel that reduces methylation age and its applications. The composition comprises Sophora japonica bud powder and dried tangerine peel powder in a mass ratio of 1:(0.5-2). This invention optimizes the preparation of Sophora japonica bud powder through a process combining enzymatic hydrolysis with cellulase, pectinase, and xylanase, along with synergistic fermentation with Lactobacillus plantarum and Lactobacillus rhamnosus, significantly improving the dissolution rate and bioavailability of active ingredients. This, in conjunction with the dried tangerine peel powder, achieves bidirectional regulation of DNA methylation. The above anti-aging composition can be widely used in the preparation of products that reduce methylation age, delay aging, and improve tissue homeostasis, including health foods, dietary supplements, functional foods, skincare products, and pharmaceuticals.

The present invention belongs to the technical fields of DNA methylation library construction and DNA methylation detection, and specifically relates to a method for constructing a high-throughput sequencing library for enriched methylated DNA and use thereof. The construction method, on the basis of existing high-throughput sequencing library construction methods, incorporates two steps of restriction endonuclease digestion, and, combined with a specially designed linker, can achieve selective library construction for methylated CpG. Compared with existing conventional high-throughput sequencing library construction methods, the construction method incorporates only a small number of steps, making the overall procedure relatively simple. Moreover, high-throughput sequencing is directly performed on the prepared library, so that methylation states in widely distributed intervals on the whole genome can be obtained, thereby eliminating cumbersome steps of base conversion and targeted enrichment.

The present invention provides a method for generating a biological clock containing a DNA methylation map applicable to at least two different sample types, the method comprising: (i) providing a first set of DNA methylation maps generated from at least two different sample types from multiple subjects; (ii) generating a composite DNA methylation map from the first set of DNA methylation maps, wherein the composite DNA methylation map contains methylation sites having a matching state in the different sample types; and (iii) generating a biological clock using the composite DNA methylation map with a reference DNA methylation map from one of the at least two sample types.

This invention provides a method for determining the biological age, risk of death, and / or probability of healthy lifespan of a dog; the method comprising: a) determining the biological age, risk of death, and / or probability of healthy lifespan of a dog using the levels of one or more biomarkers selected from one or more samples obtained from the dog, wherein the one or more biomarkers are selected from white blood cell count, serum albumin, serum alkaline phosphatase, serum creatine kinase, hemoglobin, hematocrit, mean corpuscular hemoglobin, serum glucose, mean corpuscular volume, serum globulin, serum calcium, platelet count, and / or red blood cell count; and b) determining the biological age, risk of death, and / or probability of healthy lifespan of a dog using DNA methylation profiles from the dog.