iMGEins

iMGEins identifies novel mobile genetic elements (MGEs) in personal genomes by detecting insertion breakpoints from sequencing reads and assembling inserted sequences to characterize MGEs and their impact on genome stability.

Key Features:

• Discordant read-pair mapping: identifies read pairs with unexpected distances or orientations indicative of MGE insertions.
• Split-read mapping: maps reads that span breakpoints to precisely localize insertion sites and characterize insertion structure.
• Insertion sequence assembly: assembles sequences from reads spanning insertion sites to reconstruct full MGE sequences.
• Breakpoint support analysis: uses supporting reads to validate detected MGEs and refine breakpoint positions.
• Performance metrics: reported average recall of 96.67% and precision of 100% on simulated and real personal genomes, including high accuracy within 20 base pairs of annotated breakpoints in NA12878.

Scientific Applications:

• Novel MGE discovery: detection and assembly of previously unannotated mobile genetic elements in individual genomes.
• Genome instability analysis: characterization of MGE insertions that contribute to insertion, mutation, and rearrangement events affecting genome stability.
• Disease association studies: investigation of MGE-related structural variation in contexts such as cancer by mapping insertions and assembled sequences.

Methodology:

iMGEins integrates discordant read-pair mapping, split-read mapping, and insertion sequence assembly to detect breakpoints from sequencing reads and reconstruct inserted MGE sequences.