146 results about "CpG site" patented technology

There is disclosed a cancer diagnostic method based upon DNA methylation differences at specific CpG sites. Specifically, the inventive method provides for a bisulfite treatment of DNA, followed by methylation-sensitive single nucleotide primer extension (Ms-SNuPE), for determination of strand-specific methylation status at cytosine residues.

The present invention relates to methods for identifying among the genes that are down-regulated in cells or tissues having disease including cancer, the CpG sites within the CpG islands of said genes, wherein the identified CpG sites show great potential for diagnostic utility. In another aspect, the present invention also provides methods of using the selected CpG sites for purposes of diagnosis, prognosis, staging, assessing or monitoring the therapy of or recovery from a disease such as cancer.

The present invention relates to methods for identifying among the genes that are down-regulated in cells or tissues having disease including cancer, the CpG sites within the CpG islands of said genes, wherein the identified CpG sites show great potential for diagnostic utility. In another aspect, the present invention also provides methods of using the selected CpG sites for purposes of diagnosis, prognosis, staging, assessing or monitoring the therapy of or recovery from a disease such as cancer.

The present invention provides a method for identifying a methylated CpG containing nucleic acid by contacting a nucleic acid with a methylation sensitive restriction endonuclease that cleaves unmethylated CpG sites and contacting the sample with an isoschizomer of the methylation sensitive restriction endonuclease, which cleaves both methylated and unmethylated CpG sites. The method also includes amplification of the CpG-containing nucleic acid using CpG-specific oligonucleotide primers A method is also provided for detecting an age associated disorder by identification of a methylated CpG containing nucleic acid. A method is further provided for evaluation the response of a cell to an agent A kit useful for detection of a CpG containing nucleic acid is also provided. Nucleic acid sequences encoding novel methylated clones.

The present invention is to provide a computer readable medium comprising a computer program for enabling a computer to carry out provision of information on hepatocellular carcinoma in a subject based on an analysis result on methylation status of a novel marker specific for hepatocellular carcinoma.

The above object is achieved by obtaining the analysis result on methylation status of a CpG site located in a promoter region of at least one gene selected from CELF6 and RNF135 in a DNA sample derived from the subject and providing information on hepatocellular carcinoma in the subject based on the resulting analysis result.

A gene marker for the detection of oral cancer, comprising methylated CpG sites in target genes, is provided. The CpG sites in the target genes are selected from a group consisting of the following CpG sites: FLT4_E206_F, ASCL1_E24_F, KDR_E79_F, TFPI2_P9_F, TERT_E20_F, ADCYAP1_P455_R, MT1A_P49_R, and combinations thereof. A method for the detection of oral cancer, comprising the following steps is also provided: a) providing a sample to be examined from an individual; b) detecting a methylation state of at least one CpG site in a target gene on the genomic DNA from cells of the sample, wherein the CpG site in the target gene is selected from a group consisting of the following CpG sites: FLT4_E206_F, ASCL1_E24_F, KDR_E79_F, TFPI2_P9_F, TERT_E20_F, ADCYAP1_P455_R, and MT1A_P49_R; and c) determining if the individual has oral cancer based on the methylation state of the selected CpG site in the target gene.

The invention provides a method and kit for quantitatively detecting the methylation degree of a DNA specific site. The method provided by the invention comprises the following steps: 1) designing a PCR primer in accordance with a DNA sequence to be detected, and using the PCR primer for amplifying the DNA to be detected; 2) designing a pair of TaqMan probes in accordance with a CpG site-enriched region in the PCR product obtained by amplification in the step 1), wherein one probe is a CG probe designed in accordance with the DNA of which the CpG site is completely methylated, and the other probe is a TG probe designed in accordance with the DNA of which the CpG site is completely non-methylated and is used for specifically combining the PCR product and detecting the PCR product; and 3) carrying out real-time quantitative PCR based on the primer designed in the step 1) and the probes designed in the step 2), thus detecting the methylation degree of the DNA to be detected. By using the method, a specific methylated site can be detected, and the methylation states of other sites can not affect the detection result. The kit provided by the invention can be used for detecting the methylation degree of a DNA specific site.

The invention discloses a method for detecting the activity of DNA methylase and DNA methyltranseferase based on restriction endonuclease Hpa pi and exonuclease III. An unlabeled DNA probe is prepared and the sequence of the probe comprises a cleavage site of the restriction endonuclease and a methylated CpG site. The purpose of detecting the activity of the methylase and methyltranseferase is reached by steps of hybridizing the unlabeled DNA probe with the target DNA, carrying out methylation treatment by the methylase, carrying out the specific cleavage of the restriction endonuclease Hpa pi and enabling exonuclease III having the activity of 3'->5' exonuclease to act on the double-stranded DNA and then adding fluorescence signal molecules thiazole orange which having different signals to single-stranded DNA and double-stranded DNA. According to the method, since no complex material or labeling of DNA probes need to be prepared, the defects of high detection cost, cumbersome operations and poor reproducibility caused by the preparation of the material and labeling of DNA probes are avoided. The method disclosed by the invention has the advantages of low cost and high sensitivity and is fast and simple.

