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Cancer tissue positioning method and system based on chromatin region coverage depth

A positioning method and area coverage technology, applied in the biological field, can solve the problems of low data output and poor data quality, etc.

Pending Publication Date: 2020-01-31
深圳吉因加医学检验实验室 +1
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Problems solved by technology

Therefore, there is a serious lack of C bases in the methylation library, that is, the bases are unbalanced, resulting in poor quality data obtained by sequencing, and the effective data yield obtained by PE filtering will also be low.

Method used

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  • Cancer tissue positioning method and system based on chromatin region coverage depth
  • Cancer tissue positioning method and system based on chromatin region coverage depth
  • Cancer tissue positioning method and system based on chromatin region coverage depth

Examples

Experimental program
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Embodiment

[0116] In this example, a lung cancer tissue localization model was constructed based on the coverage depth of lung tissue-specific open chromatin regions of cfDNA samples from lung cancer patients and healthy human cfDNA samples, and this model was used to predict cancer tissue localization for two samples with unknown cancer locations, as shown in figure 2 shown, including the following steps:

[0117] 1. Taking lung cancer tissue location as an example: obtain samples from 30 lung cancer patients and 30 healthy people, and build a lung cancer tissue location model, including:

[0118] 1-1 Use a 10mL Streck tube to collect the peripheral blood of the user to be tested. The blood collection volume is not less than 8mL. Immediately after blood collection, turn it upside down and mix slowly. Centrifuge the blood collection tube at 1600g for 10min at 4°C. After centrifugation, divide the upper layer of plasma into centrifuge tubes for secondary separation under the same conditi...

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Abstract

The invention relates to a cancer tissue positioning method and system based on chromatin region coverage depth, and the positioning method comprises the steps: constructing different cancer tissue positioning models according to different cancer cfDNA data, cfDNA data of a healthy person and a tissue-specific open chromatin region OCHROdb database; calculating the homogenization correction coverage depth of each tissue specific open chromatin region of the cfDNA to be detected, carrying out machine learning prediction analysis through each cancer tissue positioning model to obtain scores of different cancer tissue positioning models, and positioning cancer tissues according to the scores. The positioning method and system do not cause radiation damage to a human body, are low in library building and sequencing cost and simple and convenient in operation and analysis process, avoid artificial introduction of errors during sample preparation, and ensure the accuracy of a positioning result.

Description

technical field [0001] The invention belongs to the field of biotechnology, and in particular relates to a cancer tissue localization method and system based on coverage depth of chromatin regions. Background technique [0002] Liquid biopsy has broad application prospects in early tumor screening. It mainly detects peripheral blood free DNA (circulating cell-free DNA, cfDNA), which is mainly composed of DNA that is protected by nucleosomes during apoptosis and falls into the blood circulation. , cfDNA includes the sum of DNA fragments derived from tumor cells and all other somatic cells in the human metabolic cycle. Due to the small amount of DNA released by the tumor into the circulating blood and the limited number of mutation sites, it has brought great challenges to tumor liquid biopsy. As a result, even if mutations can monitor tumor-derived cfDNA, they can only weakly inform tumor tissue-of-origin and cannot accurately inform tumor tissue. [0003] DNA methylation c...

Claims

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Application Information

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IPC IPC(8): G16B20/00G16B20/40G16B30/10G16B50/30G16B40/00
CPCG16B20/00G16B20/40G16B30/10G16B50/30G16B40/00Y02A90/10
Inventor 黄毅易鑫吴玲清陈海新李俊刘久成杨玲
Owner 深圳吉因加医学检验实验室
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