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Method for rebuilding individual single somatotype based on optimizing solution aggregate

A haplotype and optimized solution technology, applied in the field of bioinformatics, to achieve high haplotype reconstruction rate, high practical value, and reduce loss probability

Inactive Publication Date: 2008-09-03
CENT SOUTH UNIV
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Problems solved by technology

[0009] The present invention solves the problem of individual haplotype reconstruction based on the MEC model, comprising the following steps: preprocessing the SNP matrix to obtain the SNP matrix containing only heterozygous sites

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  • Method for rebuilding individual single somatotype based on optimizing solution aggregate
  • Method for rebuilding individual single somatotype based on optimizing solution aggregate
  • Method for rebuilding individual single somatotype based on optimizing solution aggregate

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Embodiment Construction

[0016] The specific implementation of the present invention will be further described below in conjunction with the accompanying drawings. see figure 1 , figure 1 It is a flow chart of the present invention, and the dotted box represents the particle swarm optimization method. Pretreatment SNP matrix M in the present invention m×n , to remove redundant information that is not helpful to the reconstruction work, that is, to delete all satisfying conditions f in M 0 ≤t or f 1 ≤t columns (in matrix M, let n x is the number of elements whose value is x in a certain column, and f x =n x / (n x +n 1-x )), where t is set to 0.2, if most of the non-empty elements in the deleted column are 0, it is called 0-column, otherwise it is called 1-column. After deleting all the columns that meet the above conditions, some rows will become empty rows (element values ​​are all -), they are not helpful for the reconstruction work, so they are also deleted. After preprocessing, the SNP ma...

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Abstract

The invention discloses an individual haplotype rebuilding method based on an optimization solution assembling, which comprises the following steps: pre-processing a single nucleotide polymorphism matrix, removing redundant information which is helpless for a rebuilding work, obtaining a SNP matrix which only includes heterozygous locus numbers. A small scale optimization solution assembling is obtained by a particle group optimization strategy, that is, a haplotype pair assembling with only heterozygous locus numbers. The invention provides an individual haplotype rebuilding method based on a small scale optimization solution assembling solving MEC mould. The method can obtain more high haplotype rebuilding rate than bygone relative methods, and still processes relative high execution efficiency in solving large scale problems.

Description

technical field [0001] The present invention relates to bioinformatics, in particular to the reconstruction of individual haplotypes. Background technique [0002] After the completion of the human genome sequencing work, the study of genetic differences has become one of the hot spots in genome research. As we all know, almost 99.9% of human genes are the same, so the external differences we present are only caused by 0.1% genetic differences. Among various genetic variations, single nucleotide polymorphisms (single nucleotide polymorphisms, SNPs) are the most prominent form, which is a base change at a certain site on a human chromosome. Studying SNP is of great significance and practical application value in elucidating the mechanism of disease susceptibility, designing individualized treatment plan and drug development. [0003] However, the cost of detecting all 10 million common SNPs on human chromosomes is extremely expensive. Fortunately, due to linkage disequilibr...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/00C12Q1/68G06F19/10
Inventor 王建新吴璟莉
Owner CENT SOUTH UNIV
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