2020
DOI: 10.1186/s13059-020-02017-z
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ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data

Abstract: Repeat expansions are responsible for over 40 monogenic disorders, and undoubtedly more pathogenic repeat expansions remain to be discovered. Existing methods for detecting repeat expansions in short-read sequencing data require predefined repeat catalogs. Recent discoveries emphasize the need for methods that do not require pre-specified candidate repeats. To address this need, we introduce ExpansionHunter Denovo, an efficient catalog-free method for genome-wide repeat expansion detection. Analysis of real an… Show more

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Cited by 122 publications
(117 citation statements)
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“…While our work was under review, a study conducted by Trost et al 41 was published that investigated STRs of 2–20 bp in a genome-wide setting and in relation to autism spectrum disorder 41 . In our study, we detected a much higher number of CGG STR loci than Trost and colleagues, as the emphasis of their work was on expanded STR loci utilizing ExpansionHunter Denovo 42 . This algorithm only detects repeat expansions that exceed the length of the sequencing reads, typically 150 bp, corresponding to 50 CGG repeat expansions.…”
Section: Discussionmentioning
confidence: 49%
“…While our work was under review, a study conducted by Trost et al 41 was published that investigated STRs of 2–20 bp in a genome-wide setting and in relation to autism spectrum disorder 41 . In our study, we detected a much higher number of CGG STR loci than Trost and colleagues, as the emphasis of their work was on expanded STR loci utilizing ExpansionHunter Denovo 42 . This algorithm only detects repeat expansions that exceed the length of the sequencing reads, typically 150 bp, corresponding to 50 CGG repeat expansions.…”
Section: Discussionmentioning
confidence: 49%
“…To screen for extremely long STR expansions (similar to the C9orf72 repeat expansion) at loci that not included in the predefined STR catalogues, we applied ExpansionHunter-Denovo 74 . This method aims to only find STR expansions that exceed the sequencing read-length (> 150 bp) by identifying reads (mapped, mismapped and unmapped) that contain STR motifs, using their mate pairs for de novo mapping to the reference genome.…”
Section: Methodsmentioning
confidence: 99%
“…For all individuals that were sequenced on the HiSeqX dataset (5,392 cases, 1,795 controls) we screened all loci harboring SNPs associated with ALS meeting genome-wide significance for expansions of known and new short tandem repeats (STRs) using ExpansionHunter 73 and ExpansionHunter Denovo 74 .…”
Section: Short Tandem Repeat Screenmentioning
confidence: 99%
“…GeneBreaker is hosted on a virtual web server at the Centre for Molecular Medicine and Therapeutics, with 12 GB of RAM and 4 CPUs running CentOS 7. The variant data within the underlying repository comes from open‐source variant catalogs including ClinVar (Landrum et al, 2018), ClinGen (Rehm et al, 2015), and a manually curated set of pathogenic short tandem repeat expansions (Table S1) (Dolzhenko et al, 2020). Gene models come from the RefSeq annotation database provided by the UCSC Genome Browser (NCBI Homo sapiens Annotation Release 109 (March 29, 2018); Haeussler et al, 2019).…”
Section: Methodsmentioning
confidence: 99%