The invention discloses a DNA methylation marker used for diagnosis, screening, and prediction of male colorectal cancer. The DNA methylation marker is obtained via methylation of a combination of thefirst groups, or the first group with the second group, or the third groups, (1), +22, +27, and +29; (2), -24,-18, +89, and +92; and (3) +136; of three CpG sites in the front and back sequence of gene RPS24 transcription start site. The sequence number is based on sequence number in SEQ ID NO.1. The 143th site transcription start site A is recorded as +1. The invention also discloses a probe, a method, and a kit used for detecting the DNA methylation marker, and a computer module used for prediction of male colorectal cancer risk using the data of the DNA methylation sites.

The invention relates to a methylation quantitative test method of APC gene in the DNA of human blood plasma. The methylation quantitative test method obtains venous blood and the blood plasma, prepares a DNA standard curve sample of the blood plasma, extracts the DNA of the blood plasma to be detected, the DNA of a standard curve blood plasma sample and the DNA of healthy human blood plasma, realizes chemical modification of the DNA of the blood plasma to be detected, the standard curve blood plasma sample and the healthy human blood plasma, designs particularity primers and Taqman fluorescent probes according to 707 CpG locus of a 1A sequence in a human APC gene sub-promoter, builds a standard curve according to the augmentation result of the DNA of the standard blood plasma after the augmentation, and implements methylation quantitative result analysis of the sample to be detected. The methylation quantitative test method of the APC gene solves the defects that the blood plasma has less DNA content, high loss rate, DNA degradation and carcinogenic pollutant, etc. The methylation quantitative test method of the APC gene utilizes a primer pair and a Taqman fluorescent probe that aim at the 1A sequence in the APC gene sub-promoter, realizes the detection aiming at the 707 CpG locus in the APC gene sub-promoter with high methylation developing rate, implements quantitative analysis, and can be used in the aspects of cure effect observing as well as prognosis and relapse monitoring of tumor patients.

The invention relates to a detection kit and method for DNA methylation, especially to a detection kit and method for DNA methylation without CpG sites at flanking sequences. The kit and method employa Taqman probe binding to a minor groove binder (MGB) and can determine the methylation of both a CpG island (CGI) and isolated CpG sites in CpG open sea and the like without CpG at two flanking sequences. The kit and method provided by the invention are specific and sensitive, simple to operate, and does not require a control reaction or a fully-methylated standard DNA substance as a reference,thereby overcoming defects resulting from the control reaction and the fully-methylated standard DNA substance. In addition, the kit and method have higher repeatability and accuracy than the existingMethyLight technology.

A novel epigenetic biomarker for detecting bladder cancer and a method thereof. The method comprises following steps: (1) providing a to-be-detected specimen; (2) detecting a CpG sequence methylation status of at least one targeted gene in genome DNA of the to-be-detected specimen, wherein the targeted gene is selected from at least one of the group consisting of ZNF671, PTPRR, SOX1, PAX1, ZNF582, AJAP1, SOX17, EDN3, ST6GAL2, ZNF614, PTGDR, SYT9, SOX8, HS3ST2, POU4F3, ADRA1D, MAGI2, EPO, NEFH, POU4F2, STC2 and THRB; and determining whether the specimen is suffered from cancer or precancerous lesions or not according to whether the methylation status of the targeted gene exists or not, or employing the determination of the existence of the methylation status of the targeted gene as treatment prognosis. The invention also discloses a novel epigenetic biomarker for detecting the bladder cancer, wherein the biomarker comprises a methylated CpG locus of the target gene. The methylated CpG locus can be detected in urine.

The invention relates to a urine-based method and kit for diagnosing the relapse risk of a bladder cancer patient. The invention discloses two methylation-sensitive genes, namely an LMX1A gene and a VAX1 gene. A urine sample is kept before the operation of a detected bladder cancer patient, and the specific CpG sites of the genes are subjected to high methylation among people who are determined to suffer from a relapse in the follow-up visit process. Thus, the two genes can be used as biological markers for the relapse of bladder cancer. The invention can be used as the basis for designing a kit for prognosing and diagnosing the relapse of bladder cancer, and is applicable to the prognosis detection of bladder cancer in hospital, the postoperative follow-up visit and the postoperative monitoring of the community health center on people subjected to bladder cancer operation.

The invention discloses a nucleic acid combination and kit for detecting septin9 gene methylation, and relates to the field of molecular biology. The nucleic acid combination includes a primer pair for detecting septin9 gene methylation. The primer pair includes an upstream primer having a base sequence shown as SEQ ID NO.11 and a downstream primer having a base sequence shown as SEQ ID NO.17. Theprimer pair can specifically amplify the target site of a septin9 gene, wherein the target site is the third CpG island containing six CpG sites in a septin9 gene promoter region, so that specific detection of septin9 gene methylation is achieved. The nucleic acid combination and kit are high in sensitivity and have the detection limit as low as 100 copies, and the difficulty that the content ofctDNA in blood plasma is low and ctDNA cannot be detected is overcome.

