422 results about "DNA methylation" patented technology

The invention belongs to the technical field of molecular biology and genetics, and particularly relates to a method for editing cattle genes based on Pro-iCHI. The invention provides a method for editing cattle genes based on Pro-iCHI, which comprises the following steps: transiently expressing protamine in cattle AG-haESCs after gene editing, and injecting into mature oocytes to obtain reconstructed embryos. The protamine can remove abnormal DNA methylation generated by an oocyte cytoplasm injection haploid stem cell technology, cell nucleuses are compressed into a sperm-like structure, the obtained bovine Pro-iCHI embryo can smoothly develop into a blastocyst, and the ratio of the blastocyst to the blastocyst obtained by in-vitro fertilization is equivalent. Moreover, the protamine coding gene is inserted into the saccharomyces cerevisiae protein expression vector and then is subjected to transient expression, so that the protamine coding gene cannot be integrated into a genome to cause insertion of an exogenous gene while abnormal DNA methylation is erased.

The invention provides a human body biological age detection method based on DNA methylation, which comprises the following steps: step S1, aiming at at least one subject, collecting a peripheral blood sample of the subject, and extracting DNA in blood from the sample; the method comprises the following steps: S1, extracting DNA, S2, measuring a methylation map of the extracted DNA to obtain detailed information of the methylation state of the DNA, and S3, calculating a corresponding methylation rate according to the strength of a methylation signal and a non-methylation signal in the obtained methylation map; and step S4, inputting the calculated DNA methylation rate into a biological age model obtained by pre-training to obtain the biological age corresponding to the subject. The method has the beneficial effects that the biological age can be accurately predicted by acquiring methylation information of DNA data, a novel biomarker-based assessment means is provided, and the method has important application value in health management, disease risk assessment and the like.

The invention provides an individualized management system and method for colorectal cancer risk prediction, and relates to the technical field of medical diagnosis and individualized medical treatment. The system comprises a multi-omics data processing module used for collecting a blood sample of a subject, extracting circulating free DNA, and sequencing cfDNA by adopting a simplified methylation sequencing technology to obtain final original data of DNA methylation characteristics; the risk prediction module is used for carrying out bioinformatics analysis on the original data of the final DNA methylation features by adopting a machine learning algorithm, extracting a methylation feature set, a tail end motif feature set and a breakpoint motif feature set, and carrying out risk prediction on the basis of the extracted feature sets; and predicting the colorectal cancer disease risk of the subject by using a pre-trained prediction model to obtain a prediction result. The problem that the risk prediction accuracy of the colorectal cancer is low is solved.

The invention discloses a DNA methylation biomarker combination for prostate cancer detection and application of the DNA methylation biomarker combination, and belongs to the technical field of biological medicine. The DNA methylation biomarker combination comprises a combination of methylation sites indicated by CG in the SEQ ID NO: 1 sequence of the USP44 gene and the SEQ ID NO: 2 sequence of the HIF3A gene. It is reported for the first time that the methylation levels of the USP44 gene and the HIF3A gene are detected at the same time to conduct auxiliary diagnosis on the prostatic cancer, a sample urine detection result shows that the sensitivity is 97.14%, the specificity is 97.78%, and the non-invasive and reliable prostatic cancer detection method is provided and has good application prospects in early screening of the prostatic cancer.

The application provides a novel DNA methylation marker TAGMe-3 for tumor identification and use thereof. The TAGMe-3 gene sequence region has significant methylation difference between cancer tissues and paracancer tissues. As long as abnormal high methylation state of the TAGMe-3 gene sequence region is detected, the subject is determined to belong to a tumor high-risk population. Moreover, the significant difference of the TAGMe-3 presented between tumor tissues and non-tumor tissues exists in different types of tumors (Pan-cancer) in a wide range.

