TypeTE

TypeTE genotypes mobile element insertions, primarily Alu retrotransposons, from whole-genome sequencing data to reconstruct presence/absence alleles and compute genotype likelihoods for population-genomic analyses.

Key Features:

• Targeted genotyping: Specializes in genotyping segregating mobile element insertions, with a focus on Alu retrotransposons.
• Improved accuracy: Identifies hallmarks such as poly-A tails and target site duplications and uses local re-assembly to reconstruct presence and absence alleles and determine insertion orientation.
• Genotype likelihood computation: Remaps sequencing reads to reconstructed allele sequences to compute genotype likelihoods.
• Adaptability: Applicable to other retrotransposon families beyond Alu when provided with candidate insertion calls.

Scientific Applications:

• Population genomics of structural variation: Enables genotyping of Alu insertions to study population structure and the distribution of mobile element polymorphisms.
• Functional impact assessment: Supports investigation of how Alu insertions affect gene expression and genome function by providing presence/absence genotypes.
• Benchmarking and validation: Supports validation against PCR-based genotyping, with reported genotype accuracy improvements (from 83% to 92%) across a gold-standard set of >200 loci.

Methodology:

Starts from a list of polymorphic Alu insertions (e.g., from MELT), performs local re-assembly to reconstruct presence and absence alleles while assessing poly-A tails, target site duplications, and orientation, and remaps sequencing reads to the reconstructed alleles to compute genotype likelihoods.