Method and device for detecting gene fusion of target areas and storage medium

A gene fusion, target area technology, applied in special data processing applications, instruments, electrical digital data processing, etc., can solve the problems of insufficient data consideration, sensitivity defects, inability to maximize computing resources and running time, etc., to achieve optimization Resource requirements and detection speed, effects of improved sensitivity and specificity

Active Publication Date: 2018-05-04
深圳裕策生物科技有限公司
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AI Technical Summary

Problems solved by technology

Due to the limitations of the target area and clustering, it will cause defects in sensitivity; the data used does not fully consider the impact of comparison errors on the detect

Method used

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  • Method and device for detecting gene fusion of target areas and storage medium
  • Method and device for detecting gene fusion of target areas and storage medium
  • Method and device for detecting gene fusion of target areas and storage medium

Examples

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Embodiment 1

[0065] according to figure 1 In the process shown, BWA is used to compare the PE sequencing data of the target region of the quality-assessed gene fusion positive sample (ALK exon 20-EML4exon13, 45-55%) with the human reference genome, after marking duplicated reads (duplicated reads) Wait for the processing process to obtain the comparison result in BAM format, and then use it as the input data of the method of the present invention to detect the gene fusion in the target region. Specifically, the method steps and detection parameter settings are as follows:

[0066] Obtain the result of comparing the paired-end sequencing data of the target region to the human reference genome; filter out sequences with multiple indels (InDel) or short tandem repeats; extract the abnormal size of the insert within the target region and within 200 bp ( Valid information (including alignment position, sequence base, quality value and alignment) of high-quality (quality value higher than 20) u...

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Abstract

The invention discloses a method and device for detecting gene fusion of target areas and a storage medium. The method comprises a comparison result obtaining step, a target area information extraction step, a paired extension area information extraction step, an information annotation step, a breakpoint statistic scoring step, a local clustering step and a local splicing step. According to the method, advantages of double-tail end sequencing reads and comparison information are sufficiently utilized, the detection process does not re-comparison and a complicated assembling process, and the target area can detect gene fusion events through covering one fusion area, so that the sensitivity and specificity of detecting the gene fusion of target areas are greatly enhanced while the resource demand and detection speed are optimized.

Description

technical field [0001] The invention relates to the technical field of gene detection, in particular to a method, device and storage medium for detecting gene fusion in a target region. Background technique [0002] A fused gene is a gene product formed by the fusion of two unrelated genes as a result of a chromosomal translocation, deletion, or chromosomal inversion. [0003] Most of the current mainstream methods for detecting gene fusions are aimed at genome-wide structural variation, such as CREST (clipping reveals structure). The CREST method uses soft shearing information to perform two assembly comparisons, which has the disadvantages of high resource requirements and slow detection speed. At the same time, this method still considers the detection of the whole genome, and the detection effect of sequencing the target region is poor. [0004] The existing method for detecting gene fusion in the target region is mainly FACTERA (Fusion And ChromosomalTranslocation Enum...

Claims

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Application Information

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IPC IPC(8): G06F19/22G06F19/24
CPCG16B30/00G16B40/00
Inventor 陈龙昀高志博李淼王佳茜陈超杨洁
Owner 深圳裕策生物科技有限公司
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