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SNP (single nucleotide polymorphism) data filtering method

A screening method and data technology, applied in the intersection of computer and biomedicine, can solve the problems of high cost, lack of persuasiveness of SNP sites, no consideration of interaction, etc., and achieve the effect of enhancing reliability and accurate classification weight value

Inactive Publication Date: 2012-07-11
SHANGHAI UNIV
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Problems solved by technology

[0002] The development of gene chip technology has brought high-throughput SNP test equipment, which can detect up to hundreds of thousands of single nucleotide polymorphism sites (SNP) at a time, helping us to carry out genome-wide association analysis research, However, because the cost of the experiment is very expensive, the SNP data has the characteristics of high latitude and small samples
In view of the high latitude and small sample characteristics of SNP data, traditional genome-wide association studies only consider the role of a single SNP site, and do not consider the interaction between them, and the screened SNP sites associated with diseases are not convincing.

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  • SNP (single nucleotide polymorphism) data filtering method
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  • SNP (single nucleotide polymorphism) data filtering method

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Embodiment Construction

[0027] The present invention will be described in further detail below in conjunction with the accompanying drawings and preferred embodiments.

[0028] refer to figure 1 , a screening method for SNP data, the specific steps are as follows:

[0029] 1. Using the effect of a single SNP and the interaction between SNPs to calculate the SNP classification weight;

[0030] (1) Initialize the SNP data set and the classification weight of the SNP, and set them to N and 0 respectively;

[0031] (2) Select the i-th sample from the experimental data set N, if i>N, it will end, and take the current classification weight value as the final weight value, otherwise continue;

[0032] (3) Find the nearest neighbor sample m of the same category and the nearest neighbor sample n of different categories of the i sample, and the sample category only has two states: normal and diseased;

[0033] (4) Calculate the distance between the selected sample i at the location j and the nearest neighb...

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Abstract

The invention relates to an SNP (single nucleotide polymorphism) data filtering method, which includes the following steps: firstly, computing SNP classification weight by means of the action of a single SNP and the interaction among the SNPs; and secondly, filtering SNP loci by means of a support vector machine. The action of the single SNP is taken into consideration, and the interaction among the SNPs is sufficiently researched, so that reliability in filtering of the SNPs relevant with diseases is improved.

Description

technical field [0001] The invention relates to related technologies for screening high-latitude and small-sample data, in particular to design a screening method for SNP data, which belongs to the interdisciplinary field of computer and biomedicine. Background technique [0002] The development of gene chip technology has brought high-throughput SNP test equipment, which can detect up to hundreds of thousands of single nucleotide polymorphism sites (SNP) at a time, helping us to carry out genome-wide association analysis research, However, because the cost of the experiment is very expensive, the SNP data has the characteristics of high latitude and small samples. In view of the high latitude and small sample characteristics of SNP data, traditional genome-wide association studies only consider the role of a single SNP site, and do not consider the interaction between them, and the screened SNP sites associated with diseases are not convincing. In order to solve this probl...

Claims

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Application Information

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IPC IPC(8): G06F19/10
Inventor 吴悦张文宾雷州刘宗田吴红霞
Owner SHANGHAI UNIV
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