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System for determining sample type based on DNA methylation level, readable medium and application thereof

A technology of methylation and methylation rate, which is applied in the field of determining sample types based on DNA methylation level, can solve the problems of rare tumor DNA, difficulty in methylation rate, and too much loss of details, achieving reliable results and solving problems The effect of low detection rate and high sensitivity

Pending Publication Date: 2022-05-31
SHENZHEN HUADA GENE INST
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Problems solved by technology

However, on the one hand, due to the complex and changeable peripheral fluid environment and the scarcity of free tumor DNA (especially for early-stage tumors), it is very difficult to accurately obtain the methylation rate of each site, which provides a basis for analyzing tumor signals at the site level. brings great uncertainty
[0005] On the other hand, most detection methods based on methylation variation tend to take the promoter region of a gene as a whole and analyze the overall indicators, resulting in too much loss of details and decreased sensitivity

Method used

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  • System for determining sample type based on DNA methylation level, readable medium and application thereof
  • System for determining sample type based on DNA methylation level, readable medium and application thereof
  • System for determining sample type based on DNA methylation level, readable medium and application thereof

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Embodiment 1

[0059] like Figure 1~3 As shown, this embodiment includes: a methylation sequencing module, a data analysis module, a feature extraction module and a scoring and typing module, wherein: suspected bladder cancer patients and confirmed bladder cancer patients (tumor types) that have not yet received treatment are collected and Peripheral fluid samples of healthy people (healthy type) were subjected to DNA methylation sequencing using the BGI-seq500 sequencing platform, and methylation sequencing libraries were constructed respectively.

[0060] The methylation sequencing module performs DNA methylation sequencing on the constructed methylation sequencing library to obtain sequencing data; the sequencing data includes several sequencing reads.

[0061] The data analysis module is used to divide the reference genome into windows, and calculate the window methylation rate of each sample based on the sequencing reads of the methylation sequencing library of the sample to be tested,...

Embodiment 3

[0093] The source of samples in this example is the urine of donors (30 bladder cancer patients and 10 healthy individuals). Methylation sequencing used conventional methylation library construction, BGQ-seq500 sequencing platform, and sequencing depth 30×. The number of methylation sites included in each window is set to 50, the threshold of the proportion of high-frequency homosequence subsequences is 50%, and the weight is the reciprocal of the p value of Fisher's exact test (transformed using the log function and multiplied by -1) , and perform 10-fold cross-validation for a total of 10 rounds of testing.

[0094] In this example, 50 methylation sites as a window is the optimal parameter for this batch of data. Generally speaking, the more methylation sites a window contains, the more stable the statistical features are, because it refers to more sites, but the more details are lost, because the same window only considers the overall index (window A methylation rate), whi...

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Abstract

The invention discloses a system for determining a sample type based on a DNA methylation level, a readable medium and application thereof. The system comprises a data analysis module, a feature extraction module and a scoring and typing module, and the specific content is shown in the text of the invention. The methylation information of the known sample type can be analyzed based on the input information, and the sample type to which the to-be-detected sample belongs is judged; the method has the advantages of high sensitivity (up to 100%) and reliable result, can effectively solve the problem of low detection rate of existing products (such as CT), and can noninvasively obtain tumor methylation variation information which can only be provided by invasively obtaining tissue samples in the prior art.

Description

technical field [0001] The invention relates to the fields of bioinformatics, in vitro diagnosis and detection, in particular to a system for determining a sample type based on DNA methylation level, a readable medium and an application thereof. Background technique [0002] DNA methylation is an important way for organisms to regulate the physiological activity of the genome. By methylating the gene promoter region, the expression ability of the gene can be adjusted, so that the same DNA can express different proteins in different cells without changing the DNA structure, so that the cells can perform different functions. At present, a large number of studies have reported the phenomenon of specific methylation of cancer-related genes observed in tumor tissues. In theory, statistical induction of such phenomena can be used to judge / predict the risk of an individual suffering from a certain cancer. However, in practice, since tissue samples cannot be obtained for analysis i...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B30/10G16B50/00
CPCG16B30/10G16B50/00
Inventor 梁瀚李南南吴逵赵鑫李甫强林从罗甜
Owner SHENZHEN HUADA GENE INST
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