Inferring short tandem repeat variation from paired-end short reads

Nucleic Acids Research
Minh Duc CaoMikael Bodén

Abstract

The advances of high-throughput sequencing offer an unprecedented opportunity to study genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive DNA regions. We present a Bayesian method to estimate repeat-length variation from paired-end sequence read data. The method makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats at lengths of relevance to a range of phenotypes. We demonstrate the method's ability to detect and quantify changes in repeat lengths from short read genomic sequence data across genotypes. We use the method to estimate repeat variation among 12 strains of Arabidopsis thaliana and demonstrate experimentally that our method compares favourably against existing methods. Using this method, we have identified all repeats across the genome, which are likely to be polymorphic. In addition, our predicted polymorphic repeats also included the only known repeat expansion in A. thaliana, suggesting an ability to discover potential unstable repeats.

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Citations

Dec 30, 2014·Ecology and Evolution·Alexander I Putman, Ignazio Carbone
Apr 20, 2016·Advanced Drug Delivery Reviews·Dmitriy KhodakovDavid Yu Zhang
Mar 10, 2015·Computational Biology and Chemistry·Kai-Chiang LiangH Sunny Sun
Sep 4, 2014·Trends in Genetics : TIG·Maximilian O PressChristine Queitsch
Jul 19, 2016·Mathematical Biosciences·Seyed Amir MalekpourMehdi Sadeghi
Feb 6, 2018·Nature Reviews. Genetics·Anthony J Hannan
Feb 14, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Sima TaheriRedmond Ramin Shamshiri
Aug 22, 2018·Genome Biology·Harriet DashnowAlicia Oshlack
Dec 4, 2016·BMC Genomics·Kaname KojimaMasao Nagasaki
Jul 16, 2020·F1000Research·Andreas Halman, Alicia Oshlack
Jul 14, 2021·Chemical Reviews·Min LiQiang Xia

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Datasets Mentioned

BETA
CS76310

Methods Mentioned

BETA
Illumina sequencing
PCR
electrophoresis
genotyping

Software Mentioned

Dindel
MoDIL
Bowtie
BWA
Samtools mpileup
STRViper
IMR
Samtools
lobSTR
DENOM

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