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DNA methylation markers and their application in the diagnosis of early liver cancer by peripheral blood

A marker and methylation technology, used in recombinant DNA technology, DNA/RNA fragments, biochemical equipment and methods, etc., can solve problems such as poor specificity, loss of radical resection, etc., and achieve high specificity and sensitivity.

Active Publication Date: 2021-05-14
TSINGHUA UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] Liver cancer is a common malignant tumor. Due to the poor specificity of existing markers (such as alpha-fetoprotein), many patients with liver cancer are often diagnosed at the middle and late stage, and the chance of radical resection is lost

Method used

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  • DNA methylation markers and their application in the diagnosis of early liver cancer by peripheral blood
  • DNA methylation markers and their application in the diagnosis of early liver cancer by peripheral blood
  • DNA methylation markers and their application in the diagnosis of early liver cancer by peripheral blood

Examples

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Effect test

Embodiment 1

[0051] Example 1 Genome-wide methylation sequencing data screening of differential CpG sites on ribosomal DNA

[0052] We used peripheral blood bisulfite sequencing data published in PNAS titled "Noninvasive detection of cancer-associated genome-wide hypomethylation and copy number aberrations by plasmaDNA bisulfite sequencing" in 2013, and the data were deposited in the European Genome-Table Phenome Archives (European Genome-Phenome Archive), accession number is EGAS00001000566. Here we use the peripheral blood DNA methylation data of healthy people (32), HBV-infected non-cancer patients (8), early liver cancer patients (stage I, stage II, 26), and 15 pairs of liver cancer tissues and white blood cells Layer DNA methylation data.

[0053] Download the reference sequence U13369.1 of the human ribosomal DNA repeat fragment unit in GENBANK, with a total length of 42999 bases and 3288 CpG sites. Use the bs-seeker2 software to match the sequencing data back to U13369.1 on the re...

Embodiment 2

[0064] Embodiment 2 test concentrates the effect of test marker

[0065] In the 100 random splits of the training set and the test set, the regularized logistic model was trained using the training set, the model was applied to the test set, and the accuracy in the test set was calculated. Figure 4 A boxplot of the accuracy of the model on the test set is given for 100 random splits of the dataset. The average accuracy rate is 0.9513, and the standard deviation of the accuracy rate is 0.0686, indicating that a very good discrimination effect has been achieved.

[0066] Herein, the terms "first" and "second" are only used for descriptive purposes, and cannot be understood as indicating or implying relative importance or implicitly specifying the quantity of indicated technical features. Thus, the features defined as "first" and "second" may explicitly or implicitly include at least one of these features. In the description of the present invention, "plurality" means at least...

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Abstract

DNA methylation markers and their application in peripheral blood diagnosis of early liver cancer. The invention belongs to the field of biological detection, and relates to a marker for liver cancer and its application. These markers include at least one of the following CpG sites: based on the human ribosomal DNA repeat unit reference sequence U13369.1, Nos. Either a CpG site at position 34805 or a modified CpG site. At the same time, it also provides a system and kit for the combination of these markers to be used in the diagnosis of liver cancer. The methylation status of these markers was significantly different between tumor tissue and non-tumor tissue, and the methylation was low in tumor tissue. The accuracy of these marker combinations in the test set to distinguish whether patients had liver cancer reached 95%.

Description

technical field [0001] The invention belongs to the field of biological detection, and relates to a marker for liver cancer and its application, in particular to a DNA methylation marker and its application for diagnosing early liver cancer by peripheral blood. Background technique [0002] Detection of diseases in peripheral blood is a minimally invasive or even non-invasive detection method. There are free DNA in peripheral blood, and these free DNA comes from the DNA released into the blood by apoptosis. Therefore, some problems in the body can be identified through the analysis of free DNA. [0003] DNA methylation is an important part of epigenetics, and DNA methylation plays a vital role in gene regulation. Existing studies have shown that the occurrence of cancer is very closely related to genomic DNA methylation, which makes it a reality to detect cancer by identifying the variation of DNA methylation. DNA methylation refers to the process of transferring a methyl ...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6886C12N15/11
Inventor 汪小我张祥林方欢李衍达
Owner TSINGHUA UNIV
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