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STRetch: detecting and discovering pathogenic short tandem repeats expansions

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

Posted 04 Jul 2017
bioRxiv DOI: 10.1101/159228 (published DOI: 10.1186/s13059-018-1505-2)

Short tandem repeat (STR) expansions have been identified as the causal DNA mutation in dozens of Mendelian diseases. Historically, pathogenic STR expansions could only be detected by single locus techniques, such as PCR and electrophoresis. The ability to use short read sequencing data to screen for STR expansions has the potential to reduce both the time and cost to reaching diagnosis and enable the discovery of new causal STR loci. Most existing tools detect STR variation within the read length, and so are unable to detect the majority of pathogenic expansions. Those tools that can detect large expansions are limited to a set of known disease loci and as yet no new disease causing STR expansions have been identified with high-throughput sequencing technologies. Here we address this by presenting STRetch, a new genome-wide method to detect STR expansions at all loci across the human genome. We demonstrate the use of STRetch for detecting pathogenic STR expansions in short-read whole genome sequencing data and apply it to the analysis of 97 whole genomes to reveal variation at STR loci. We further demonstrate the application of STRetch to solve cases of patients with undiagnosed disease, in which STR expansions are a likely cause. STRetch assesses expansions at all STR loci in the genome and allows screening for novel disease-causing STRs. STRetch is open source software, available from github.com/Oshlack/STRetch.

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