ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Rustagi, Navin; Hampton, Oliver; Li, Jie; Xi, Liu; Gibbs, Richard; Plon, Sharon; Kimmel, Marek; Wheeler, David
• Is Part Of: BMC bioinformatics. Volume 17:Issue 1(2016)
• Page Start: 1
• Page End: 8
• Publication Date: 2016-12
• Subjects: Tandem duplication -- De Bruijn graphs -- Assembly -- FLT3 -- Data mining -- Cancer genetics -- AML -- Clustering -- Somatic mutations; Bioinformatics -- Periodicals; Computational biology -- Periodicals; 570.285
• DOI: 10.1186/s12859-016-1031-8
• Languages: English
• ISSNs: 1471-2105

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 inFLT3, 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.