The invention relates to the technical field of cancer risk prediction, in particular to a deep learning cancer risk prediction method and system based on a methylation sequence. The method comprises the following steps: acquiring DNA methylation sequencing data and reference genome annotation data in a blood sample of a cancer patient; performing functional region classification processing on the DNA methylation sequencing data according to the reference genome annotation data to obtain promoter subregion methylation data, enhancement subregion methylation data and transcription factor binding site methylation data; performing dynamic sequence similarity calculation processing on the methylation data of the promoter region to obtain a first feature vector containing importance weight of the promoter region of the cancer-related gene; the methylation sites are classified according to the functions of the methylation sites in the transcriptional regulation pathway, so that the biological interpretation of the characteristics is improved, and the synergistic effect among different functional regions can be captured.

The disclosure provides methods for storage solutions for preserving DNA methylation patterns over a period of time. The disclosure also provides for methods of using methylated DNA stored in such storage solutions.

The invention belongs to the technical field of biological diagnosis, and particularly relates to application of a reagent for detecting DNA methylation of an RPL10 promoter region in preparation of a sow pregnancy diagnosis product. Through methylation high-throughput sequencing of blood DNA of pregnant sows and non-pregnant sows, it is found that the methylation level of a gene promoter region of the ribosomal protein L10 in the early pregnancy stage of the sows is remarkably reduced. The methylation level of the pregnant sow RPL10 is analyzed by using MSP, BSP and qMSP methods, and meanwhile, the ROC curve analysis result also shows that the RPL10 has diagnostic value. The results show that the method for detecting the RPL10 gene in the pig blood sample can be an effective method for diagnosing the early pregnancy of pigs. According to the invention, a pregnancy diagnosis technology based on RPL10 promoter region DNA methylation is preliminarily established, pig pregnancy detection methods are enriched, and a reference is provided for further exploring the DNA methylation level and the regulation mechanism of the pig pregnancy early stage.

The invention relates to the technical field of tumor data processing, in particular to a methylation-based tumor data processing system. The system comprises the following modules: a methylated sample sequencing module, a sequencing difference site recognition module, a tumor gene sequence analysis module and a tumor subtype classification module, performing high-throughput sequencing on the to-be-detected clinical tumor DNA sample to obtain methylated tumor sequencing data; performing methylation level quantification on the methylated tumor sequencing data, and performing tumor difference site analysis to generate tumor difference site data; performing tumor generation key gene sequence identification according to the tumor difference site data to generate tumor methylation characteristic data; and performing tumor subtype tag identification according to the tumor methylation characteristic data to generate tumor type tag data. According to the method, accurate tumor typing is realized on the basis of tumor DNA methylation characteristic analysis, and the false negative rate of low-concentration sample detection is effectively reduced.

The present invention discloses a cell-labeling microbead, a preparation method and an application thereof, relating to the field of biological detection. The cell-labeling microbead includes a microbead, a universal primer sequence, a cell label and a linking sequence that are sequentially coupled to the microbead; wherein, the universal primer sequence is used to bind to a primer compatible with a sequencer, and dC in the universal primer sequence is 5-Methyl dC; the cell label is used to trace and identify target cells, and the bases in the cell label include A base, T base, G base; the linking sequence is used to link the cell label to the target cells. The technical solution of the present invention avoids base conversion by removing unmethylated C bases in the universal primer sequence and the cell label sequence, and realizes the construction of a high-throughput single-cell DNA methylation library; by labeling multiple sequences on the microbead, the number of primer syntheses and costs are significantly reduced, which helps to promote the development and application of high-throughput sequencing technology for single-cell DNA methylomes.

Methods, compositions and kits are provided to amplify an amount of genomic methylated DNA that can be subsequently analyzed and / or sequenced. It has particular use with small amounts of DNA, including, but not limited to cell free DNA samples. In some embodiments, the ratio of polymerase and methyltransferase is controlled in order to provide maximum yields. In some embodiments, a dual primase / polymerase is used.

The present disclosure includes, among other things, methods, kits, and systems for determining the 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 that that are characteristic of the status of lung cancer. In some embodiments, differential modifications and / or differential accessibility are detected and quantified at one or more genomic loci of a biological sample, e.g., in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from a subject with lung cancer. In various embodiments a determined status is useful, e.g., in selecting treatment for and / or treating a lung cancer.

