ME-Scan

ME-Scan identifies polymorphic mobile element insertions (pMEIs) from the AluYb, L1HS, and SVA retrotransposon families in mammalian genomes, with a focus on human samples, to characterize genomic variation and impacts on gene expression, genome integrity, and disease.

Key Features:

• Targeted identification: Detects insertions from the three major active human mobile element families AluYb, L1HS, and SVA.
• High sensitivity and accuracy: Demonstrates reported sensitivity >90% and accuracy >95% for pMEI detection.
• Library pooling for single-run detection: Pools libraries of the three element families to enable simultaneous identification of pMEIs in a single Illumina sequencing run.
• Flexibility and adaptability: Protocol can be adapted for genomes beyond human to extend utility across species.
• Comprehensive experimental and computational framework: Provides library design, sequencing protocols, and computational pipelines for downstream analyses.

Scientific Applications:

• Genomic variation studies: Identification of pMEIs to analyze sources and consequences of genomic variation.
• Gene expression regulation research: Examination of how mobile elements influence gene expression patterns.
• Disease association studies: Investigation of the roles of pMEIs in disease etiology and progression.
• Genome integrity analysis: Studies of mobile element impacts on genome stability and integrity.

Methodology:

The protocol includes computational pipelines for downstream analyses of Illumina sequencing data derived from selectively amplified insertion sites of active retrotransposons.