AluMine: alignment-free method for the discovery of polymorphic Alu element insertions

Mobile DNA
Tarmo PuurandMaido Remm

Abstract

Recently, alignment-free sequence analysis methods have gained popularity in the field of personal genomics. These methods are based on counting frequencies of short k-mer sequences, thus allowing faster and more robust analysis compared to traditional alignment-based methods. We have created a fast alignment-free method, AluMine, to analyze polymorphic insertions of Alu elements in the human genome. We tested the method on 2,241 individuals from the Estonian Genome Project and identified 28,962 potential polymorphic Alu element insertions. Each tested individual had on average 1,574 Alu element insertions that were different from those in the reference genome. In addition, we propose an alignment-free genotyping method that uses the frequency of insertion/deletion-specific 32-mer pairs to call the genotype directly from raw sequencing reads. Using this method, the concordance between the predicted and experimentally observed genotypes was 98.7%. The running time of the discovery pipeline is approximately 2 h per individual. The genotyping of potential polymorphic insertions takes between 0.4 and 4 h per individual, depending on the hardware configuration. AluMine provides tools that allow discovery of novel Alu element inserti...Continue Reading

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Citations

Feb 19, 2020·Nucleic Acids Research·Clément GoubertCédric Feschotte
May 3, 2020·Genome Biology and Evolution·W Scott WatkinsLynn B Jorde
Dec 10, 2020·European Journal of Human Genetics : EJHG·Gou YamamotoKiwamu Akagi
Mar 15, 2021·Human Mutation·Lauris KaplinskiMaido Remm

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Datasets Mentioned

BETA
NA12878

Methods Mentioned

BETA
PCR
genotyping

Software Mentioned

lex2
RetroSeq
VariationHunter
GenomeTester4
Hydra
STEAK
+ script
FastGT
me
TEA

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