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A method and system for detecting epistasis in complex diseases based on chromatin regulatory loops

A loop detection and chromatin technology, applied in hybridization, genomics, proteomics, etc., can solve the problems of large computing resources and time, consumption, and epistasis that has not been seen, so as to reduce the amount of calculation and reduce false negatives The effect of the result

Active Publication Date: 2020-07-28
XI AN JIAOTONG UNIV
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Problems solved by technology

Aimless and random research on the interaction between SNP sites will consume huge computing resources and time, and will produce many false negative results
So far, there have been no reports on the calculation of epistasis between SNPs using these chromatin long-range interaction data as screening criteria

Method used

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  • A method and system for detecting epistasis in complex diseases based on chromatin regulatory loops

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Embodiment Construction

[0031] The present invention will be described in further detail below in conjunction with the accompanying drawings and embodiments. The examples are only used to explain the content of the present invention.

[0032] Based on the existing chromatin long-range interaction data, gene-enhancer regulatory data and super-enhancer data, the applicant defined the chromatin regulatory loop that interacts with the target gene, and invented a chromatin-based regulatory loop Methods for detecting epistasis in complex diseases. The basic steps are as follows:

[0033] P1: Collect and organize chromatin long-range interaction data and corresponding chromatin segmentation state data, gene-enhancer regulation data, and super-enhancer data of complex disease-related cell lines;

[0034] P2: Use the above data to establish chromatin regulatory loops that interact with target genes;

[0035] P3: Using the established chromatin regulatory circuit, calculate the SNP interactions in the regul...

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Abstract

The invention discloses a method and a system of detecting epistasis of a complex disease on the basis of chromatin regulation loops. Chromatin remote-interaction data and chromatin segmentation status data of cell lines related to the complex disease are collected and arranged; the above-mentioned data are utilized to establish the chromatin regulation loops; and SNP (Single nucleotide polymorphism) interaction which is in the regulation loops and can influence phenotypes of the complex disease is calculated. According to the method, the data of chromatin remote-interaction and the like are utilized to establish the chromatin regulation loops based on gene interaction, and the epistasis is calculated according to the chromatin regulation loops. Compared with the prior art, the method cangreatly decrease a calculation amount, can also reduce false negative results, thus rapidly and accurately explores SNP interaction related to the complex disease, and provides potential targets for subsequent drug design and the like.

Description

technical field [0001] The invention relates to the technical field of complex disease epistasis detection, in particular to a method and system for detecting complex disease epistasis based on chromatin regulatory loops. Background technique [0002] Genome-wide Association Study (GWASs) is currently an effective research method for revealing complex disease / trait susceptibility genes. Using this method, more than 2,000 papers have been published in international high-level journals, and nearly 10,000 complex disease susceptibility loci marked by SNP (Single nucleotide polymorphism) have been successfully identified. For a specific complex disease, the reported disease susceptibility loci accumulatively explain less than 15% of the genetic variation of the disease, and there are still a large number of unknown genetic factors, that is, "lost heritability" that needs to be discovered urgently. This is a common problem faced in all studies of complex disease genetics. There...

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): G16B20/20G16B40/00
CPCG16B20/00G16B25/00
Inventor 杨铁林姚石陈一霄牛慧敏董珊珊郭燕
Owner XI AN JIAOTONG UNIV
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