PopAlu: population-scale discovery of Alu polymorphisms
- Published
- Accepted
- Subject Areas
- Bioinformatics, Computational Biology, Genomics
- Keywords
- structural variation, mobile element insertion, Alu elements, paired-end sequencing, polymorphism genotyping
- Copyright
- © 2015 Qian et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ PrePrints) and either DOI or URL of the article must be cited.
- Cite this article
- 2015. PopAlu: population-scale discovery of Alu polymorphisms. PeerJ PrePrints 3:e1174v1 https://doi.org/10.7287/peerj.preprints.1174v1
Abstract
Alu elements are sequences of approximately 300 basepairs that combined comprise more than 10% of the human genome. Due to their recent origin in primate evolution some Alu elements are polymorphic in humans, present in some individuals while absent in others. We present PopAlu, a tool to detect polymorphic Alu elements on a population scale from paired-end sequencing data. PopAlu uses read pair distance and orientation as well as split reads to identify the location and precise breakpoints of polymorphic Alus. Genotype calling enables us to differentiate between homozygous and heterozygous carriers, making the output of PopAlu suitable for use in downstream analyses such as genome-wide association studies (GWAS). We show on a simulated dataset that PopAlu calls Alu elements inserted and deleted with respect to a reference genome with high accuracy and high precision. Our analysis of real data of a human trio from the 1000 Genomes Project confirms that PopAlu is able to produce highly accurate genotype calls. To our knowledge, PopAlu is the first tool that identifies polymorphic Alu elements from multiple individuals simultaneously, pinpoints the precise breakpoints and calls genotypes with high accuracy.
Author Comment
This is a submission to PeerJ for review.