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Cluster analysis method based on peripheral blood plasma free DNA nucleosome footprint difference, and application thereof

A cluster analysis and nucleosome technology, applied in the biological field, can solve problems such as treatment failure, patient suffering, and inability to alleviate the condition, and achieve high coverage and good accuracy.

Inactive Publication Date: 2019-08-30
广州市雄基生物信息技术有限公司
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Problems solved by technology

Because chemotherapy drugs generally have strong toxicity, inappropriate chemotherapy can not only cause pain to patients, but also fail to alleviate the disease. More importantly, it may induce multi-drug resistance, leading to treatment failure.
Radiotherapy is a treatment method that uses high-energy radiation to kill cancer cells. The treatment range is relatively limited and the local control effect is better. However, while radiotherapy inhibits or kills tumor cells, it also has toxic effects on normal cells in the body. Not every patient suitable for radiotherapy

Method used

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  • Cluster analysis method based on peripheral blood plasma free DNA nucleosome footprint difference, and application thereof
  • Cluster analysis method based on peripheral blood plasma free DNA nucleosome footprint difference, and application thereof
  • Cluster analysis method based on peripheral blood plasma free DNA nucleosome footprint difference, and application thereof

Examples

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Embodiment 1

[0024] Example 1: Cluster analysis of chemotherapy-sensitive group and chemotherapy-insensitive group of lung cancer

[0025] Based on the high-throughput sequencing data of cell-free DNA in peripheral blood plasma of 5 lung cancer chemotherapy-sensitive and 6 insensitive patients, the coverage difference analysis of TSSs and TTSs regions was performed, and it was found that chemotherapy-sensitive patients had different TSSs and TTSs from insensitive patients There were 178 regions (see Table 2), of which the coverage of 88 differential TSSs regions was upregulated in the sensitive patient group, and the coverage of 90 differential TSSs regions was downregulated in sensitive patients. By using differentially expressed genes for unsupervised hierarchical clustering analysis, it was found that based on 178 differential genes, samples can be clustered into sensitive and insensitive categories, and the patterns of coverage differential genes of the two groups are significantly diff...

Embodiment 2

[0042] Example 2: Cluster comparative analysis based on the complete remission group and the insensitive group of neoadjuvant chemoradiotherapy for colorectal cancer DNA high-throughput sequencing data (see Table 3), and the coverage difference analysis of TSSs and TTSs regions, found that there were 597 TSSs and TTSs regions (see Table 4) that were different between radiotherapy and chemotherapy-sensitive patients and insensitive patients (see Table 4), of which 368 The coverage of regions with 10 differential TSSs was upregulated in the sensitive patient group, and the coverage of 229 regions with differential TSSs was downregulated in sensitive patients. Through unsupervised hierarchical clustering analysis using differentially expressed genes, it was found that based on 597 differential genes, samples could be clustered into two categories: complete remission and insensitivity, and the patterns of coverage differential genes of the two groups were significantly different. ...

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Abstract

The invention discloses a cluster analysis method based on a peripheral blood plasma free DNA nucleosome footprint difference, and an application thereof. The method comprises the steps of (1), acquiring peripheral blood plasma free DNA high-flux sequencing data; (2), constructing a standard nucleosome positioning area database; (3), performing comparative analysis on each sample sequencing data and the standard nucleosome positioning area database; (4), screening coverage data of the nucleosome footprint difference and performing standardizing; and (5), performing cluster analysis on the standardized data by means of a hierarchical clustering method according to correlation between the samples. The method according to the invention has advantages of effectively preventing dependence of anexisting method to tissues or cells, comprehensively improving depth and accuracy in high-flux sequencing data analysis, realizing noninvasive radiotherapy and chemotherapy sensitivity prediction toa tumor patient, and realizing high comprehensiveness, high accuracy and high coverage. The method belongs to the field of biotechnology.

Description

technical field [0001] The invention discloses a cluster analysis method based on the nucleosome footprint difference of peripheral blood plasma free DNA nucleosome footprint. technology field. Background technique [0002] As the basic unit of eukaryotic chromatin, nucleosome is a typical biological macromolecule in which DNA and histones are combined, and is an important content of epigenetics. In different cell states, nucleosome positioning is dynamic, and the change of its position will affect the binding of transcription factors to DNA, thereby regulating the specific expression of genes. Therefore, it is of great significance to analyze the differences in nucleosome footprints and find out the changes of nucleosome footprints under different conditions. Due to the extreme environment of low oxygen and high acidity in the tumor, and the fierce competition among tumor cells, a large number of tumor cells undergo apoptosis. When cells undergo apoptosis, the DNA in the...

Claims

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Application Information

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IPC IPC(8): G16B30/10G16B40/00
CPCG16B30/10G16B40/00
Inventor 胥顺李坤杨学习
Owner 广州市雄基生物信息技术有限公司
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