Complex structure variation detecting method based on hybrid strategy

A technology for complex structure and variation detection, applied in the field of data science, can solve problems such as deficiencies, and achieve the effect of reducing the interference of assembly performance, high reliability, and improving accuracy

Active Publication Date: 2019-07-12
XI AN JIAOTONG UNIV
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Problems solved by technology

The pairwise combination strategy has improved the sensitivity and specificity of the software for low-frequency mutations to a certain extent, but

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  • Complex structure variation detecting method based on hybrid strategy
  • Complex structure variation detecting method based on hybrid strategy
  • Complex structure variation detecting method based on hybrid strategy

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Embodiment Construction

[0049] The present invention provides a complex structural variation detection method based on a mixed strategy, which integrates three strategies of paired-end mapping method, split-read method and local assembly method to accurately identify structural variation, and improves the detection efficiency of low-frequency mutations and insertion fragments. Exact call rate for structural variants in deleted variants.

[0050] see figure 1 , a method for detecting complex structural variations based on a mixed strategy of the present invention, comprising the following steps:

[0051] S1. Information statistics

[0052] Collect the statistical information (mean value μ, variance σ) and chain orientation information of the insert fragment length of statistical read pairs. The read pairs with inconsistent alignments are determined through the above parameters. The read pairs with inconsistent alignments refer to the read pairs with abnormalities in the alignment of the read alignme...

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Abstract

The invention discloses a complex structure variation detecting method based on a hybrid strategy. The method comprises the steps of collecting and performing statistics on inserting fragment length distribution and chain direction information of a read pair in double-end sequencing, determining a read pair contrasting chain direction, an inserting fragment length and the read pair with an abnormal chromosome through two-end read segment contrasting; identifying breakpoints by means of a hybrid strategy of a double-end mapping method, a local assembling method and a split read segment method;wherein the breakpoints are coordinates on a pair of reference genome and are adjacent in a sample and are separated in the reference genome; updating breakpoint position information according to a contrasting result, and changing the breakpoint interval which records the structure variation breakpoint information to an accurate position; wherein the structure variation breakpoint information comprises a structure variation type, a breakpoint starting position and a support read segment number; and recording the contrast quality of the read pair and the read pair number of the support breakpoints, thereby finishing accurate structure variation identification. The complex structure variation detecting method improves variation detecting precision and supplies a checkout method for complex structure variations.

Description

technical field [0001] The invention belongs to the technical field of data science with the application background of precision medicine, and in particular relates to a complex structure variation detection method based on a mixed strategy. Background technique [0002] Cancer is currently the disease with the highest morbidity and mortality in China. In the past two decades, modern oncology, especially tumor genomics, has developed rapidly, resulting in precise diagnosis and treatment of tumors, which has greatly improved the five-year survival rate of cancer. The basis of precision treatment is to analyze and detect key gene mutations with high sensitivity, high specificity, and high efficiency. The efficacy of precision treatment greatly depends on the accuracy of data analysis. [0003] According to the definition of genomics, gene mutation can be divided into single nucleotide variation (English name: singlenucleotide variants, English abbreviation: SNV) and structura...

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Application Information

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IPC IPC(8): G16B15/00G16B20/20G16B40/00
Inventor 王妙王嘉寅张选平韩博刘涛管彦芳王旭文王申杰
Owner XI AN JIAOTONG UNIV
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