Paper Info
Title
ITD assembler: an algorithm for internal tandem duplication discovery from short-read sequencing data.
Abstract
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.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.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.
Year
DOI
Venue
2016
10.1186/s12859-016-1031-8
BMC Bioinformatics
Keywords
Field
DocType
AML,Assembly,Cancer genetics,Clustering,Data mining,De Bruijn graphs,FLT3,Somatic mutations,Tandem duplication
Biology,Molecular diagnostic techniques,Fms-Like Tyrosine Kinase 3,Exome,Tandem Repeat Sequence,Coding (social sciences),Bioinformatics,Tandem exon duplication,Genetics,Reference genome,DNA microarray
Journal
Volume
Issue
ISSN
17
1
1471-2105
Citations 
PageRank 
References 
0
0.34
7
Authors
8
Name
Order
Citations
PageRank
Navin Rustagi1231.91
Oliver A. Hampton200.34
Jie Li300.34
Liu Xi400.34
Richard A. Gibbs55610.04
sharon e plon691.55
Marek Kimmel714520.47
David A. Wheeler8183.65