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dc.contributor.authorBahlo, M
dc.contributor.authorBennett, MF
dc.contributor.authorDegorski, P
dc.contributor.authorTankard, RM
dc.contributor.authorDelatycki, MB
dc.contributor.authorLockhart, PJ
dc.date.accessioned2020-12-17T04:35:19Z
dc.date.available2020-12-17T04:35:19Z
dc.date.issued2018
dc.identifier.citationBahlo, M., Bennett, M. F., Degorski, P., Tankard, R. M., Delatycki, M. B. & Lockhart, P. J. (2018). Recent advances in the detection of repeat expansions with short-read next-generation sequencing.. F1000Res, 7, pp.736-736. https://doi.org/10.12688/f1000research.13980.1.
dc.identifier.issn2046-1402
dc.identifier.urihttp://hdl.handle.net/11343/255373
dc.description.abstractShort tandem repeats (STRs), also known as microsatellites, are commonly defined as consisting of tandemly repeated nucleotide motifs of 2-6 base pairs in length. STRs appear throughout the human genome, and about 239,000 are documented in the Simple Repeats Track available from the UCSC (University of California, Santa Cruz) genome browser. STRs vary in size, producing highly polymorphic markers commonly used as genetic markers. A small fraction of STRs (about 30 loci) have been associated with human disease whereby one or both alleles exceed an STR-specific threshold in size, leading to disease. Detection of repeat expansions is currently performed with polymerase chain reaction-based assays or with Southern blots for large expansions. The tests are expensive and time-consuming and are not always conclusive, leading to lengthy diagnostic journeys for patients, potentially including missed diagnoses. The advent of whole exome and whole genome sequencing has identified the genetic cause of many genetic disorders; however, analysis pipelines are focused primarily on the detection of short nucleotide variations and short insertions and deletions (indels). Until recently, repeat expansions, with the exception of the smallest expansion (SCA6), were not detectable in next-generation short-read sequencing datasets and would have been ignored in most analyses. In the last two years, four analysis methods with accompanying software (ExpansionHunter, exSTRa, STRetch, and TREDPARSE) have been released. Although a comprehensive comparative analysis of the performance of these methods across all known repeat expansions is still lacking, it is clear that these methods are a valuable addition to any existing analysis pipeline. Here, we detail how to assess short-read data for evidence of expansions, reviewing all four methods and outlining their strengths and weaknesses. Implementation of these methods should lead to increased diagnostic yield of repeat expansion disorders for known STR loci and has the potential to detect novel repeat expansions.
dc.languageeng
dc.publisherF1000 Research Ltd
dc.rights.urihttps://creativecommons.org/licenses/by/4.0
dc.titleRecent advances in the detection of repeat expansions with short-read next-generation sequencing.
dc.typeJournal Article
dc.identifier.doi10.12688/f1000research.13980.1
melbourne.affiliation.departmentPaediatrics (RCH)
melbourne.affiliation.departmentMelbourne School of Population and Global Health
melbourne.affiliation.departmentSchool of Mathematics and Statistics
melbourne.affiliation.departmentMedical Biology (W.E.H.I.)
melbourne.source.titleF1000Research
melbourne.source.volume7
melbourne.source.pages736-736
dc.rights.licenseCC BY
melbourne.elementsid1337809
melbourne.openaccess.pmchttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC6008857
melbourne.contributor.authorLockhart, Paul
melbourne.contributor.authorBahlo, Melanie
melbourne.contributor.authorBennett, Mark
melbourne.contributor.authorDelatycki, Martin
melbourne.contributor.authorDegorski, Peter
melbourne.contributor.authorTankard, Rick
dc.identifier.eissn2046-1402
melbourne.accessrightsOpen Access


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