Ribosome DNA methylation marker for detection of cancer in peripheral blood and application thereof

A marker, ribosome technology, applied in recombinant DNA technology, DNA/RNA fragment, microbial determination/inspection, etc., can solve the problems of poor marker specificity, loss of radical resection, etc., to achieve high specificity and sensitivity Effect

Active Publication Date: 2019-09-03
TSINGHUA UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

[0005] Cancer is a serious threat to human life and health. Due to the poor specificity of existing markers...

Method used

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  • Ribosome DNA methylation marker for detection of cancer in peripheral blood and application thereof
  • Ribosome DNA methylation marker for detection of cancer in peripheral blood and application thereof
  • Ribosome DNA methylation marker for detection of cancer in peripheral blood and application thereof

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0056] Example 1 Genome-wide methylation sequencing data screening of differential CpG sites on ribosomal DNA

[0057] 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.

[0058] 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

[0065] Example 2 Using the model and screening sites obtained in Example 1 to predict the effect of lung cancer, breast cancer, and nasopharyngeal cancer

[0066] The data used the reference data given in Example 1, including 5 breast cancers, 4 lung cancers, and 9 nasopharyngeal carcinomas. The number of cancer patients here is limited, and these types of cancer do not distinguish between cancer types. The models and loci obtained from liver cancer training in Example 1 were used to predict the distinction between these three types of cancer and reserve healthy people. The purpose of this example is to verify that the sites and models screened in Example 1 can also be used for the detection of other cancer types. figure 2 Gives a plot of the predicted ROC curve. From figure 2 It can be seen that the average AUC reaches 0.82, which has achieved a good prediction effect. It illustrates that the sites screened in Example 1 can be used for the prediction of breast cancer, l...

Embodiment 3

[0067] Example 3 Using Peripheral Blood RRBS Data to Predict Lung Cancer and Colorectal Cancer

[0068] We used the degenerate representative bisulfite sequencing (RRBS) of peripheral blood published in the PNAS article titled "Identification of methylation haplotypeblocks aids in deconvolution of heterogeneous tissue samples and tumorissue-of-origin mapping from plasma DNA" in 2017 Data, data deposited in Gene Expression Omnibus (GEO), accession number is GSE79279. Here, the peripheral blood DNA methylation data of healthy people (75), lung cancer patients (29), and peripheral blood DNA methylation data of 30 colorectal cancer patients were used.

[0069] 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 reference sequence, and no longer remove the sequencing repeats, because the sequencing ...

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Abstract

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%.

Description

technical field [0001] The invention belongs to the field of biological detection, and relates to a marker for cancer detection or postoperative evaluation and its application, in particular to a DNA methylation marker for cancer diagnosis by using peripheral blood and its application. 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 ...

Claims

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Application Information

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IPC IPC(8): C12Q1/6886C12N15/11
CPCC12Q1/6886C12Q2600/154
Inventor 汪小我张祥林方欢
Owner TSINGHUA UNIV
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