A method and device for detecting precise breakpoints of CNV and features around the breakpoints

Abstract

The invention discloses a method for detecting precise breakpoints of CNV and features around the breakpoints, comprising the following steps: using known CNV detection software to detect ambiguous CNV breakpoints; extracting abnormal read pairs around the ambiguous CNV breakpoints; Find out the read pairs that are aligned at one end and truncated at the other end. When such read pairs are located near the breakpoint and there are more than 3 high-quality reads that are truncated by more than 10 bp, we calculate the mapping part of the high-quality reads and the truncated reads. Cut the part to obtain two precise CNV breakpoints; verify whether the two precise CNV breakpoints are the two breakpoints of the target CNV according to the read pairs of abnormal insert size; obtain the features around the breakpoint; the present invention Also disclosed is a device for detecting the exact breakpoint of CNV and features around the breakpoint; the method and device for detecting the exact breakpoint of CNV and features around the breakpoint of the present invention focus on alignment errors, sequencing errors and the existence of similar sequences and other factors to help detect the precise breakpoint of CNV and the features around the breakpoint.

Description

technical field [0001] The invention relates to the field of CNV breakpoint detection, in particular to a method and device for detecting the precise breakpoint of CNV and the features around the breakpoint. Background technique [0002] At present, there are many methods used to detect CNV, such as split-read method (AGE, Pindel, ClipCrop), paired-end method (BreakDancer, PEMer), read-depth method (ReadDepth, CNVnator, CNV-seq) , sequence assembly methods, and comprehensive methods (DELLY:), many of these methods can achieve single-base level accuracy, and have high accuracy and sensitivity. However, affected by many factors, such as mapping error, sequencing errors, and the presence of microhomology, the breakpoints detected by these methods still have a difference of tens of bp from the real accurate breakpoints. At the same time, many methods for detecting CNVs are designed to detect CNVs in the whole genome, so the general functions are limited, the details cannot be p...

AI Technical Summary

Problems solved by technology

However, affected by many factors, such as mapping error, sequencing errors, and the presence of microhomology, the breakpoints detected by these methods still have a difference of tens of bp from the real accurate breakpoints.

At the same time, many methods for detecting CNVs are designed to detect CNVs in the whole genome, so the general functions are limited, the details cannot be perfected, and the features around the breakpoints (micro-mutations, insert sequence and microhomology, etc.) cannot be detected at the same time. Only some features can be detected, such as Breakseq software can detect microhomology

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