The present disclosure includes, among other things, methods, kits, and systems for determining HER2 status of cancer, e.g., a breast, gastric / gastroesophageal, colorectal, or 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 that that are characteristic of HER2 status of cancer. In some embodiments, differential modifications and / or differential accessibility are detected and quantified at one or more genomic loci of a biological sample, e.g., in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from a subject with cancer. In various embodiments a determined HER2 status is useful, e.g., in selecting treatment for and / or treating a cancer, e.g., a breast, gastric / gastroesophageal, colorectal, or lung cancer.

The present disclosure includes, among other things, methods, kits, and systems for determining ER status of cancer, e.g., a breast 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 that that are characteristic of ER status of cancer. In some embodiments, differential modifications and / or differential accessibility are detected and quantified at one or more genomic loci of a biological sample, e.g., in cell-free DNA (cfDNA) from a liquid biopsy sample obtained or derived from a subject with cancer. In various embodiments a determined ER status is useful, e.g., in selecting treatment for and / or treating a cancer, e.g., a breast cancer.

System, methods, and non-transitory computer readable medium (CRM) are provided that are directed to a biological age model utilizing metabolomic and proteomic data. Additional clinical variables and DNA methylation data may also be delivered to the methods, systems, and CRM. The biological age model determines a morbidity parameter based on a comparison between a patient's determined biological age and their chronological age to determine a time until death and possible treatment strategies.

The invention belongs to the technical field of bioinformatics, and particularly relates to a method for detecting abnormal DNA methylation fragments from cell free DNA (cell free DNA, cfDNA) and classifying the abnormal DNA methylation fragments from the cell free DNA, and the method comprises the following steps: based on a healthy cfDNA sample and a tumor cfDNA sample, selecting methylation haplotype regions (Methylation Haplotype Block, MHB) having significant difference between the two samples by adopting seven DNA methylation measurement indexes; on the basis of the selected methylated haplotype regions with significant differences, constructing total distribution of seven DNA methylation measurement indexes in the healthy cfDNA sample and the tumor cfDNA sample, and carrying out differential analysis; seven DNA methylation measurement indexes are adopted to construct classification models for abnormal DNA methylation fragments, and the classification models of the seven abnormal DNA methylation fragments are integrated on the basis of differential analysis results of overall distribution of the seven DNA methylation measurement indexes. According to the application, the abnormal DNA methylation fragments in the cell free DNA are detected by adopting seven DNA methylation measurement indexes, and the abnormal DNA methylation fragment classification model based on the seven DNA methylation measurement indexes is integrated, so that the improvement of the sensitivity of tumor early screening is facilitated.

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.

Disclosed herein are methods, compositions, and devices for use in diagnosis and treatment of cancer. The methods include sequencing a panel of regions in cell-free nucleic acid molecules and detecting one or more biomarkers that are indicative of a cancer and capability for cancer subtyping.

The invention discloses a method for simultaneously determining gene point mutation and DNA methylation based on a CRISPR / Cas12a system. The method is characterized by comprising four steps of enzyme digestion, recognition, conversion and detection, wherein in the enzyme digestion step, methylation-sensitive restriction endonuclease (MSRE) is selected according to a target site sequence, unmethylated DNA is not hydrolyzed by MSRE and is kept complete, methylated DNA is hydrolyzed and broken under the action of MSRE, and the broken 3'end can be used as a primer P1 to trigger SDA1 amplification; wherein in the recognition step, a Flap primer and an Invading primer are designed according to a point mutation sequence, and an enzyme digestion product generated under the action of FEN1 enzyme can be used as a primer P2 to trigger SDA2 amplification; wherein in the conversion step, two different SDA amplification templates are designed according to sequences of P1 and P2, and amplification of SDA1 and SDA2 is triggered by enzyme digestion products P1 and P2 respectively, so that DNA methylation and gene mutation information are quickly converted into two different amplification products T1 and T2; wherein in the detection step, crRNA1 and crRNA2 are respectively designed as guide chains of a CRISPR / Cas12a reaction system according to sequences of T1 and T2, and synchronous detection of gene point mutation and DNA methylation is realized through'strong 'and'weak' of fluorescence signals. Based on a CRISPR / Cas12a system, the method solves the problem that a traditional detection method cannot realize simultaneous detection of gene point mutation and DNA methylation, can be used for scientific research analysis and clinical detection, and has a wide market prospect.

