Detection device and method for gene fusion

Abstract

The invention discloses a detection device and method for gene fusion. The detection method is executed between sequence alignment and local assembly verification and comprises the step of local sequence clustering. The method for local sequence clustering comprises the steps that local clustering is conducted on a second A type sequence which is partially matched with a first position and is also partially matched with a second position of a reference genome and a second B type sequence which is partially matched with the first position and is not partially matched with the second position based on the distance between the first position and the second position, so that a series of first position clusters and a series of second position clusters are obtained; local assembly is conducted on second A type sequences and second B type sequences in the series of second position clusters, so that an assembly sequence is obtained; the assembly sequence is compared with the reference genome again, whether the comparison result of the assembly sequence is consistent with a comparison result for second A type sequences in the second position clusters is checked, if yes, it is proved that the first position and the second position are the gene fusion positions. According to the detection method, the true positive rate is high, and the result is more reliable.

Description

technical field [0001] The invention relates to the field of biological information, in particular to a detection device and method for gene fusion. Background technique [0002] In agricultural economic species, especially agricultural animals and plants with important economic value, differences in genome structure lead to differences in individual traits, in which gene fusion plays an important role. Gene fusion refers to the phenomenon that two translocated genes on the chromosome are chimerized together to form a chimeric gene. This phenomenon is generally due to chromosomal translocations, deletions, or inversions. Gene fusion is an important type of variation in organisms, which may cause overexpression of genes, etc., resulting in great changes in the traits of organisms, and these changes are usually unfavorable. [0003] Therefore, accurate detection of gene fusion in individual genomes can provide a new platform for the further exploration and utilization of agr...

AI Technical Summary

Problems solved by technology

[0007] Among the above two detection methods, the detection method based on PE relationship is to perform fusion detection (for example, Break Dancer) based on the information of abnormal paired-end alignment sequences (reads), which can only roughly give the fusion position, but cannot determine the exact position. breakpoint information, and the false positives of such methods are high

like figure 1 As shown, each pair of black lines in opposite directions and the dotted line in the middle indicate the size of the insert fragment in the sequencing library, the direction of the arrow indicates the direction of library sequencing, and a pair of black lines in opposite directions indicates a pair of sequences obtained by double-end sequencing (reads ), figure 1 It shows that when each pair of sequences (reads) in multiple pairs of sequences (reads) obtained by sequencing is compared with the reference genome sequence, it can be compared to different chromosome positions in the reference genome, but the exact breakpoint cannot be determined Location

[0008] The detection method based on truncated alignment is a method of using incompletely aligned sequence information to determine the position of the breakpoint and then determine the fusion method, or does not perform local assembly so that the fusion breakpoint is not verified (for example, Pindel), or there is no Time-consuming assembly due to full use of sequence alignment information (e.g., CREST)

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