ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data
| dc.citation.articleNumber | 188 | en_US |
| dc.citation.journalTitle | BMC Bioinformatics | en_US |
| dc.citation.volumeNumber | 17 | en_US |
| dc.contributor.author | Rustagi, Navin | en_US |
| dc.contributor.author | Hampton, Oliver A. | en_US |
| dc.contributor.author | Li, Jie | en_US |
| dc.contributor.author | Xi, Liu | en_US |
| dc.contributor.author | Gibbs, Richard A. | en_US |
| dc.contributor.author | Plon, Sharon E. | en_US |
| dc.contributor.author | Kimmel, Marek | en_US |
| dc.contributor.author | Wheeler, David A. | en_US |
| dc.date.accessioned | 2016-08-11T13:50:05Z | en_US |
| dc.date.available | 2016-08-11T13:50:05Z | en_US |
| dc.date.issued | 2016 | en_US |
| dc.date.updated | 2016-08-11T13:50:05Z | en_US |
| dc.description.abstract | Abstract Background Detection of tandem duplication within coding exons, referred to as internal tandem duplication (ITD), remains challenging due to inefficiencies in alignment of ITD-containing reads to the reference genome. There is a critical need to develop efficient methods to recover these important mutational events. Results In this paper we introduce ITD Assembler, a novel approach that rapidly evaluates all unmapped and partially mapped reads from whole exome NGS data using a De Bruijn graphs approach to select reads that harbor cycles of appropriate length, followed by assembly using overlap-layout-consensus. We tested ITD Assembler on The Cancer Genome Atlas AML dataset as a truth set. ITD Assembler identified the highest percentage of reported FLT3-ITDs when compared to other ITD detection algorithms, and discovered additional ITDs in FLT3, KIT, CEBPA, WT1 and other genes. Evidence of polymorphic ITDs in 54 genes were also found. Novel ITDs were validated by analyzing the corresponding RNA sequencing data. Conclusions ITD Assembler is a very sensitive tool which can detect partial, large and complex tandem duplications. This study highlights the need to more effectively look for ITD’s in other cancers and Mendelian diseases. | en_US |
| dc.identifier.citation | Rustagi, Navin, Hampton, Oliver A., Li, Jie, et al.. "ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data." <i>BMC Bioinformatics,</i> 17, (2016) BioMed Central: http://dx.doi.org/10.1186/s12859-016-1031-8. | en_US |
| dc.identifier.doi | http://dx.doi.org/10.1186/s12859-016-1031-8 | en_US |
| dc.identifier.uri | https://hdl.handle.net/1911/91216 | en_US |
| dc.language.iso | eng | en_US |
| dc.publisher | BioMed Central | en_US |
| dc.rights | This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. | en_US |
| dc.rights.holder | Rustagi et al. | en_US |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | en_US |
| dc.title | ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data | en_US |
| dc.type | Journal article | en_US |
| dc.type.dcmi | Text | en_US |
| dc.type.publication | publisher version | en_US |
| local.sword.agent | BioMed Central | en_US |