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There is a critical need to develop efficient methods to recover these important mutational events.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>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 <jats:italic>FLT3<\/jats:italic>, <jats:italic>KIT<\/jats:italic>, <jats:italic>CEBPA, WT1<\/jats:italic> and other genes. Evidence of polymorphic ITDs in 54 genes were also found. Novel ITDs were validated by analyzing the corresponding RNA sequencing data.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>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\u00a0ITD\u2019s in other cancers and Mendelian diseases.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-016-1031-8","type":"journal-article","created":{"date-parts":[[2016,4,27]],"date-time":"2016-04-27T04:19:41Z","timestamp":1461730781000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data"],"prefix":"10.1186","volume":"17","author":[{"given":"Navin","family":"Rustagi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oliver A","family":"Hampton","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liu","family":"Xi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard A.","family":"Gibbs","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sharon E.","family":"Plon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marek","family":"Kimmel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David A.","family":"Wheeler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2016,4,27]]},"reference":[{"key":"1031_CR1","doi-asserted-by":"publisher","first-page":"444","DOI":"10.1182\/blood-2008-02-140392","volume":"112","author":"AJ Mead","year":"2008","unstructured":"Mead AJ et al. 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