Method of discovering SNP group related to complex disease from SNP information

A disease and data technology, applied in the field of data processing, can solve the problems that the discovery of multiple SNP groups cannot be used, and the large-scale calculation amount cannot use the whole genome data, etc.

Inactive Publication Date: 2010-11-24
XIDIAN UNIV
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Problems solved by technology

Computationally, either only a single causative SNP can be found, and it cannot be used for the discovery of mul

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  • Method of discovering SNP group related to complex disease from SNP information
  • Method of discovering SNP group related to complex disease from SNP information
  • Method of discovering SNP group related to complex disease from SNP information

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Embodiment Construction

[0035] refer to figure 1 , the specific implementation steps of the present invention are as follows:

[0036] Step 1, preprocessing and initializing the SNP data.

[0037] (1.1) According to the principle that the influence of any gene variation in homologous chromosome alleles on the disease can be treated equally, the SNP data is processed into data containing only 0, 1, 2, and 3, where 0 indicates missing data;

[0038] (1.2) order Indicates the preprocessed data, where N is the number of samples in the SNP data, x i ∈ {0, 1, 2, 3} d , d is the number of SNPs in the data, y i∈ {1, 2} for sample x i , 1 represents the disease group, 2 represents the control group, y=[y 1 ,y 2 ,...,y N ];

[0039] (1.3) Let C be the set of SNP groups associated with complex diseases, initialized to be empty; let M be the number of SNP groups that are scheduled to be found associated with complex diseases, and the default value is 6; let L be a single nucleotide polymorphism The up...

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Abstract

The invention discloses a method of discovering SNP group related to complex disease from SNP information, solving the that problem that the multiple nosogenesis of susceptibilitytodiseases and SNP combination related to each reason can not be found in the SNP data of the complex disease in the prior art. The method comprises the steps of: preprocessing an SNP data set of the complex disease; searching an SNP group of candidate suspected nosogenesis in the preprocessed data set according to the measure of the relevance of the SNP group; calculating the stability measure of the relevance of the SNP group of all candidate suspected nosogenesis; adding the SNP group with maximum relevance stability measure as the suspected nosogenesis into a set of the SNP groups related to the complex disease; and outputting the SNP group in the set of the SNP groups related to the complex disease, and evaluating the degree of the SNP groups being the suspected nosogenesis by using the degree of the relevance stability close to 1. The invention can simultaneously find a plurality of nosogenesis SNP groups hidden in the data, and can be used for the pathogenic mechanism research and the early diagnosis of the complex disease and the development of the biomedicine.

Description

technical field [0001] The invention belongs to the technical field of data processing, and specifically relates to a method for discovering SNP groups related to complex diseases from single nucleotide polymorphism SNP data by using the maximum stability criterion, which can be used for the research on the pathogenic mechanism of complex diseases, Early diagnosis and biopharmaceutical development. Background technique [0002] Complex diseases are caused by multiple genetic factors and environmental factors, and their occurrence and development are affected by multiple genes in a complex network structure. Complex diseases are different from Mendelian genetic diseases. In most cases, there are often no major genes that are sufficient to cause disease, and the effect of a single gene on disease may be negligible or even non-existent, but these single gene combinations that may play a negligible role Together, their combined effects may be the cause of complex diseases. The...

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Application Information

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IPC IPC(8): G06F19/00
Inventor 张军英耿耀君于国强赵晓雪尚军亮王跃
Owner XIDIAN UNIV
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