title: Inferring short tandem repeat variation from paired-end short reads.
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.
authors.affiliation: School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, St Lucia QLD 4072, Australia, Clayton School of Information Technology, Monash University, Clayton, VIC 3800, Australia, School of Biological Sciences, Monash University, Melbourne, Australia and Advanced Water Management Centre, The University of Queensland, Queensland, Australia.
authors.forename: Minh Duc
authors.initials: MD
authors.lastname: Cao
authors.forename: Edward
authors.initials: E
authors.lastname: Tasker
authors.forename: Kai
authors.initials: K
authors.lastname: Willadsen
authors.forename: Michael
authors.initials: M
authors.lastname: Imelfort
authors.forename: Sailaja
authors.initials: S
authors.lastname: Vishwanathan
authors.forename: Sridevi
authors.initials: S
authors.lastname: Sureshkumar
authors.forename: Sureshkumar
authors.initials: S
authors.lastname: Balasubramanian
authors.forename: Mikael
authors.initials: M
authors.lastname: Bodén
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D001499:Bayes Theorem; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D020080:Tandem Repeat Sequences