STRetch: detecting and discovering pathogenic short tandem repeat expansions.

TitleSTRetch: detecting and discovering pathogenic short tandem repeat expansions.
Publication TypeJournal Article
Year of Publication2018
AuthorsDashnow, H, Lek, M, Phipson, B, Halman, A, Sadedin, S, Lonsdale, A, Davis, M, Lamont, P, Clayton, JS, Laing, NG, MacArthur, DG, Oshlack, A
JournalGenome Biol
Date Published2018 08 21
KeywordsAlleles, Chromosomes, Human, DNA Repeat Expansion, Genetic Loci, Genome, Human, Humans, Microsatellite Repeats, Polymerase Chain Reaction, Software

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 .

Alternate JournalGenome Biol.
PubMed ID30129428
PubMed Central IDPMC6102892
Grant ListUM1 HG008900 / HG / NHGRI NIH HHS / United States
GNT1126157 / / National Health and Medical Research Council / International