The invention relates to a DNA methylation standard substance as well as a preparation method and application thereof. The DNA methylation standard substance comprises a 100% negative DNA methylation standard substance and a 100% positive DNA methylation standard substance, and the preparation method comprises the following steps: (1) carrying out first PCR amplification on a target gene, diluting an amplification product, and then carrying out second PCR amplification to obtain the 100% negative DNA methylation standard substance; and (2) carrying out methylation treatment on the 100% negative DNA methylation standard substance to obtain the 100% positive DNA methylation standard substance. According to the DNA methylation standard substance prepared by the invention, whether the MSP-qPCR primer has specificity or not can be judged, a primary basis is provided for establishment of an MSP-qPCR detection method, the sensitivity of the MSP-qPCR detection method can be evaluated, and a preparation scheme is simple and easy to implement.

The invention provides a DNA methylation marker gene combination for detecting liver tumor related diseases, a reagent and application, and belongs to the technical field of biology. Gene subregions of liver tumor related diseases are further optimized, a subregion combination with a better effect is provided, and when the genome provided by the invention cooperates as a biomarker for plasma separation DNA methylation detection, better sensitivity and specificity are achieved; the accuracy of early screening or re-screening of liver tumor related diseases can be remarkably improved, and the screening efficiency can be improved.

The invention belongs to the technical field of biology, and provides a medium-flux single cell four recombinant library construction and sequencing technology mtCOOL-seq (mid-throughput single cell multi-gene sequencing), and the four recombinant library construction and sequencing technology comprises a transcriptome, a DNA (deoxyribonucleic acid) methylation group, copy number variation and chromatin openness. The combination of the omics can comprehensively reveal a gene expression regulation mechanism and a functional state of a single cell. The mtCOOL-seq technology overcomes the defects of scRRBS, iscCOOL-seq and the like in the prior art, integrates the advantages of the scRRBS, the iscCOOL-seq and the like, and provides a more powerful and practical tool for single-cell multi-omics research.

The present invention relates to the field of gene detection, and particularly to a primer-probe combination, a kit and their applications for detecting the benign and malignant nature of pulmonary nodules. The primer-probe combination includes primer pairs and probes for detecting gene mutation sites and methylation sites, and can achieve simultaneous detection covering the EGFR L858R mutation site, the EGFR 19Del mutation site, and the methylation sites of the HOXA7, CCNA1, and ZNF808 genes at one time. Thus, the present invention is a simple, rapid and accurate combined detection scheme for DNA methylation and gene mutation to assist in differentiating the benign and malignant nature of pulmonary nodules; at the same time, the primer-probe combination can achieve rapid pre-cancer screening, and also has application values such as accurate medication guidance and prognosis and metastasis risk prediction.

The invention discloses a cancer profiling classification and prognosis prediction method based on generic cancer multi-omics data, and relates to a cancer profiling classification and prognosis prediction method. The invention aims to solve the problems of cancer subtype classification and prognosis prediction in generic cancer multi-omics. The method comprises the following steps: step 1, acquiring a multi-omics generic cancer data set, wherein the multi-omics generic cancer data set comprises a data set consisting of mRNA (messenger ribonucleic acid), DNA (deoxyribonucleic acid) methylation, miRNA (micro Ribonucleic Acid) and clinical prognosis data; 2, preprocessing the multi-omics cancer data set in the step 1; step 3, constructing a deep neural network model; 4, training the deep neural network model constructed in the step 3 based on the multi-omics generic cancer data set preprocessed in the step 2; and 5, carrying out cancer subtype classification and prognosis prediction on to-be-detected data based on the deep neural network model trained in the step 4. The invention belongs to the technical field of bioinformatics.

The invention discloses an application of leukocyte DNA methylation markers in colorectal tumor risk prediction, a series of leukocyte DNA methylation biomarkers related to colorectal tumors are researched, screened and verified, finally five methylation areas are obtained, a novel risk prediction model is constructed based on the five methylation areas, and the leukocyte DNA methylation markers have high clinical transformation potential and can be used for predicting the risk of colorectal tumors. And a novel risk stratification tool is provided for prevention and early screening of colorectal cancer.

