Three-generation sequencing-based whole genome structure variation analysis method and system

Abstract

The invention discloses a three-generation sequencing-based whole genome structure variation analysis method and system. The method comprises the steps of 1) performing sequence splitting; 2) performing sequence comparison; 3) performing genome structure variation preliminary detection; 4) combining and screening genome structure variation preliminary detection results; and 5) performing genome structure variation function annotation. The system comprises a sequence splitting module, a sequence comparison module, a genome structure variation preliminary detection module, a genome structure variation preliminary detection result combining and screening module and a genome structure variation function annotation module. According to the method and the system, by integrating existing three-generation genome structure variation detection technologies PBhoney and Sniffles, the accuracy and sensitiveness of genome structure variation detection under low coverage degree can be effectively improved, and the reliability of the detection results is ensured while the detection cost is reduced.

Description

technical field [0001] The invention belongs to the field of genome structure variation detection, and in particular relates to a method and system for analysis of whole genome structure variation based on three-generation sequencing. Background technique [0002] Genome structural variation usually refers to the insertion, deletion, duplication, inversion, translocation, and DNA copy number variation (CNV) of large fragments in the genome. Genome structural variants affect more genome sequences (~13%) than short sequence variants (SNPs, Indels, etc.), and thus also play a very important role in various diseases. At present, the detection of genomic structural variation mainly includes first-generation sequencing technologies such as oligonucleotide-based array-CGH, ​​SNP array, MLPA, and QPCR, Breakdancer, readdepth, delly, and PIndel analysis technologies based on second-generation sequencing, and PBhoney and Sniffles based on third-generation sequencing. analytical skill...

AI Technical Summary

Problems solved by technology

However, due to the characteristics of the second-generation sequencing read length (about 100-150bp), the reads cannot span the entire variation region. Although a variety of algorithms are used, the detection of genome structure variation still has the disadvantages of low accuracy and low sensitivity; The third-generation sequencing technology has the characteristics of extremely long read length (up to 40K or more), high single-base error rate (15%), and good error randomness (basically not affected by GC content). Currently, the genome structure based on the third generation Although the mutation detection technology (PBhoney, Sniffles, etc.) has greatly improved the problem of low sensitivity of the second-generation technology, the disadvantage of low accuracy still exists

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