Discovery and characterization of Alu repeat sequences via precise local read assembly

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Alu elements comprise over 11% of the human genome, with active subfamilies contributing to genetic diversity.
• Characterizing polymorphic Alu insertions from short-read sequencing data presents significant computational challenges.

Purpose of the Study:

• To develop and validate a computational method for accurate reconstruction and characterization of Alu insertion events using whole genome sequencing (WGS) data.
• To generate a high-confidence dataset of assembled Alu variants and investigate their insertion mechanisms and structural variations.

Main Methods:

• Combined Alu detection with de novo assembly of WGS data to reconstruct full Alu insertion sequences from Illumina paired-end reads.
• Validated assembled Alu variants against long-read sequencing data and PCR genotyping.
• Analyzed assembled sequences for evidence of premature insertion mechanisms and structural features like 5' truncation.

Main Results:

• Generated a call set of 1614 fully assembled Alu variants from 53 Human Genome Diversity Project (HGDP) samples with a false discovery rate below 5%.
• Achieved >99% agreement with PCR-based genotypes for 1010 assembled insertions.
• Identified 5' truncation in 16% of AluYa5 and AluYb8 insertions, linked to RNA structures and L1 ORF2p pausing.
• Discovered variable AluJ and AluS elements potentially generated by non-retrotransposition mechanisms.

Conclusions:

• The developed computational approach enables accurate characterization of polymorphic Alu insertions from short-read WGS data.
• The study provides insights into Alu insertion mechanisms, including premature insertion and 5' truncation, and identifies novel Alu variants.
• This work enhances the understanding of Alu element dynamics and their contribution to human genome variation.