System for detecting potential pathogenic variants of exome based on family

A mutation detection and exon technology, which is applied in the determination/inspection of microorganisms, special data processing applications, instruments, etc., can solve the problems of high heterogeneity, high noise, high mutation rate, etc.

Inactive Publication Date: 2016-08-17
WANKANGYUAN TIANJIN GENE TECH CO LTD
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Problems solved by technology

[0005] In view of this, the present invention proposes a family-based exome potential pathogenic variant detection system, focusing on s

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  • System for detecting potential pathogenic variants of exome based on family
  • System for detecting potential pathogenic variants of exome based on family

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Embodiment Construction

[0028] It should be noted that, in the case of no conflict, the embodiments of the present invention and the features in the embodiments can be combined with each other.

[0029] The present invention will be described in detail below with reference to the accompanying drawings and examples.

[0030] Such as figure 1 Shown flow process, software system of the present invention mainly comprises 4 modules:

[0031] (1) The annotation integration module, including the variantMatrix.pl program, reads the result file of the exome sequencing data processing flow, merges the variant vcf file of each sample and the ANNOVAR annotation file, performs functional filtering, and obtains a preliminary integration file, Each sample is divided into two files, SNP and INDEL, according to the variation type;

[0032] Among them, the ANNOVAR annotation result file must be input from the vcf file corresponding to the name, and obtained by using ANNOVAR annotation. It is a table, each row record...

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Abstract

The invention provides a system for detecting potential pathogenic variants of exome based on a family. The system comprises a comment integration module for reading a result file of exome sequencing data processing flow, a matrix segmentation module for extracting variants in all samples t, solving a union set and then combining all the samples to form a matrix, a potential pathogenic variant mining module for extracting variant information from the obtained matrix for being enumerated, evaluating pathogenicity of individual variants and combined double-site variants to obtain a list of potential pathogenic variants, and a potential pathogenic variant recording module for recording occurrence of a site in each sample and a target gene and displaying with icons. Output results of conventional exome sequencing low processing are used as input conditions to complete the integration and basic filtration of data; a candidate set of potential pathogenic variants is obtained according to a special variant screening algorithm, so that the system provided by the invention solves the problem of mining of potential pathogenic variants of sequencing data with high heterogeneity, high mutation rate and high noise.

Description

technical field [0001] The invention belongs to the field of gene information data processing, and in particular relates to a family-based exome potential pathogenic variation detection system. Background technique [0002] Exome sequencing technology is well established, and the number of studies applying this technology to detect pathogenic variants is numerous. As a result, algorithms to detect pathogenic variants have emerged in an endless stream. Usually, a whole exome sequencing with an average sequencing depth as low as 20 can detect 50,000 variant sites for each sample. common problems. [0003] In the past, the search space for causative variants has been narrowed by the degree to which the variant is shared among case or control samples. For irrelevant people, this is almost the only means of filtering. Therefore, pedigree information provides important clues for the study of genetic diseases, and a variety of genetic models have been constructed for further sc...

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Application Information

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IPC IPC(8): C12Q1/68G06F19/24
Inventor 薛成海马熹马飞张广发
Owner WANKANGYUAN TIANJIN GENE TECH CO LTD
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