The invention discloses a detection kit for TMEM101 gene methylation in human peripheral blood circulating tumor DNA for early screening of endometrial cancer. The detection kit is applied to early screening of endometrial cancer and comprises a methylation specific primer of a TMEM101 gene target site, a hydrolysis probe which is specific to the TMEM101 gene, and a primer of a reference gene and a hydrolysis probe of the reference gene, wherein the target site of the TMEM101 gene is at least one CpG site in an upstream and downstream 2000bp interval of a transcription start site of the TMEM101 gene; the reference gene is one or more of GAPDH and beta-actin; and the kit comprises a PCR pre-amplification reaction system and a PCR amplification reaction system. According to the provided detection kit for TMEM101 gene methylation in human peripheral blood circulating tumor DNA for early screening of endometrial cancer, the technical defects that in the prior art, the process is tedious, the detection time is long, the false positive is high, and the early screening of the endometrial cancer blood cannot be traced are overcome.

The invention provides a method and a system for acquiring the age of a male individual in a Chinese population. The method comprises the following steps: extracting DNA of the male individual; acquiring the methylation rates of 9 CpG sites of the DNA; and according to the methylation rates of the respective CpG loci, performing regression analysis on the 9 CpG loci and the age by R software to construct a regression model so as to acquire the age of the male individual in the Chinese population. According to a scheme provided by the invention, the age of the male individual in the Chinese population can be accurately acquired, and the age of the individual can be inferred from biodetection materials, such as blood or a blood mark sample, which are left on a crime scene in an actual publicsecurity combat, so that quick locking of a criminal suspect scope is facilitated, a clue is provided for case detection and the speed of the case detection is increased.

The invention provides a ribosome DNA methylation marker for detection of cancer in peripheral blood and an application thereof. The markers comprise at least one selected from the group consisting of, by taking a human ribosomal DNA repeat fragment unit reference sequence U13369.1 as a reference, CpG sites at positions of 38974, 37148, 37013, 37082, 37076, 32936, 21740, 23407, 34657, and 28277 orthe modified CpG site. The invention also provides a system, a kit, and the like for any combination of the markers for cancer diagnosis. The methylation status of the markers is significantly different between tumor tissues and non-tumor tissues, and the markers are hypomethylated in tumor tissues, and the ROC of combination of the markers in a test set to distinguish patients with liver cancer,lung cancer, and colorectal cancer can respectively reach 96%, 94%, and 92%.

The invention relates to a method for centralized expanding and detecting the gene region of a genome DNA, which aims to verify the characteristics of the gene area in the genome. The characteristics comprise single nucleotide polymorphism (SNP), point mutuation, sequence insertion/deletion and the levels of dideoxy nucleotide (DNA) methylated CpG sites. With an Alu family, particularly an AluY subfamily common sequence as the main oligonucleotide primer, the method expands the DNA and copies all gene regions which are mostly concentrated in the genome with the oligonucleotide primer inter-alu PCR expanded genome DNA. The method is characterized in that the inter-Alu PCR can filter some non-gene sequences, so that a novel generation of sequencing technology detects the SNP, the point mutuation, the sequence insertion/deletion and the levels of DNA methylated CpG sites of the gene region in a centralized way, so as to save the consumption of the genome DNA required by the sequencing.

The invention discloses an expansion method for DNA methylation chip data. Expansion of the DNA methylation chip data is realized by predicting a CpG locus not covered by a DNA methylation chip. Specifically, first, features of the CpG locus to be predicted are extracted based on measured data of the DNA methylation chip and sequencing data of other whole-genome sulfite with similar tissue; second, a methylation value measured through a whole-genome sulfite sequencing method of the CpG locus to be predicted is combined to train a Logistic regression model; and last, the trained regression model is used to predict new data.

Provided are a primer set, a method and a kit therefor, which can easily perform with high accuracy the detection of a cancer cell caused by HPV and the determination of whether or not a tissue is a tissue with high-grade dysplasia or in a more severe phase. As a primer set, used is a primer set consisting of a first primer which hybridizes with a nucleic acid consisting of a nucleotide sequence in which cytosine present in a site other than a CpG site is converted into another base in a nucleotide sequence having a CpG site in L1 region or L2 region of HPV and a second primer which hybridizes with a nucleic acid consisting of a nucleotide sequence in which cytosine is converted into another base in a nucleotide sequence having a CpG site in LCR or E6 region of HPV.

The invention discloses an human repeat element DNA methylation as markers for early diagnosis of liver cancer and an application thereof.The invention belongs to the field of biological detection, and relates to markers for liver cancer and the application thereof.These markers are selected from one or more of the CpG sites modified at positions 64 on AluYg6,72,231 on AluSp,447,493,673 on L1HS,380,448 on L1,230 on AluYba3a2,1569 on LSAU, and 446 on LTR12E in Repbase data published by the Genetic Information Research Institute (GIRI).The invention further provides a system for diagnosing livercancer or predicting the risk of liver cancer by using the combination of the markers.The methylation states of the markers are obviously different in tumor tissues and non-tumor tissues; the methylation of the markers is low in the tumor tissues, and the accuracy rate of distinguishing whether or not a patient suffers from liver cancer in a test set by the marker combination reaches 90 percent.