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PopAlu: population-scale detection of Alu polymorphisms

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DOI

  • Yu Qian
  • ,
  • Birte Kehr, deCODE Genet Amgen
  • ,
  • Bjarni V. Halldorsson, Reykjavik Univ, Reykjavik University, Inst Biomed & Neural Engn, Sch Sci & Engn

Alu elements are sequences of approximately 300 basepairs that together 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.

Original languageEnglish
Article number1269
JournalPeerJ
Volume3
Number of pages15
ISSN2167-8359
DOIs
Publication statusPublished - 22 Sep 2015

    Research areas

  • Structural variation, Mobile element insertion, Alu elements, Paired-end sequencing, Polymorphism genotyping, GENERATION SEQUENCING DATA, WHOLE-GENOME, INSERTIONS, RETROTRANSPOSITION, DISCOVERY, ELEMENTS, REPEATS

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