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Genome Biol. 2018 Aug 21;19(1):121. doi: 10.1186/s13059-018-1505-2.

STRetch: detecting and discovering pathogenic short tandem repeat expansions.

Author information

1
Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.
2
School of Biosciences, The University of Melbourne, Parkville, VIC, Australia.
3
Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
4
Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
5
Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC, Australia.
6
Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA, Australia.
7
Neurogenetic Unit, Royal Perth Hospital, Perth, WA, Australia.
8
Harry Perkins Institute of Medical Research, Centre for Medical Research, University of Western Australia, Nedlands, WA, Australia.
9
Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia. alicia.oshlack@mcri.edu.au.
10
School of Biosciences, The University of Melbourne, Parkville, VIC, Australia. alicia.oshlack@mcri.edu.au.

Abstract

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 github.com/Oshlack/STRetch .

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