Inferring short tandem repeat variation from paired-end short reads

Cao, Minh Duc, Tasker, Edward, Willadsen, Kai, Imelfort, Michael, Vishwanathan, Sailaja, Sureshkumar, Sridevi, Balasubramanian, Sureshkumar and Bodén, Mikael (2014) Inferring short tandem repeat variation from paired-end short reads. Nucleic Acids Research, 42 3: e16.1-e16.11. doi:10.1093/nar/gkt1313

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Author Cao, Minh Duc
Tasker, Edward
Willadsen, Kai
Imelfort, Michael
Vishwanathan, Sailaja
Sureshkumar, Sridevi
Balasubramanian, Sureshkumar
Bodén, Mikael
Title Inferring short tandem repeat variation from paired-end short reads
Journal name Nucleic Acids Research   Check publisher's open access policy
ISSN 0305-1048
1362-4962
1362-4954
Publication date 2014-01-01
Year available 2013
Sub-type Article (original research)
DOI 10.1093/nar/gkt1313
Open Access Status DOI
Volume 42
Issue 3
Start page e16.1
End page e16.11
Total pages 11
Place of publication Oxford, United Kingdom
Publisher Oxford University Press
Language eng
Formatted abstract
The advances of high-throughput sequencing offer an unprecedented opportunity to study genetic variation. This is challenged by the difficulty of resolving variant calls in repetitive DNA regions. We present a Bayesian method to estimate repeat-length variation from paired-end sequence read data. The method makes variant calls based on deviations in sequence fragment sizes, allowing the analysis of repeats at lengths of relevance to a range of phenotypes. We demonstrate the method’s ability to detect and quantify changes in repeat lengths from short read genomic sequence data across genotypes. We use the method to estimate repeat variation among 12 strains of Arabidopsis thaliana and demonstrate experimentally that our method compares favourably against existing methods. Using this method, we have identified all repeats across the genome, which are likely to be polymorphic. In addition, our predicted polymorphic repeats also included the only known repeat expansion in A. thaliana, suggesting an ability to discover potential unstable repeats.
Keyword Biochemistry & Molecular Biology
Biochemistry & Molecular Biology
Q-Index Code C1
Q-Index Status Confirmed Code
Grant ID 1004112
DP1095325
DP110100964
FT100100377
FT100100377
Institutional Status UQ
Additional Notes First published online: 17 December 2013.

Document type: Journal Article
Sub-type: Article (original research)
Collections: Official 2014 Collection
School of Chemistry and Molecular Biosciences
Advanced Water Management Centre Publications
 
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Citation counts: TR Web of Science Citation Count  Cited 15 times in Thomson Reuters Web of Science Article | Citations
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Created: Fri, 10 Jan 2014, 21:18:11 EST by Miss Abigail Downie on behalf of School of Chemistry & Molecular Biosciences