July 7, 2019  |  

STRetch: detecting and discovering pathogenic short tandem repeat expansions.

Authors: Dashnow, Harriet and Lek, Monkol and Phipson, Belinda and Halman, Andreas and Sadedin, Simon and Lonsdale, Andrew and Davis, Mark and Lamont, Phillipa and Clayton, Joshua S and Laing, Nigel G and MacArthur, Daniel G and Oshlack, Alicia

Short tandem repeat (STR) expansions have been identified as the causal DNA mutation in dozens of Mendelian diseases. Most existing tools for detecting STR variation with short reads do so within the read length and so are unable to detect the majority of pathogenic expansions. Here we present STRetch, a new genome-wide method to scan for STR expansions at all loci across the human genome. We demonstrate the use of STRetch for detecting STR expansions using short-read whole-genome sequencing data at known pathogenic loci as well as novel STR loci. STRetch is open source software, available from .

Journal: Genome biology
DOI: 10.1186/s13059-018-1505-2
Year: 2018

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