The invention relates to sgRNAs for demethylation editing of an fgf2 gene of oryzias melastigma, an editing system and application, and belongs to the technical field of gene editing, and the sgRNAs are sgRNA1 + sgRNA2 + sgRNA3 or sgRNA2 + sgRNA3 + sgRNA4 + sgRNA5; the system comprises a Fuw-UbC-dCas9-tet1 plasmid and a pGL3-U6-sgRNAs plasmid, and the sequence of a conserved structural domain of a tet1 gene is as shown in SEQ ID NO. 1 (sequence identifier number 1). Through co-transfection of Mix1 or Mix2, the DNA methylation level of the fgf2 gene promoter can be effectively reduced by about 20.41% at most, the off-target efficiency is extremely low, the cell growth speed is remarkably increased, and stable inheritance is achieved.

The invention belongs to the technical field of gene detection, and particularly relates to a DNA methylation label-free fluorescence detection method, a reagent composition and application. The method comprises the following steps: cracking target DNA (Deoxyribose Nucleic Acid) by adopting GLaI endonuclease, and carrying out GLaI endonuclease reaction to obtain a digestion product; carrying out a double-cascade chain displacement amplification reaction on the obtained digestion product to obtain a double-cascade chain displacement amplification reaction product; carrying out CRISPR / Cas12a reaction on the obtained double-cascade chain displacement amplification reaction product, so as to obtain a CRISPR / Cas12a reaction product; in the CRISPR / Cas12a reaction, a G triplex is used as a signal source; and adding a fluorescent reaction reagent into the CRISPR / Cas12a reaction product, and measuring the fluorescence intensity of the CRISPR / Cas12a reaction product to obtain a methylation detection result of the target DNA. The detection method has the characteristics of low cost, universality, high sensitivity, high accuracy, good selectivity and the like.

The present disclosure relates to methods of analyzing the methylation level of differential DNA methylation regions (DMRs) obtained from buccal and blood monocyte cells. Also disclosed herein are methods of analyzing methylation level of DMRs for identification and preventative treatments of rheumatoid arthritis in human subjects.

The invention discloses a reagent combination for protecting fragment integrity in DNA methylation detection, the reagent combination is used for protecting fragment integrity in DNA methylation detection sample transformation, and the reagent combination comprises tetrahydrofurfuryl alcohol, L-ascorbyl palmitate and ethylenediamine tetraacetic acid; wherein the volume concentration of the tetrahydrofurfuryl alcohol is 10%-80%; the molar concentration of the L-ascorbyl palmitate is 10 mM to 100 mM; the molar concentration of the ethylenediamine tetraacetic acid is 1 mM to 10 mM. The invention also provides a kit and a method for DNA conversion by using the kit. According to the reagent combination, damage of sulfite to DNA in the transformation process can be reduced, DNA degradation is prevented, a transformed fragment is longer than that of a traditional transformation method, the DNA recovery concentration and the library concentration are higher, follow-up detection is facilitated, and the sensitivity of a follow-up detection method is improved.

The present invention discloses a nucleic acid composition, a kit and a detection method for detecting methylation of liver cancer-related genes. The nucleic acid composition is a first nucleic acid composition, a second nucleic acid composition or a combination of the first nucleic acid composition and the second nucleic acid composition. The first nucleic acid composition comprises: a methylation-specific primer and a probe for a target site of the EMX1 gene, a methylation-specific primer and a probe for a target site of the OTX2 gene, and a methylation-specific primer and probe for a target site of the DAB2IP gene. The second nucleic acid composition comprises: a methylation-specific primer and a probe for a target site of the Septin9 gene, a methylation-specific primer and a probe for a target site of the CDKL2 gene, and a methylation-specific primer and probe for a target site of the GSTP1 gene. The kit configured with the nucleic acid composition discovered in the present invention determines whether a test sample has become cancerous based on the degree of DNA methylation of the test sample, thereby providing a clinically simple and accurate liver cancer screening method, which has a very positive significance for the detection of liver cancer.