Journal article

STRetch: detecting and discovering pathogenic short tandem repeat expansions

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

GENOME BIOLOGY | BMC | Published : 2018

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 .

Grants

Awarded by Australian Genomics Health Alliance PhD Award - NHMRC


Awarded by NHMRC Fellowship


Awarded by NHMRC Project


Awarded by EU Collaborative Grant


Awarded by National Health and Medical Research Council, Career Development Fellowship


Awarded by National Heart, Lung and Blood Institute


Awarded by NATIONAL HUMAN GENOME RESEARCH INSTITUTE


Funding Acknowledgements

HD is supported by an Australian Government Research Training Program (RTP) Scholarship, a Murdoch Children's Research Institute Top Up Scholarship, and an Australian Genomics Health Alliance PhD Award, funded by NHMRC (GNT1113531). NGL is supported by NHMRC Fellowship APP1117510, NHMRC Project Grant APP1080587, and EU Collaborative Grant APP1055295. AO is funded by a National Health and Medical Research Council, Career Development Fellowship GNT1126157. This work was supported in part by the National Human Genome Research Institute, the National Eye Institute, and the National Heart, Lung and Blood Institute grant UM1 HG008900.