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dc.contributor.authorMc Laughlin, Russell
dc.contributor.authorHardiman, Orla
dc.date.accessioned2019-10-30T10:26:35Z
dc.date.available2019-10-30T10:26:35Z
dc.date.issued2017
dc.date.submitted2017en
dc.identifier.citationMc Laughlin, R., Hardiman, O., et al., Detection of long repeat expansions from PCR-free whole-genome sequence data; Genome Research, 2017, 27, 11, 1895–1903en
dc.identifier.otherY
dc.identifier.urihttp://dx.doi.org/10.1101/gr.225672.117
dc.identifier.urihttp://hdl.handle.net/2262/89949
dc.descriptionPUBLISHEDen
dc.description.abstractIdentifying large expansions of short tandem repeats (STRs), such as those that cause amyotrophic lateral sclerosis (ALS) andfragile X syndrome, is challenging for short-read whole-genome sequencing (WGS) data. A solution to this problem is animportant step toward integrating WGS into precision medicine. We developed a software tool called ExpansionHunter that,using PCR-free WGS short-read data, can genotype repeats at the locus of interest, even if the expanded repeat is larger thanthe read length. We applied our algorithm to WGS data from 3001 ALS patients who have been tested for the presence oftheC9orf72repeat expansion with repeat-primed PCR (RP-PCR). Compared against this truth data, ExpansionHunter cor-rectly classified all (212/212, 95% CI [0.98, 1.00]) of the expanded samples as either expansions (208) or potential expansions(4). Additionally, 99.9% (2786/2789, 95% CI [0.997, 1.00]) of the wild-type samples were correctly classified as wild typeby this method with the remaining three samples identified as possible expansions. We further applied our algorithm to a setof 152 samples in which every sample had one of eight different pathogenic repeat expansions, including those associatedwith fragile X syndrome, Friedreich’s ataxia, and Huntington’s disease, and correctly flagged all but one of the known repeatexpansions. Thus, ExpansionHunter can be used to accurately detect known pathogenic repeat expansions and provides re-searchers with a tool that can be used to identify new pathogenic repeat expansionen
dc.format.extent1895-1903en
dc.language.isoenen
dc.relation.ispartofseriesGenome Res.;
dc.relation.ispartofseries27;
dc.rightsYen
dc.subjectShort tandem repeats (STRs)en
dc.subjectAmyotrophic lateral sclerosis (ALS)en
dc.subjectFragile X syndromeen
dc.subjectWhole-genome sequencing (WGS) dataen
dc.subjectSoftware toolsen
dc.subjectExpansionHunteren
dc.titleDetection of long repeat expansions from PCR-free whole-genome sequence dataen
dc.typeJournal Articleen
dc.type.supercollectionscholarly_publicationsen
dc.type.supercollectionrefereed_publicationsen
dc.identifier.peoplefinderurlhttp://people.tcd.ie/hardimao
dc.identifier.peoplefinderurlhttp://people.tcd.ie/mclaugr1
dc.identifier.rssinternalid181572
dc.rights.ecaccessrightsopenAccess
dc.identifier.orcid_id0000-0003-2610-1291


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