iMGEins: detecting novel mobile genetic elements inserted in individual genomes

Area of Science:

• Genomics
• Bioinformatics
• Molecular Biology

Background:

• Advances in sequencing technology enable investigation of structural variations and their role in disease physiology, such as cancer.
• Mobile genetic elements (MGEs) are significant components of human genomes, contributing to genome instability through various mechanisms.

Purpose of the Study:

• To develop a novel computational tool, iMGEins, for identifying mobile genetic elements (MGEs) in individual genomes.
• To explore the breakpoints and supporting reads associated with MGE insertions.

Main Methods:

• iMGEins integrates discordant read-pair mapping, split-read mapping, and insertion sequence assembly for MGE detection.
• The program was evaluated using simulated and real personal genome data, including the NA12878 sample.

Main Results:

• iMGEins demonstrated outstanding performance in detecting novel MGEs with average recall and precision rates of 96.67% and 100%, respectively.
• It achieved the highest accuracy in detecting MGEs within 20 bp proximity of annotated breakpoints compared to other programs.
• The tool successfully identified novel MGEs and assembled inserted sequences.

Conclusions:

• iMGEins accurately detects MGE breakpoints and reports inserted MGEs, facilitating the study of MGE dynamics in individual genomes.
• Its key features include the identification and assembly of novel MGEs, surpassing existing MGE detection programs.