Exome potential pathogenic mutation detection method based on family line

A technology for exome sequencing and mutation detection, which is applied in biochemical equipment and methods, microbial measurement/testing, instruments, etc., and can solve problems such as high heterogeneity, pathogenic variant mining of sequencing data, and high mutation rate

Inactive Publication Date: 2016-09-07
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 method for detecting potential pathogenic variants in exomes, focusing on solving the problem of mining potential pathogenic variants in sequencing data with high heterogeneity, high mutation rate, and high noise

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  • Exome potential pathogenic mutation detection method based on family line
  • Exome potential pathogenic mutation detection method based on family line

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Embodiment Construction

[0031] 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.

[0032] The present invention will be described in detail below with reference to the accompanying drawings and examples.

[0033] Such as figure 1 Shown, the present invention mainly comprises 4 steps:

[0034] (1) Read the result file of the exome sequencing data processing flow, merge the variation vcf file and ANNOVAR annotation file of each sample, and perform functional filtering to obtain a preliminary integration file. Each sample is divided into SNP and SNP according to the variation type. INDEL two files;

[0035] 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 records a variation, and each column records an annotation, including and only including the following columns:

[...

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Abstract

The invention provides an exome potential pathogenic mutation detection method based on a family line. The detection method comprises the following steps: 1) reading a result file of an exome sequencing data processing flow, and conducting function filtering; 2) reading the file obtained in the last step, extracting mutations in all samples, calculating a union set, and then combining all samples, so that a matrix is constituted; 3) extracting mutation information in the matrix obtained in the last step, enumerating and assessing pathogenicity of single mutation and pathogenicity of combined dual-site mutation, so that a potential pathogenic mutation list is obtained; and 4) in accordance with the list obtained in the last step, calculating the appearance situations of sites in various samples and target genes. According to the method disclosed by the invention, data integration and basic filtration are completed by taking an output result of the common exome sequencing processing flow as an input condition; by virtue of a special mutation screening algorithm, a candidate set of the potential pathogenic mutations is provided; and the method focuses on solving a problem on potential pathogenic mutation mining 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, in particular to a family-based method for detecting potential pathogenic variants of exomes. 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 screeni...

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): C12Q1/68G06F19/24
CPCC12Q1/6883C12Q2600/156G16B40/00
Inventor 薛成海李连硕关晋霞吕艳玲
Owner WANKANGYUAN TIANJIN GENE TECH CO LTD
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