Sequencing technologies and tools for short tandem repeat variation detection

Cao, Minh Duc, Balasubramanian, Sureshkumar and Boden, Mikael (2015) Sequencing technologies and tools for short tandem repeat variation detection. Briefings in Bioinformatics, 16 2: 193-204. doi:10.1093/bib/bbu001

Author Cao, Minh Duc
Balasubramanian, Sureshkumar
Boden, Mikael
Title Sequencing technologies and tools for short tandem repeat variation detection
Journal name Briefings in Bioinformatics   Check publisher's open access policy
ISSN 1477-4054
Publication date 2015-03-01
Year available 2014
Sub-type Article (original research)
DOI 10.1093/bib/bbu001
Open Access Status
Volume 16
Issue 2
Start page 193
End page 204
Total pages 12
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Collection year 2015
Language eng
Abstract Short tandem repeats are highly polymorphic and associated with a wide range of phenotypic variation, some of which cause neurodegenerative disease in humans. With advances in high-throughput sequencing technologies, there are novel opportunities to study genetic variation. While available sequencing technologies and bioinformatics tools provide options for mining high-throughput sequencing data, their suitability for analysis of repeat variation is an open question, with tools for quantifying variability in repetitive sequence still in their infancy. We present here a comprehensive survey and empirical evaluation of current sequencing technologies and bioinformatics tools in all stages of an analysis pipeline. While there is not one optimal pipeline to suit all circumstances, we find that the choice of alignment and repeat genotyping tools greatly impacts the accuracy and efficiency by which short tandem repeat variation can be detected. We further note that to detect variation relevant to many repeat diseases, it is essential to choose technologies that offer either long read-lengths or paired-end sequencing, coupled with specific genotyping tools.
Keyword Short tandemrepeat variation
High-throughput sequencing
Bioinformatics tools
Sequence alignment
Variant calling
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Published online ahead of print 6 Feb 2014

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2015 Collection
Official Audit
School of Chemistry and Molecular Biosciences
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