On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing
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On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing

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On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing

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dc.contributor.author Lucas Lledó, José Ignacio
dc.contributor.author Cáceres, Mario
dc.date.accessioned 2015-06-25T09:00:10Z
dc.date.available 2015-06-25T09:00:10Z
dc.date.issued 2013
dc.identifier.uri http://hdl.handle.net/10550/44729
dc.description.abstract One of the most used techniques to study structural variation at a genome level is paired-end mapping (PEM). PEM has the advantage of being able to detect balanced events, such as inversions and translocations. However, inversions are still quite difficult to predict reliably, especially from high-throughput sequencing data. We simulated realistic PEM experiments with different combinations of read and library fragment lengths, including sequencing erros and meaningful base-qualities, to quantify and track down the origin of false positives and negatives along sequencing, mapping, and downstream analysis. We show that PEM is very appropriate to detect a wide range of inversions, even with low coverage data. However, >80% of inversions located between segmental duplications are expected to go undetected by the most common sequencing strategies. In general, longer DNA libraries improve the detectability of inversions far better than increments of the coverage depth or the read length. Finally, we review the performance of three algorithms to detect inversions ¿SVDetect, GRIAL, and VariationHunter¿, identify common pitfalls, and reveal important differences in their breakpoint precisions. These results stress the importance of the sequencing strategy for the detection of structural variants, especially inversions, and offer guidelines for the design of future genome sequencing projects.
dc.language.iso eng
dc.relation.ispartof Plos One, 2013, vol. 8, num. 4, p. e61292
dc.rights.uri info:eu-repo/semantics/openAccess
dc.source Lucas Lledó, José Ignacio; Cáceres, Mario (2013) On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing Plos One 8 4 e61292
dc.title On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing
dc.type info:eu-repo/semantics/article
dc.date.updated 2015-06-25T09:00:10Z
dc.identifier.doi http://dx.doi.org/10.1371/journal.pone.0061292
dc.identifier.idgrec 105224

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