STRetch: detecting and discovering pathogenic short tandem repeat expansions

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 pres...

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Main Authors:	Harriet Dashnow, Monkol Lek, Belinda Phipson, Andreas Halman, Simon Sadedin, Andrew Lonsdale, Mark Davis, Phillipa Lamont, Joshua S. Clayton, Nigel G. Laing, Daniel G. MacArthur, Alicia Oshlack
Format:	Article
Language:	English
Published:	BMC 2018-08-01
Series:	Genome Biology
Online Access:	http://link.springer.com/article/10.1186/s13059-018-1505-2

id	doaj-4551a90d1c484cf283843fa6e6c0815d
record_format	Article
spelling	doaj-4551a90d1c484cf283843fa6e6c0815d2020-11-24T21:22:57ZengBMCGenome Biology1474-760X2018-08-0119111310.1186/s13059-018-1505-2STRetch: detecting and discovering pathogenic short tandem repeat expansionsHarriet Dashnow0Monkol Lek1Belinda Phipson2Andreas Halman3Simon Sadedin4Andrew Lonsdale5Mark Davis6Phillipa Lamont7Joshua S. Clayton8Nigel G. Laing9Daniel G. MacArthur10Alicia Oshlack11Murdoch Children’s Research Institute, Royal Children’s HospitalAnalytic and Translational Genetics Unit, Massachusetts General HospitalMurdoch Children’s Research Institute, Royal Children’s HospitalMurdoch Children’s Research Institute, Royal Children’s HospitalMurdoch Children’s Research Institute, Royal Children’s HospitalMurdoch Children’s Research Institute, Royal Children’s HospitalDepartment of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical CentreNeurogenetic Unit, Royal Perth HospitalHarry Perkins Institute of Medical Research, Centre for Medical Research, University of Western AustraliaHarry Perkins Institute of Medical Research, Centre for Medical Research, University of Western AustraliaAnalytic and Translational Genetics Unit, Massachusetts General HospitalMurdoch Children’s Research Institute, Royal Children’s HospitalAbstract 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.http://link.springer.com/article/10.1186/s13059-018-1505-2
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Harriet Dashnow Monkol Lek Belinda Phipson Andreas Halman Simon Sadedin Andrew Lonsdale Mark Davis Phillipa Lamont Joshua S. Clayton Nigel G. Laing Daniel G. MacArthur Alicia Oshlack
spellingShingle	Harriet Dashnow Monkol Lek Belinda Phipson Andreas Halman Simon Sadedin Andrew Lonsdale Mark Davis Phillipa Lamont Joshua S. Clayton Nigel G. Laing Daniel G. MacArthur Alicia Oshlack STRetch: detecting and discovering pathogenic short tandem repeat expansions Genome Biology
author_facet	Harriet Dashnow Monkol Lek Belinda Phipson Andreas Halman Simon Sadedin Andrew Lonsdale Mark Davis Phillipa Lamont Joshua S. Clayton Nigel G. Laing Daniel G. MacArthur Alicia Oshlack
author_sort	Harriet Dashnow
title	STRetch: detecting and discovering pathogenic short tandem repeat expansions
title_short	STRetch: detecting and discovering pathogenic short tandem repeat expansions
title_full	STRetch: detecting and discovering pathogenic short tandem repeat expansions
title_fullStr	STRetch: detecting and discovering pathogenic short tandem repeat expansions
title_full_unstemmed	STRetch: detecting and discovering pathogenic short tandem repeat expansions
title_sort	stretch: detecting and discovering pathogenic short tandem repeat expansions
publisher	BMC
series	Genome Biology
issn	1474-760X
publishDate	2018-08-01
description	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.
url	http://link.springer.com/article/10.1186/s13059-018-1505-2
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STRetch: detecting and discovering pathogenic short tandem repeat expansions

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