Feb 6, 2015

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

BioRxiv : the Preprint Server for Biology
Julia H WildschutteJeffrey M Kidd

Abstract

Alu insertions have contributed to >11% of the human genome and ~30-35 Alu subfamilies remain actively mobile, yet the characterization of polymorphic Alu insertions from short-read data remains a challenge. We build on existing computational methods to combine Alu detection and de novo assembly of WGS data as a means to reconstruct the full sequence of insertion events from Illumina paired end reads. Comparison with published calls obtained using PacBio long-reads indicates a false discovery rate below 5%, at the cost of reduced sensitivity due to the colocation of reference and non-reference repeats. We generate a highly accurate call set of 1,614 completely assembled Alu variants from 53 samples from the Human Genome Diversity Project panel. We utilize the reconstructed alternative insertion haplotypes to genotype 1,010 fully assembled insertions, obtaining >99% accuracy. In our assembled sequences, we find evidence of non-classical insertion mechanisms and observe 5? truncation in 16% of AluYa5 and AluYb8 insertions. The sites of truncation coincide with stem-loop structures and SRP9/14 binding sites in the Alu RNA, implicating L1 ORF2p pausing in the generation of 5? truncations.

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Mentioned in this Paper

Gene Polymorphism
Genome
SRP9
SRP9 gene
Site
Alu Elements
Protein Domain
Protein Truncation
Local
LINE-1 Elements

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