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Method for determining influence of genetic variation on function based on genomic environment

A genetic variation and genome technology, applied in the field of determining the functional impact of genetic variation based on the genome environment, can solve the problem of not being able to accurately and directly point out the specific impact of variation on biological pathways, avoiding annotation errors and improving accuracy.

Inactive Publication Date: 2017-05-31
PEKING UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

However, the statistical test analysis aims to find out those biological pathways that are significantly affected by the variation, and cannot accurately and directly point out the specific impact of the variation on the biological pathway

Method used

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  • Method for determining influence of genetic variation on function based on genomic environment
  • Method for determining influence of genetic variation on function based on genomic environment
  • Method for determining influence of genetic variation on function based on genomic environment

Examples

Experimental program
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Effect test

Embodiment 1

[0027] Example 1: Annotation of protein-coding genes

[0028] In this example, the method of the present invention is used to annotate protein-coding genes.

[0029] For the annotation of protein-coding genes, the following steps can be carried out: 1) Map the variation to each gene of a given gene model according to its coordinate position; 2) Infer the protein-coding region of the gene according to all the variations on each gene; specifically Specifically, for transcripts containing variants that affect splicing, search for hidden splicing sites within a given interval (+ / -100bp by default), as well as new splicing sites caused by other variants. For transcripts for which no alternative splice sites could be found, both exon skipping and intron retention were considered. 3) Translate it into a protein sequence according to the sequence of the obtained protein coding region; 4) Compare the obtained protein sequence with the known reference protein sequence to determine the ...

Embodiment 2

[0032] Example 2: Annotation of transcription factor binding sites

[0033] In this example, the method of the present invention is used to annotate transcription factor binding sites.

[0034] The annotation of transcription factor binding sites is divided into loss of transcription factor binding sites (TFBS loss) and transcription factor binding site gain (TFBS gain). For the prediction of the loss of transcription factor binding sites, it is judged whether there is a loss of transcription factor binding sites by comparing the score of the site weight matrix corresponding to the sequence before and after the mutation. On the other hand, for the prediction of transcription factor binding sites, first find out all the variations in the promoter, and then reconstruct the promoter sequence. Then, the transcription factor binding sites were predicted according to the site weight matrix. Figure 4 A flowchart showing the annotation of transcription factor binding sites using th...

Embodiment 3

[0037] Example 3: Annotation to microRNA

[0038] In this example, the method of the present invention is used to annotate microRNA.

[0039] For the annotation of miRNA, the individualized sequence is also reconstructed according to the given variation to comprehensively judge the impact of the variation on miRNA production and miRNA target sites. For the annotation of microRNA generation, it aims to predict the effect of genomic variation located on pre-microRNA on the minimum free energy of pre-microRNA secondary structure. The tool used here to calculate the minimum free energy of pre-microRNA is RNAfold. First, find all variants on the same pre-microRNA. Then, the real pre-microRNA sequence is reconstructed. Finally, calculate the change of the minimum free energy of the pre-microRNA before and after the genomic variation occurs, and take it as the influence on the generation of microRNA. MicroRNA target binding annotation refers to the effect of predicting variants o...

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Abstract

The invention provides a method for determining the influence of genetic variations on function based on a genomic environment. According to the method, each gene serves as a unit, and the common influence of all variations on the gene is annotated. The method includes the following steps: 1, all the variations are mapped to all genes of a given genetic model according to the coordinate positions of the variations; 2, according to all the variations on all the genes, the individualized sequence of each gene is reconstructed; 3, all the individualized sequences are analyzed, and the influences of the variations on the genes are obtained. The method fully considers the genomic environment where the variations are located, a large quantity of annotation errors are avoided, and the accuracy of the annotation variation effect is remarkably improved.

Description

technical field [0001] The invention relates to the field of bioinformatics, and more specifically relates to a method for determining the functional influence of genetic variation based on genome environment. Background technique [0002] With the rapid development of high-throughput genetic variation detection technology represented by deep sequencing, it is now possible to quickly identify genetic variation in individual genomes. However, how to accurately determine the impact of these genetic variations on biomolecular functions, so as to provide clues, guidance and support for subsequent applications such as personalized medicine and molecular breeding, is still a major challenge in this field. [0003] Currently commonly used methods in the field of variant annotation (e.g., VEP [1] 、ANNOVAR [2] ) is usually taken as a unit of variation, and the impact of each variation is independently processed based on a reference gene model. Obviously, this approach of assuming ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18
CPCG16B20/00
Inventor 高歌程斯进
Owner PEKING UNIV
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